From 3dc45fd7cda60a120acfdf0a8bd4e3da3db584de Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Mon, 12 Aug 2024 15:16:55 -0700
Subject: [PATCH 01/20] Move recan_bundle_tdr script to attic (#6491)

---
 {scripts => attic/scripts}/recan_bundle_tdr.py | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename {scripts => attic/scripts}/recan_bundle_tdr.py (100%)

diff --git a/scripts/recan_bundle_tdr.py b/attic/scripts/recan_bundle_tdr.py
similarity index 100%
rename from scripts/recan_bundle_tdr.py
rename to attic/scripts/recan_bundle_tdr.py

From 62df7fb65227e912b51f3953d8555c308060f012 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Wed, 7 Aug 2024 19:32:45 -0700
Subject: [PATCH 02/20] Fix JSON indentation

---
 .../data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
index abf7dd5f9..e8f318774 100644
--- a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
+++ b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
@@ -1445,13 +1445,13 @@
                 }
             ],
             "hca_bionetworks": [
-                 {
+                {
                     "name": "Immune",
                     "atlas_project": false,
                     "hca_tissue_atlas": "Blood",
                     "hca_tissue_atlas_version": "v1.0",
                     "schema_version": "1.0.1"
-                 }
+                }
             ],
             "provenance": {
                 "document_id": "6615efae-fca8-4dd2-a223-9cfcf30fe94d",

From fd24a5dd8f1963e2d72dc763f8e08e38a576e693 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Wed, 7 Aug 2024 15:21:29 -0700
Subject: [PATCH 03/20] Fix type warnings

---
 src/humancellatlas/data/metadata/api.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/humancellatlas/data/metadata/api.py b/src/humancellatlas/data/metadata/api.py
index 39c4e7a77..5aa7c4f6d 100644
--- a/src/humancellatlas/data/metadata/api.py
+++ b/src/humancellatlas/data/metadata/api.py
@@ -42,6 +42,7 @@
 )
 from azul.collections import (
     OrderedSet,
+    dict_merge,
 )
 from humancellatlas.data.metadata.age_range import (
     AgeRange,
@@ -940,7 +941,7 @@ class Link:
     link_type: str = 'process_link'
 
     @classmethod
-    def from_json(cls, json: JSON, schema_version: Tuple[int]) -> Iterable['Link']:
+    def from_json(cls, json: JSON, schema_version: tuple[int, ...]) -> Iterable['Link']:
         if 'source_id' in json:
             # DCP/1 v5 (obsolete)
             yield cls(source_id=UUID4(json['source_id']),
@@ -1132,7 +1133,7 @@ def recurse(entities: Iterable[Entity]) -> Mapping[UUID4, L]:
                 except StopIteration:
                     return visit(entity)
                 else:
-                    return dict(chain.from_iterable(map(dict.items, map(visit, entities))))
+                    return dict_merge(map(visit, entities))
 
         def visit(entity: Entity) -> Mapping[UUID4, L]:
             if isinstance(entity, LinkedEntity):

From 9d26075c0efde61c4c8c5e6d8d803cc75b4b41c1 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Thu, 22 Aug 2024 14:56:51 -0700
Subject: [PATCH 04/20] Remove duplicated Azul code in src/humancellatlas/

---
 .../plugins/repository/canned/__init__.py     |  7 ++--
 src/humancellatlas/data/metadata/api.py       | 36 +++++--------------
 .../data/metadata/helpers/exception.py        | 36 -------------------
 .../metadata/helpers/schema_validation.py     |  8 ++---
 .../data/metadata/helpers/staging_area.py     | 20 ++++++-----
 5 files changed, 26 insertions(+), 81 deletions(-)
 delete mode 100644 src/humancellatlas/data/metadata/helpers/exception.py

diff --git a/src/azul/plugins/repository/canned/__init__.py b/src/azul/plugins/repository/canned/__init__.py
index d4ec63bae..566945205 100644
--- a/src/azul/plugins/repository/canned/__init__.py
+++ b/src/azul/plugins/repository/canned/__init__.py
@@ -25,7 +25,6 @@
 from typing import (
     Optional,
     Type,
-    cast,
 )
 
 from furl import (
@@ -64,8 +63,6 @@
 )
 from azul.types import (
     JSON,
-    MutableJSON,
-    MutableJSONs,
 )
 from azul.uuids import (
     validate_uuid_prefix,
@@ -201,8 +198,8 @@ def fetch_bundle(self, bundle_fqid: CannedBundleFQID) -> CannedBundle:
                                            uuid=bundle_fqid.uuid,
                                            version=version)
         bundle = CannedBundle(fqid=bundle_fqid,
-                              manifest=cast(MutableJSONs, manifest),
-                              metadata_files=cast(MutableJSON, metadata))
+                              manifest=manifest,
+                              metadata_files=metadata)
         assert version == bundle.version, (version, bundle)
         log.info('It took %.003fs to download bundle %s.%s',
                  time.time() - now, bundle.uuid, bundle.version)
diff --git a/src/humancellatlas/data/metadata/api.py b/src/humancellatlas/data/metadata/api.py
index 5aa7c4f6d..4244fe7c1 100644
--- a/src/humancellatlas/data/metadata/api.py
+++ b/src/humancellatlas/data/metadata/api.py
@@ -18,8 +18,6 @@
     chain,
 )
 from typing import (
-    Any,
-    Dict,
     Iterable,
     Iterator,
     List,
@@ -44,6 +42,12 @@
     OrderedSet,
     dict_merge,
 )
+from azul.types import (
+    JSON,
+    MutableJSON,
+    MutableJSONs,
+    is_optional,
+)
 from humancellatlas.data.metadata.age_range import (
     AgeRange,
 )
@@ -58,10 +62,6 @@
 # A few helpful type aliases
 #
 UUID4 = UUID
-AnyJSON2 = Union[str, int, float, bool, None, Dict[str, Any], List[Any]]
-AnyJSON1 = Union[str, int, float, bool, None, Dict[str, AnyJSON2], List[AnyJSON2]]
-AnyJSON = Union[str, int, float, bool, None, Dict[str, AnyJSON1], List[AnyJSON1]]
-JSON = Dict[str, AnyJSON]
 
 
 @dataclass(init=False)
@@ -83,7 +83,7 @@ class ManifestEntry:
     version: str
     is_stitched: bool = field(init=False)
 
-    def __init__(self, json: JSON):
+    def __init__(self, json: MutableJSON):
         # '/' was once forbidden in file paths and was encoded with '!'. Now
         # '/' is allowed and we force it in the metadata so that backwards
         # compatibility is simplified downstream.
@@ -822,26 +822,6 @@ class ImagingPreparationProtocol(Protocol):
     pass
 
 
-def is_optional(t):
-    """
-    https://stackoverflow.com/a/62641842/4171119
-
-    >>> is_optional(str)
-    False
-    >>> is_optional(Optional[str])
-    True
-    >>> is_optional(Union[str, None])
-    True
-    >>> is_optional(Union[None, str])
-    True
-    >>> is_optional(Union[str, None, int])
-    True
-    >>> is_optional(Union[str, int])
-    False
-    """
-    return t == Optional[t]
-
-
 @dataclass(init=False)
 class File(LinkedEntity):
     format: str
@@ -1020,7 +1000,7 @@ class Bundle:
     entities: MutableMapping[UUID4, Entity] = field(repr=False)
     links: List[Link]
 
-    def __init__(self, uuid: str, version: str, manifest: List[JSON], metadata_files: Mapping[str, JSON]):
+    def __init__(self, uuid: str, version: str, manifest: MutableJSONs, metadata_files: Mapping[str, JSON]):
         self.uuid = UUID4(uuid)
         self.version = version
         self.manifest = {m.name: m for m in map(ManifestEntry, manifest)}
diff --git a/src/humancellatlas/data/metadata/helpers/exception.py b/src/humancellatlas/data/metadata/helpers/exception.py
deleted file mode 100644
index af1c704cc..000000000
--- a/src/humancellatlas/data/metadata/helpers/exception.py
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copied from https://github.com/DataBiosphere/azul/blob/develop/src/azul/__init__.py
-
-
-class RequirementError(RuntimeError):
-    """
-    Unlike assertions, unsatisfied requirements do not constitute a bug in the program.
-    """
-
-
-def require(condition: bool, *args, exception: type = RequirementError):
-    """
-    Raise a RequirementError, or an instance of the given exception class, if the given condition is False.
-
-    :param condition: the boolean condition to be required
-
-    :param args: optional positional arguments to be passed to the exception constructor. Typically only one such
-                 argument should be provided: a string containing a textual description of the requirement.
-
-    :param exception: a custom exception class to be instantiated and raised if the condition does not hold
-    """
-    reject(not condition, *args, exception=exception)
-
-
-def reject(condition: bool, *args, exception: type = RequirementError):
-    """
-    Raise a RequirementError, or an instance of the given exception class, if the given condition is True.
-
-    :param condition: the boolean condition to be rejected
-
-    :param args: optional positional arguments to be passed to the exception constructor. Typically only one such
-                 argument should be provided: a string containing a textual description of the rejected condition.
-
-    :param exception: a custom exception class to be instantiated and raised if the condition occurs
-    """
-    if condition:
-        raise exception(*args)
diff --git a/src/humancellatlas/data/metadata/helpers/schema_validation.py b/src/humancellatlas/data/metadata/helpers/schema_validation.py
index fd6632266..a6adc96e7 100644
--- a/src/humancellatlas/data/metadata/helpers/schema_validation.py
+++ b/src/humancellatlas/data/metadata/helpers/schema_validation.py
@@ -11,12 +11,12 @@
 )
 import requests
 
-from humancellatlas.data.metadata.api import (
-    JSON,
-)
-from humancellatlas.data.metadata.helpers.exception import (
+from azul import (
     RequirementError,
 )
+from azul.types import (
+    JSON,
+)
 
 log = logging.getLogger(__name__)
 
diff --git a/src/humancellatlas/data/metadata/helpers/staging_area.py b/src/humancellatlas/data/metadata/helpers/staging_area.py
index c510d2095..8d915f589 100644
--- a/src/humancellatlas/data/metadata/helpers/staging_area.py
+++ b/src/humancellatlas/data/metadata/helpers/staging_area.py
@@ -26,14 +26,18 @@
 
 import git
 
-from humancellatlas.data.metadata.api import (
-    Bundle,
-    JSON,
-)
-from humancellatlas.data.metadata.helpers.exception import (
+from azul import (
     reject,
     require,
 )
+from azul.types import (
+    JSON,
+    MutableJSON,
+    MutableJSONs,
+)
+from humancellatlas.data.metadata.api import (
+    Bundle,
+)
 from humancellatlas.data.metadata.helpers.schema_validation import (
     SchemaValidator,
 )
@@ -49,14 +53,14 @@ class JsonFile:
     uuid: str
     version: str
     name: str
-    content: JSON
+    content: MutableJSON
     _validator: ClassVar[SchemaValidator] = SchemaValidator()
 
     def __attrs_post_init__(self):
         self._validator.validate_json(self.content, self.name)
 
     @classmethod
-    def from_json(cls, file_name: str, content: JSON) -> 'JsonFile':
+    def from_json(cls, file_name: str, content: MutableJSON) -> 'JsonFile':
         def parse_file_name(file_name: str) -> Sequence[str]:
             suffix = '.json'
             assert file_name.endswith(suffix), file_name
@@ -141,7 +145,7 @@ def get_bundle(self, subgraph_id: str) -> Bundle:
         version, manifest, metadata = self.get_bundle_parts(subgraph_id)
         return Bundle(subgraph_id, version, manifest, metadata)
 
-    def get_bundle_parts(self, subgraph_id: str) -> tuple[str, list[JSON], JSON]:
+    def get_bundle_parts(self, subgraph_id: str) -> tuple[str, MutableJSONs, MutableJSON]:
         """
         Return the components to create a bundle from the staging area
         """

From f1d8212e56624a5d68f7f4c62a81883c928d73e2 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Thu, 22 Aug 2024 15:11:23 -0700
Subject: [PATCH 05/20] Eliminate old-style type annotations in
 src/humancellatlas

---
 src/humancellatlas/data/metadata/age_range.py |   5 +-
 src/humancellatlas/data/metadata/api.py       | 174 +++++++++---------
 src/humancellatlas/data/metadata/datetime.py  |   5 +-
 .../data/metadata/helpers/staging_area.py     |   3 +-
 src/humancellatlas/data/metadata/lookup.py    |   4 +-
 5 files changed, 88 insertions(+), 103 deletions(-)

diff --git a/src/humancellatlas/data/metadata/age_range.py b/src/humancellatlas/data/metadata/age_range.py
index f94f71fe8..da96ece00 100644
--- a/src/humancellatlas/data/metadata/age_range.py
+++ b/src/humancellatlas/data/metadata/age_range.py
@@ -1,9 +1,6 @@
 from dataclasses import (
     dataclass,
 )
-from typing import (
-    Optional,
-)
 
 
 @dataclass(frozen=True)
@@ -89,7 +86,7 @@ def fail():
             else:
                 raise fail() from e1
 
-        def cvt(value: str, default: float) -> Optional[float]:
+        def cvt(value: str, default: float) -> float | None:
             assert isinstance(default, float)
             try:
                 return factor * float(value) if value else default
diff --git a/src/humancellatlas/data/metadata/api.py b/src/humancellatlas/data/metadata/api.py
index 4244fe7c1..c3c8e135b 100644
--- a/src/humancellatlas/data/metadata/api.py
+++ b/src/humancellatlas/data/metadata/api.py
@@ -20,15 +20,9 @@
 from typing import (
     Iterable,
     Iterator,
-    List,
     Mapping,
     MutableMapping,
-    Optional,
-    Set,
-    Tuple,
-    Type,
     TypeVar,
-    Union,
 )
 from uuid import (
     UUID,
@@ -71,12 +65,12 @@ class ManifestEntry:
     crc32c: str
     indexed: bool
     name: str
-    s3_etag: Optional[str]
-    sha1: Optional[str]
+    s3_etag: str | None
+    sha1: str | None
     sha256: str
     size: int
     # only populated if bundle was requested with `directurls` or `directurls` set
-    url: Optional[str]
+    url: str | None
     uuid: UUID4 = field(init=False)
     # FIXME: Change Bundle.version and ManifestEntry.version from string to datetime
     #        https://github.com/DataBiosphere/hca-metadata-api/issues/48
@@ -105,10 +99,10 @@ def __init__(self, json: MutableJSON):
 class Entity:
     json: JSON = field(repr=False)
     document_id: UUID4
-    submitter_id: Optional[str]
-    metadata_manifest_entry: Optional[ManifestEntry]
+    submitter_id: str | None
+    metadata_manifest_entry: ManifestEntry | None
     submission_date: datetime
-    update_date: Optional[datetime]
+    update_date: datetime | None
 
     @property
     def is_stitched(self):
@@ -120,7 +114,7 @@ def is_stitched(self):
     @classmethod
     def from_json(cls,
                   json: JSON,
-                  metadata_manifest_entry: Optional[ManifestEntry],
+                  metadata_manifest_entry: ManifestEntry | None,
                   **kwargs):
         content = json.get('content', json)
         described_by = content['describedBy']
@@ -133,7 +127,7 @@ def from_json(cls,
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__()
         self.json = json
@@ -154,7 +148,7 @@ def __init__(self,
     def _datetime(self, s: str) -> datetime:
         return parse_jsonschema_date_time(s).astimezone(timezone.utc)
 
-    def _optional_datetime(self, s: Optional[str]) -> Optional[datetime]:
+    def _optional_datetime(self, s: str | None) -> datetime | None:
         return s if s is None else self._datetime(s)
 
     @property
@@ -212,7 +206,7 @@ def _connect_to(self, other: Entity, forward: bool) -> None:
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         self.children = {}
@@ -248,9 +242,9 @@ def __init__(self, entity: LinkedEntity, other_entity: Entity, forward: bool) ->
 @dataclass(frozen=True)
 class ProjectPublication:
     title: str
-    url: Optional[str]
-    official_hca: Optional[bool]
-    doi: Optional[str]
+    url: str | None
+    official_hca: bool | None
+    doi: str | None
 
     @classmethod
     def from_json(cls, json: JSON) -> 'ProjectPublication':
@@ -277,11 +271,11 @@ def publication_url(self):
 @dataclass(frozen=True)
 class ProjectContact:
     name: str
-    email: Optional[str]
-    institution: Optional[str]  # optional up to project/5.3.0/contact
-    laboratory: Optional[str]
-    corresponding_contributor: Optional[bool]
-    project_role: Optional[str]
+    email: str | None
+    institution: str | None  # optional up to project/5.3.0/contact
+    laboratory: str | None
+    corresponding_contributor: bool | None
+    project_role: str | None
 
     @classmethod
     def from_json(cls, json: JSON) -> 'ProjectContact':
@@ -310,27 +304,27 @@ class Accession:
 @dataclass(eq=True, frozen=True)
 class Bionetwork:
     name: str
-    atlas_project: Optional[bool] = None
-    hca_tissue_atlas: Optional[str] = None
-    hca_tissue_atlas_version: Optional[str] = None
-    schema_version: Optional[str] = None
+    atlas_project: bool | None = None
+    hca_tissue_atlas: str | None = None
+    hca_tissue_atlas_version: str | None = None
+    schema_version: str | None = None
 
 
 @dataclass(init=False)
 class Project(Entity):
     project_short_name: str
     project_title: str
-    project_description: Optional[str]  # optional up to core/project/5.2.2/project_core
+    project_description: str | None  # optional up to core/project/5.2.2/project_core
     publications: OrderedSet[ProjectPublication]
     contributors: OrderedSet[ProjectContact]
     accessions: OrderedSet[Accession]
     supplementary_links: OrderedSet[str]
-    estimated_cell_count: Optional[int]
+    estimated_cell_count: int | None
     bionetworks: OrderedSet[Bionetwork]
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
@@ -356,29 +350,29 @@ def __init__(self,
                                       for bionetwork in content.get('hca_bionetworks', ())
                                       if bionetwork)
 
-    def _accessions(self, namespace: str) -> Set[str]:
+    def _accessions(self, namespace: str) -> set[str]:
         return {a.accession for a in self.accessions if a.namespace == namespace}
 
     @property
-    def insdc_project_accessions(self) -> Set[str]:
+    def insdc_project_accessions(self) -> set[str]:
         warnings.warn("Project.insdc_project_accessions is deprecated. "
                       "Use Project.accessions instead.", DeprecationWarning)
         return self._accessions('insdc_project')
 
     @property
-    def geo_series_accessions(self) -> Set[str]:
+    def geo_series_accessions(self) -> set[str]:
         warnings.warn("Project.geo_series_accessions is deprecated. "
                       "Use Project.accessions instead.", DeprecationWarning)
         return self._accessions('geo_series')
 
     @property
-    def array_express_accessions(self) -> Set[str]:
+    def array_express_accessions(self) -> set[str]:
         warnings.warn("Project.array_express_accessions is deprecated. "
                       "Use Project.accessions instead.", DeprecationWarning)
         return self._accessions('array_express')
 
     @property
-    def insdc_study_accessions(self) -> Set[str]:
+    def insdc_study_accessions(self) -> set[str]:
         warnings.warn("Project.insdc_study_accessions is deprecated. "
                       "Use Project.accessions instead.", DeprecationWarning)
         return self._accessions('insdc_study')
@@ -399,14 +393,14 @@ def project_shortname(self) -> str:
 @dataclass(init=False)
 class Biomaterial(LinkedEntity):
     biomaterial_id: str
-    ncbi_taxon_id: List[int]
-    has_input_biomaterial: Optional[str]
+    ncbi_taxon_id: list[int]
+    has_input_biomaterial: str | None
     from_processes: MutableMapping[UUID4, 'Process'] = field(repr=False)
     to_processes: MutableMapping[UUID4, 'Process']
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
@@ -428,16 +422,16 @@ def _connect_to(self, other: Entity, forward: bool) -> None:
 
 @dataclass(init=False)
 class DonorOrganism(Biomaterial):
-    genus_species: Set[str]
-    diseases: Set[str]
+    genus_species: set[str]
+    diseases: set[str]
     organism_age: str
     organism_age_unit: str
     sex: str
-    development_stage: Optional[str]
+    development_stage: str | None
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
@@ -449,7 +443,7 @@ def __init__(self,
         self.development_stage = ontology_label(content.get('development_stage'), default=None)
 
     @property
-    def organism_age_in_seconds(self) -> Optional[AgeRange]:
+    def organism_age_in_seconds(self) -> AgeRange | None:
         if self.organism_age and self.organism_age_unit:
             return AgeRange.parse(self.organism_age, self.organism_age_unit)
         else:
@@ -470,15 +464,15 @@ def disease(self):
 
 @dataclass(init=False)
 class SpecimenFromOrganism(Biomaterial):
-    storage_method: Optional[str]
-    preservation_method: Optional[str]
-    diseases: Set[str]
-    organ: Optional[str]
-    organ_parts: Set[str]
+    storage_method: str | None
+    preservation_method: str | None
+    diseases: set[str]
+    organ: str | None
+    organ_parts: set[str]
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
@@ -510,11 +504,11 @@ def organ_part(self):
 
 @dataclass(init=False)
 class ImagedSpecimen(Biomaterial):
-    slice_thickness: Union[float, int]
+    slice_thickness: float | int
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         self.slice_thickness = json['slice_thickness']
@@ -522,12 +516,12 @@ def __init__(self,
 
 @dataclass(init=False)
 class CellSuspension(Biomaterial):
-    estimated_cell_count: Optional[int]
-    selected_cell_types: Set[str]
+    estimated_cell_count: int | None
+    selected_cell_types: set[str]
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
@@ -542,7 +536,7 @@ def total_estimated_cells(self) -> int:
         return self.estimated_cell_count
 
     @property
-    def selected_cell_type(self) -> Set[str]:
+    def selected_cell_type(self) -> set[str]:
         warnings.warn("CellSuspension.selected_cell_type is deprecated. "
                       "Use CellSuspension.selected_cell_types instead.", DeprecationWarning)
         return self.selected_cell_types
@@ -551,11 +545,11 @@ def selected_cell_type(self) -> Set[str]:
 @dataclass(init=False)
 class CellLine(Biomaterial):
     type: str
-    model_organ: Optional[str]
+    model_organ: str | None
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
@@ -572,11 +566,11 @@ def cell_line_type(self) -> str:
 @dataclass(init=False)
 class Organoid(Biomaterial):
     model_organ: str
-    model_organ_part: Optional[str]
+    model_organ_part: str | None
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
@@ -587,7 +581,7 @@ def __init__(self,
 @dataclass(init=False)
 class Process(LinkedEntity):
     process_id: str
-    process_name: Optional[str]
+    process_name: str | None
     input_biomaterials: MutableMapping[UUID4, Biomaterial] = field(repr=False)
     input_files: MutableMapping[UUID4, 'File'] = field(repr=False)
     output_biomaterials: MutableMapping[UUID4, Biomaterial]
@@ -596,7 +590,7 @@ class Process(LinkedEntity):
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
@@ -638,7 +632,7 @@ class DissociationProcess(Process):
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         warnings.warn(f"{type(self)} is deprecated", DeprecationWarning)
         super().__init__(json, metadata_manifest_entry)
@@ -649,7 +643,7 @@ class EnrichmentProcess(Process):
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         warnings.warn(f"{type(self)} is deprecated", DeprecationWarning)
         super().__init__(json, metadata_manifest_entry)
@@ -661,7 +655,7 @@ class LibraryPreparationProcess(Process):
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         warnings.warn(f"{type(self)} is deprecated", DeprecationWarning)
         super().__init__(json, metadata_manifest_entry)
@@ -675,7 +669,7 @@ class SequencingProcess(Process):
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         warnings.warn(f"{type(self)} is deprecated", DeprecationWarning)
         super().__init__(json, metadata_manifest_entry)
@@ -699,11 +693,11 @@ def from_json(cls, json: JSON) -> 'ImagingProbe':
 @dataclass(init=False)
 class Protocol(LinkedEntity):
     protocol_id: str
-    protocol_name: Optional[str]
+    protocol_name: str | None
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
@@ -721,11 +715,11 @@ def _connect_to(self, other: Entity, forward: bool) -> None:
 @dataclass(init=False)
 class LibraryPreparationProtocol(Protocol):
     library_construction_method: str
-    nucleic_acid_source: Optional[str]
+    nucleic_acid_source: str | None
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
@@ -743,11 +737,11 @@ def library_construction_approach(self) -> str:
 @dataclass(init=False)
 class SequencingProtocol(Protocol):
     instrument_manufacturer_model: str
-    paired_end: Optional[bool]
+    paired_end: bool | None
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
@@ -797,11 +791,11 @@ class TreatmentProtocol(Protocol):
 
 @dataclass(init=False)
 class ImagingProtocol(Protocol):
-    probe: List[ImagingProbe]  # A list so all the ImagingProbe objects can be tallied when indexed
+    probe: list[ImagingProbe]  # A list so all the ImagingProbe objects can be tallied when indexed
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry]
+                 metadata_manifest_entry: ManifestEntry | None
                  ) -> None:
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
@@ -811,7 +805,7 @@ def __init__(self,
         ]
 
     @property
-    def target(self) -> List[ImagingProbe]:
+    def target(self) -> list[ImagingProbe]:
         warnings.warn('ImagingProtocol.target is deprecated. '
                       'Use ImagingProtocol.probe instead.', DeprecationWarning)
         return self.probe
@@ -828,12 +822,12 @@ class File(LinkedEntity):
     from_processes: MutableMapping[UUID4, Process] = field(repr=False)
     to_processes: MutableMapping[UUID4, Process]
     manifest_entry: ManifestEntry
-    content_description: Set[str]
+    content_description: set[str]
     file_source: str
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: Optional[ManifestEntry],
+                 metadata_manifest_entry: ManifestEntry | None,
                  manifest: Mapping[str, ManifestEntry]):
         super().__init__(json, metadata_manifest_entry)
         content = json.get('content', json)
@@ -872,7 +866,7 @@ def is_matrix(self) -> bool:
 @dataclass(init=False)
 class SequenceFile(File):
     read_index: str
-    lane_index: Optional[str]
+    lane_index: str | None
 
     def __init__(self,
                  json: JSON,
@@ -998,15 +992,15 @@ class Bundle:
 
     manifest: MutableMapping[str, ManifestEntry]
     entities: MutableMapping[UUID4, Entity] = field(repr=False)
-    links: List[Link]
+    links: list[Link]
 
     def __init__(self, uuid: str, version: str, manifest: MutableJSONs, metadata_files: Mapping[str, JSON]):
         self.uuid = UUID4(uuid)
         self.version = version
         self.manifest = {m.name: m for m in map(ManifestEntry, manifest)}
 
-        def from_json(core_cls: Type[E],
-                      json_entities: List[Tuple[JSON, ManifestEntry]],
+        def from_json(core_cls: type[E],
+                      json_entities: list[tuple[JSON, ManifestEntry]],
                       **kwargs
                       ) -> MutableMapping[UUID4, E]:
             entities = (
@@ -1017,7 +1011,7 @@ def from_json(core_cls: Type[E],
 
         if 'project.json' in metadata_files:
 
-            def from_json_v5(core_cls: Type[E], file_name, key=None, **kwargs) -> MutableMapping[UUID4, E]:
+            def from_json_v5(core_cls: type[E], file_name, key=None, **kwargs) -> MutableMapping[UUID4, E]:
                 file_content = metadata_files.get(file_name)
                 if file_content:
                     manifest_entry = self.manifest.get(file_name)
@@ -1035,7 +1029,7 @@ def from_json_v5(core_cls: Type[E], file_name, key=None, **kwargs) -> MutableMap
 
         elif 'project_0.json' in metadata_files:
 
-            json_by_core_cls: MutableMapping[Type[E], List[Tuple[JSON, ManifestEntry]]] = defaultdict(list)
+            json_by_core_cls: MutableMapping[type[E], list[tuple[JSON, ManifestEntry]]] = defaultdict(list)
             for file_name, json in metadata_files.items():
                 assert file_name.endswith('.json')
                 schema_name, _, suffix = file_name[:-5].rpartition('_')
@@ -1044,7 +1038,7 @@ def from_json_v5(core_cls: Type[E], file_name, key=None, **kwargs) -> MutableMap
                     core_cls = core_types[entity_cls]
                     json_by_core_cls[core_cls].append((json, self.manifest.get(file_name)))
 
-            def from_json_vx(core_cls: Type[E], **kwargs) -> MutableMapping[UUID4, E]:
+            def from_json_vx(core_cls: type[E], **kwargs) -> MutableMapping[UUID4, E]:
                 json_entities = json_by_core_cls[core_cls]
                 return from_json(core_cls, json_entities, **kwargs)
 
@@ -1091,7 +1085,7 @@ def visit(self, entity: Entity) -> None:
 
         return roots
 
-    def leaf_entities(self, entity_type: Type[L]) -> Mapping[UUID4, L]:
+    def leaf_entities(self, entity_type: type[L]) -> Mapping[UUID4, L]:
         """
         Return a set of all leaf entities in this bundle. A leaf entity is a
         linked entity of a given type that has no descendants of that type.
@@ -1131,16 +1125,16 @@ def leaf_cell_suspensions(self) -> Mapping[UUID4, CellSuspension]:
         return self.leaf_entities(CellSuspension)
 
     @property
-    def specimens(self) -> List[SpecimenFromOrganism]:
+    def specimens(self) -> list[SpecimenFromOrganism]:
         return [s for s in self.biomaterials.values() if isinstance(s, SpecimenFromOrganism)]
 
     @property
-    def sequencing_input(self) -> List[Biomaterial]:
+    def sequencing_input(self) -> list[Biomaterial]:
         return [bm for bm in self.biomaterials.values()
                 if any(ps.is_sequencing_process() for ps in bm.to_processes.values())]
 
     @property
-    def sequencing_output(self) -> List[SequenceFile]:
+    def sequencing_output(self) -> list[SequenceFile]:
         return [f for f in self.files.values()
                 if isinstance(f, SequenceFile)
                 and any(ps.is_sequencing_process() for ps in f.from_processes.values())]
@@ -1202,8 +1196,8 @@ def sequencing_output(self) -> List[SequenceFile]:
 assert len(entity_types) == len(schema_names), "The mapping from schema name to entity type is not bijective"
 
 
-def ontology_label(ontology: Optional[Mapping[str, str]],
-                   default: Union[str, None, LookupDefault] = LookupDefault.RAISE) -> str:
+def ontology_label(ontology: Mapping[str, str] | None,
+                   default: str | LookupDefault | None = LookupDefault.RAISE) -> str:
     """
     Return the best-suited value from the given ontology dictionary.
 
diff --git a/src/humancellatlas/data/metadata/datetime.py b/src/humancellatlas/data/metadata/datetime.py
index 23a37a71e..66502b4c0 100644
--- a/src/humancellatlas/data/metadata/datetime.py
+++ b/src/humancellatlas/data/metadata/datetime.py
@@ -4,12 +4,9 @@
     timezone,
 )
 import re
-from typing import (
-    Optional,
-)
 
 
-def parse_jsonschema_date_time(s: str) -> Optional[datetime]:
+def parse_jsonschema_date_time(s: str) -> datetime | None:
     """
     Convert a string in JSONSchema `date-time` format
 
diff --git a/src/humancellatlas/data/metadata/helpers/staging_area.py b/src/humancellatlas/data/metadata/helpers/staging_area.py
index 8d915f589..716f9d570 100644
--- a/src/humancellatlas/data/metadata/helpers/staging_area.py
+++ b/src/humancellatlas/data/metadata/helpers/staging_area.py
@@ -11,7 +11,6 @@
     Mapping,
     Self,
     Sequence,
-    Set,
     TypeVar,
 )
 from uuid import (
@@ -184,7 +183,7 @@ def get_bundle_parts(self, subgraph_id: str) -> tuple[str, MutableJSONs, Mutable
 
     def _entity_ids_by_type(self,
                             subgraph_id: str
-                            ) -> dict[str, Set[str]]:
+                            ) -> dict[str, set[str]]:
         """
         Return a mapping of entity types (e.g. 'analysis_file',
         'cell_suspension') to a set of entity IDs
diff --git a/src/humancellatlas/data/metadata/lookup.py b/src/humancellatlas/data/metadata/lookup.py
index 9e1adf86d..41fd21f67 100644
--- a/src/humancellatlas/data/metadata/lookup.py
+++ b/src/humancellatlas/data/metadata/lookup.py
@@ -3,9 +3,7 @@
 )
 from typing import (
     Mapping,
-    Optional,
     TypeVar,
-    Union,
 )
 
 K = TypeVar('K')
@@ -19,7 +17,7 @@ class LookupDefault(Enum):
 def lookup(d: Mapping[K, V],
            k: K,
            *ks: K,
-           default: Union[Optional[V], LookupDefault] = LookupDefault.RAISE
+           default: V | LookupDefault | None = LookupDefault.RAISE
            ) -> V:
     """
     Look up a value in the specified dictionary given one or more candidate keys.

From 9124390415660cd003d365607b5b8ecd5c52c5b7 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Fri, 9 Aug 2024 11:41:24 -0700
Subject: [PATCH 06/20] Fix mismatched entity IDs in canned TDR table

Some canned table rows contain conflicting values for the entities' UUIDs: the
primary keys do not match the document IDs in the `content` column. We suspect
this is the result of a bug in the recently-retired `recan_bundle_tdr` script.
Soon, we will replace file names in HCA bundles with entity references, at
which point these inconsistent UUIDs would break the build.
---
 ...8-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json | 22 +++++-----
 ...39f-4e7d-9161-b720953432ce.tables.tdr.json | 44 +++++++++----------
 2 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
index cb5961843..5f92b228c 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
@@ -711,7 +711,7 @@
                 "schema_minor_version": 5
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file_6.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -765,7 +765,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_2.json": {
+        "sequence_file_4.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -819,7 +819,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_4.json": {
+        "sequence_file_7.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -846,7 +846,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_5.json": {
+        "sequence_file_8.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -873,7 +873,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_6.json": {
+        "sequence_file_5.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -900,7 +900,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_7.json": {
+        "sequence_file_10.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -927,7 +927,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_8.json": {
+        "sequence_file_9.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -954,7 +954,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_9.json": {
+        "sequence_file_2.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -981,7 +981,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_10.json": {
+        "sequence_file_0.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1313,7 +1313,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_2.json": {
+        "process_3.json": {
             "process_core": {
                 "process_id": "process_id_1"
             },
@@ -1327,7 +1327,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_3.json": {
+        "process_2.json": {
             "process_core": {
                 "process_id": "process_id_3"
             },
diff --git a/test/indexer/data/d8c20944-739f-4e7d-9161-b720953432ce.tables.tdr.json b/test/indexer/data/d8c20944-739f-4e7d-9161-b720953432ce.tables.tdr.json
index 6aaff0ce4..5b304b391 100644
--- a/test/indexer/data/d8c20944-739f-4e7d-9161-b720953432ce.tables.tdr.json
+++ b/test/indexer/data/d8c20944-739f-4e7d-9161-b720953432ce.tables.tdr.json
@@ -504,8 +504,8 @@
         "sequence_file": {
             "rows": [
                 {
-                    "sequence_file_id": "133f2a25-f3aa-49a7-b9b6-d185d302fb26",
-                    "version": "2019-09-20T13:51:28.379000Z",
+                    "sequence_file_id": "5f68ea73-350b-4d37-a341-3004139fb699",
+                    "version": "2019-09-20T13:50:35.660000Z",
                     "content": {
                         "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
                         "schema_type": "file",
@@ -590,8 +590,8 @@
                     }
                 },
                 {
-                    "sequence_file_id": "27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6",
-                    "version": "2019-09-20T13:50:35.338000Z",
+                    "sequence_file_id": "3c3d882a-cc38-4eea-ac53-0885f906852e",
+                    "version": "2019-09-20T13:52:19.666000Z",
                     "content": {
                         "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
                         "schema_type": "file",
@@ -676,8 +676,8 @@
                     }
                 },
                 {
-                    "sequence_file_id": "3c3d882a-cc38-4eea-ac53-0885f906852e",
-                    "version": "2019-09-20T13:52:19.666000Z",
+                    "sequence_file_id": "63051b9f-87d4-4853-a4a0-5cc742ef6e72",
+                    "version": "2019-09-20T13:50:59.836000Z",
                     "content": {
                         "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
                         "schema_type": "file",
@@ -719,8 +719,8 @@
                     }
                 },
                 {
-                    "sequence_file_id": "3dffc456-caaf-4823-9f65-fc0db7abacbc",
-                    "version": "2019-09-20T13:49:42.771000Z",
+                    "sequence_file_id": "6ca8e43f-5f40-4eb9-bfa9-294c54dbeade",
+                    "version": "2019-09-20T13:52:17.560000Z",
                     "content": {
                         "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
                         "schema_type": "file",
@@ -762,8 +762,8 @@
                     }
                 },
                 {
-                    "sequence_file_id": "5f68ea73-350b-4d37-a341-3004139fb699",
-                    "version": "2019-09-20T13:50:35.660000Z",
+                    "sequence_file_id": "3dffc456-caaf-4823-9f65-fc0db7abacbc",
+                    "version": "2019-09-20T13:49:42.771000Z",
                     "content": {
                         "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
                         "schema_type": "file",
@@ -805,8 +805,8 @@
                     }
                 },
                 {
-                    "sequence_file_id": "63051b9f-87d4-4853-a4a0-5cc742ef6e72",
-                    "version": "2019-09-20T13:50:59.836000Z",
+                    "sequence_file_id": "a2f4b05d-0dae-4655-acfd-ef3b91ae0ad0",
+                    "version": "2019-09-20T13:50:08.492000Z",
                     "content": {
                         "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
                         "schema_type": "file",
@@ -848,8 +848,8 @@
                     }
                 },
                 {
-                    "sequence_file_id": "6ca8e43f-5f40-4eb9-bfa9-294c54dbeade",
-                    "version": "2019-09-20T13:52:17.560000Z",
+                    "sequence_file_id": "98ee0901-d34c-48a5-915a-0511bac325ec",
+                    "version": "2019-09-20T13:53:16.941000Z",
                     "content": {
                         "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
                         "schema_type": "file",
@@ -891,8 +891,8 @@
                     }
                 },
                 {
-                    "sequence_file_id": "98ee0901-d34c-48a5-915a-0511bac325ec",
-                    "version": "2019-09-20T13:53:16.941000Z",
+                    "sequence_file_id": "27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6",
+                    "version": "2019-09-20T13:50:35.338000Z",
                     "content": {
                         "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
                         "schema_type": "file",
@@ -934,8 +934,8 @@
                     }
                 },
                 {
-                    "sequence_file_id": "a2f4b05d-0dae-4655-acfd-ef3b91ae0ad0",
-                    "version": "2019-09-20T13:50:08.492000Z",
+                    "sequence_file_id": "133f2a25-f3aa-49a7-b9b6-d185d302fb26",
+                    "version": "2019-09-20T13:51:28.379000Z",
                     "content": {
                         "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
                         "schema_type": "file",
@@ -1527,8 +1527,8 @@
                     }
                 },
                 {
-                    "process_id": "c5cf9180-535a-4d1c-bdee-4f6ce7845b1e",
-                    "version": "2019-09-20T13:43:52.368000Z",
+                    "process_id": "df5114c9-9f52-451b-afde-3673392fc864",
+                    "version": "2019-09-20T13:43:52.607000Z",
                     "content": {
                         "process_core": {
                             "process_id": "process_id_1"
@@ -1545,8 +1545,8 @@
                     }
                 },
                 {
-                    "process_id": "df5114c9-9f52-451b-afde-3673392fc864",
-                    "version": "2019-09-20T13:43:52.607000Z",
+                    "process_id": "c5cf9180-535a-4d1c-bdee-4f6ce7845b1e",
+                    "version": "2019-09-20T13:43:52.368000Z",
                     "content": {
                         "process_core": {
                             "process_id": "process_id_3"

From bd3bffd901fec6cfd312be10d89ba55e4bf5fdb7 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Fri, 23 Aug 2024 02:51:05 -0700
Subject: [PATCH 07/20] Remove dangling manifest entries in canned bundles

There are no metadata documents associated with these entries. Soon we will
convert the manifest to a dictionary using entity references as keys, at which
point it will become impossible for bundles to include such dangling entries.
Removing them preemptively proves that they have no effect on any of our tests.
---
 .../2019-05-15T222432.561000Z/manifest.json   | 24 -------------------
 ...7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json | 14 +----------
 2 files changed, 1 insertion(+), 37 deletions(-)

diff --git a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439/2019-05-15T222432.561000Z/manifest.json b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439/2019-05-15T222432.561000Z/manifest.json
index 41ef55acc..24e16c231 100644
--- a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439/2019-05-15T222432.561000Z/manifest.json
+++ b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439/2019-05-15T222432.561000Z/manifest.json
@@ -143,18 +143,6 @@
         "uuid": "e4d9ebe5-2e62-47cf-bc35-1fb8ef7c1ef7",
         "version": "2019-05-16T015324.490566Z"
     },
-    {
-        "content-type": "application/gzip; dcp-type=data",
-        "crc32c": "56a9e200",
-        "indexed": false,
-        "name": "21784_6#51_2.fastq.gz",
-        "s3_etag": "86b0f2604a0aa1dbe3bd72d316f077f3",
-        "sha1": "d138b7a22c6fd4834f03564921a6436ebed5076e",
-        "sha256": "6a95e7f0792fe70dfcf174ee585c6900f2ed5fb401c5c8d0d15bef5e95271726",
-        "size": 7553715,
-        "uuid": "60f17b79-74d9-49b5-a6da-48580a67f11f",
-        "version": "2019-05-16T015324.739985Z"
-    },
     {
         "content-type": "application/pdf; dcp-type=data",
         "crc32c": "847325b6",
@@ -178,17 +166,5 @@
         "size": 29230,
         "uuid": "cd8e02d1-d0f9-4094-9a31-329931df60dc",
         "version": "2019-05-16T015325.251968Z"
-    },
-    {
-        "content-type": "application/pdf; dcp-type=data",
-        "crc32c": "3658ec51",
-        "indexed": false,
-        "name": "SmartSeq2_sequencing_protocol.pdf",
-        "s3_etag": "2742e1e78f6d4663bf41d3080396695c",
-        "sha1": "9ec6ee2b6e2093681c1fed694b3a8c78a2aa3438",
-        "sha256": "9c93a354a8636c041a31ba6f3fb00ef20352e1b853d8080d63a654221cb35673",
-        "size": 61134,
-        "uuid": "bf92ef4a-c422-44fb-bfc1-c2f86528b86b",
-        "version": "2019-05-16T015325.498431Z"
     }
 ]
diff --git a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
index 9c6007653..69e0dacd8 100644
--- a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
+++ b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
@@ -228,18 +228,6 @@
             "uuid": "f2b6c6f0-8d25-4aae-b255-1974cc110cfe",
             "version": "2018-09-14T12:33:43.720332Z"
         },
-        {
-            "content-type": "application/gzip; dcp-type=data",
-            "crc32c": "180453cc",
-            "indexed": false,
-            "name": "22030_5#300_1.fastq.gz",
-            "s3_etag": "e00937999e7f6e6df279c7501c846a04",
-            "sha1": "1ade3a1627214dba42db59b0f7cd138f25f096a4",
-            "sha256": "1125f2f86092798b85be93fbc66f4e733e9aec0929b558589c06929627115582",
-            "size": 64718465,
-            "uuid": "12b6c6f0-8d25-4aae-b255-1974cc110cfe",
-            "version": "1018-09-14T12:33:43.720332Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "d2417d49",
@@ -835,4 +823,4 @@
             ]
         }
     }
-}
\ No newline at end of file
+}

From eac456213e9d5b55b460afab0c06d33e92829abe Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Fri, 16 Aug 2024 20:56:30 -0700
Subject: [PATCH 08/20] Drop support for old v5 DSS bundles

---
 src/humancellatlas/data/metadata/api.py       |    64 +-
 .../2018-03-29T142048.835519Z/metadata.json   |   662 +-
 ...8-01a0-464a-9599-7375fda3353d.dss.hca.json |   868 +-
 ...c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json | 13078 ++++++++--------
 ...a-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json | 13078 ++++++++--------
 ...e-7554-4b5d-96a2-7df127a7640b.dss.hca.json |   626 +-
 ...f-4c01-48d5-a79f-1c5439659da3.dss.hca.json |   698 +-
 ...6-ced8-448a-8e45-1fc7846d8995.dss.hca.json |   626 +-
 ...9-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json | 13078 ++++++++--------
 ...8-7eaa-45f4-8077-5a3fb4204953.dss.hca.json |   660 +-
 ...9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json | 12686 ++++++++-------
 test/indexer/test_indexer.py                  |     6 +-
 12 files changed, 27911 insertions(+), 28219 deletions(-)

diff --git a/src/humancellatlas/data/metadata/api.py b/src/humancellatlas/data/metadata/api.py
index c3c8e135b..b1591af21 100644
--- a/src/humancellatlas/data/metadata/api.py
+++ b/src/humancellatlas/data/metadata/api.py
@@ -999,58 +999,30 @@ def __init__(self, uuid: str, version: str, manifest: MutableJSONs, metadata_fil
         self.version = version
         self.manifest = {m.name: m for m in map(ManifestEntry, manifest)}
 
-        def from_json(core_cls: type[E],
-                      json_entities: list[tuple[JSON, ManifestEntry]],
-                      **kwargs
-                      ) -> MutableMapping[UUID4, E]:
+        json_by_core_cls: MutableMapping[type[E], list[tuple[JSON, ManifestEntry]]] = defaultdict(list)
+        for file_name, json in metadata_files.items():
+            assert file_name.endswith('.json')
+            schema_name, _, suffix = file_name[:-5].rpartition('_')
+            if schema_name and suffix.isdigit():
+                entity_cls = entity_types[schema_name]
+                core_cls = core_types[entity_cls]
+                json_by_core_cls[core_cls].append((json, self.manifest.get(file_name)))
+
+        def from_json_vx(core_cls: type[E],
+                         **kwargs
+                         ) -> MutableMapping[UUID4, E]:
+            json_entities = json_by_core_cls[core_cls]
             entities = (
                 core_cls.from_json(entity, manifest_entry, **kwargs)
                 for entity, manifest_entry in json_entities
             )
             return {entity.document_id: entity for entity in entities}
 
-        if 'project.json' in metadata_files:
-
-            def from_json_v5(core_cls: type[E], file_name, key=None, **kwargs) -> MutableMapping[UUID4, E]:
-                file_content = metadata_files.get(file_name)
-                if file_content:
-                    manifest_entry = self.manifest.get(file_name)
-                    json_entities = file_content[key] if key else [file_content]
-                    json_entities = [(json_entity, manifest_entry) for json_entity in json_entities]
-                    return from_json(core_cls, json_entities, **kwargs)
-                else:
-                    return {}
-
-            self.projects = from_json_v5(Project, 'project.json')
-            self.biomaterials = from_json_v5(Biomaterial, 'biomaterial.json', 'biomaterials')
-            self.processes = from_json_v5(Process, 'process.json', 'processes')
-            self.protocols = from_json_v5(Protocol, 'protocol.json', 'protocols')
-            self.files = from_json_v5(File, 'file.json', 'files', manifest=self.manifest)
-
-        elif 'project_0.json' in metadata_files:
-
-            json_by_core_cls: MutableMapping[type[E], list[tuple[JSON, ManifestEntry]]] = defaultdict(list)
-            for file_name, json in metadata_files.items():
-                assert file_name.endswith('.json')
-                schema_name, _, suffix = file_name[:-5].rpartition('_')
-                if schema_name and suffix.isdigit():
-                    entity_cls = entity_types[schema_name]
-                    core_cls = core_types[entity_cls]
-                    json_by_core_cls[core_cls].append((json, self.manifest.get(file_name)))
-
-            def from_json_vx(core_cls: type[E], **kwargs) -> MutableMapping[UUID4, E]:
-                json_entities = json_by_core_cls[core_cls]
-                return from_json(core_cls, json_entities, **kwargs)
-
-            self.projects = from_json_vx(Project)
-            self.biomaterials = from_json_vx(Biomaterial)
-            self.processes = from_json_vx(Process)
-            self.protocols = from_json_vx(Protocol)
-            self.files = from_json_vx(File, manifest=self.manifest)
-
-        else:
-
-            raise RuntimeError('Unable to detect bundle structure')
+        self.projects = from_json_vx(Project)
+        self.biomaterials = from_json_vx(Biomaterial)
+        self.processes = from_json_vx(Process)
+        self.protocols = from_json_vx(Protocol)
+        self.files = from_json_vx(File, manifest=self.manifest)
 
         self.entities = {**self.projects, **self.biomaterials, **self.processes, **self.protocols, **self.files}
 
diff --git a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-03-29T142048.835519Z/metadata.json b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-03-29T142048.835519Z/metadata.json
index b147d5293..49a0fdfdd 100644
--- a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-03-29T142048.835519Z/metadata.json
+++ b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-03-29T142048.835519Z/metadata.json
@@ -1,5 +1,5 @@
 {
-    "project.json": {
+    "project_0.json": {
         "content": {
             "describedBy": "https://schema.humancellatlas.org/type/project/5.1.0/project",
             "project_core": {
@@ -98,365 +98,337 @@
         "schema_version": "5.1.0",
         "schema_type": "project_bundle"
     },
-    "biomaterial.json": {
-        "biomaterials": [
-            {
-                "content": {
-                    "genus_species": [
-                        {
-                            "text": "Mus musculus",
-                            "ontology": "NCBITaxon:10090"
-                        }
-                    ],
-                    "total_estimated_cells": 1,
-                    "target_cell_type": [
-                        {
-                            "text": "CD11b+ Macrophages/monocytes"
-                        }
-                    ],
-                    "schema_type": "biomaterial",
-                    "biomaterial_core": {
-                        "has_input_biomaterial": "1139_T",
-                        "ncbi_taxon_id": [
-                            10090
-                        ],
-                        "biomaterial_id": "22011_1#268"
-                    },
-                    "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/cell_suspension"
-                },
-                "hca_ingest": {
-                    "accession": "",
-                    "submissionDate": "2018-03-28T14:00:05.544Z",
-                    "updateDate": "2018-03-28T14:39:28.596Z",
-                    "document_id": "603a818f-dbe7-466a-8241-58b9c1618846"
-                }
-            },
-            {
-                "content": {
-                    "biomaterial_core": {
-                        "has_input_biomaterial": "1139",
-                        "ncbi_taxon_id": [
-                            10090
-                        ],
-                        "biomaterial_id": "1139_T",
-                        "supplementary_files": [
-                            "FACS_sorting_markers.pdf"
-                        ],
-                        "biomaterial_name": "Mouse_day11_T_rep5"
-                    },
-                    "genus_species": [
-                        {
-                            "text": "Mus musculus",
-                            "ontology": "NCBITaxon:10090"
-                        }
-                    ],
-                    "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/specimen_from_organism",
-                    "organ": {
-                        "text": "tumor"
-                    },
-                    "schema_type": "biomaterial"
-                },
-                "hca_ingest": {
-                    "accession": "",
-                    "submissionDate": "2018-03-28T13:55:31.072Z",
-                    "updateDate": "2018-03-28T14:15:11.657Z",
-                    "document_id": "4e41a067-dbb7-439f-b72f-80240ce858f6"
+    "cell_suspension_0.json": {
+        "content": {
+            "genus_species": [
+                {
+                    "text": "Mus musculus",
+                    "ontology": "NCBITaxon:10090"
                 }
-            },
-            {
-                "content": {
-                    "is_living": false,
-                    "mus_musculus_specific": {
-                        "strain": [
-                            {
-                                "text": "C57BL/6"
-                            }
-                        ]
-                    },
-                    "biological_sex": "female",
-                    "genus_species": [
-                        {
-                            "text": "Mus musculus",
-                            "ontology": "NCBITaxon:10090"
-                        }
-                    ],
-                    "disease": [
-                        {
-                            "text": "subcutaneous melanoma",
-                            "ontology": "EFO:0000756"
-                        }
-                    ],
-                    "organism_age": "6-12",
-                    "schema_type": "biomaterial",
-                    "biomaterial_core": {
-                        "ncbi_taxon_id": [
-                            10090
-                        ],
-                        "biomaterial_id": "1139",
-                        "biomaterial_name": "Mouse_day11_rep5"
-                    },
-                    "organism_age_unit": {
-                        "text": "week",
-                        "ontology": "UO:0000034"
-                    },
-                    "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/donor_organism"
-                },
-                "hca_ingest": {
-                    "accession": "",
-                    "submissionDate": "2018-03-28T13:58:05.518Z",
-                    "updateDate": "2018-03-28T14:01:13.757Z",
-                    "document_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410"
+            ],
+            "total_estimated_cells": 1,
+            "target_cell_type": [
+                {
+                    "text": "CD11b+ Macrophages/monocytes"
                 }
-            }
-        ],
-        "describedBy": "https://schema.humancellatlas.org/bundle/5.1.0/biomaterial",
-        "schema_version": "5.1.0",
-        "schema_type": "biomaterial_bundle"
+            ],
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "has_input_biomaterial": "1139_T",
+                "ncbi_taxon_id": [
+                    10090
+                ],
+                "biomaterial_id": "22011_1#268"
+            },
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/cell_suspension"
+        },
+        "hca_ingest": {
+            "accession": "",
+            "submissionDate": "2018-03-28T14:00:05.544Z",
+            "updateDate": "2018-03-28T14:39:28.596Z",
+            "document_id": "603a818f-dbe7-466a-8241-58b9c1618846"
+        }
     },
-    "file.json": {
-        "files": [
-            {
-                "content": {
-                    "file_core": {
-                        "file_name": "22011_1#268_1.fastq.gz",
-                        "file_format": "fastq.gz"
-                    },
-                    "lane_index": 1,
-                    "read_index": "read1",
-                    "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
-                    "schema_type": "file"
-                },
-                "hca_ingest": {
-                    "submissionDate": "2018-03-28T14:00:30.935Z",
-                    "document_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1"
+    "specimen_from_organism_1.json": {
+        "content": {
+            "biomaterial_core": {
+                "has_input_biomaterial": "1139",
+                "ncbi_taxon_id": [
+                    10090
+                ],
+                "biomaterial_id": "1139_T",
+                "supplementary_files": [
+                    "FACS_sorting_markers.pdf"
+                ],
+                "biomaterial_name": "Mouse_day11_T_rep5"
+            },
+            "genus_species": [
+                {
+                    "text": "Mus musculus",
+                    "ontology": "NCBITaxon:10090"
                 }
+            ],
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/specimen_from_organism",
+            "organ": {
+                "text": "tumor"
             },
-            {
-                "content": {
-                    "file_core": {
-                        "file_name": "22011_1#268_2.fastq.gz",
-                        "file_format": "fastq.gz"
-                    },
-                    "lane_index": 1,
-                    "read_index": "read2",
-                    "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
-                    "schema_type": "file"
-                },
-                "hca_ingest": {
-                    "submissionDate": "2018-03-28T14:00:30.947Z",
-                    "document_id": "aa662c76-d220-49f4-8316-f4af5820d60b"
-                }
-            }
-        ],
-        "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/file",
-        "schema_version": "1.0.0",
-        "schema_type": "file_bundle"
+            "schema_type": "biomaterial"
+        },
+        "hca_ingest": {
+            "accession": "",
+            "submissionDate": "2018-03-28T13:55:31.072Z",
+            "updateDate": "2018-03-28T14:15:11.657Z",
+            "document_id": "4e41a067-dbb7-439f-b72f-80240ce858f6"
+        }
     },
-    "process.json": {
-        "processes": [
-            {
-                "content": {
-                    "nucleic_acid_source": "single cell",
-                    "process_core": {
-                        "process_id": "TissueDissociationProcess",
-                        "process_name": "Extracting cells from lymph nodes"
-                    },
-                    "dissociation_method": "mechanical",
-                    "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/dissociation_process",
-                    "schema_type": "process"
-                },
-                "hca_ingest": {
-                    "accession": "",
-                    "submissionDate": "2018-03-28T14:04:14.574Z",
-                    "updateDate": "2018-03-28T14:13:28.361Z",
-                    "document_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902"
+    "donor_organism_2.json": {
+        "content": {
+            "is_living": false,
+            "mus_musculus_specific": {
+                "strain": [
+                    {
+                        "text": "C57BL/6"
+                    }
+                ]
+            },
+            "biological_sex": "female",
+            "genus_species": [
+                {
+                    "text": "Mus musculus",
+                    "ontology": "NCBITaxon:10090"
                 }
-            },
-            {
-                "content": {
-                    "process_core": {
-                        "process_id": "sampling_process_6"
-                    },
-                    "describedBy": "https://schema.humancellatlas.org/type/process/1.0.0/process",
-                    "schema_type": "process"
-                },
-                "hca_ingest": {
-                    "accession": "",
-                    "submissionDate": "2018-03-28T14:00:15.938Z",
-                    "updateDate": "2018-03-28T14:51:13.100Z",
-                    "document_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9"
+            ],
+            "disease": [
+                {
+                    "text": "subcutaneous melanoma",
+                    "ontology": "EFO:0000756"
                 }
+            ],
+            "organism_age": "6-12",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "ncbi_taxon_id": [
+                    10090
+                ],
+                "biomaterial_id": "1139",
+                "biomaterial_name": "Mouse_day11_rep5"
+            },
+            "organism_age_unit": {
+                "text": "week",
+                "ontology": "UO:0000034"
+            },
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/donor_organism"
+        },
+        "hca_ingest": {
+            "accession": "",
+            "submissionDate": "2018-03-28T13:58:05.518Z",
+            "updateDate": "2018-03-28T14:01:13.757Z",
+            "document_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410"
+        }
+    },
+    "sequence_file_0.json": {
+        "content": {
+            "file_core": {
+                "file_name": "22011_1#268_1.fastq.gz",
+                "file_format": "fastq.gz"
+            },
+            "lane_index": 1,
+            "read_index": "read1",
+            "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
+            "schema_type": "file"
+        },
+        "hca_ingest": {
+            "submissionDate": "2018-03-28T14:00:30.935Z",
+            "document_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1"
+        }
+    },
+    "sequence_file_1.json": {
+        "content": {
+            "file_core": {
+                "file_name": "22011_1#268_2.fastq.gz",
+                "file_format": "fastq.gz"
+            },
+            "lane_index": 1,
+            "read_index": "read2",
+            "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
+            "schema_type": "file"
+        },
+        "hca_ingest": {
+            "submissionDate": "2018-03-28T14:00:30.947Z",
+            "document_id": "aa662c76-d220-49f4-8316-f4af5820d60b"
+        }
+    },
+    "dissociation_process_0.json": {
+        "content": {
+            "nucleic_acid_source": "single cell",
+            "process_core": {
+                "process_id": "TissueDissociationProcess",
+                "process_name": "Extracting cells from lymph nodes"
+            },
+            "dissociation_method": "mechanical",
+            "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/dissociation_process",
+            "schema_type": "process"
+        },
+        "hca_ingest": {
+            "accession": "",
+            "submissionDate": "2018-03-28T14:04:14.574Z",
+            "updateDate": "2018-03-28T14:13:28.361Z",
+            "document_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902"
+        }
+    },
+    "process_1.json": {
+        "content": {
+            "process_core": {
+                "process_id": "sampling_process_6"
             },
-            {
-                "content": {
-                    "enrichment_method": "FACS",
-                    "process_core": {
-                        "process_id": "FACS2"
-                    },
-                    "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/enrichment_process",
-                    "markers": "CD45+ CD3e- B220- CD11c+",
-                    "schema_type": "process"
-                },
-                "hca_ingest": {
-                    "accession": "",
-                    "submissionDate": "2018-03-28T14:05:22.289Z",
-                    "updateDate": "2018-03-28T14:29:50.280Z",
-                    "document_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78"
-                }
+            "describedBy": "https://schema.humancellatlas.org/type/process/1.0.0/process",
+            "schema_type": "process"
+        },
+        "hca_ingest": {
+            "accession": "",
+            "submissionDate": "2018-03-28T14:00:15.938Z",
+            "updateDate": "2018-03-28T14:51:13.100Z",
+            "document_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9"
+        }
+    },
+    "enrichment_process_2.json": {
+        "content": {
+            "enrichment_method": "FACS",
+            "process_core": {
+                "process_id": "FACS2"
             },
-            {
-                "content": {
-                    "enrichment_method": "FACS",
-                    "process_core": {
-                        "process_id": "FACS3.7"
-                    },
-                    "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/enrichment_process",
-                    "markers": "CD45+ CD3e- B220- CD11b+",
-                    "schema_type": "process"
-                },
-                "hca_ingest": {
-                    "accession": "",
-                    "submissionDate": "2018-03-28T14:04:02.056Z",
-                    "updateDate": "2018-03-28T14:32:20.272Z",
-                    "document_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215"
-                }
+            "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/enrichment_process",
+            "markers": "CD45+ CD3e- B220- CD11c+",
+            "schema_type": "process"
+        },
+        "hca_ingest": {
+            "accession": "",
+            "submissionDate": "2018-03-28T14:05:22.289Z",
+            "updateDate": "2018-03-28T14:29:50.280Z",
+            "document_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78"
+        }
+    },
+    "enrichment_process_3.json": {
+        "content": {
+            "enrichment_method": "FACS",
+            "process_core": {
+                "process_id": "FACS3.7"
             },
-            {
-                "content": {
-                    "input_nucleic_acid_molecule": {
-                        "text": "polyA RNA",
-                        "ontology": "OBI:0000869"
-                    },
-                    "process_core": {
-                        "process_id": "lib_prep_1",
-                        "process_name": "Library preparation process"
-                    },
-                    "umi_barcode": {
-                        "barcode_offset": 0,
-                        "barcode_length": 16,
-                        "barcode_read": "Read 1"
-                    },
-                    "library_construction_approach": "Smart-seq2",
-                    "schema_type": "process",
-                    "end_bias": "full length",
-                    "primer": "poly-dT",
-                    "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/library_preparation_process",
-                    "strand": "unstranded"
-                },
-                "hca_ingest": {
-                    "accession": "",
-                    "submissionDate": "2018-03-28T14:05:43.803Z",
-                    "updateDate": "2018-03-28T14:43:01.679Z",
-                    "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
-                }
+            "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/enrichment_process",
+            "markers": "CD45+ CD3e- B220- CD11b+",
+            "schema_type": "process"
+        },
+        "hca_ingest": {
+            "accession": "",
+            "submissionDate": "2018-03-28T14:04:02.056Z",
+            "updateDate": "2018-03-28T14:32:20.272Z",
+            "document_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215"
+        }
+    },
+    "library_preparation_process_4.json": {
+        "content": {
+            "input_nucleic_acid_molecule": {
+                "text": "polyA RNA",
+                "ontology": "OBI:0000869"
+            },
+            "process_core": {
+                "process_id": "lib_prep_1",
+                "process_name": "Library preparation process"
+            },
+            "umi_barcode": {
+                "barcode_offset": 0,
+                "barcode_length": 16,
+                "barcode_read": "Read 1"
+            },
+            "library_construction_approach": "Smart-seq2",
+            "schema_type": "process",
+            "end_bias": "full length",
+            "primer": "poly-dT",
+            "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/library_preparation_process",
+            "strand": "unstranded"
+        },
+        "hca_ingest": {
+            "accession": "",
+            "submissionDate": "2018-03-28T14:05:43.803Z",
+            "updateDate": "2018-03-28T14:43:01.679Z",
+            "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
+        }
+    },
+    "sequencing_process_5.json": {
+        "content": {
+            "paired_ends": true,
+            "instrument_manufacturer_model": {
+                "text": "Illumina HiSeq 2500",
+                "ontology": "EFO:0008567"
             },
-            {
-                "content": {
-                    "paired_ends": true,
-                    "instrument_manufacturer_model": {
-                        "text": "Illumina HiSeq 2500",
-                        "ontology": "EFO:0008567"
-                    },
-                    "process_core": {
-                        "process_id": "seq_264",
-                        "process_name": "Sequencing process"
-                    },
-                    "smartseq2": {
-                        "well_name": "F02",
-                        "plate_id": "575"
-                    },
-                    "schema_type": "process",
-                    "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/sequencing_process"
-                },
-                "hca_ingest": {
-                    "accession": "",
-                    "submissionDate": "2018-03-28T14:03:27.156Z",
-                    "updateDate": "2018-03-28T14:32:54.422Z",
-                    "document_id": "2580dcf9-3f7d-4421-b962-ab860e10d072"
-                }
-            }
-        ],
-        "describedBy": "https://schema.humancellatlas.org/bundle/5.2.1/process",
-        "schema_version": "5.2.1",
-        "schema_type": "process_bundle"
+            "process_core": {
+                "process_id": "seq_264",
+                "process_name": "Sequencing process"
+            },
+            "smartseq2": {
+                "well_name": "F02",
+                "plate_id": "575"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/sequencing_process"
+        },
+        "hca_ingest": {
+            "accession": "",
+            "submissionDate": "2018-03-28T14:03:27.156Z",
+            "updateDate": "2018-03-28T14:32:54.422Z",
+            "document_id": "2580dcf9-3f7d-4421-b962-ab860e10d072"
+        }
     },
-    "protocol.json": {
-        "protocols": [
-            {
-                "content": {
-                    "protocol_core": {
-                        "protocol_name": "Extracting cells from lymph nodes",
-                        "document": "TissueDissociationProtocol.pdf",
-                        "protocol_id": "tissue_dissociation_protocol"
-                    },
-                    "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                    "schema_type": "protocol"
-                },
-                "hca_ingest": {
-                    "accession": "",
-                    "submissionDate": "2018-03-28T13:55:26.033Z",
-                    "updateDate": "2018-03-28T14:14:33.716Z",
-                    "document_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127"
-                }
+    "protocol_0.json": {
+        "content": {
+            "protocol_core": {
+                "protocol_name": "Extracting cells from lymph nodes",
+                "document": "TissueDissociationProtocol.pdf",
+                "protocol_id": "tissue_dissociation_protocol"
             },
-            {
-                "content": {
-                    "protocol_core": {
-                        "protocol_name": "FACS sorting cells by surface markers",
-                        "document": "FACSsortingProtocol.pdf",
-                        "protocol_id": "FACS_sorting_protocol"
-                    },
-                    "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                    "schema_type": "protocol"
-                },
-                "hca_ingest": {
-                    "accession": "",
-                    "submissionDate": "2018-03-28T13:55:26.040Z",
-                    "updateDate": "2018-03-28T14:45:43.500Z",
-                    "document_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6"
-                }
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+            "schema_type": "protocol"
+        },
+        "hca_ingest": {
+            "accession": "",
+            "submissionDate": "2018-03-28T13:55:26.033Z",
+            "updateDate": "2018-03-28T14:14:33.716Z",
+            "document_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127"
+        }
+    },
+    "protocol_1.json": {
+        "content": {
+            "protocol_core": {
+                "protocol_name": "FACS sorting cells by surface markers",
+                "document": "FACSsortingProtocol.pdf",
+                "protocol_id": "FACS_sorting_protocol"
             },
-            {
-                "content": {
-                    "protocol_core": {
-                        "protocol_name": "Make/amplify cDNA for each cell",
-                        "document": "SmartSeq2_RTPCR_protocol.pdf",
-                        "protocol_id": "SmartSeq2_RTPCR_protocol"
-                    },
-                    "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                    "protocol_type": {
-                        "text": "Smart-seq2 protocol",
-                        "ontology": "EFO:0008442"
-                    },
-                    "schema_type": "protocol"
-                },
-                "hca_ingest": {
-                    "accession": "",
-                    "submissionDate": "2018-03-28T13:55:26.044Z",
-                    "updateDate": "2018-03-28T14:24:04.790Z",
-                    "document_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643"
-                }
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+            "schema_type": "protocol"
+        },
+        "hca_ingest": {
+            "accession": "",
+            "submissionDate": "2018-03-28T13:55:26.040Z",
+            "updateDate": "2018-03-28T14:45:43.500Z",
+            "document_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6"
+        }
+    },
+    "protocol_2.json": {
+        "content": {
+            "protocol_core": {
+                "protocol_name": "Make/amplify cDNA for each cell",
+                "document": "SmartSeq2_RTPCR_protocol.pdf",
+                "protocol_id": "SmartSeq2_RTPCR_protocol"
             },
-            {
-                "content": {
-                    "protocol_core": {
-                        "protocol_name": "Sequencing SmartSeq2 cells",
-                        "protocol_id": "SmartSeq2_sequencing_protocol"
-                    },
-                    "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                    "schema_type": "protocol"
-                },
-                "hca_ingest": {
-                    "accession": "",
-                    "submissionDate": "2018-03-28T13:55:26.050Z",
-                    "updateDate": "2018-03-28T14:30:39.321Z",
-                    "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
-                }
-            }
-        ],
-        "describedBy": "https://schema.humancellatlas.org/bundle/5.1.0/protocol",
-        "schema_version": "5.1.0",
-        "schema_type": "protocol_bundle"
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+            "protocol_type": {
+                "text": "Smart-seq2 protocol",
+                "ontology": "EFO:0008442"
+            },
+            "schema_type": "protocol"
+        },
+        "hca_ingest": {
+            "accession": "",
+            "submissionDate": "2018-03-28T13:55:26.044Z",
+            "updateDate": "2018-03-28T14:24:04.790Z",
+            "document_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643"
+        }
+    },
+    "protocol_3.json": {
+        "content": {
+            "protocol_core": {
+                "protocol_name": "Sequencing SmartSeq2 cells",
+                "protocol_id": "SmartSeq2_sequencing_protocol"
+            },
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+            "schema_type": "protocol"
+        },
+        "hca_ingest": {
+            "accession": "",
+            "submissionDate": "2018-03-28T13:55:26.050Z",
+            "updateDate": "2018-03-28T14:30:39.321Z",
+            "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
+        }
     },
     "links.json": {
         "links": [
@@ -603,4 +575,4 @@
         "schema_version": "1.0.0",
         "schema_type": "link_bundle"
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json b/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
index 5e757ec1c..e387a8926 100644
--- a/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
+++ b/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
@@ -146,7 +146,7 @@
         }
     ],
     "metadata": {
-        "project.json": {
+        "project_0.json": {
             "content": {
                 "contributors": [
                     {
@@ -250,462 +250,434 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
         },
-        "biomaterial.json": {
-            "biomaterials": [
-                {
-                    "content": {
-                        "biomaterial_core": {
-                            "has_input_biomaterial": "A1-Spl-0-TL5",
-                            "ncbi_taxon_id": [
-                                9606
-                            ],
-                            "biomaterial_id": "A1-Spl-0-TL5_cells",
-                            "biomaterial_name": "cells from fresh spleen"
-                        },
-                        "genus_species": [
-                            {
-                                "text": "Homo sapiens",
-                                "ontology": "NCBITaxon:9606"
-                            }
-                        ],
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/cell_suspension",
-                        "total_estimated_cells": 39300000,
-                        "schema_type": "biomaterial"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-27T13:10:38.189Z",
-                        "updateDate": "2018-03-27T13:10:43.316Z",
-                        "document_id": "a86b1fda-bb1d-4ef8-87d9-392517d4a937"
-                    }
-                },
-                {
-                    "content": {
-                        "state_of_specimen": {
-                            "ischemic_time": 7200,
-                            "gross_image": [
-                                "284C_IMAGE_spleen_annotated.jpg"
-                            ],
-                            "postmortem_interval": 19800,
-                            "ischemic_temperature": "warm",
-                            "microscopic_description": "dead cells are quite faint on microscope at LMB"
-                        },
-                        "organ": {
-                            "text": "spleen",
-                            "ontology": "UBERON:0002106"
-                        },
-                        "genus_species": [
-                            {
-                                "text": "Homo sapiens",
-                                "ontology": "NCBITaxon:9606"
-                            }
-                        ],
-                        "schema_type": "biomaterial",
-                        "biomaterial_core": {
-                            "biomaterial_description": "fresh spleen",
-                            "has_input_biomaterial": "284C-A1",
-                            "biomaterial_name": "284C_spleen_fresh",
-                            "supplementary_files": [
-                                "284C_IMAGE_spleen_annotated.jpeg"
-                            ],
-                            "ncbi_taxon_id": [
-                                9606
-                            ],
-                            "biomaterial_id": "A1-Spl-0-TL5"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/specimen_from_organism"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-27T13:10:38.291Z",
-                        "updateDate": "2018-03-27T13:10:43.420Z",
-                        "document_id": "d231b8f3-8fa3-4f3b-a8e5-66eca6228ae7"
-                    }
-                },
-                {
-                    "content": {
-                        "is_living": false,
-                        "death": {
-                            "cause_of_death": "Hypoxic brain damage",
-                            "cold_perfused": false
-                        },
-                        "biological_sex": "male",
-                        "weight": "80-85",
-                        "disease": [
-                            {
-                                "text": "normal",
-                                "ontology": "PATO:0000461"
-                            }
-                        ],
-                        "genus_species": [
-                            {
-                                "text": "Homo sapiens",
-                                "ontology": "NCBITaxon:9606"
-                            }
-                        ],
-                        "height_unit": {
-                            "text": "meter",
-                            "ontology": "UO:0000008"
-                        },
-                        "height": "1.75-1.8",
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/donor_organism",
-                        "organism_age": "55-60",
-                        "schema_type": "biomaterial",
-                        "biomaterial_core": {
-                            "biomaterial_id": "284C-A1",
-                            "ncbi_taxon_id": [
-                                9606
-                            ],
-                            "biomaterial_description": "Spleen",
-                            "biomaterial_name": "284C-spleen"
-                        },
-                        "medical_history": {
-                            "alcohol_history": "3-6 units/day",
-                            "smoking_history": "Smoker, 20/day for 25 years, stopped 2000"
-                        },
-                        "organism_age_unit": {
-                            "text": "year",
-                            "ontology": "UO:0000036"
-                        },
-                        "development_stage": {
-                            "text": "adult",
-                            "ontology": "EFO:0001272"
-                        },
-                        "weight_unit": {
-                            "text": "kg",
-                            "ontology": "UO:0000009"
-                        }
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-27T13:10:38.212Z",
-                        "updateDate": "2018-03-27T13:10:46.762Z",
-                        "document_id": "9a7acc6d-8352-497e-b162-5e63b380366f"
-                    }
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/5.1.0/biomaterial",
-            "schema_version": "5.1.0",
-            "schema_type": "biomaterial_bundle"
-        },
-        "file.json": {
-            "files": [
-                {
-                    "content": {
-                        "file_core": {
-                            "file_name": "HCATisStabAug177078016_S1_L001_I1_001.fastq.gz",
-                            "file_format": "fastq.gz"
-                        },
-                        "lane_index": 1,
-                        "read_index": "index1",
-                        "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
-                        "schema_type": "file"
-                    },
-                    "hca_ingest": {
-                        "submissionDate": "2018-03-27T13:10:38.480Z",
-                        "document_id": "49fddace-4c59-41c1-8930-0707460132d7"
-                    }
-                },
-                {
-                    "content": {
-                        "file_core": {
-                            "file_name": "HCATisStabAug177078016_S1_L001_R1_001.fastq.gz",
-                            "file_format": "fastq.gz"
-                        },
-                        "lane_index": 1,
-                        "read_index": "read1",
-                        "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
-                        "schema_type": "file"
-                    },
-                    "hca_ingest": {
-                        "submissionDate": "2018-03-27T13:10:38.490Z",
-                        "document_id": "771d9bcb-a5ff-43b5-b3e8-e738cc4c05bf"
-                    }
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+                    "ontology": "OBI:0000869"
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                 },
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+                    "ontology": "EFO:0008563"
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+                    "protocol_description": "ChromiumTM Single Cell 3' Library & Gel Bead Kit v2",
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diff --git a/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json b/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
index 3aaf5bcb5..6955a5cb9 100644
--- a/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
+++ b/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
@@ -2306,7 +2306,7 @@
         }
     ],
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             "content": {
                 "describedBy": "https://schema.humancellatlas.org/type/project/5.1.0/project",
                 "project_core": {
@@ -2435,6727 +2435,6699 @@
             "schema_version": "5.1.0",
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         },
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-                {
-                    "content": {
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-                            {
-                                "text": "Homo sapiens",
-                                "ontology": "NCBITaxon:9606"
-                            }
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-                        "target_cell_type": [
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-                                "text": "bone marrow hematopoietic cell",
-                                "ontology": "CL:1001610"
-                            }
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-                        "biomaterial_core": {
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-                            "ncbi_taxon_id": [
-                                9606
-                            ],
-                            "biomaterial_id": "3_BM1_cells"
-                        },
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-                        "document_id": "78e48232-86ed-4b68-ae64-df114f02fa80"
+        "cell_suspension_0.json": {
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+                "genus_species": [
+                    {
+                        "text": "Homo sapiens",
+                        "ontology": "NCBITaxon:9606"
                     }
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+                ],
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+                "target_cell_type": [
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+                        "text": "bone marrow hematopoietic cell",
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                     }
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+                    "ontology": "UBERON:0002390"
                 },
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-                        "document_id": "01f2d4b7-7746-4dc0-88d7-4cb0b3dbb370"
+                "genus_species": [
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+                "biological_sex": "female",
+                "genus_species": [
+                    {
+                        "text": "Homo sapiens",
+                        "ontology": "NCBITaxon:9606"
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+                        "text": "Homo sapiens",
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diff --git a/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json b/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json
index a2ec29415..860e0de64 100644
--- a/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json
+++ b/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json
@@ -2306,7 +2306,7 @@
         }
     ],
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@@ -2435,6727 +2435,6699 @@
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+        "sequencing_process_65.json": {
+            "content": {
+                "paired_ends": true,
+                "local_machine_name": "HXH",
+                "instrument_manufacturer_model": {
+                    "text": "Illumina Hiseq X 10",
+                    "ontology": "EFO:0008567"
+                },
+                "process_type": {
+                    "text": "10x sequencing process"
+                },
+                "process_core": {
+                    "process_description": "Single cell sequencing of cDNAs by 10x",
+                    "process_name": "Sequencing cord blood donor 1-4",
+                    "process_id": "10x_v2_sequencing_process_3",
+                    "start_time": "2017-09-26T05:01:00Z",
+                    "process_location": "Broad Institute"
+                },
+                "schema_type": "process",
+                "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/sequencing_process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-26T17:00:06.910Z",
+                "updateDate": "2018-03-26T17:00:53.514Z",
+                "document_id": "49aa3970-895a-44bb-9433-3b49373794f3"
+            }
+        },
+        "protocol_0.json": {
+            "content": {
+                "protocol_core": {
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                 },
-                {
-                    "content": {
-                        "process_core": {
-                            "process_id": "sampling_process_83"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/process/1.0.0/process",
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-                        "submissionDate": "2018-03-26T16:59:40.948Z",
-                        "updateDate": "2018-03-26T17:00:00.142Z",
-                        "document_id": "f963aea9-4016-4570-88f3-66f2046be874"
-                    }
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "schema_type": "protocol"
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+                "submissionDate": "2018-03-26T16:59:18.834Z",
+                "updateDate": "2018-03-26T16:59:27.584Z",
+                "document_id": "3cbebf0a-4aab-4525-80f4-222703d14b98"
+            }
+        },
+        "protocol_1.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_id": "library_preparation_protocol_1"
                 },
-                {
-                    "content": {
-                        "input_nucleic_acid_molecule": {
-                            "text": "polyA RNA",
-                            "ontology": "OBI:0000869"
-                        },
-                        "process_type": {
-                            "text": "10x sequencing process"
-                        },
-                        "process_core": {
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-                            "process_name": "Preparing RNA for sequencing by 10x"
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-                            "barcode_length": 10,
-                            "barcode_read": "Read 1"
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-                        "cell_barcode": {
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-                            "barcode_length": 16,
-                            "barcode_read": "Read 1"
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-                        "schema_type": "process",
-                        "end_bias": "3 prime tag",
-                        "primer": "poly-dT",
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-                        "document_id": "12ea2953-06a4-4e80-8910-a27aba936b9c"
-                    }
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "protocol_type": {
+                    "text": "10x sequencing protocol",
+                    "ontology": "EFO:0008443"
                 },
-                {
-                    "content": {
-                        "paired_ends": true,
-                        "local_machine_name": "HXH",
-                        "instrument_manufacturer_model": {
-                            "text": "Illumina Hiseq X 10",
-                            "ontology": "EFO:0008567"
-                        },
-                        "process_type": {
-                            "text": "10x sequencing process"
-                        },
-                        "process_core": {
-                            "process_description": "Single cell sequencing of cDNAs by 10x",
-                            "process_name": "Sequencing cord blood donor 1-4",
-                            "process_id": "10x_v2_sequencing_process_3",
-                            "start_time": "2017-09-26T05:01:00Z",
-                            "process_location": "Broad Institute"
-                        },
-                        "schema_type": "process",
-                        "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/sequencing_process"
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-                    "content": {
-                        "protocol_core": {
-                            "protocol_id": "dissociation_protocol_1"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
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-                        "document_id": "3cbebf0a-4aab-4525-80f4-222703d14b98"
-                    }
+                "schema_type": "protocol"
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+                "updateDate": "2018-03-26T16:59:29.761Z",
+                "document_id": "81b97ec1-f68c-4d69-be78-50d1aad7bbef"
+            }
+        },
+        "protocol_2.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_id": "10x_v2_sequencing_protocol_1"
                 },
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_id": "library_preparation_protocol_1"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "protocol_type": {
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-                        },
-                        "schema_type": "protocol"
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-                        "document_id": "81b97ec1-f68c-4d69-be78-50d1aad7bbef"
-                    }
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "protocol_type": {
+                    "text": "10x sequencing protocol",
+                    "ontology": "EFO:0008443"
                 },
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_id": "10x_v2_sequencing_protocol_1"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "protocol_type": {
-                            "text": "10x sequencing protocol",
-                            "ontology": "EFO:0008443"
-                        },
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-                        "submissionDate": "2018-03-26T16:59:18.860Z",
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-            "describedBy": "https://schema.humancellatlas.org/bundle/5.1.0/protocol",
-            "schema_version": "5.1.0",
-            "schema_type": "protocol_bundle"
+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-26T16:59:18.860Z",
+                "updateDate": "2018-03-26T16:59:27.537Z",
+                "document_id": "e99eed63-5794-4d8d-baf9-9c6888e91e6d"
+            }
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         "links.json": {
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diff --git a/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json b/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json
index cfaa555d8..9ac543d2c 100644
--- a/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json
+++ b/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json
@@ -26,83 +26,76 @@
         }
     ],
     "metadata": {
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-            "protocols": [
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_name": "Extracting cells from lymph nodes",
-                            "document": "TissueDissociationProtocol.pdf",
-                            "protocol_id": "tissue_dissociation_protocol"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "schema_type": "protocol"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:55:26.033Z",
-                        "updateDate": "2018-03-28T14:14:33.716Z",
-                        "document_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127"
-                    }
+        "protocol_0.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_name": "Extracting cells from lymph nodes",
+                    "document": "TissueDissociationProtocol.pdf",
+                    "protocol_id": "tissue_dissociation_protocol"
                 },
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_name": "FACS sorting cells by surface markers",
-                            "document": "FACSsortingProtocol.pdf",
-                            "protocol_id": "FACS_sorting_protocol"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "schema_type": "protocol"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:55:26.040Z",
-                        "updateDate": "2018-03-28T14:45:43.500Z",
-                        "document_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6"
-                    }
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:26.033Z",
+                "updateDate": "2018-03-28T14:14:33.716Z",
+                "document_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127"
+            }
+        },
+        "protocol_1.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_name": "FACS sorting cells by surface markers",
+                    "document": "FACSsortingProtocol.pdf",
+                    "protocol_id": "FACS_sorting_protocol"
                 },
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_name": "Make/amplify cDNA for each cell",
-                            "document": "SmartSeq2_RTPCR_protocol.pdf",
-                            "protocol_id": "SmartSeq2_RTPCR_protocol"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "protocol_type": {
-                            "text": "Smart-seq2 protocol",
-                            "ontology": "EFO:0008442"
-                        },
-                        "schema_type": "protocol"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:55:26.044Z",
-                        "updateDate": "2018-03-28T14:24:04.790Z",
-                        "document_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643"
-                    }
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "schema_type": "protocol"
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+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:26.040Z",
+                "updateDate": "2018-03-28T14:45:43.500Z",
+                "document_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6"
+            }
+        },
+        "protocol_2.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_name": "Make/amplify cDNA for each cell",
+                    "document": "SmartSeq2_RTPCR_protocol.pdf",
+                    "protocol_id": "SmartSeq2_RTPCR_protocol"
                 },
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_name": "Sequencing SmartSeq2 cells",
-                            "protocol_id": "SmartSeq2_sequencing_protocol"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "schema_type": "protocol"
-                    },
-                    "hca_ingest": {
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-                        "submissionDate": "2018-03-28T13:55:26.050Z",
-                        "updateDate": "2018-03-28T14:30:39.321Z",
-                        "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
-                    }
-                }
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-            "describedBy": "https://schema.humancellatlas.org/bundle/5.1.0/protocol",
-            "schema_version": "5.1.0",
-            "schema_type": "protocol_bundle"
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "protocol_type": {
+                    "text": "Smart-seq2 protocol",
+                    "ontology": "EFO:0008442"
+                },
+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:26.044Z",
+                "updateDate": "2018-03-28T14:24:04.790Z",
+                "document_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643"
+            }
+        },
+        "protocol_3.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_name": "Sequencing SmartSeq2 cells",
+                    "protocol_id": "SmartSeq2_sequencing_protocol"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:26.050Z",
+                "updateDate": "2018-03-28T14:30:39.321Z",
+                "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
+            }
         },
         "links.json": {
             "links": [
@@ -219,7 +212,7 @@
             "schema_version": "1.0.0",
             "schema_type": "link_bundle"
         },
-        "project.json": {
+        "project_0.json": {
             "content": {
                 "describedBy": "https://schema.humancellatlas.org/type/project/9.0.2/project",
                 "project_core": {
@@ -343,270 +336,249 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
         },
-        "biomaterial.json": {
-            "biomaterials": [
-                {
-                    "content": {
-                        "genus_species": [
-                            {
-                                "text": "Mus musculus",
-                                "ontology": "NCBITaxon:10090"
-                            }
-                        ],
-                        "total_estimated_cells": 1,
-                        "target_cell_type": [
-                            {
-                                "text": "CD11b+ Macrophages/monocytes"
-                            }
-                        ],
-                        "schema_type": "biomaterial",
-                        "biomaterial_core": {
-                            "has_input_biomaterial": "1117_T",
-                            "ncbi_taxon_id": [
-                                10090
-                            ],
-                            "biomaterial_id": "22467_6#209"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/cell_suspension"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:58:57.160Z",
-                        "updateDate": "2018-03-28T14:27:46.870Z",
-                        "document_id": "04e58fb0-384e-4997-a9e9-575d9887e737"
+        "cell_suspension_0.json": {
+            "content": {
+                "genus_species": [
+                    {
+                        "text": "Mus musculus",
+                        "ontology": "NCBITaxon:10090"
                     }
-                },
-                {
-                    "content": {
-                        "biomaterial_core": {
-                            "has_input_biomaterial": "1117",
-                            "ncbi_taxon_id": [
-                                10090
-                            ],
-                            "biomaterial_id": "1117_T",
-                            "supplementary_files": [
-                                "FACS_sorting_markers.pdf"
-                            ],
-                            "biomaterial_name": "Mouse_day5_T_rep8"
-                        },
-                        "genus_species": [
-                            {
-                                "text": "Mus musculus",
-                                "ontology": "NCBITaxon:10090"
-                            }
-                        ],
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/specimen_from_organism",
-                        "organ": {
-                            "text": "tumor"
-                        },
-                        "schema_type": "biomaterial"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:56:12.647Z",
-                        "updateDate": "2018-03-28T14:19:05.173Z",
-                        "document_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c"
+                ],
+                "total_estimated_cells": 1,
+                "target_cell_type": [
+                    {
+                        "text": "CD11b+ Macrophages/monocytes"
                     }
+                ],
+                "schema_type": "biomaterial",
+                "biomaterial_core": {
+                    "has_input_biomaterial": "1117_T",
+                    "ncbi_taxon_id": [
+                        10090
+                    ],
+                    "biomaterial_id": "22467_6#209"
                 },
-                {
-                    "content": {
-                        "is_living": false,
-                        "mus_musculus_specific": {
-                            "strain": [
-                                {
-                                    "text": "C57BL/6"
-                                }
-                            ]
-                        },
-                        "biological_sex": "female",
-                        "genus_species": [
-                            {
-                                "text": "Mus musculus",
-                                "ontology": "NCBITaxon:10090"
-                            }
-                        ],
-                        "disease": [
-                            {
-                                "text": "subcutaneous melanoma",
-                                "ontology": "EFO:0000756"
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-                        "organism_age": "6-12",
-                        "schema_type": "biomaterial",
-                        "biomaterial_core": {
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-                                10090
-                            ],
-                            "biomaterial_id": "1117",
-                            "biomaterial_name": "Mouse_day5_rep8"
-                        },
-                        "organism_age_unit": {
-                            "text": "week",
-                            "ontology": "UO:0000034"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/donor_organism"
-                    },
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-                        "submissionDate": "2018-03-28T13:56:00.553Z",
-                        "updateDate": "2018-03-28T14:00:16.892Z",
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-            "describedBy": "https://schema.humancellatlas.org/bundle/5.1.0/biomaterial",
-            "schema_version": "5.1.0",
-            "schema_type": "biomaterial_bundle"
+                "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/cell_suspension"
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+                "accession": "",
+                "submissionDate": "2018-03-28T13:58:57.160Z",
+                "updateDate": "2018-03-28T14:27:46.870Z",
+                "document_id": "04e58fb0-384e-4997-a9e9-575d9887e737"
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-                    "content": {
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-                        "process_core": {
-                            "process_id": "TissueDissociationProcess",
-                            "process_name": "Extracting cells from lymph nodes"
-                        },
-                        "dissociation_method": "mechanical",
-                        "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/dissociation_process",
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-                        "submissionDate": "2018-03-28T14:04:14.574Z",
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-                        "document_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902"
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+        "specimen_from_organism_1.json": {
+            "content": {
+                "biomaterial_core": {
+                    "has_input_biomaterial": "1117",
+                    "ncbi_taxon_id": [
+                        10090
+                    ],
+                    "biomaterial_id": "1117_T",
+                    "supplementary_files": [
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                 },
-                {
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-                        "process_core": {
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-                        "document_id": "0763320a-e0c4-4c07-b150-b83650fbef68"
+                "genus_species": [
+                    {
+                        "text": "Mus musculus",
+                        "ontology": "NCBITaxon:10090"
                     }
+                ],
+                "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/specimen_from_organism",
+                "organ": {
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                 },
-                {
-                    "content": {
-                        "enrichment_method": "FACS",
-                        "process_core": {
-                            "process_id": "FACS3.2"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/enrichment_process",
-                        "markers": "CD45+ CD3e- B220- CD11b+",
-                        "schema_type": "process"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T14:04:02.006Z",
-                        "updateDate": "2018-03-28T14:15:18.962Z",
-                        "document_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4"
-                    }
+                "schema_type": "biomaterial"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:56:12.647Z",
+                "updateDate": "2018-03-28T14:19:05.173Z",
+                "document_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c"
+            }
+        },
+        "donor_organism_2.json": {
+            "content": {
+                "is_living": false,
+                "mus_musculus_specific": {
+                    "strain": [
+                        {
+                            "text": "C57BL/6"
+                        }
+                    ]
                 },
-                {
-                    "content": {
-                        "input_nucleic_acid_molecule": {
-                            "text": "polyA RNA",
-                            "ontology": "OBI:0000869"
-                        },
-                        "process_core": {
-                            "process_id": "lib_prep_1",
-                            "process_name": "Library preparation process"
-                        },
-                        "umi_barcode": {
-                            "barcode_offset": 0,
-                            "barcode_length": 16,
-                            "barcode_read": "Read 1"
-                        },
-                        "library_construction_approach": "Smart-seq2",
-                        "schema_type": "process",
-                        "end_bias": "full length",
-                        "primer": "poly-dT",
-                        "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/library_preparation_process",
-                        "strand": "unstranded"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T14:05:43.803Z",
-                        "updateDate": "2018-03-28T14:43:01.679Z",
-                        "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
+                "biological_sex": "female",
+                "genus_species": [
+                    {
+                        "text": "Mus musculus",
+                        "ontology": "NCBITaxon:10090"
                     }
-                },
-                {
-                    "content": {
-                        "paired_ends": true,
-                        "instrument_manufacturer_model": {
-                            "text": "Illumina HiSeq 2500",
-                            "ontology": "EFO:0008567"
-                        },
-                        "process_core": {
-                            "process_id": "seq_5656",
-                            "process_name": "Sequencing process"
-                        },
-                        "smartseq2": {
-                            "well_name": "D5",
-                            "plate_id": "537"
-                        },
-                        "schema_type": "process",
-                        "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/sequencing_process"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T14:05:51.198Z",
-                        "updateDate": "2018-03-28T14:10:52.303Z",
-                        "document_id": "4624400f-00c5-476a-9bd6-589e87ddb0fe"
+                ],
+                "disease": [
+                    {
+                        "text": "subcutaneous melanoma",
+                        "ontology": "EFO:0000756"
                     }
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/5.2.1/process",
-            "schema_version": "5.2.1",
-            "schema_type": "process_bundle"
+                ],
+                "organism_age": "6-12",
+                "schema_type": "biomaterial",
+                "biomaterial_core": {
+                    "ncbi_taxon_id": [
+                        10090
+                    ],
+                    "biomaterial_id": "1117",
+                    "biomaterial_name": "Mouse_day5_rep8"
+                },
+                "organism_age_unit": {
+                    "text": "week",
+                    "ontology": "UO:0000034"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/donor_organism"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:56:00.553Z",
+                "updateDate": "2018-03-28T14:00:16.892Z",
+                "document_id": "689311a2-bfaf-4196-a753-554e69ab59b2"
+            }
         },
-        "file.json": {
-            "files": [
-                {
-                    "content": {
-                        "file_core": {
-                            "file_name": "22467_6#209_1.fastq.gz",
-                            "file_format": "fastq.gz"
-                        },
-                        "lane_index": 6,
-                        "read_index": "read1",
-                        "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
-                        "schema_type": "file"
-                    },
-                    "hca_ingest": {
-                        "submissionDate": "2018-03-28T14:02:56.078Z",
-                        "document_id": "2d8cdf91-8162-4321-9923-e00e90fd9133"
-                    }
+        "dissociation_process_0.json": {
+            "content": {
+                "nucleic_acid_source": "single cell",
+                "process_core": {
+                    "process_id": "TissueDissociationProcess",
+                    "process_name": "Extracting cells from lymph nodes"
                 },
-                {
-                    "content": {
-                        "file_core": {
-                            "file_name": "22467_6#209_2.fastq.gz",
-                            "file_format": "fastq.gz"
-                        },
-                        "lane_index": 6,
-                        "read_index": "read2",
-                        "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
-                        "schema_type": "file"
-                    },
-                    "hca_ingest": {
-                        "submissionDate": "2018-03-28T14:02:56.090Z",
-                        "document_id": "d9087c74-a41e-4702-8481-cea3ef68379c"
-                    }
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/file",
-            "schema_version": "1.0.0",
-            "schema_type": "file_bundle"
+                "dissociation_method": "mechanical",
+                "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/dissociation_process",
+                "schema_type": "process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:04:14.574Z",
+                "updateDate": "2018-03-28T14:13:28.361Z",
+                "document_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902"
+            }
+        },
+        "process_1.json": {
+            "content": {
+                "process_core": {
+                    "process_id": "sampling_process_12"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/process/1.0.0/process",
+                "schema_type": "process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:00:16.640Z",
+                "updateDate": "2018-03-28T14:00:59.234Z",
+                "document_id": "0763320a-e0c4-4c07-b150-b83650fbef68"
+            }
+        },
+        "enrichment_process_2.json": {
+            "content": {
+                "enrichment_method": "FACS",
+                "process_core": {
+                    "process_id": "FACS3.2"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/enrichment_process",
+                "markers": "CD45+ CD3e- B220- CD11b+",
+                "schema_type": "process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:04:02.006Z",
+                "updateDate": "2018-03-28T14:15:18.962Z",
+                "document_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4"
+            }
+        },
+        "library_preparation_process_3.json": {
+            "content": {
+                "input_nucleic_acid_molecule": {
+                    "text": "polyA RNA",
+                    "ontology": "OBI:0000869"
+                },
+                "process_core": {
+                    "process_id": "lib_prep_1",
+                    "process_name": "Library preparation process"
+                },
+                "umi_barcode": {
+                    "barcode_offset": 0,
+                    "barcode_length": 16,
+                    "barcode_read": "Read 1"
+                },
+                "library_construction_approach": "Smart-seq2",
+                "schema_type": "process",
+                "end_bias": "full length",
+                "primer": "poly-dT",
+                "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/library_preparation_process",
+                "strand": "unstranded"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:05:43.803Z",
+                "updateDate": "2018-03-28T14:43:01.679Z",
+                "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
+            }
+        },
+        "sequencing_process_4.json": {
+            "content": {
+                "paired_ends": true,
+                "instrument_manufacturer_model": {
+                    "text": "Illumina HiSeq 2500",
+                    "ontology": "EFO:0008567"
+                },
+                "process_core": {
+                    "process_id": "seq_5656",
+                    "process_name": "Sequencing process"
+                },
+                "smartseq2": {
+                    "well_name": "D5",
+                    "plate_id": "537"
+                },
+                "schema_type": "process",
+                "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/sequencing_process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:05:51.198Z",
+                "updateDate": "2018-03-28T14:10:52.303Z",
+                "document_id": "4624400f-00c5-476a-9bd6-589e87ddb0fe"
+            }
+        },
+        "sequence_file_0.json": {
+            "content": {
+                "file_core": {
+                    "file_name": "22467_6#209_1.fastq.gz",
+                    "file_format": "fastq.gz"
+                },
+                "lane_index": 6,
+                "read_index": "read1",
+                "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
+                "schema_type": "file"
+            },
+            "hca_ingest": {
+                "submissionDate": "2018-03-28T14:02:56.078Z",
+                "document_id": "2d8cdf91-8162-4321-9923-e00e90fd9133"
+            }
+        },
+        "sequence_file_1.json": {
+            "content": {
+                "file_core": {
+                    "file_name": "22467_6#209_2.fastq.gz",
+                    "file_format": "fastq.gz"
+                },
+                "lane_index": 6,
+                "read_index": "read2",
+                "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
+                "schema_type": "file"
+            },
+            "hca_ingest": {
+                "submissionDate": "2018-03-28T14:02:56.090Z",
+                "document_id": "d9087c74-a41e-4702-8481-cea3ef68379c"
+            }
         }
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json b/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
index 2299f575b..0f18ef57e 100644
--- a/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
+++ b/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
@@ -26,7 +26,7 @@
         }
     ],
     "metadata": {
-        "project.json": {
+        "project_0.json": {
             "content": {
                 "describedBy": "https://schema.humancellatlas.org/type/project/5.1.0/project",
                 "project_core": {
@@ -150,386 +150,358 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
         },
-        "biomaterial.json": {
-            "biomaterials": [
-                {
-                    "content": {
-                        "genus_species": [
-                            {
-                                "text": "Mus musculus",
-                                "ontology": "NCBITaxon:10090"
-                            }
-                        ],
-                        "total_estimated_cells": 1,
-                        "target_cell_type": [
-                            {
-                                "text": "CD4+ T cell",
-                                "ontology": "CL:0000624"
-                            }
-                        ],
-                        "schema_type": "biomaterial",
-                        "biomaterial_core": {
-                            "has_input_biomaterial": "1134_LN",
-                            "ncbi_taxon_id": [
-                                10090
-                            ],
-                            "biomaterial_id": "21935_7#154"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/cell_suspension"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T14:00:04.041Z",
-                        "updateDate": "2018-03-28T14:47:04.573Z",
-                        "document_id": "54a80c57-0409-4f57-9699-8a2f8cbace43"
+        "cell_suspension_0.json": {
+            "content": {
+                "genus_species": [
+                    {
+                        "text": "Mus musculus",
+                        "ontology": "NCBITaxon:10090"
                     }
-                },
-                {
-                    "content": {
-                        "organ": {
-                            "text": "lymph node"
-                        },
-                        "genus_species": [
-                            {
-                                "text": "Mus musculus",
-                                "ontology": "NCBITaxon:10090"
-                            }
-                        ],
-                        "schema_type": "biomaterial",
-                        "biomaterial_core": {
-                            "has_input_biomaterial": "1134",
-                            "ncbi_taxon_id": [
-                                10090
-                            ],
-                            "biomaterial_id": "1134_LN",
-                            "supplementary_files": [
-                                "FACS_sorting_markers.pdf"
-                            ],
-                            "biomaterial_name": "Mouse_day11_LN_rep1"
-                        },
-                        "organ_part": {
-                            "text": "UBERON:0000029"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/specimen_from_organism"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:59:13.295Z",
-                        "updateDate": "2018-03-28T14:12:34.135Z",
-                        "document_id": "b3623b88-c369-46c9-a2e9-a16042d2c589"
+                ],
+                "total_estimated_cells": 1,
+                "target_cell_type": [
+                    {
+                        "text": "CD4+ T cell",
+                        "ontology": "CL:0000624"
                     }
+                ],
+                "schema_type": "biomaterial",
+                "biomaterial_core": {
+                    "has_input_biomaterial": "1134_LN",
+                    "ncbi_taxon_id": [
+                        10090
+                    ],
+                    "biomaterial_id": "21935_7#154"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/cell_suspension"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:00:04.041Z",
+                "updateDate": "2018-03-28T14:47:04.573Z",
+                "document_id": "54a80c57-0409-4f57-9699-8a2f8cbace43"
+            }
+        },
+        "specimen_from_organism_1.json": {
+            "content": {
+                "organ": {
+                    "text": "lymph node"
                 },
-                {
-                    "content": {
-                        "is_living": false,
-                        "mus_musculus_specific": {
-                            "strain": [
-                                {
-                                    "text": "C57BL/6"
-                                }
-                            ]
-                        },
-                        "biological_sex": "female",
-                        "genus_species": [
-                            {
-                                "text": "Mus musculus",
-                                "ontology": "NCBITaxon:10090"
-                            }
-                        ],
-                        "disease": [
-                            {
-                                "text": "subcutaneous melanoma",
-                                "ontology": "EFO:0000756"
-                            }
-                        ],
-                        "organism_age": "6-12",
-                        "schema_type": "biomaterial",
-                        "biomaterial_core": {
-                            "ncbi_taxon_id": [
-                                10090
-                            ],
-                            "biomaterial_id": "1134",
-                            "biomaterial_name": "Mouse_day11_rep1"
-                        },
-                        "organism_age_unit": {
-                            "text": "week",
-                            "ontology": "UO:0000034"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/donor_organism"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:55:51.172Z",
-                        "updateDate": "2018-03-28T14:22:45.353Z",
-                        "document_id": "665b75b4-8638-4a15-83e5-f3928dd29314"
+                "genus_species": [
+                    {
+                        "text": "Mus musculus",
+                        "ontology": "NCBITaxon:10090"
                     }
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/5.1.0/biomaterial",
-            "schema_version": "5.1.0",
-            "schema_type": "biomaterial_bundle"
+                ],
+                "schema_type": "biomaterial",
+                "biomaterial_core": {
+                    "has_input_biomaterial": "1134",
+                    "ncbi_taxon_id": [
+                        10090
+                    ],
+                    "biomaterial_id": "1134_LN",
+                    "supplementary_files": [
+                        "FACS_sorting_markers.pdf"
+                    ],
+                    "biomaterial_name": "Mouse_day11_LN_rep1"
+                },
+                "organ_part": {
+                    "text": "UBERON:0000029"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/specimen_from_organism"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:59:13.295Z",
+                "updateDate": "2018-03-28T14:12:34.135Z",
+                "document_id": "b3623b88-c369-46c9-a2e9-a16042d2c589"
+            }
         },
-        "file.json": {
-            "files": [
-                {
-                    "content": {
-                        "file_core": {
-                            "file_name": "21935_7#154_1.fastq.gz",
-                            "file_format": "fastq.gz"
-                        },
-                        "lane_index": 7,
-                        "read_index": "read1",
-                        "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
-                        "schema_type": "file"
-                    },
-                    "hca_ingest": {
-                        "submissionDate": "2018-03-28T14:01:07.788Z",
-                        "document_id": "b2cd6fb7-6612-4ab9-a1c5-e475663437e3"
+        "donor_organism_2.json": {
+            "content": {
+                "is_living": false,
+                "mus_musculus_specific": {
+                    "strain": [
+                        {
+                            "text": "C57BL/6"
+                        }
+                    ]
+                },
+                "biological_sex": "female",
+                "genus_species": [
+                    {
+                        "text": "Mus musculus",
+                        "ontology": "NCBITaxon:10090"
                     }
-                },
-                {
-                    "content": {
-                        "file_core": {
-                            "file_name": "21935_7#154_2.fastq.gz",
-                            "file_format": "fastq.gz"
-                        },
-                        "lane_index": 7,
-                        "read_index": "read2",
-                        "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
-                        "schema_type": "file"
-                    },
-                    "hca_ingest": {
-                        "submissionDate": "2018-03-28T14:01:07.794Z",
-                        "document_id": "f599ea3f-14bb-4504-82ce-d9c1f26e55fa"
+                ],
+                "disease": [
+                    {
+                        "text": "subcutaneous melanoma",
+                        "ontology": "EFO:0000756"
                     }
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/file",
-            "schema_version": "1.0.0",
-            "schema_type": "file_bundle"
+                ],
+                "organism_age": "6-12",
+                "schema_type": "biomaterial",
+                "biomaterial_core": {
+                    "ncbi_taxon_id": [
+                        10090
+                    ],
+                    "biomaterial_id": "1134",
+                    "biomaterial_name": "Mouse_day11_rep1"
+                },
+                "organism_age_unit": {
+                    "text": "week",
+                    "ontology": "UO:0000034"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/donor_organism"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:51.172Z",
+                "updateDate": "2018-03-28T14:22:45.353Z",
+                "document_id": "665b75b4-8638-4a15-83e5-f3928dd29314"
+            }
         },
-        "process.json": {
-            "processes": [
-                {
-                    "content": {
-                        "nucleic_acid_source": "single cell",
-                        "process_core": {
-                            "process_id": "TissueDissociationProcess",
-                            "process_name": "Extracting cells from lymph nodes"
-                        },
-                        "dissociation_method": "mechanical",
-                        "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/dissociation_process",
-                        "schema_type": "process"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T14:04:14.574Z",
-                        "updateDate": "2018-03-28T14:13:28.361Z",
-                        "document_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902"
-                    }
+        "sequence_file_0.json": {
+            "content": {
+                "file_core": {
+                    "file_name": "21935_7#154_1.fastq.gz",
+                    "file_format": "fastq.gz"
+                },
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                 },
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                 },
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                 },
-                {
-                    "content": {
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-                        "process_core": {
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-                        "document_id": "5a801f3d-12b0-4374-aed9-deee905b55ef"
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+                "document_id": "5a801f3d-12b0-4374-aed9-deee905b55ef"
+            }
+        },
+        "library_preparation_process_5.json": {
+            "content": {
+                "input_nucleic_acid_molecule": {
+                    "text": "polyA RNA",
+                    "ontology": "OBI:0000869"
+                },
+                "process_core": {
+                    "process_id": "lib_prep_1",
+                    "process_name": "Library preparation process"
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+                    "barcode_length": 16,
+                    "barcode_read": "Read 1"
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+                "schema_type": "process",
+                "end_bias": "full length",
+                "primer": "poly-dT",
+                "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/library_preparation_process",
+                "strand": "unstranded"
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+                "submissionDate": "2018-03-28T14:05:43.803Z",
+                "updateDate": "2018-03-28T14:43:01.679Z",
+                "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
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+        "sequencing_process_6.json": {
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+                "instrument_manufacturer_model": {
+                    "text": "Illumina HiSeq 2500",
+                    "ontology": "EFO:0008567"
                 },
-                {
-                    "content": {
-                        "input_nucleic_acid_molecule": {
-                            "text": "polyA RNA",
-                            "ontology": "OBI:0000869"
-                        },
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                 },
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-                        "instrument_manufacturer_model": {
-                            "text": "Illumina HiSeq 2500",
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-                            "plate_id": "569"
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+                "smartseq2": {
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+                    "plate_id": "569"
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+                "schema_type": "process",
+                "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/sequencing_process"
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-                            "document": "TissueDissociationProtocol.pdf",
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+                    "document": "TissueDissociationProtocol.pdf",
+                    "protocol_id": "tissue_dissociation_protocol"
                 },
-                {
-                    "content": {
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-                            "document": "FACSsortingProtocol.pdf",
-                            "protocol_id": "FACS_sorting_protocol"
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+                    "document": "FACSsortingProtocol.pdf",
+                    "protocol_id": "FACS_sorting_protocol"
                 },
-                {
-                    "content": {
-                        "protocol_core": {
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-                            "document": "SmartSeq2_RTPCR_protocol.pdf",
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-                        "protocol_type": {
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+                "submissionDate": "2018-03-28T13:55:26.040Z",
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+                    "document": "SmartSeq2_RTPCR_protocol.pdf",
+                    "protocol_id": "SmartSeq2_RTPCR_protocol"
                 },
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_name": "Sequencing SmartSeq2 cells",
-                            "protocol_id": "SmartSeq2_sequencing_protocol"
-                        },
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-            "describedBy": "https://schema.humancellatlas.org/bundle/5.1.0/protocol",
-            "schema_version": "5.1.0",
-            "schema_type": "protocol_bundle"
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "protocol_type": {
+                    "text": "Smart-seq2 protocol",
+                    "ontology": "EFO:0008442"
+                },
+                "schema_type": "protocol"
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+                "submissionDate": "2018-03-28T13:55:26.044Z",
+                "updateDate": "2018-03-28T14:24:04.790Z",
+                "document_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643"
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+        "protocol_3.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_name": "Sequencing SmartSeq2 cells",
+                    "protocol_id": "SmartSeq2_sequencing_protocol"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "schema_type": "protocol"
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+                "submissionDate": "2018-03-28T13:55:26.050Z",
+                "updateDate": "2018-03-28T14:30:39.321Z",
+                "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
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         "links.json": {
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diff --git a/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json b/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
index 5a558a892..57d87c415 100644
--- a/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
+++ b/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
@@ -26,7 +26,7 @@
         }
     ],
     "metadata": {
-        "project.json": {
+        "project_0.json": {
             "content": {
                 "describedBy": "https://schema.humancellatlas.org/type/project/9.0.0/project",
                 "project_core": {
@@ -150,233 +150,212 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
         },
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-                            "file_format": "fastq.gz"
-                        },
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-                        "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
-                        "schema_type": "file"
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-                    "hca_ingest": {
-                        "submissionDate": "2018-03-28T14:03:00.756Z",
-                        "document_id": "e080459e-e4ab-40ea-ab75-a2646b5fdd29"
-                    }
+        "sequence_file_0.json": {
+            "content": {
+                "file_core": {
+                    "file_name": "22467_6#373_1.fastq.gz",
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                 },
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-            "schema_version": "1.0.0",
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+                "read_index": "read1",
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+                "schema_type": "file"
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+                "document_id": "e080459e-e4ab-40ea-ab75-a2646b5fdd29"
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-                        "process_core": {
-                            "process_id": "TissueDissociationProcess",
-                            "process_name": "Extracting cells from lymph nodes"
-                        },
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-                        "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/dissociation_process",
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-                        "document_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902"
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+        "sequence_file_1.json": {
+            "content": {
+                "file_core": {
+                    "file_name": "22467_6#373_2.fastq.gz",
+                    "file_format": "fastq.gz"
                 },
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-                        "submissionDate": "2018-03-28T14:00:16.640Z",
-                        "updateDate": "2018-03-28T14:00:59.234Z",
-                        "document_id": "0763320a-e0c4-4c07-b150-b83650fbef68"
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+                "lane_index": 6,
+                "read_index": "read2",
+                "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
+                "schema_type": "file"
+            },
+            "hca_ingest": {
+                "submissionDate": "2018-03-28T14:03:00.761Z",
+                "document_id": "3417cdb5-5618-4c0c-bc27-62a4eb78916a"
+            }
+        },
+        "dissociation_process_0.json": {
+            "content": {
+                "nucleic_acid_source": "single cell",
+                "process_core": {
+                    "process_id": "TissueDissociationProcess",
+                    "process_name": "Extracting cells from lymph nodes"
                 },
-                {
-                    "content": {
-                        "enrichment_method": "FACS",
-                        "process_core": {
-                            "process_id": "FACS3.2"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/enrichment_process",
-                        "markers": "CD45+ CD3e- B220- CD11b+",
-                        "schema_type": "process"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T14:04:02.006Z",
-                        "updateDate": "2018-03-28T14:15:18.962Z",
-                        "document_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4"
-                    }
+                "dissociation_method": "mechanical",
+                "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/dissociation_process",
+                "schema_type": "process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:04:14.574Z",
+                "updateDate": "2018-03-28T14:13:28.361Z",
+                "document_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902"
+            }
+        },
+        "process_1.json": {
+            "content": {
+                "process_core": {
+                    "process_id": "sampling_process_12"
                 },
-                {
-                    "content": {
-                        "input_nucleic_acid_molecule": {
-                            "text": "polyA RNA",
-                            "ontology": "OBI:0000869"
-                        },
-                        "process_core": {
-                            "process_id": "lib_prep_1",
-                            "process_name": "Library preparation process"
-                        },
-                        "umi_barcode": {
-                            "barcode_offset": 0,
-                            "barcode_length": 16,
-                            "barcode_read": "Read 1"
-                        },
-                        "library_construction_approach": "Smart-seq2",
-                        "schema_type": "process",
-                        "end_bias": "full length",
-                        "primer": "poly-dT",
-                        "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/library_preparation_process",
-                        "strand": "unstranded"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T14:05:43.803Z",
-                        "updateDate": "2018-03-28T14:43:01.679Z",
-                        "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
-                    }
+                "describedBy": "https://schema.humancellatlas.org/type/process/1.0.0/process",
+                "schema_type": "process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:00:16.640Z",
+                "updateDate": "2018-03-28T14:00:59.234Z",
+                "document_id": "0763320a-e0c4-4c07-b150-b83650fbef68"
+            }
+        },
+        "enrichment_process_2.json": {
+            "content": {
+                "enrichment_method": "FACS",
+                "process_core": {
+                    "process_id": "FACS3.2"
                 },
-                {
-                    "content": {
-                        "paired_ends": true,
-                        "instrument_manufacturer_model": {
-                            "text": "Illumina HiSeq 2500",
-                            "ontology": "EFO:0008567"
-                        },
-                        "process_core": {
-                            "process_id": "seq_5834",
-                            "process_name": "Sequencing process"
-                        },
-                        "smartseq2": {
-                            "well_name": "D85",
-                            "plate_id": "537"
-                        },
-                        "schema_type": "process",
-                        "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/sequencing_process"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T14:04:09.031Z",
-                        "updateDate": "2018-03-28T14:10:22.768Z",
-                        "document_id": "b8a6acbe-6b57-4efb-b6c7-bceaa6d9924d"
-                    }
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/5.2.1/process",
-            "schema_version": "5.2.1",
-            "schema_type": "process_bundle"
+                "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/enrichment_process",
+                "markers": "CD45+ CD3e- B220- CD11b+",
+                "schema_type": "process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:04:02.006Z",
+                "updateDate": "2018-03-28T14:15:18.962Z",
+                "document_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4"
+            }
         },
-        "protocol.json": {
-            "protocols": [
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_name": "Extracting cells from lymph nodes",
-                            "document": "TissueDissociationProtocol.pdf",
-                            "protocol_id": "tissue_dissociation_protocol"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "schema_type": "protocol"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:55:26.033Z",
-                        "updateDate": "2018-03-28T14:14:33.716Z",
-                        "document_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127"
-                    }
+        "library_preparation_process_3.json": {
+            "content": {
+                "input_nucleic_acid_molecule": {
+                    "text": "polyA RNA",
+                    "ontology": "OBI:0000869"
                 },
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_name": "FACS sorting cells by surface markers",
-                            "document": "FACSsortingProtocol.pdf",
-                            "protocol_id": "FACS_sorting_protocol"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "schema_type": "protocol"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:55:26.040Z",
-                        "updateDate": "2018-03-28T14:45:43.500Z",
-                        "document_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6"
-                    }
+                "process_core": {
+                    "process_id": "lib_prep_1",
+                    "process_name": "Library preparation process"
                 },
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_name": "Make/amplify cDNA for each cell",
-                            "document": "SmartSeq2_RTPCR_protocol.pdf",
-                            "protocol_id": "SmartSeq2_RTPCR_protocol"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "protocol_type": {
-                            "text": "Smart-seq2 protocol",
-                            "ontology": "EFO:0008442"
-                        },
-                        "schema_type": "protocol"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:55:26.044Z",
-                        "updateDate": "2018-03-28T14:24:04.790Z",
-                        "document_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643"
-                    }
+                "umi_barcode": {
+                    "barcode_offset": 0,
+                    "barcode_length": 16,
+                    "barcode_read": "Read 1"
                 },
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_name": "Sequencing SmartSeq2 cells",
-                            "protocol_id": "SmartSeq2_sequencing_protocol"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "schema_type": "protocol"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:55:26.050Z",
-                        "updateDate": "2018-03-28T14:30:39.321Z",
-                        "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
-                    }
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/5.1.0/protocol",
-            "schema_version": "5.1.0",
-            "schema_type": "protocol_bundle"
+                "library_construction_approach": "Smart-seq2",
+                "schema_type": "process",
+                "end_bias": "full length",
+                "primer": "poly-dT",
+                "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/library_preparation_process",
+                "strand": "unstranded"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:05:43.803Z",
+                "updateDate": "2018-03-28T14:43:01.679Z",
+                "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
+            }
+        },
+        "sequencing_process_4.json": {
+            "content": {
+                "paired_ends": true,
+                "instrument_manufacturer_model": {
+                    "text": "Illumina HiSeq 2500",
+                    "ontology": "EFO:0008567"
+                },
+                "process_core": {
+                    "process_id": "seq_5834",
+                    "process_name": "Sequencing process"
+                },
+                "smartseq2": {
+                    "well_name": "D85",
+                    "plate_id": "537"
+                },
+                "schema_type": "process",
+                "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/sequencing_process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:04:09.031Z",
+                "updateDate": "2018-03-28T14:10:22.768Z",
+                "document_id": "b8a6acbe-6b57-4efb-b6c7-bceaa6d9924d"
+            }
+        },
+        "protocol_0.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_name": "Extracting cells from lymph nodes",
+                    "document": "TissueDissociationProtocol.pdf",
+                    "protocol_id": "tissue_dissociation_protocol"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:26.033Z",
+                "updateDate": "2018-03-28T14:14:33.716Z",
+                "document_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127"
+            }
+        },
+        "protocol_1.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_name": "FACS sorting cells by surface markers",
+                    "document": "FACSsortingProtocol.pdf",
+                    "protocol_id": "FACS_sorting_protocol"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:26.040Z",
+                "updateDate": "2018-03-28T14:45:43.500Z",
+                "document_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6"
+            }
+        },
+        "protocol_2.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_name": "Make/amplify cDNA for each cell",
+                    "document": "SmartSeq2_RTPCR_protocol.pdf",
+                    "protocol_id": "SmartSeq2_RTPCR_protocol"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "protocol_type": {
+                    "text": "Smart-seq2 protocol",
+                    "ontology": "EFO:0008442"
+                },
+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:26.044Z",
+                "updateDate": "2018-03-28T14:24:04.790Z",
+                "document_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643"
+            }
+        },
+        "protocol_3.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_name": "Sequencing SmartSeq2 cells",
+                    "protocol_id": "SmartSeq2_sequencing_protocol"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:26.050Z",
+                "updateDate": "2018-03-28T14:30:39.321Z",
+                "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
+            }
         },
         "links.json": {
             "links": [
@@ -493,120 +472,113 @@
             "schema_version": "1.0.0",
             "schema_type": "link_bundle"
         },
-        "biomaterial.json": {
-            "biomaterials": [
-                {
-                    "content": {
-                        "genus_species": [
-                            {
-                                "text": "Mus musculus",
-                                "ontology": "NCBITaxon:10090"
-                            }
-                        ],
-                        "total_estimated_cells": 1,
-                        "target_cell_type": [
-                            {
-                                "text": "CD11b+ Macrophages/monocytes"
-                            }
-                        ],
-                        "schema_type": "biomaterial",
-                        "biomaterial_core": {
-                            "has_input_biomaterial": "1117_T",
-                            "ncbi_taxon_id": [
-                                10090
-                            ],
-                            "biomaterial_id": "22467_6#373"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/cell_suspension"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:58:01.823Z",
-                        "updateDate": "2018-03-28T14:27:21.201Z",
-                        "document_id": "f59292f0-318f-40d0-bce5-29413b59a790"
+        "cell_suspension_0.json": {
+            "content": {
+                "genus_species": [
+                    {
+                        "text": "Mus musculus",
+                        "ontology": "NCBITaxon:10090"
+                    }
+                ],
+                "total_estimated_cells": 1,
+                "target_cell_type": [
+                    {
+                        "text": "CD11b+ Macrophages/monocytes"
                     }
+                ],
+                "schema_type": "biomaterial",
+                "biomaterial_core": {
+                    "has_input_biomaterial": "1117_T",
+                    "ncbi_taxon_id": [
+                        10090
+                    ],
+                    "biomaterial_id": "22467_6#373"
                 },
-                {
-                    "content": {
-                        "biomaterial_core": {
-                            "has_input_biomaterial": "1117",
-                            "ncbi_taxon_id": [
-                                10090
-                            ],
-                            "biomaterial_id": "1117_T",
-                            "supplementary_files": [
-                                "FACS_sorting_markers.pdf"
-                            ],
-                            "biomaterial_name": "Mouse_day5_T_rep8"
-                        },
-                        "genus_species": [
-                            {
-                                "text": "Mus musculus",
-                                "ontology": "NCBITaxon:10090"
-                            }
-                        ],
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/specimen_from_organism",
-                        "organ": {
-                            "text": "tumor"
-                        },
-                        "schema_type": "biomaterial"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:56:12.647Z",
-                        "updateDate": "2018-03-28T14:19:05.173Z",
-                        "document_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c"
+                "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/cell_suspension"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:58:01.823Z",
+                "updateDate": "2018-03-28T14:27:21.201Z",
+                "document_id": "f59292f0-318f-40d0-bce5-29413b59a790"
+            }
+        },
+        "specimen_from_organism_1.json": {
+            "content": {
+                "biomaterial_core": {
+                    "has_input_biomaterial": "1117",
+                    "ncbi_taxon_id": [
+                        10090
+                    ],
+                    "biomaterial_id": "1117_T",
+                    "supplementary_files": [
+                        "FACS_sorting_markers.pdf"
+                    ],
+                    "biomaterial_name": "Mouse_day5_T_rep8"
+                },
+                "genus_species": [
+                    {
+                        "text": "Mus musculus",
+                        "ontology": "NCBITaxon:10090"
                     }
+                ],
+                "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/specimen_from_organism",
+                "organ": {
+                    "text": "tumor"
                 },
-                {
-                    "content": {
-                        "is_living": false,
-                        "mus_musculus_specific": {
-                            "strain": [
-                                {
-                                    "text": "C57BL/6"
-                                }
-                            ]
-                        },
-                        "biological_sex": "female",
-                        "genus_species": [
-                            {
-                                "text": "Mus musculus",
-                                "ontology": "NCBITaxon:10090"
-                            }
-                        ],
-                        "disease": [
-                            {
-                                "text": "subcutaneous melanoma",
-                                "ontology": "EFO:0000756"
-                            }
-                        ],
-                        "organism_age": "6-12",
-                        "schema_type": "biomaterial",
-                        "biomaterial_core": {
-                            "ncbi_taxon_id": [
-                                10090
-                            ],
-                            "biomaterial_id": "1117",
-                            "biomaterial_name": "Mouse_day5_rep8"
-                        },
-                        "organism_age_unit": {
-                            "text": "week",
-                            "ontology": "UO:0000034"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/donor_organism"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:56:00.553Z",
-                        "updateDate": "2018-03-28T14:00:16.892Z",
-                        "document_id": "689311a2-bfaf-4196-a753-554e69ab59b2"
+                "schema_type": "biomaterial"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:56:12.647Z",
+                "updateDate": "2018-03-28T14:19:05.173Z",
+                "document_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c"
+            }
+        },
+        "donor_organism_2.json": {
+            "content": {
+                "is_living": false,
+                "mus_musculus_specific": {
+                    "strain": [
+                        {
+                            "text": "C57BL/6"
+                        }
+                    ]
+                },
+                "biological_sex": "female",
+                "genus_species": [
+                    {
+                        "text": "Mus musculus",
+                        "ontology": "NCBITaxon:10090"
                     }
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/5.1.0/biomaterial",
-            "schema_version": "5.1.0",
-            "schema_type": "biomaterial_bundle"
+                ],
+                "disease": [
+                    {
+                        "text": "subcutaneous melanoma",
+                        "ontology": "EFO:0000756"
+                    }
+                ],
+                "organism_age": "6-12",
+                "schema_type": "biomaterial",
+                "biomaterial_core": {
+                    "ncbi_taxon_id": [
+                        10090
+                    ],
+                    "biomaterial_id": "1117",
+                    "biomaterial_name": "Mouse_day5_rep8"
+                },
+                "organism_age_unit": {
+                    "text": "week",
+                    "ontology": "UO:0000034"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/donor_organism"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:56:00.553Z",
+                "updateDate": "2018-03-28T14:00:16.892Z",
+                "document_id": "689311a2-bfaf-4196-a753-554e69ab59b2"
+            }
         }
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json b/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
index cedf87567..7de7ec75a 100644
--- a/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
+++ b/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
@@ -2306,7 +2306,7 @@
         }
     ],
     "metadata": {
-        "project.json": {
+        "project_0.json": {
             "content": {
                 "describedBy": "https://schema.humancellatlas.org/type/project/5.1.0/project",
                 "project_core": {
@@ -2435,6727 +2435,6699 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
         },
-        "biomaterial.json": {
-            "biomaterials": [
-                {
-                    "content": {
-                        "genus_species": [
-                            {
-                                "text": "Homo sapiens",
-                                "ontology": "NCBITaxon:9606"
-                            }
-                        ],
-                        "total_estimated_cells": 4753,
-                        "target_cell_type": [
-                            {
-                                "text": "umbilical cord blood cell",
-                                "ontology": "CL:2000095"
-                            }
-                        ],
-                        "schema_type": "biomaterial",
-                        "biomaterial_core": {
-                            "has_input_biomaterial": "2_CB5",
-                            "ncbi_taxon_id": [
-                                9606
-                            ],
-                            "biomaterial_id": "2_CB5_cells"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/cell_suspension"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-26T16:59:18.961Z",
-                        "updateDate": "2018-03-26T17:00:44.422Z",
-                        "document_id": "81bdd959-6a0c-45e8-a95f-9e94362ac234"
-                    }
-                },
-                {
-                    "content": {
-                        "organ": {
-                            "text": "hematopoietic system",
-                            "ontology": "UBERON:0002390"
-                        },
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diff --git a/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json b/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
index d19d2b8f8..50e8ccded 100644
--- a/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
+++ b/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
@@ -26,7 +26,7 @@
         }
     ],
     "metadata": {
-        "project.json": {
+        "project_0.json": {
             "content": {
                 "describedBy": "https://schema.humancellatlas.org/type/project/5.1.0/project",
                 "project_core": {
@@ -150,365 +150,337 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
         },
-        "biomaterial.json": {
-            "biomaterials": [
-                {
-                    "content": {
-                        "genus_species": [
-                            {
-                                "text": "Mus musculus",
-                                "ontology": "NCBITaxon:10090"
-                            }
-                        ],
-                        "total_estimated_cells": 1,
-                        "target_cell_type": [
-                            {
-                                "text": "CD11b+ Macrophages/monocytes"
-                            }
-                        ],
-                        "schema_type": "biomaterial",
-                        "biomaterial_core": {
-                            "has_input_biomaterial": "1139_T",
-                            "ncbi_taxon_id": [
-                                10090
-                            ],
-                            "biomaterial_id": "22011_1#268"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/cell_suspension"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T14:00:05.544Z",
-                        "updateDate": "2018-03-28T14:39:28.596Z",
-                        "document_id": "603a818f-dbe7-466a-8241-58b9c1618846"
-                    }
-                },
-                {
-                    "content": {
-                        "biomaterial_core": {
-                            "has_input_biomaterial": "1139",
-                            "ncbi_taxon_id": [
-                                10090
-                            ],
-                            "biomaterial_id": "1139_T",
-                            "supplementary_files": [
-                                "FACS_sorting_markers.pdf"
-                            ],
-                            "biomaterial_name": "Mouse_day11_T_rep5"
-                        },
-                        "genus_species": [
-                            {
-                                "text": "Mus musculus",
-                                "ontology": "NCBITaxon:10090"
-                            }
-                        ],
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/specimen_from_organism",
-                        "organ": {
-                            "text": "tumor"
-                        },
-                        "schema_type": "biomaterial"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:55:31.072Z",
-                        "updateDate": "2018-03-28T14:15:11.657Z",
-                        "document_id": "4e41a067-dbb7-439f-b72f-80240ce858f6"
+        "cell_suspension_0.json": {
+            "content": {
+                "genus_species": [
+                    {
+                        "text": "Mus musculus",
+                        "ontology": "NCBITaxon:10090"
                     }
-                },
-                {
-                    "content": {
-                        "is_living": false,
-                        "mus_musculus_specific": {
-                            "strain": [
-                                {
-                                    "text": "C57BL/6"
-                                }
-                            ]
-                        },
-                        "biological_sex": "female",
-                        "genus_species": [
-                            {
-                                "text": "Mus musculus",
-                                "ontology": "NCBITaxon:10090"
-                            }
-                        ],
-                        "disease": [
-                            {
-                                "text": "subcutaneous melanoma",
-                                "ontology": "EFO:0000756"
-                            }
-                        ],
-                        "organism_age": "6-12",
-                        "schema_type": "biomaterial",
-                        "biomaterial_core": {
-                            "ncbi_taxon_id": [
-                                10090
-                            ],
-                            "biomaterial_id": "1139",
-                            "biomaterial_name": "Mouse_day11_rep5"
-                        },
-                        "organism_age_unit": {
-                            "text": "week",
-                            "ontology": "UO:0000034"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/donor_organism"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T13:58:05.518Z",
-                        "updateDate": "2018-03-28T14:01:13.757Z",
-                        "document_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410"
+                ],
+                "total_estimated_cells": 1,
+                "target_cell_type": [
+                    {
+                        "text": "CD11b+ Macrophages/monocytes"
                     }
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/5.1.0/biomaterial",
-            "schema_version": "5.1.0",
-            "schema_type": "biomaterial_bundle"
+                ],
+                "schema_type": "biomaterial",
+                "biomaterial_core": {
+                    "has_input_biomaterial": "1139_T",
+                    "ncbi_taxon_id": [
+                        10090
+                    ],
+                    "biomaterial_id": "22011_1#268"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/cell_suspension"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:00:05.544Z",
+                "updateDate": "2018-03-28T14:39:28.596Z",
+                "document_id": "603a818f-dbe7-466a-8241-58b9c1618846"
+            }
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-            "files": [
-                {
-                    "content": {
-                        "file_core": {
-                            "file_name": "22011_1#268_1.fastq.gz",
-                            "file_format": "fastq.gz"
-                        },
-                        "lane_index": 1,
-                        "read_index": "read1",
-                        "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
-                        "schema_type": "file"
-                    },
-                    "hca_ingest": {
-                        "submissionDate": "2018-03-28T14:00:30.935Z",
-                        "document_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1"
+        "specimen_from_organism_1.json": {
+            "content": {
+                "biomaterial_core": {
+                    "has_input_biomaterial": "1139",
+                    "ncbi_taxon_id": [
+                        10090
+                    ],
+                    "biomaterial_id": "1139_T",
+                    "supplementary_files": [
+                        "FACS_sorting_markers.pdf"
+                    ],
+                    "biomaterial_name": "Mouse_day11_T_rep5"
+                },
+                "genus_species": [
+                    {
+                        "text": "Mus musculus",
+                        "ontology": "NCBITaxon:10090"
                     }
+                ],
+                "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/specimen_from_organism",
+                "organ": {
+                    "text": "tumor"
                 },
-                {
-                    "content": {
-                        "file_core": {
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-            "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/file",
-            "schema_version": "1.0.0",
-            "schema_type": "file_bundle"
+                "schema_type": "biomaterial"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:31.072Z",
+                "updateDate": "2018-03-28T14:15:11.657Z",
+                "document_id": "4e41a067-dbb7-439f-b72f-80240ce858f6"
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-        "process.json": {
-            "processes": [
-                {
-                    "content": {
-                        "nucleic_acid_source": "single cell",
-                        "process_core": {
-                            "process_id": "TissueDissociationProcess",
-                            "process_name": "Extracting cells from lymph nodes"
-                        },
-                        "dissociation_method": "mechanical",
-                        "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/dissociation_process",
-                        "schema_type": "process"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T14:04:14.574Z",
-                        "updateDate": "2018-03-28T14:13:28.361Z",
-                        "document_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902"
+        "donor_organism_2.json": {
+            "content": {
+                "is_living": false,
+                "mus_musculus_specific": {
+                    "strain": [
+                        {
+                            "text": "C57BL/6"
+                        }
+                    ]
+                },
+                "biological_sex": "female",
+                "genus_species": [
+                    {
+                        "text": "Mus musculus",
+                        "ontology": "NCBITaxon:10090"
                     }
-                },
-                {
-                    "content": {
-                        "process_core": {
-                            "process_id": "sampling_process_6"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/process/1.0.0/process",
-                        "schema_type": "process"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T14:00:15.938Z",
-                        "updateDate": "2018-03-28T14:51:13.100Z",
-                        "document_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9"
+                ],
+                "disease": [
+                    {
+                        "text": "subcutaneous melanoma",
+                        "ontology": "EFO:0000756"
                     }
+                ],
+                "organism_age": "6-12",
+                "schema_type": "biomaterial",
+                "biomaterial_core": {
+                    "ncbi_taxon_id": [
+                        10090
+                    ],
+                    "biomaterial_id": "1139",
+                    "biomaterial_name": "Mouse_day11_rep5"
+                },
+                "organism_age_unit": {
+                    "text": "week",
+                    "ontology": "UO:0000034"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/donor_organism"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:58:05.518Z",
+                "updateDate": "2018-03-28T14:01:13.757Z",
+                "document_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410"
+            }
+        },
+        "sequence_file_0.json": {
+            "content": {
+                "file_core": {
+                    "file_name": "22011_1#268_1.fastq.gz",
+                    "file_format": "fastq.gz"
+                },
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+                "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
+                "schema_type": "file"
+            },
+            "hca_ingest": {
+                "submissionDate": "2018-03-28T14:00:30.935Z",
+                "document_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1"
+            }
+        },
+        "sequence_file_1.json": {
+            "content": {
+                "file_core": {
+                    "file_name": "22011_1#268_2.fastq.gz",
+                    "file_format": "fastq.gz"
+                },
+                "lane_index": 1,
+                "read_index": "read2",
+                "describedBy": "https://schema.humancellatlas.org/type/file/5.1.0/sequence_file",
+                "schema_type": "file"
+            },
+            "hca_ingest": {
+                "submissionDate": "2018-03-28T14:00:30.947Z",
+                "document_id": "aa662c76-d220-49f4-8316-f4af5820d60b"
+            }
+        },
+        "dissociation_process_0.json": {
+            "content": {
+                "nucleic_acid_source": "single cell",
+                "process_core": {
+                    "process_id": "TissueDissociationProcess",
+                    "process_name": "Extracting cells from lymph nodes"
+                },
+                "dissociation_method": "mechanical",
+                "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/dissociation_process",
+                "schema_type": "process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:04:14.574Z",
+                "updateDate": "2018-03-28T14:13:28.361Z",
+                "document_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902"
+            }
+        },
+        "process_1.json": {
+            "content": {
+                "process_core": {
+                    "process_id": "sampling_process_6"
                 },
-                {
-                    "content": {
-                        "enrichment_method": "FACS",
-                        "process_core": {
-                            "process_id": "FACS2"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/enrichment_process",
-                        "markers": "CD45+ CD3e- B220- CD11c+",
-                        "schema_type": "process"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T14:05:22.289Z",
-                        "updateDate": "2018-03-28T14:29:50.280Z",
-                        "document_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78"
-                    }
+                "describedBy": "https://schema.humancellatlas.org/type/process/1.0.0/process",
+                "schema_type": "process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:00:15.938Z",
+                "updateDate": "2018-03-28T14:51:13.100Z",
+                "document_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9"
+            }
+        },
+        "enrichment_process_2.json": {
+            "content": {
+                "enrichment_method": "FACS",
+                "process_core": {
+                    "process_id": "FACS2"
                 },
-                {
-                    "content": {
-                        "enrichment_method": "FACS",
-                        "process_core": {
-                            "process_id": "FACS3.7"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/enrichment_process",
-                        "markers": "CD45+ CD3e- B220- CD11b+",
-                        "schema_type": "process"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-28T14:04:02.056Z",
-                        "updateDate": "2018-03-28T14:32:20.272Z",
-                        "document_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215"
-                    }
+                "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/enrichment_process",
+                "markers": "CD45+ CD3e- B220- CD11c+",
+                "schema_type": "process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:05:22.289Z",
+                "updateDate": "2018-03-28T14:29:50.280Z",
+                "document_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78"
+            }
+        },
+        "enrichment_process_3.json": {
+            "content": {
+                "enrichment_method": "FACS",
+                "process_core": {
+                    "process_id": "FACS3.7"
                 },
-                {
-                    "content": {
-                        "input_nucleic_acid_molecule": {
-                            "text": "polyA RNA",
-                            "ontology": "OBI:0000869"
-                        },
-                        "process_core": {
-                            "process_id": "lib_prep_1",
-                            "process_name": "Library preparation process"
-                        },
-                        "umi_barcode": {
-                            "barcode_offset": 0,
-                            "barcode_length": 16,
-                            "barcode_read": "Read 1"
-                        },
-                        "library_construction_approach": "Smart-seq2",
-                        "schema_type": "process",
-                        "end_bias": "full length",
-                        "primer": "poly-dT",
-                        "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/library_preparation_process",
-                        "strand": "unstranded"
-                    },
-                    "hca_ingest": {
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-                        "submissionDate": "2018-03-28T14:05:43.803Z",
-                        "updateDate": "2018-03-28T14:43:01.679Z",
-                        "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
-                    }
+                "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/enrichment_process",
+                "markers": "CD45+ CD3e- B220- CD11b+",
+                "schema_type": "process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:04:02.056Z",
+                "updateDate": "2018-03-28T14:32:20.272Z",
+                "document_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215"
+            }
+        },
+        "library_preparation_process_4.json": {
+            "content": {
+                "input_nucleic_acid_molecule": {
+                    "text": "polyA RNA",
+                    "ontology": "OBI:0000869"
+                },
+                "process_core": {
+                    "process_id": "lib_prep_1",
+                    "process_name": "Library preparation process"
+                },
+                "umi_barcode": {
+                    "barcode_offset": 0,
+                    "barcode_length": 16,
+                    "barcode_read": "Read 1"
+                },
+                "library_construction_approach": "Smart-seq2",
+                "schema_type": "process",
+                "end_bias": "full length",
+                "primer": "poly-dT",
+                "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/library_preparation_process",
+                "strand": "unstranded"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T14:05:43.803Z",
+                "updateDate": "2018-03-28T14:43:01.679Z",
+                "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
+            }
+        },
+        "sequencing_process_5.json": {
+            "content": {
+                "paired_ends": true,
+                "instrument_manufacturer_model": {
+                    "text": "Illumina HiSeq 2500",
+                    "ontology": "EFO:0008567"
                 },
-                {
-                    "content": {
-                        "paired_ends": true,
-                        "instrument_manufacturer_model": {
-                            "text": "Illumina HiSeq 2500",
-                            "ontology": "EFO:0008567"
-                        },
-                        "process_core": {
-                            "process_id": "seq_264",
-                            "process_name": "Sequencing process"
-                        },
-                        "smartseq2": {
-                            "well_name": "F02",
-                            "plate_id": "575"
-                        },
-                        "schema_type": "process",
-                        "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/sequencing_process"
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-            "describedBy": "https://schema.humancellatlas.org/bundle/5.2.1/process",
-            "schema_version": "5.2.1",
-            "schema_type": "process_bundle"
+                "process_core": {
+                    "process_id": "seq_264",
+                    "process_name": "Sequencing process"
+                },
+                "smartseq2": {
+                    "well_name": "F02",
+                    "plate_id": "575"
+                },
+                "schema_type": "process",
+                "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/sequencing_process"
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+                "submissionDate": "2018-03-28T14:03:27.156Z",
+                "updateDate": "2018-03-28T14:32:54.422Z",
+                "document_id": "2580dcf9-3f7d-4421-b962-ab860e10d072"
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         },
-        "protocol.json": {
-            "protocols": [
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_name": "Extracting cells from lymph nodes",
-                            "document": "TissueDissociationProtocol.pdf",
-                            "protocol_id": "tissue_dissociation_protocol"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "schema_type": "protocol"
-                    },
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-                        "submissionDate": "2018-03-28T13:55:26.033Z",
-                        "updateDate": "2018-03-28T14:14:33.716Z",
-                        "document_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127"
-                    }
+        "protocol_0.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_name": "Extracting cells from lymph nodes",
+                    "document": "TissueDissociationProtocol.pdf",
+                    "protocol_id": "tissue_dissociation_protocol"
                 },
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_name": "FACS sorting cells by surface markers",
-                            "document": "FACSsortingProtocol.pdf",
-                            "protocol_id": "FACS_sorting_protocol"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "schema_type": "protocol"
-                    },
-                    "hca_ingest": {
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-                        "submissionDate": "2018-03-28T13:55:26.040Z",
-                        "updateDate": "2018-03-28T14:45:43.500Z",
-                        "document_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6"
-                    }
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+                "schema_type": "protocol"
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+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:26.033Z",
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diff --git a/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json b/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
index 50f1a8ea4..4efdb0de7 100644
--- a/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
+++ b/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
@@ -2234,7 +2234,7 @@
         }
     ],
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                 "project_core": {
@@ -2363,6526 +2363,6498 @@
             "schema_version": "5.1.0",
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         },
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-                {
-                    "content": {
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-                                "text": "Homo sapiens",
-                                "ontology": "NCBITaxon:9606"
-                            }
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-                        "target_cell_type": [
-                            {
-                                "text": "bone marrow hematopoietic cell",
-                                "ontology": "CL:1001610"
-                            }
-                        ],
-                        "schema_type": "biomaterial",
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-                            "ncbi_taxon_id": [
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-                            ],
-                            "biomaterial_id": "3_BM8_cells"
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-                            "ontology": "UBERON:0002390"
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-                                "ontology": "NCBITaxon:9606"
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+        "cell_suspension_0.json": {
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+                    {
+                        "text": "Homo sapiens",
+                        "ontology": "NCBITaxon:9606"
                     }
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+                "target_cell_type": [
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                     }
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+                "biological_sex": "female",
+                "genus_species": [
+                    {
+                        "text": "Homo sapiens",
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+                    "biomaterial_name": "Bone Marrow donor 8"
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+                "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/dissociation_process",
+                "schema_type": "process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-26T17:00:58.313Z",
+                "updateDate": "2018-03-26T17:01:07.329Z",
+                "document_id": "e3515c4a-944a-4f0e-aeff-e872fe44d677"
+            }
+        },
+        "process_61.json": {
+            "content": {
+                "process_core": {
+                    "process_id": "sampling_process_122"
                 },
-                {
-                    "content": {
-                        "nucleic_acid_source": "single cell",
-                        "process_core": {
-                            "process_name": "mononuclear cell isolation",
-                            "process_description": "We isolated mononuclear cells for all samples in preparation for 10x sequencing.",
-                            "process_id": "dissociation_process_54"
-                        },
-                        "dissociation_method": "10x_v2",
-                        "describedBy": "https://schema.humancellatlas.org/type/process/biomaterial_collection/5.1.0/dissociation_process",
-                        "schema_type": "process"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-26T17:00:58.313Z",
-                        "updateDate": "2018-03-26T17:01:07.329Z",
-                        "document_id": "e3515c4a-944a-4f0e-aeff-e872fe44d677"
-                    }
+                "describedBy": "https://schema.humancellatlas.org/type/process/1.0.0/process",
+                "schema_type": "process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-26T16:59:46.490Z",
+                "updateDate": "2018-03-26T17:00:03.343Z",
+                "document_id": "d46f0814-1caf-4668-ab2e-cec3af24b1fb"
+            }
+        },
+        "library_preparation_process_62.json": {
+            "content": {
+                "input_nucleic_acid_molecule": {
+                    "text": "polyA RNA",
+                    "ontology": "OBI:0000869"
+                },
+                "process_type": {
+                    "text": "10x sequencing process"
+                },
+                "process_core": {
+                    "process_id": "library_preparation_process_1",
+                    "process_name": "Preparing RNA for sequencing by 10x"
+                },
+                "umi_barcode": {
+                    "barcode_offset": 16,
+                    "barcode_length": 10,
+                    "barcode_read": "Read 1"
+                },
+                "library_construction_approach": "10x_v2",
+                "cell_barcode": {
+                    "barcode_offset": 0,
+                    "barcode_length": 16,
+                    "barcode_read": "Read 1"
+                },
+                "schema_type": "process",
+                "end_bias": "3 prime tag",
+                "primer": "poly-dT",
+                "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/library_preparation_process",
+                "strand": "second"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-26T17:00:06.820Z",
+                "updateDate": "2018-03-26T17:00:44.791Z",
+                "document_id": "12ea2953-06a4-4e80-8910-a27aba936b9c"
+            }
+        },
+        "sequencing_process_63.json": {
+            "content": {
+                "paired_ends": true,
+                "local_machine_name": "HXJ",
+                "instrument_manufacturer_model": {
+                    "text": "Illumina Hiseq X 10",
+                    "ontology": "EFO:0008567"
+                },
+                "process_type": {
+                    "text": "10x sequencing process"
+                },
+                "process_core": {
+                    "process_description": "Single cell sequencing of cDNAs by 10x",
+                    "process_name": "Sequencing bone marrow donor 5-8",
+                    "process_id": "10x_v2_sequencing_process_2",
+                    "start_time": "2017-09-26T05:20:00Z",
+                    "process_location": "Broad Institute"
+                },
+                "schema_type": "process",
+                "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/sequencing_process"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-26T17:00:06.935Z",
+                "updateDate": "2018-03-26T17:00:53.534Z",
+                "document_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1"
+            }
+        },
+        "protocol_0.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_id": "dissociation_protocol_1"
                 },
-                {
-                    "content": {
-                        "process_core": {
-                            "process_id": "sampling_process_122"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/process/1.0.0/process",
-                        "schema_type": "process"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-26T16:59:46.490Z",
-                        "updateDate": "2018-03-26T17:00:03.343Z",
-                        "document_id": "d46f0814-1caf-4668-ab2e-cec3af24b1fb"
-                    }
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-26T16:59:18.834Z",
+                "updateDate": "2018-03-26T16:59:27.584Z",
+                "document_id": "3cbebf0a-4aab-4525-80f4-222703d14b98"
+            }
+        },
+        "protocol_1.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_id": "library_preparation_protocol_1"
                 },
-                {
-                    "content": {
-                        "input_nucleic_acid_molecule": {
-                            "text": "polyA RNA",
-                            "ontology": "OBI:0000869"
-                        },
-                        "process_type": {
-                            "text": "10x sequencing process"
-                        },
-                        "process_core": {
-                            "process_id": "library_preparation_process_1",
-                            "process_name": "Preparing RNA for sequencing by 10x"
-                        },
-                        "umi_barcode": {
-                            "barcode_offset": 16,
-                            "barcode_length": 10,
-                            "barcode_read": "Read 1"
-                        },
-                        "library_construction_approach": "10x_v2",
-                        "cell_barcode": {
-                            "barcode_offset": 0,
-                            "barcode_length": 16,
-                            "barcode_read": "Read 1"
-                        },
-                        "schema_type": "process",
-                        "end_bias": "3 prime tag",
-                        "primer": "poly-dT",
-                        "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/library_preparation_process",
-                        "strand": "second"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-26T17:00:06.820Z",
-                        "updateDate": "2018-03-26T17:00:44.791Z",
-                        "document_id": "12ea2953-06a4-4e80-8910-a27aba936b9c"
-                    }
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "protocol_type": {
+                    "text": "10x sequencing protocol",
+                    "ontology": "EFO:0008443"
                 },
-                {
-                    "content": {
-                        "paired_ends": true,
-                        "local_machine_name": "HXJ",
-                        "instrument_manufacturer_model": {
-                            "text": "Illumina Hiseq X 10",
-                            "ontology": "EFO:0008567"
-                        },
-                        "process_type": {
-                            "text": "10x sequencing process"
-                        },
-                        "process_core": {
-                            "process_description": "Single cell sequencing of cDNAs by 10x",
-                            "process_name": "Sequencing bone marrow donor 5-8",
-                            "process_id": "10x_v2_sequencing_process_2",
-                            "start_time": "2017-09-26T05:20:00Z",
-                            "process_location": "Broad Institute"
-                        },
-                        "schema_type": "process",
-                        "describedBy": "https://schema.humancellatlas.org/type/process/sequencing/5.1.0/sequencing_process"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-26T17:00:06.935Z",
-                        "updateDate": "2018-03-26T17:00:53.534Z",
-                        "document_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1"
-                    }
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/5.2.1/process",
-            "schema_version": "5.2.1",
-            "schema_type": "process_bundle"
-        },
-        "protocol.json": {
-            "protocols": [
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_id": "dissociation_protocol_1"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "schema_type": "protocol"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-26T16:59:18.834Z",
-                        "updateDate": "2018-03-26T16:59:27.584Z",
-                        "document_id": "3cbebf0a-4aab-4525-80f4-222703d14b98"
-                    }
+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-26T16:59:18.848Z",
+                "updateDate": "2018-03-26T16:59:29.761Z",
+                "document_id": "81b97ec1-f68c-4d69-be78-50d1aad7bbef"
+            }
+        },
+        "protocol_2.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_id": "10x_v2_sequencing_protocol_1"
                 },
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_id": "library_preparation_protocol_1"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "protocol_type": {
-                            "text": "10x sequencing protocol",
-                            "ontology": "EFO:0008443"
-                        },
-                        "schema_type": "protocol"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-26T16:59:18.848Z",
-                        "updateDate": "2018-03-26T16:59:29.761Z",
-                        "document_id": "81b97ec1-f68c-4d69-be78-50d1aad7bbef"
-                    }
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "protocol_type": {
+                    "text": "10x sequencing protocol",
+                    "ontology": "EFO:0008443"
                 },
-                {
-                    "content": {
-                        "protocol_core": {
-                            "protocol_id": "10x_v2_sequencing_protocol_1"
-                        },
-                        "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
-                        "protocol_type": {
-                            "text": "10x sequencing protocol",
-                            "ontology": "EFO:0008443"
-                        },
-                        "schema_type": "protocol"
-                    },
-                    "hca_ingest": {
-                        "accession": "",
-                        "submissionDate": "2018-03-26T16:59:18.860Z",
-                        "updateDate": "2018-03-26T16:59:27.537Z",
-                        "document_id": "e99eed63-5794-4d8d-baf9-9c6888e91e6d"
-                    }
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/5.1.0/protocol",
-            "schema_version": "5.1.0",
-            "schema_type": "protocol_bundle"
+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-26T16:59:18.860Z",
+                "updateDate": "2018-03-26T16:59:27.537Z",
+                "document_id": "e99eed63-5794-4d8d-baf9-9c6888e91e6d"
+            }
         },
         "links.json": {
             "links": [
diff --git a/test/indexer/test_indexer.py b/test/indexer/test_indexer.py
index f8b485f47..229bc5cb7 100644
--- a/test/indexer/test_indexer.py
+++ b/test/indexer/test_indexer.py
@@ -1464,9 +1464,9 @@ def mocked_mget(self, body, _source_includes):
         self.assertEqual(4, len(file_uuids))
         for bundle_fqid in bundles:
             bundle = self._load_canned_bundle(bundle_fqid)
-            files: JSONs = bundle.metadata_files['file.json']['files']
-            for file in files:
-                file_document_ids.add(file['hca_ingest']['document_id'])
+            for doc in bundle.metadata_files.values():
+                if doc.get('content', {}).get('schema_type') == 'file':
+                    file_document_ids.add(doc['hca_ingest']['document_id'])
         self.assertEqual(file_document_ids, file_uuids)
 
     def test_indexing_matrix_related_files(self):

From 115d4db42d7b546d4574c65640cf0414733a7007 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Tue, 20 Aug 2024 15:40:55 -0700
Subject: [PATCH 09/20] Convert hca_metadata_api cans to new format

---
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   607 +
 .../2018-08-03T082009.272868Z/manifest.json   |   158 -
 .../2018-08-03T082009.272868Z/metadata.json   |   447 -
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   659 +
 .../2018-08-03T082009.272868Z/manifest.json   |   194 -
 .../2018-08-03T082009.272868Z/metadata.json   |   463 -
 ...a3fb4204953.2018-08-03T082009.272868Z.json |  1982 +++
 .../2018-08-03T082009.272868Z/manifest.json   |   602 -
 .../2018-08-03T082009.272868Z/metadata.json   |  1378 --
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   563 +
 .../2018-08-03T082009.272868Z/manifest.json   |   158 -
 .../2018-08-03T082009.272868Z/metadata.json   |   403 -
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   592 +
 .../2018-08-03T082009.272868Z/manifest.json   |   170 -
 .../2018-08-03T082009.272868Z/metadata.json   |   420 -
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   498 +
 .../2018-08-03T082009.272868Z/manifest.json   |   170 -
 .../2018-08-03T082009.272868Z/metadata.json   |   326 -
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   878 ++
 .../2018-08-03T082009.272868Z/manifest.json   |   338 -
 .../2018-08-03T082009.272868Z/metadata.json   |   538 -
 ...318dbb86000.2019-01-03T163633.780215Z.json |  2049 +++
 .../2019-01-03T163633.780215Z/manifest.json   |   598 -
 .../2019-01-03T163633.780215Z/metadata.json   |  1449 --
 ...61d6da02d44.2019-09-20T103932.395795Z.json |  1072 ++
 .../2019-09-20T103932.395795Z/manifest.json   |   326 -
 .../2019-09-20T103932.395795Z/metadata.json   |   744 -
 ...a3fb4204953.2018-03-29T142048.835519Z.json |   678 +
 .../2018-03-29T142048.835519Z/manifest.json   |    98 -
 .../2018-03-29T142048.835519Z/metadata.json   |   578 -
 ...d019d1c9439.2019-05-15T222432.561000Z.json |   401 +
 .../2019-05-15T222432.561000Z/manifest.json   |   170 -
 .../2019-05-15T222432.561000Z/metadata.json   |   233 -
 ...08092b2dabe.2019-04-17T175706.867000Z.json |   933 ++
 .../2019-04-17T175706.867000Z/manifest.json   |   230 -
 .../2019-04-17T175706.867000Z/metadata.json   |   701 -
 ...68e20ec4a2e.2019-02-02T065454.662896Z.json |  2704 ++++
 .../2019-02-02T065454.662896Z/manifest.json   |  1046 --
 .../2019-02-02T065454.662896Z/metadata.json   |  1656 ---
 ...19c1c2d9018.2018-10-07T130111.835234Z.json |   672 +
 .../2018-10-07T130111.835234Z/manifest.json   |   194 -
 .../2018-10-07T130111.835234Z/metadata.json   |   476 -
 ...406a478d5ab.2018-09-05T182535.846470Z.json |   501 +
 .../2018-09-05T182535.846470Z/manifest.json   |   194 -
 .../2018-09-05T182535.846470Z/metadata.json   |   305 -
 ...95a3f8deb9c.2019-04-03T103426.471000Z.json | 11982 ++++++++++++++++
 .../2019-04-03T103426.471000Z/manifest.json   |  5582 -------
 .../2019-04-03T103426.471000Z/metadata.json   |  6398 ---------
 ...720f33a5dde.2019-03-17T220646.332108Z.json |   790 +
 .../2019-03-17T220646.332108Z/manifest.json   |   230 -
 .../2019-03-17T220646.332108Z/metadata.json   |   558 -
 test/hca_metadata_api/test.py                 |    27 +-
 52 files changed, 27573 insertions(+), 27546 deletions(-)
 create mode 100644 test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
 delete mode 100644 test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json
 delete mode 100644 test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
 create mode 100644 test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
 delete mode 100644 test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json
 delete mode 100644 test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
 create mode 100644 test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
 delete mode 100644 test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json
 delete mode 100644 test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
 create mode 100644 test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
 delete mode 100644 test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json
 delete mode 100644 test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
 create mode 100644 test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
 delete mode 100644 test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json
 delete mode 100644 test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
 create mode 100644 test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
 delete mode 100644 test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json
 delete mode 100644 test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
 create mode 100644 test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
 delete mode 100644 test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json
 delete mode 100644 test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
 create mode 100644 test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
 delete mode 100644 test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000/2019-01-03T163633.780215Z/manifest.json
 delete mode 100644 test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000/2019-01-03T163633.780215Z/metadata.json
 create mode 100644 test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
 delete mode 100644 test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44/2019-09-20T103932.395795Z/manifest.json
 delete mode 100644 test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44/2019-09-20T103932.395795Z/metadata.json
 create mode 100644 test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
 delete mode 100644 test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-03-29T142048.835519Z/manifest.json
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diff --git a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
new file mode 100644
index 000000000..01627b98e
--- /dev/null
+++ b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
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+                "project_short_name": "1M Immune Cells",
+                "project_title": "Census of Immune Cells",
+                "project_description": "Diverse cells of the immune system maintain and protect tissue function, integrity, and homeostasis upon changes in functional demands and diverse perturbations. Recent advances such as massively parallel single-cell RNA-sequencing and sophisticated computational methods help shed new light on this complexity. This immune cell census aims to profile up to 2M immunocytes, the first tranche of this is currently available. With computational methods optimized to a massive scale, we can readily identify cell types and markers, as well as the process of hematopoietic differentiation. The high quality and comprehensive reference map is provided as an open community resource for understanding human health and disease."
+            },
+            "contributors": [
+                {
+                    "contact_name": "Aviv,,Regev",
+                    "email": "aregev@broadinstitute.org",
+                    "phone": "(617) 714-7020",
+                    "institution": "Broad Institute",
+                    "laboratory": "Regev Lab",
+                    "address": "415 Main Street, Cambridge, MA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Bo,,Li",
+                    "email": "libo@broadinstitute.org",
+                    "phone": "(617) 714-8681",
+                    "institution": "Broad Institute",
+                    "laboratory": "Regev Lab",
+                    "address": "415 Main Street, Cambridge, MA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Monika,S,Kowalczyk",
+                    "email": "msk.kowalczyk@gmail.com",
+                    "institution": "Broad Institute",
+                    "laboratory": "Regev Lab",
+                    "address": "415 Main Street, Cambridge, MA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Danielle,,Dionne",
+                    "email": "dionne@broadinstitute.org",
+                    "phone": "(617) 714-8147",
+                    "institution": "Broad Institute",
+                    "laboratory": "Regev Lab",
+                    "address": "415 Main Street, Cambridge, MA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Timothy,,Tickle",
+                    "email": "ttickle@broadinstitute.org",
+                    "phone": "(617) 714-7084",
+                    "institution": "Broad Institute",
+                    "laboratory": "Regev Lab",
+                    "address": "415 Main Street, Cambridge, MA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Jane,,Lee",
+                    "email": "janelee@broadinstitute.org",
+                    "phone": "(617) 714-7448",
+                    "institution": "Broad Institute",
+                    "laboratory": "Regev Lab",
+                    "address": "415 Main Street, Cambridge, MA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Orit,,Rozenblatt-Rosen",
+                    "email": "orit@broadinstitute.org",
+                    "phone": "(617) 714-7789",
+                    "institution": "Broad Institute",
+                    "laboratory": "Regev Lab",
+                    "address": "415 Main Street, Cambridge, MA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Orr,,Ashenberg",
+                    "email": "orr@broadinstitute.org",
+                    "phone": "(617) 714-8681",
+                    "institution": "Broad Institute",
+                    "laboratory": "Regev Lab",
+                    "address": "415 Main Street, Cambridge, MA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Marcin,,Tabaka",
+                    "email": "mtabaka@broadinstitute.org",
+                    "phone": "(617) 714-7470",
+                    "institution": "Broad Institute",
+                    "laboratory": "Regev Lab",
+                    "address": "415 Main Street, Cambridge, MA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Karthik,,Shekhar",
+                    "email": "karthik@broadinstitute.org",
+                    "phone": "(617) 714-8067",
+                    "institution": "Broad Institute",
+                    "laboratory": "Regev Lab",
+                    "address": "415 Main Street, Cambridge, MA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Michal,,Slyper",
+                    "email": "mslyper@broadinstitute.org",
+                    "phone": "(617) 714-7199",
+                    "institution": "Broad Institute",
+                    "laboratory": "Regev Lab",
+                    "address": "415 Main Street, Cambridge, MA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Julia,,Waldman",
+                    "email": "jwaldman@broadinstitute.org",
+                    "institution": "Broad Institute",
+                    "laboratory": "Regev Lab",
+                    "address": "415 Main Street, Cambridge, MA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Mallory,Ann,Freeberg",
+                    "email": "mfreeberg@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "Human Cell Atlas Data Coordination Platform",
+                    "address": "Wellcome Trust Genome Campus, Cambridge",
+                    "country": "UK",
+                    "project_role": "Human Cell Atlas wrangler",
+                    "orcid_id": "0000-0003-2949-3921",
+                    "corresponding_contributor": false
+                },
+                {
+                    "contact_name": "Danielle,,Welter",
+                    "email": "dwelter@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "Human Cell Atlas Data Coordination Platform",
+                    "address": "Wellcome Trust Genome Campus, Cambridge",
+                    "country": "UK",
+                    "project_role": "Human Cell Atlas wrangler",
+                    "orcid_id": "0000-0003-1058-2668",
+                    "corresponding_contributor": false
+                }
+            ],
+            "provenance": {
+                "document_id": "617eb7c1-a3bc-4dd3-9a2a-50a77c998e22",
+                "submission_date": "2018-09-04T12:26:40.041Z",
+                "update_date": "2018-09-04T12:27:09.930Z"
+            }
+        },
+        "sequence_file_0.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/6.5.2/sequence_file",
+            "schema_type": "file",
+            "file_core": {
+                "file_name": "MantonBM1_HiSeq_1_S1_L007_I1_001.fastq.gz",
+                "file_format": "fastq.gz"
+            },
+            "read_index": "index1",
+            "lane_index": 7,
+            "read_length": 8,
+            "technical_replicate_group": "1_BM1_cells_r1",
+            "provenance": {
+                "document_id": "36d7f891-8a43-4ae4-8472-a34dcb2be643",
+                "submission_date": "2018-09-04T12:26:43.089Z",
+                "update_date": "2018-09-04T12:27:39.827Z"
+            }
+        },
+        "sequencing_protocol_0.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "10x_v2_sequencing_protocol_1",
+                "protocol_name": "Sequencing bone marrow donor 1-4",
+                "protocol_description": "Single cell sequencing of cDNAs by 10x"
+            },
+            "instrument_manufacturer_model": {
+                "text": "Illumina Hiseq X 10",
+                "ontology": "EFO:0008567"
+            },
+            "local_machine_name": "HXE",
+            "paired_end": true,
+            "sequencing_approach": {
+                "text": "tag based single cell RNA sequencing",
+                "ontology": "EFO:0008440"
+            },
+            "provenance": {
+                "document_id": "aaa08845-5150-4a4f-9c44-5ea22add1fc3",
+                "submission_date": "2018-09-04T12:26:55.003Z",
+                "update_date": "2018-09-04T12:27:50.911Z"
+            }
+        },
+        "specimen_from_organism_0.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "1_BM1",
+                "ncbi_taxon_id": [
+                    9606
+                ]
+            },
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606"
+                }
+            ],
+            "organ": {
+                "text": "bone",
+                "ontology": "UBERON:0001474"
+            },
+            "organ_part": {
+                "text": "bone marrow",
+                "ontology": "UBERON:0002371"
+            },
+            "purchased_specimen": {
+                "manufacturer": "Stem Cell Technologies"
+            },
+            "provenance": {
+                "document_id": "6228558b-436a-46c9-9cd3-ea9b5c123070",
+                "submission_date": "2018-09-04T12:26:40.206Z",
+                "update_date": "2018-09-04T12:27:13.378Z"
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json
deleted file mode 100644
index b0a606b26..000000000
--- a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json	
+++ /dev/null
@@ -1,158 +0,0 @@
-[
-    {
-        "crc32c": "1C09FCE0",
-        "sha1": "f1aeb2b94ce28ee524388730c9b63b7dafc895c7",
-        "sha256": "b3f554280c892aecfc235a64f924843b2484f73cb0cd21aacdd1d796383a6d69",
-        "s3_etag": "bceb1c61bab478faf3f70e0ff832b4c0",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "cell_suspension_0.json",
-        "size": 770,
-        "uuid": "84354fad-8890-41df-b808-48f9ed4e1cc3",
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-    },
-    {
-        "crc32c": "28EA16F2",
-        "sha1": "7cc7ac34f3c2c00befb398a63b5303d636ca4711",
-        "sha256": "de429783e1308851f7f5e8320d8612e7c1ad90975698fec9a481c836db2e9543",
-        "s3_etag": "61eb8b831af8c1fdf1105ee9cb66fb16",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "dissociation_protocol_0.json",
-        "size": 711,
-        "uuid": "30cf9805-82f5-4725-a7ad-7411c276b4a9",
-        "version": "1"
-    },
-    {
-        "crc32c": "C2C08857",
-        "sha1": "8f1b7481a5dc77f3a6c90530a957952102a92e35",
-        "sha256": "94be68544f8a5a0171fd918e070150a29fa1c8f4380ec351a302bb56b980b491",
-        "s3_etag": "d98de4db8b42b8def2aa2591da2f8569",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "donor_organism_0.json",
-        "size": 1358,
-        "uuid": "491a22fb-3a6c-4a8f-9c5b-f009e080d280",
-        "version": "1"
-    },
-    {
-        "crc32c": "0B85C35C",
-        "sha1": "dd9a81c11165c742d94b1cb8561e3789854a8ca7",
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-        "s3_etag": "abc3a4a3dbec4beab0e2cacf50b831c4",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "library_preparation_protocol_0.json",
-        "size": 1087,
-        "uuid": "821601f1-64e8-4427-8680-34a743b35b69",
-        "version": "1"
-    },
-    {
-        "crc32c": "DDAABBB6",
-        "sha1": "82c4c5273e31923bf6e12139804c3a4cf10b338d",
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-        "s3_etag": "4dc6069c891063f28a0ee155c6cd7b65",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "links.json",
-        "size": 1856,
-        "uuid": "04e79979-489e-4cd8-93c3-1d8e99d09ec8",
-        "version": "1"
-    },
-    {
-        "crc32c": "522D96A7",
-        "sha1": "9876adb67827ea0328566811a1304bcf49a31b02",
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-        "s3_etag": "4f939c7dae692b468e4741b56ccfbe3e",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "process_0.json",
-        "size": 386,
-        "uuid": "c4175b47-1767-48c5-b408-f9e97c01f94e",
-        "version": "1"
-    },
-    {
-        "crc32c": "51B043A0",
-        "sha1": "9b17c9cd8e3d7c3bc4685e24bbcba9e528792d05",
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-        "s3_etag": "8ff1e91a29e51311d5252889599eb709",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "process_1.json",
-        "size": 386,
-        "uuid": "88b3b728-e9c6-4b1b-a030-97f6670469c2",
-        "version": "1"
-    },
-    {
-        "crc32c": "1FAD27D0",
-        "sha1": "b2a61619fa1922cb899d993aace4fa0f6b30a232",
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-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "process_2.json",
-        "size": 384,
-        "uuid": "317b3c35-e0f6-48d6-9154-80db47ff8f20",
-        "version": "1"
-    },
-    {
-        "crc32c": "68AEC241",
-        "sha1": "1296d3c9b98cef091f1aecd6d9df25fa7f780d5c",
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-        "s3_etag": "93f27be5baa191e55406b1b54af4bd1e",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "project_0.json",
-        "size": 6018,
-        "uuid": "a34d2ddc-1433-4a3c-b1de-ad3a26adca9e",
-        "version": "1"
-    },
-    {
-        "crc32c": "29B559F9",
-        "sha1": "0587673d7d88efa40a6f4d25d34d2eba14cf8e8b",
-        "sha256": "df8b88b6f32f494a53687f79724a6ebd8bbb9c5c0474b9a857d467a0bdb83c2d",
-        "s3_etag": "ef8edc4bf0ba07805a052cd7686b5ea7",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "sequence_file_0.json",
-        "size": 566,
-        "uuid": "6832e250-33c6-469a-b105-efa0d6f61309",
-        "version": "1"
-    },
-    {
-        "crc32c": "29B559F9",
-        "sha1": "0587673d7d88efa40a6f4d25d34d2eba14cf8e8b",
-        "sha256": "df8b88b6f32f494a53687f79724a6ebd8bbb9c5c0474b9a857d467a0bdb83c2d",
-        "s3_etag": "ef8edc4bf0ba07805a052cd7686b5ea7",
-        "content-type": "application/octet-stream",
-        "indexed": false,
-        "name": "MantonBM1_HiSeq_1_S1_L007_I1_001.fastq.gz",
-        "size": 566,
-        "uuid": "c8a4ea32-6d66-48f3-b480-9421743b9c0a",
-        "version": "1"
-    },
-    {
-        "crc32c": "5B68EDBD",
-        "sha1": "189a903531d1b9fe78e035945ed29bc004636526",
-        "sha256": "87854958090c0868f38be4ac5c7aa2324ff027b2b4803a5a2fd9a8eb01af4f21",
-        "s3_etag": "2c0a2cf2cc963e8f01e85cc324763c4c",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "sequencing_protocol_0.json",
-        "size": 864,
-        "uuid": "86417b00-f90f-409d-a9dd-717d077c3cf4",
-        "version": "1"
-    },
-    {
-        "crc32c": "290F5DCB",
-        "sha1": "3d4837dacac05df3adb29fa05874a5841b4661f7",
-        "sha256": "62e38c88e4038b73e52abafeb08440ccb6eb4417c1f56fd3fc7bc10a2aec32ff",
-        "s3_etag": "9512af43df021d47adc83a34d49046b9",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "specimen_from_organism_0.json",
-        "size": 852,
-        "uuid": "169096e5-f310-4c67-9a70-e139a3576e9e",
-        "version": "1"
-    }
-]
diff --git a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
deleted file mode 100644
index 3a2e44de9..000000000
--- a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json	
+++ /dev/null
@@ -1,447 +0,0 @@
-{
-    "cell_suspension_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "1_BM1_cells",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "selected_cell_type": [
-            {
-                "text": "bone marrow hematopoietic cell",
-                "ontology": "CL:1001610"
-            }
-        ],
-        "total_estimated_cells": 4294,
-        "provenance": {
-            "document_id": "7b53bae2-2424-44c0-9d80-ad72e8bca136",
-            "submission_date": "2018-09-04T12:26:41.629Z",
-            "update_date": "2018-09-04T12:27:19.625Z"
-        }
-    },
-    "dissociation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "dissociation_protocol_1",
-            "protocol_name": "mononuclear cell isolation",
-            "protocol_description": "We isolated mononuclear cells for all samples in preparation for 10x sequencing."
-        },
-        "dissociation_method": {
-            "text": "10x sequencing",
-            "ontology": "EFO:0008995"
-        },
-        "provenance": {
-            "document_id": "eebf404f-4fbb-41b0-a9c6-81586f729599",
-            "submission_date": "2018-09-04T12:26:54.982Z",
-            "update_date": "2018-09-04T12:26:56.433Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "BM1",
-            "biomaterial_name": "Bone Marrow donor 1",
-            "biomaterial_description": "Bone Marrow donor 1",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "organism_age": "52",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036"
-        },
-        "development_stage": {
-            "text": "adult",
-            "ontology": "EFO:0001272"
-        },
-        "is_living": "yes",
-        "sex": "female",
-        "medical_history": {
-            "smoking_history": "no"
-        },
-        "human_specific": {
-            "ethnicity": [
-                {
-                    "text": "Caucasian"
-                }
-            ]
-        },
-        "weight": "69",
-        "weight_unit": {
-            "text": "kilogram",
-            "ontology": "UO:0000009"
-        },
-        "height": "165",
-        "height_unit": {
-            "text": "centimeter",
-            "ontology": "UO:0000015"
-        },
-        "provenance": {
-            "document_id": "628e8b1d-a1ce-4dee-b15a-3fd33290eafe",
-            "submission_date": "2018-09-04T12:26:40.051Z",
-            "update_date": "2018-09-04T12:27:10.175Z"
-        }
-    },
-    "library_preparation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/4.3.2/library_preparation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "library_preparation_protocol_1",
-            "protocol_name": "Preparing RNA for sequencing by 10x"
-        },
-        "cell_barcode": {
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diff --git a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
new file mode 100644
index 000000000..1a798a5a8
--- /dev/null
+++ b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
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+                "project_title": "Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis",
+                "project_description": "CD4+ cytotoxic T lymphocytes (CD4-CTLs) have been reported to play a protective role in several viral infections. However, little is known in humans about the biology of CD4-CTL generation, their functional properties, heterogeneity and clonal diversity, especially in relation to other well-described CD4+ memory T cell subsets. We performed single-cell RNA-seq in over 9000 cells to unravel CD4-CTL heterogeneity, transcriptional profile and clonality in humans. The single-cell differential gene expression analysis, revealed a spectrum of known transcripts, including several linked to cytotoxic and co-stimulatory function, and transcripts of unknown cytotoxicity-related function that are expressed at higher levels in the TEMRA subset, which is highly enriched for CD4-CTLs, compared to cells in the central and effector memory subsets (TCM, TEM). Simultaneous T cells antigen receptor (TCR) analysis in single-cells and bulk subsets revealed that CD4-TEMRA cells show marked clonal expansion compared to TCM and TEM cells and that the majority of CD4-TEMRA were dengue virus (DENV)-specific in subjects with previous DENV infection. The profile of CD4-TEMRA was highly heterogeneous across subjects, with four distinct clusters identified by the single-cell analysis. Most importantly, we identified distinct clusters of CD4-CTL effector and precursor cells in the TEMRA subset; the precursor cells shared TCR clonotypes with CD4-CTL effectors and were distinguished by high expression of the interleukin-7 receptor. Our identification of a CD4-CTL precursor population may allow further investigation of how CD4-CTLs arise in humans and thus could provide insights into the mechanisms that may be utilized to generate durable and effective CD4-CTL immunity."
+            },
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+            "geo_series": "GSE106540",
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+            "supplementary_links": [
+                "https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-106540/Results"
+            ],
+            "contributors": [
+                {
+                    "contact_name": "Pandurangan,,Vijayanand",
+                    "email": "vijay@lji.org",
+                    "institution": "La Jolla Institute for Allergy and Immunology",
+                    "laboratory": "Division of Vaccine Discovery",
+                    "address": "La Jolla, CA 92037",
+                    "country": "USA",
+                    "corresponding_contributor": true
+                },
+                {
+                    "contact_name": "Mallory,Ann,Freeberg",
+                    "email": "mfreeberg@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "Human Cell Atlas Data Coordination Platform",
+                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
+                    "country": "UK",
+                    "project_role": "Human Cell Atlas wrangler",
+                    "orcid_id": "0000-0003-2949-3921",
+                    "corresponding_contributor": false
+                },
+                {
+                    "contact_name": "Laura,,Huerta",
+                    "email": "lauhuema@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "Molecular Atlas",
+                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
+                    "country": "UK",
+                    "project_role": "external curator",
+                    "orcid_id": "0000-0002-8748-599X",
+                    "corresponding_contributor": false
+                }
+            ],
+            "funders": [
+                {
+                    "grant_id": "U19AI118626",
+                    "funder_name": "National Institutes of Health (NIH)"
+                },
+                {
+                    "grant_id": "U19AI118610",
+                    "funder_name": "National Institutes of Health (NIH)"
+                },
+                {
+                    "grant_id": "R01HL114093",
+                    "funder_name": "National Institutes of Health (NIH)"
+                },
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+                    "funder_name": "National Institutes of Health (NIH)"
+                },
+                {
+                    "funder_name": "William K. Bowes Jr. Foundation"
+                }
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+                {
+                    "authors": [
+                        "Patil VS, Madrigal A, Schmiedel BJ, Clarke J, O'Rourke P, Harris E, de Silva AD, Harris E, Peters B, Seumois G, Weiskopf D, Sette A, Vijayanand P"
+                    ],
+                    "publication_title": "Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis.",
+                    "doi": "10.1126/sciimmunol.aan8664",
+                    "pmid": 29352091,
+                    "publication_url": "http://immunology.sciencemag.org/content/3/19/eaan8664.long"
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+            "preservation_storage": {
+                "preservation_method": "cryopreservation, other",
+                "storage_method": "frozen, liquid nitrogen"
+            },
+            "provenance": {
+                "document_id": "ff63b5d7-e702-40da-bbe9-619e52131b63",
+                "submission_date": "2018-09-05T09:47:21.215Z",
+                "update_date": "2018-09-05T09:50:44.523Z"
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json
deleted file mode 100644
index c4871bb0e..000000000
--- a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json	
+++ /dev/null
@@ -1,194 +0,0 @@
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-]
diff --git a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
deleted file mode 100644
index a534b298f..000000000
--- a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json	
+++ /dev/null
@@ -1,463 +0,0 @@
-{
-    "cell_suspension_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "Single-cell_RNA-seq_Subject10_TEMRA_Cell001",
-            "biomaterial_name": "Single-cell_RNA-seq_Subject10_TEMRA_Cell001",
-            "biomaterial_description": "Single-cell_RNA-seq_Subject10_TEMRA_Cell001",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "insdc_biomaterial": "SRS2661967"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "selected_cell_type": [
-            {
-                "text": "TEMRA",
-                "ontology": "CL:0000625"
-            }
-        ],
-        "total_estimated_cells": 1,
-        "plate_based_sequencing": {
-            "plate_id": "subject9-10_batch1",
-            "cell_quality": "OK"
-        },
-        "provenance": {
-            "document_id": "cc0d9bf0-6ad5-4489-994b-db26ff761c5a",
-            "submission_date": "2018-09-05T09:47:21.355Z",
-            "update_date": "2018-09-05T09:53:09.415Z"
-        }
-    },
-    "collection_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/8.2.6/collection_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "collection_protocol_2",
-            "protocol_name": "Blood sample collection",
-            "protocol_description": "Blood sample collection",
-            "publication_doi": "10.1126/sciimmunol.aan8664"
-        },
-        "collection_method": {
-            "text": "blood draw",
-            "ontology": "EFO:0009121"
-        },
-        "provenance": {
-            "document_id": "f8d9778f-0f72-4432-a929-1096fd9ca2f4",
-            "submission_date": "2018-09-05T09:48:40.196Z",
-            "update_date": "2018-09-05T09:52:05.472Z"
-        }
-    },
-    "dissociation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "dissociation_protocol_1",
-            "protocol_name": "Dissociation by FACS into single cells",
-            "protocol_description": "Dissociation by FACS into single cells",
-            "publication_doi": "10.1126/sciimmunol.aan8664"
-        },
-        "dissociation_method": {
-            "text": "fluorescence-activated cell sorting",
-            "ontology": "EFO:0009108"
-        },
-        "provenance": {
-            "document_id": "a934e15c-e1ce-423b-b554-9203d4e93f41",
-            "submission_date": "2018-09-05T09:48:40.205Z",
-            "update_date": "2018-09-05T09:51:59.418Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "Subject10",
-            "biomaterial_name": "Subject10",
-            "biomaterial_description": "Subject10",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "is_living": "yes",
-        "sex": "unknown",
-        "medical_history": {
-            "test_results": "dengue virus negative"
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461"
-            }
-        ],
-        "development_stage": {
-            "text": "adult",
-            "ontology": "EFO:0001272"
-        },
-        "organism_age": "18-60",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036"
-        },
-        "provenance": {
-            "document_id": "25e083e3-d747-4295-86c8-c7ddc4b975be",
-            "submission_date": "2018-09-05T09:47:20.947Z",
-            "update_date": "2018-09-05T09:50:15.914Z"
-        }
-    },
-    "enrichment_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "enrichment_protocol_1",
-            "protocol_name": "PBMC Enrichment",
-            "protocol_description": "CD4 memory cell types were isolated from PBMCs and directly sorted by Flow cytometry into a 96-well plate wells with lysis buffer with RNAase inhibitor (Takara) - Described in Picelli et al. Nat Protoc. 2014, PMID:24385147. No particular cell growth procedure was required.",
-            "publication_doi": "10.1073/pnas.1305227110"
-        },
-        "enrichment_method": {
-            "text": "Ficoll-Hypaque method",
-            "ontology": "EFO:0009110"
-        },
-        "provenance": {
-            "document_id": "80921b90-fe8d-45e1-a5e5-4fdb55f9a3fa",
-            "submission_date": "2018-09-05T09:48:40.213Z",
-            "update_date": "2018-09-05T09:52:05.683Z"
-        }
-    },
-    "enrichment_protocol_1.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "enrichment_protocol_2",
-            "protocol_name": "TEMRA Enrichment",
-            "protocol_description": "For single-cell RNA-seq experiments, live and singlet gated cells were further gated to sort 1) TCM; CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA-CCR7+, 2) TEM; CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA-CCR7-, 3) TEMRA; CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA+CCR7-, 4) IL-7Rhigh TEMRA (CD4-CTL precursors); CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA+CCR7-CD127high, 5) IL-7R- TEMRA (CD4-CTL effectors); CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA+CCR7- CD127-. Single cells were directly sorted into 96 well plate with lysis buffer for downstream processing using Smart-seq2 method",
-            "publication_doi": "10.1126/sciimmunol.aan8664"
-        },
-        "enrichment_method": {
-            "text": "fluorescence-activated cell sorting",
-            "ontology": "EFO:0009108"
-        },
-        "markers": "CD3+CD4+CD8alpha/CD14/CD19-CD45RA+CCR7-",
-        "provenance": {
-            "document_id": "77c71448-fb32-472f-9d44-ea9a42867a41",
-            "submission_date": "2018-09-05T09:48:40.222Z",
-            "update_date": "2018-09-05T09:51:58.823Z"
-        }
-    },
-    "library_preparation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/4.3.2/library_preparation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "library_preparation_protocol_1",
-            "protocol_name": "Preparation of mRNAs for single cell SmartSeq2 sequencing",
-            "protocol_description": "Single cell RNAseq was performed as described in Picelli et al.Nat Protoc. 2014, PMID:24385147. We performed 23 cycles of amplification. Barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina) were prepared as following manufacturers protocol.",
-            "publication_doi": "10.1038/nprot.2014.006"
-        },
-        "library_construction_approach": {
-            "text": "Smart-seq2",
-            "ontology": "EFO:0008931"
-        },
-        "nucleic_acid_source": "single cell",
-        "end_bias": "full length",
-        "primer": "poly-dT",
-        "strand": "unstranded",
-        "input_nucleic_acid_molecule": {
-            "text": "polyA RNA",
-            "ontology": "OBI:0000869"
-        },
-        "library_construction_kit": {
-            "retail_name": "Nextera XT library preparation kit",
-            "manufacturer": "Illumina"
-        },
-        "library_preamplification_method": {
-            "text": "PCR",
-            "ontology": "OBI:0000415"
-        },
-        "provenance": {
-            "document_id": "0ea30fa0-7183-4ffc-a4b8-537c6de32e65",
-            "submission_date": "2018-09-05T09:48:40.286Z",
-            "update_date": "2018-09-05T09:52:00.867Z"
-        }
-    },
-    "links.json": {
-        "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
-        "schema_type": "link_bundle",
-        "schema_version": "1.1.1",
-        "links": [
-            {
-                "process": "bcfcb3d7-674a-429f-8bf9-347a0f222db2",
-                "inputs": [
-                    "cc0d9bf0-6ad5-4489-994b-db26ff761c5a"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "a5806f2e-3f85-486a-9015-e02e5c805285"
-                ],
-                "output_type": "file",
-                "protocols": [
-                    {
-                        "protocol_type": "library_preparation_protocol",
-                        "protocol_id": "0ea30fa0-7183-4ffc-a4b8-537c6de32e65"
-                    },
-                    {
-                        "protocol_type": "sequencing_protocol",
-                        "protocol_id": "2d0f835b-ced1-4cf1-a053-0cf109fdefeb"
-                    }
-                ]
-            },
-            {
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-            "project_description": "CD4+ cytotoxic T lymphocytes (CD4-CTLs) have been reported to play a protective role in several viral infections. However, little is known in humans about the biology of CD4-CTL generation, their functional properties, heterogeneity and clonal diversity, especially in relation to other well-described CD4+ memory T cell subsets. We performed single-cell RNA-seq in over 9000 cells to unravel CD4-CTL heterogeneity, transcriptional profile and clonality in humans. The single-cell differential gene expression analysis, revealed a spectrum of known transcripts, including several linked to cytotoxic and co-stimulatory function, and transcripts of unknown cytotoxicity-related function that are expressed at higher levels in the TEMRA subset, which is highly enriched for CD4-CTLs, compared to cells in the central and effector memory subsets (TCM, TEM). Simultaneous T cells antigen receptor (TCR) analysis in single-cells and bulk subsets revealed that CD4-TEMRA cells show marked clonal expansion compared to TCM and TEM cells and that the majority of CD4-TEMRA were dengue virus (DENV)-specific in subjects with previous DENV infection. The profile of CD4-TEMRA was highly heterogeneous across subjects, with four distinct clusters identified by the single-cell analysis. Most importantly, we identified distinct clusters of CD4-CTL effector and precursor cells in the TEMRA subset; the precursor cells shared TCR clonotypes with CD4-CTL effectors and were distinguished by high expression of the interleukin-7 receptor. Our identification of a CD4-CTL precursor population may allow further investigation of how CD4-CTLs arise in humans and thus could provide insights into the mechanisms that may be utilized to generate durable and effective CD4-CTL immunity."
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-                "funder_name": "National Institutes of Health (NIH)"
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-                "funder_name": "National Institutes of Health (NIH)"
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-                ],
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-                "pmid": 29352091,
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diff --git a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
new file mode 100644
index 000000000..eb9525ed0
--- /dev/null
+++ b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
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+                "project_description": "The purpose of this project is to assess the relevance of pluripotent stem cell-derived cerebral and liver organoids to recapitulate the variation in cell-type specific gene expression programs between individuals. Towards this aim, we will generate reference atlases of the developing cortex and liver from multiple individuals, derive iPSC lines from these same individuals, and determine if inter-individual gene expression variation is recapitulated in cerebral and liver organoids from the same individual from which we have reference maps. In parallel we will assess the genetic contribution to variablity between organoids from different iPSCs of multiple human individuals that are available in existing iPSC resources (e.g. HipSci)."
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+                    "contact_name": "Zhisong,,He",
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+                    "address": "Deutscher Pl. 6, 04103 Leipzig",
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+        }
+    }
+}
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diff --git a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json
deleted file mode 100644
index f8f6f0ed8..000000000
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-        "crc32c": "47985515",
-        "sha1": "b12c361c6d4ebb7c255ddb3e67e3babbd1fe0e25",
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diff --git a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
deleted file mode 100644
index ef933bc83..000000000
--- a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
+++ /dev/null
@@ -1,1378 +0,0 @@
-{
-    "cell_line_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.2/cell_line",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0214i-kucg_2",
-            "biomaterial_name": "iPS cell line kucg_2",
-            "biomaterial_description": "iPS cell line kucg_2",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA2645814"
-        },
-        "diseases": {
-            "text": "normal",
-            "ontology": "PATO:0000461"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "cell_type": {
-            "text": "pluripotent stem cell",
-            "ontology": "CL:0002248"
-        },
-        "catalog_number": "77650065",
-        "catalog_url": "http://www.hipsci.org/lines/#/lines/HPSI0214i-kucg_2",
-        "cell_line_type": "induced pluripotent",
-        "cell_morphology": {
-            "cell_viability_method": "Growth to confluence post-thaw"
-        },
-        "growth_conditions": {
-            "passage_number": 25,
-            "growth_medium": "E8",
-            "feeder_layer_type": "feeder-free",
-            "drug_treatment": "Cells were cultured in presence of Penicillin and Streptomycin",
-            "mycoplasma_testing_method": "PCR",
-            "mycoplasma_testing_results": "pass"
-        },
-        "date_established": "2014-11-03T00:00:00Z",
-        "provenance": {
-            "document_id": "304fadde-e22a-4ff9-9544-f8ec097b6135",
-            "submission_date": "2018-09-05T09:25:02.372Z",
-            "update_date": "2018-09-05T09:25:11.221Z"
-        }
-    },
-    "cell_line_1.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.2/cell_line",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0214i-wibj_2",
-            "biomaterial_name": "iPS cell line wibj_2",
-            "biomaterial_description": "iPS cell line wibj_2",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA2627567"
-        },
-        "diseases": {
-            "text": "normal",
-            "ontology": "PATO:0000461"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "cell_type": {
-            "text": "pluripotent stem cell",
-            "ontology": "CL:0002248"
-        },
-        "catalog_number": "77650057",
-        "catalog_url": "http://www.hipsci.org/lines/#/lines/HPSI0214i-wibj_2",
-        "cell_line_type": "induced pluripotent",
-        "cell_morphology": {
-            "cell_viability_method": "Growth to confluence post-thaw"
-        },
-        "growth_conditions": {
-            "passage_number": 24,
-            "growth_medium": "E8",
-            "feeder_layer_type": "feeder-free",
-            "drug_treatment": "Cells were cultured in presence of Penicillin and Streptomycin",
-            "mycoplasma_testing_method": "PCR",
-            "mycoplasma_testing_results": "pass"
-        },
-        "date_established": "2014-10-24T00:00:00Z",
-        "provenance": {
-            "document_id": "cc5c8bd6-3bd6-49d6-87b3-b24ef3a577a4",
-            "submission_date": "2018-09-05T09:25:02.352Z",
-            "update_date": "2018-09-05T09:25:10.838Z"
-        }
-    },
-    "cell_line_2.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.2/cell_line",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0314i-sojd_3",
-            "biomaterial_name": "iPS cell line sojd_3",
-            "biomaterial_description": "iPS cell line sojd_3",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA2627569"
-        },
-        "diseases": {
-            "text": "normal",
-            "ontology": "PATO:0000461"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "cell_type": {
-            "text": "pluripotent stem cell",
-            "ontology": "CL:0002248"
-        },
-        "catalog_number": "77650126",
-        "catalog_url": "http://www.hipsci.org/lines/#/lines/HPSI0314i-sojd_3",
-        "cell_line_type": "induced pluripotent",
-        "cell_morphology": {
-            "cell_viability_method": "Growth to confluence post-thaw"
-        },
-        "growth_conditions": {
-            "passage_number": 22,
-            "growth_medium": "E8",
-            "feeder_layer_type": "feeder-free",
-            "drug_treatment": "Cells were cultured in presence of Penicillin and Streptomycin",
-            "mycoplasma_testing_method": "PCR",
-            "mycoplasma_testing_results": "pass"
-        },
-        "date_established": "2015-01-09T00:00:00Z",
-        "provenance": {
-            "document_id": "6953e086-13cc-4467-b059-4d5f91f6f268",
-            "submission_date": "2018-09-05T09:25:02.407Z",
-            "update_date": "2018-09-05T09:25:05.636Z"
-        }
-    },
-    "cell_line_3.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.2/cell_line",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0314i-hoik_1",
-            "biomaterial_name": "iPS cell line hoik_1",
-            "biomaterial_description": "iPS cell line hoik_1",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA2698315"
-        },
-        "diseases": {
-            "text": "normal",
-            "ontology": "PATO:0000461"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "cell_type": {
-            "text": "pluripotent stem cell",
-            "ontology": "CL:0002248"
-        },
-        "catalog_number": "77650129",
-        "catalog_url": "http://www.hipsci.org/lines/#/lines/HPSI0314i-hoik_1",
-        "cell_line_type": "induced pluripotent",
-        "cell_morphology": {
-            "cell_viability_method": "Growth to confluence post-thaw"
-        },
-        "growth_conditions": {
-            "passage_number": 20,
-            "growth_medium": "E8",
-            "feeder_layer_type": "feeder-free",
-            "drug_treatment": "Cells were cultured in presence of Penicillin and Streptomycin",
-            "mycoplasma_testing_method": "PCR",
-            "mycoplasma_testing_results": "pass"
-        },
-        "date_established": "2015-02-02T00:00:00Z",
-        "provenance": {
-            "document_id": "8bd345cb-4635-4bf5-9435-bf144013b938",
-            "submission_date": "2018-09-05T09:25:02.397Z",
-            "update_date": "2018-09-05T09:25:11.557Z"
-        }
-    },
-    "cell_suspension_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI_organoids_pooled_1",
-            "biomaterial_name": "pooled cells from 4 dissociated organoids",
-            "biomaterial_description": "pooled cells from 4 dissociated organoids (wibj_2, kucg_2, hoik_1, sojd_3)",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "selected_cell_type": [
-            {
-                "text": "neural cell",
-                "ontology": "CL:0002319"
-            }
-        ],
-        "total_estimated_cells": 6316,
-        "provenance": {
-            "document_id": "8fc8b364-98bb-4082-98af-e3fdffcf82b7",
-            "submission_date": "2018-09-05T09:25:02.595Z",
-            "update_date": "2018-09-05T09:25:12.353Z"
-        }
-    },
-    "differentiation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/1.3.0/differentiation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "Org_Lanc_2014",
-            "protocol_name": "Generation of cerebral organoids from human pluripotent stem cells",
-            "publication_doi": "10.1038/nprot.2014.158"
-        },
-        "differentiation_method": "embryoid bodies",
-        "differentiation_target_pathway": "RHO||ROCK",
-        "differentiation_validation_method": "immunostaining",
-        "differentiation_reagents": {
-            "retail_name": "ROCK inhibitor Y27632"
-        },
-        "differentiation_small_molecules": "Vitamin A (retinoic acid)",
-        "provenance": {
-            "document_id": "537b3c44-998f-43c2-8146-7e3e2932c30b",
-            "submission_date": "2018-09-05T09:25:02.643Z",
-            "update_date": "2018-09-05T09:25:11.867Z"
-        }
-    },
-    "dissociation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "Cerebral_organoid_dissociation",
-            "protocol_name": "cerebral organoid dissociation",
-            "document": "Dissociation_protocol_130-092-628.pdf"
-        },
-        "dissociation_method": {
-            "text": "Papain-based enzymatic dissociation",
-            "ontology": "EFO:0009128"
-        },
-        "protocol_reagents": [
-            {
-                "retail_name": "Neural Tissue Dissociation Kit",
-                "catalog_number": "130-092-628",
-                "manufacturer": "Miltenyi Biotec"
-            }
-        ],
-        "provenance": {
-            "document_id": "58334256-af4f-4754-9455-668fb31bbcff",
-            "submission_date": "2018-09-05T09:25:02.654Z",
-            "update_date": "2018-09-05T09:25:09.326Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0314i-sojd",
-            "biomaterial_name": "donor HPSI0314i-sojd",
-            "biomaterial_description": "donor HPSI0314i-sojd_3, iPSC, cell line, skin",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA2418245"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "sex": "female",
-        "organism_age": "45-49",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036"
-        },
-        "human_specific": {
-            "ethnicity": [
-                {
-                    "text": "White - other, Ad Mixed American",
-                    "ontology": "hancestro:0463"
-                }
-            ]
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461"
-            }
-        ],
-        "is_living": "yes",
-        "provenance": {
-            "document_id": "5554b939-a268-4619-9cef-0f09151454fc",
-            "submission_date": "2018-09-05T09:25:02.273Z",
-            "update_date": "2018-09-05T09:25:09.818Z"
-        }
-    },
-    "donor_organism_1.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0214i-wibj",
-            "biomaterial_name": "donor HPSI0214i-wibj",
-            "biomaterial_description": "donor HPSI0214i-wibj_2, iPSC, cell line, skin",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA2398911"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "sex": "female",
-        "organism_age": "55-59",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036"
-        },
-        "human_specific": {
-            "ethnicity": [
-                {
-                    "text": "European, White, British",
-                    "ontology": "hancestro:0462"
-                }
-            ]
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461"
-            }
-        ],
-        "is_living": "yes",
-        "provenance": {
-            "document_id": "eea3dd19-90e0-45c4-803d-4620d1fab90d",
-            "submission_date": "2018-09-05T09:25:02.230Z",
-            "update_date": "2018-09-05T09:25:09.806Z"
-        }
-    },
-    "donor_organism_2.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0214i-kucg",
-            "biomaterial_name": "donor HPSI0214i-kucg",
-            "biomaterial_description": "donor HPSI0214i-kucg_2, iPSC, cell line, skin",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA2397923"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "sex": "male",
-        "organism_age": "65-69",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036"
-        },
-        "human_specific": {
-            "ethnicity": [
-                {
-                    "text": "European, White, British",
-                    "ontology": "hancestro:0462"
-                }
-            ]
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461"
-            }
-        ],
-        "is_living": "yes",
-        "provenance": {
-            "document_id": "fbd4c071-58bd-4818-8ddd-2c31ddb60363",
-            "submission_date": "2018-09-05T09:25:02.247Z",
-            "update_date": "2018-09-05T09:25:09.903Z"
-        }
-    },
-    "donor_organism_3.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0314i-hoik",
-            "biomaterial_name": "donor HPSI0314i-hoik",
-            "biomaterial_description": "donor HPSI0314i-hoik_1, iPSC, cell line, skin",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA2399961"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "sex": "female",
-        "organism_age": "40-44",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036"
-        },
-        "human_specific": {
-            "ethnicity": [
-                {
-                    "text": "European, White, British",
-                    "ontology": "hancestro:0462"
-                }
-            ]
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461"
-            }
-        ],
-        "is_living": "yes",
-        "provenance": {
-            "document_id": "62ee5119-4fa1-4508-95f3-59c7b0fddd34",
-            "submission_date": "2018-09-05T09:25:02.257Z",
-            "update_date": "2018-09-05T09:25:09.841Z"
-        }
-    },
-    "ipsc_induction_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/2.0.1/ipsc_induction_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "ipsc_induction_protocol_1",
-            "protocol_name": "iPSC induction by Sendai virus",
-            "protocol_description": "Fibroblasts are thawed, transduced using Cytotune 2.0 Sendai virus (containing the Yamanaka genes encoding transcription factors Oct4, Sox2, cMyc and Klf4) and maintained until iPSC colony formation. Colonies are then picked and cultured to obtain a sizable yield of IPS cells, which are banked to a commercial grade standard. These banks then undergo quality checks to ensure the banks pass resuscitation tests and are free of mycoplasma.",
-            "document": "hipsci-ipsc-pipeline.pdf"
-        },
-        "ipsc_induction_method": "sendai virus",
-        "pluripotency_vector_removed": "yes",
-        "ipsc_induction_kit": {
-            "retail_name": "Cytotune 1.0",
-            "manufacturer": "Thermofisher"
-        },
-        "pluripotency_test": "HipSci Pluri test",
-        "ipsc_induction_produced_in_house": false,
-        "provenance": {
-            "document_id": "9e3b5ef9-cbb0-43ef-a194-1ce1969cfd62",
-            "submission_date": "2018-09-05T09:25:02.631Z",
-            "update_date": "2018-09-05T09:25:09.069Z"
-        }
-    },
-    "library_preparation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/4.3.2/library_preparation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "10x_3'_library_preparation",
-            "protocol_name": "10x 3' single cell library preparation",
-            "protocol_description": "10x Chromium single cell 3' v2 library preparation",
-            "document": "CG00052_SingleCell3_ReagentKitv2UserGuide_RevE.pdf"
-        },
-        "nucleic_acid_source": "single cell",
-        "input_nucleic_acid_molecule": {
-            "text": "polyA RNA",
-            "ontology": "OBI:0000869"
-        },
-        "library_construction_approach": {
-            "text": "Chromium 3' Single Cell v2",
-            "ontology": "EFO:0008995"
-        },
-        "end_bias": "3 prime end bias",
-        "primer": "poly-dT",
-        "strand": "unstranded",
-        "cell_barcode": {
-            "barcode_read": "Read 1",
-            "barcode_offset": 0,
-            "barcode_length": 16
-        },
-        "umi_barcode": {
-            "barcode_read": "Read 1",
-            "barcode_offset": 15,
-            "barcode_length": 10
-        },
-        "library_construction_kit": {
-            "retail_name": "10X Chromium Single Cell 3' Solution v2 Chemistry",
-            "manufacturer": "10X Genomics"
-        },
-        "provenance": {
-            "document_id": "853c2086-1ac4-488e-b3b3-fe7956e74283",
-            "submission_date": "2018-09-05T09:25:02.667Z",
-            "update_date": "2018-09-05T09:25:09.008Z"
-        }
-    },
-    "links.json": {
-        "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
-        "schema_type": "link_bundle",
-        "schema_version": "1.1.1",
-        "links": [
-            {
-                "process": "88ef68b1-0c0b-4594-be46-4bb0bcf2025d",
-                "inputs": [
-                    "8fc8b364-98bb-4082-98af-e3fdffcf82b7"
-                ],
-                "input_type": "biomaterial",
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diff --git a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
new file mode 100644
index 000000000..3f9f9b81a
--- /dev/null
+++ b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
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+            "schema_type": "biomaterial",
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+                    9606
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+            },
+            "genus_species": [
+                {
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+            "organism_age_unit": {
+                "text": "year",
+                "ontology": "UO:0000036"
+            },
+            "human_specific": {
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+            },
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+                "update_date": "2018-09-05T12:14:26.204Z"
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+        },
+        "library_preparation_protocol_0.json": {
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+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "library_preparation_protocol_1",
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+                "protocol_description": "Single-cell RNA-seq libraries were generated as described in Picelli et al., 2014, Full-length RNA-seq from single cells using Smart-seq2, Nature Protocols.",
+                "publication_doi": "10.1038/nprot.2014.006"
+            },
+            "library_construction_approach": {
+                "text": "Smart-seq2",
+                "ontology": "EFO:0008931"
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+            "nucleic_acid_source": "single cell",
+            "end_bias": "full length",
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+                "text": "polyA RNA",
+                "ontology": "OBI:0000869"
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+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "60471337-a47b-4b9c-95e7-4a19349a5e05"
+                    ],
+                    "output_type": "file",
+                    "protocols": [
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+                    "inputs": [
+                        "38002d8f-eac5-4ee4-8290-03d323bf780e"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "1200f5bf-7d45-4f26-865e-b560797f1808"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "dissociation_protocol",
+                            "protocol_id": "6029a289-861c-4349-9614-4c244103be21"
+                        }
+                    ]
+                },
+                {
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+                    "inputs": [
+                        "8bb4258a-90c7-4af6-8a1b-c4ab6c5483e2"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "38002d8f-eac5-4ee4-8290-03d323bf780e"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": []
+                }
+            ]
+        },
+        "process_0.json": {
+            "insdc_experiment": {
+                "insdc_experiment": "ERX1700368"
+            },
+            "process_core": {
+                "process_id": "process_id_3526"
+            },
+            "schema_type": "process",
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
+            "provenance": {
+                "document_id": "aa67d2ed-e4ea-4cdf-92ed-7d5e6dc1f6fa",
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+                "update_date": "2018-09-05T12:26:35.419Z"
+            }
+        },
+        "process_1.json": {
+            "process_core": {
+                "process_id": "process_id_12"
+            },
+            "schema_type": "process",
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
+            "provenance": {
+                "document_id": "443b4672-3f14-4f1e-b7be-862ae02493dc",
+                "submission_date": "2018-09-05T12:11:53.403Z",
+                "update_date": "2018-09-05T12:25:01.078Z"
+            }
+        },
+        "process_2.json": {
+            "process_core": {
+                "process_id": "process_id_1"
+            },
+            "schema_type": "process",
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
+            "provenance": {
+                "document_id": "738243c5-e336-4c55-a8b6-b192b6f98fe7",
+                "submission_date": "2018-09-05T12:11:53.128Z",
+                "update_date": "2018-09-05T12:25:00.908Z"
+            }
+        },
+        "project_0.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/project/9.0.2/project",
+            "schema_type": "project",
+            "project_core": {
+                "project_short_name": "Healthy and type 2 diabetes pancreas",
+                "project_title": "Single-cell RNA-seq analysis of human pancreas from healthy individuals and type 2 diabetes patients",
+                "project_description": "We used single-cell RNA-sequencing to generate transcriptional profiles of endocrine and exocrine cell types of the human pancreas. Pancreatic tissue and islets were obtained from six healthy and four T2D cadaveric donors. Islets were cultured and dissociated into single-cell suspension. Viable individual cells were distributed via fluorescence-activated cell sorted (FACS) into 384-well plates containing lysis buffer. Single-cell cDNA libraries were generated using the Smart-seq2 protocol. Gene expression was quantified as reads per kilobase transcript and per million mapped reads (RPKM) using rpkmforgenes. Bioinformatics analysis was used to classify cells into cell types without knowledge of cell types or prior purification of cell populations. We revealed subpopulations in endocrine and exocrine cell types, identified genes with interesting correlations to body mass index (BMI) in specific cell types and found transcriptional alterations in T2D.  Complementary whole-islet RNA-seq data have also been deposited at ArrayExpress under accession number E-MTAB-5060 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5060)."
+            },
+            "insdc_project": "ERP017126",
+            "array_express_investigation": "E-MTAB-5061",
+            "insdc_study": "PRJEB15401",
+            "supplementary_links": [
+                "https://www.ebi.ac.uk/gxa/sc/experiments/E-MTAB-5061/Results"
+            ],
+            "contributors": [
+                {
+                    "contact_name": "Athanasia,,Palasantza",
+                    "email": "Athanasia.Palasantza@ki.se",
+                    "institution": "Karolinska Institutet",
+                    "laboratory": "Department of Cell and Molecular Biology (CMB)",
+                    "address": "Nobels vag 3, 171 77, Stockholm",
+                    "country": "Sweden",
+                    "corresponding_contributor": false
+                },
+                {
+                    "contact_name": "Rickard,,Sandberg",
+                    "email": "Rickard.Sandberg@ki.se",
+                    "institution": "Karolinska Institutet",
+                    "laboratory": "Department of Cell and Molecular Biology (CMB)",
+                    "address": "Nobels vag 3, 171 77, Stockholm",
+                    "country": "Sweden",
+                    "orcid_id": "0000-0001-6473-1740",
+                    "corresponding_contributor": true
+                },
+                {
+                    "contact_name": "Asa,,Segerstolpe",
+                    "email": "Asa.Segerstolpe@ki.se",
+                    "institution": "Karolinska Institutet",
+                    "laboratory": "Department of Cell and Molecular Biology (CMB)",
+                    "address": "Nobels vag 3, 171 77, Stockholm",
+                    "country": "Sweden",
+                    "corresponding_contributor": false
+                },
+                {
+                    "contact_name": "Mallory,Ann,Freeberg",
+                    "email": "mfreeberg@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "Human Cell Atlas Data Coordination Platform",
+                    "address": "Wellcome Trust Genome Campus, Cambridge",
+                    "country": "UK",
+                    "project_role": "Human Cell Atlas wrangler",
+                    "orcid_id": "0000-0003-2949-3921",
+                    "corresponding_contributor": false
+                },
+                {
+                    "contact_name": "Laura,,Huerta",
+                    "email": "lauhuema@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "Molecular Atlas",
+                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
+                    "country": "UK",
+                    "project_role": "external curator",
+                    "orcid_id": "0000-0002-8748-599X",
+                    "corresponding_contributor": false
+                }
+            ],
+            "funders": [
+                {
+                    "grant_id": "648842",
+                    "funder_name": "European Research Council"
+                },
+                {
+                    "funder_name": "Swedish Research Council"
+                },
+                {
+                    "funder_name": "Swedish Foundation for Strategic Research"
+                },
+                {
+                    "funder_name": "Swedish Cancer Society"
+                },
+                {
+                    "funder_name": "Center for Innovative Medicine"
+                }
+            ],
+            "publications": [
+                {
+                    "authors": [
+                        "Segerstolpe A, Palasantza A, Eliasson P, Andersson EM, Andreasson AC, Sun X, Picelli S, Sabirsh A, Clausen M, Bjursell MK, Smith DM, Kasper M, Ammala C, Sandberg R"
+                    ],
+                    "publication_title": "Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes",
+                    "doi": "10.1016/j.cmet.2016.08.020",
+                    "pmid": 27667667,
+                    "publication_url": "https://europepmc.org/abstract/MED/27667667"
+                }
+            ],
+            "provenance": {
+                "document_id": "6751cc10-8cc3-452f-929c-4dcb98ee1435",
+                "submission_date": "2018-09-05T12:09:41.693Z",
+                "update_date": "2018-09-05T12:14:26.167Z"
+            }
+        },
+        "sequence_file_0.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/6.5.2/sequence_file",
+            "schema_type": "file",
+            "file_core": {
+                "file_name": "AZ_B8.fastq.gz",
+                "file_format": "fastq.gz"
+            },
+            "read_index": "read1",
+            "read_length": 43,
+            "insdc_run": [
+                "ERR1630035"
+            ],
+            "provenance": {
+                "document_id": "60471337-a47b-4b9c-95e7-4a19349a5e05",
+                "submission_date": "2018-09-05T12:10:45.476Z",
+                "update_date": "2018-09-05T12:27:42.525Z"
+            }
+        },
+        "sequencing_protocol_0.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "sequencing_protocol_1",
+                "protocol_name": "SmartSeq2 single cell sequencing",
+                "protocol_description": "Libraries were sequenced on an Illumina HiSeq 2000, generating 43 bp single-end reads.",
+                "publication_doi": "10.1038/nprot.2014.006"
+            },
+            "sequencing_approach": {
+                "text": "full length single cell RNA sequencing",
+                "ontology": "EFO:0008441"
+            },
+            "instrument_manufacturer_model": {
+                "text": "Illumina HiSeq 2000",
+                "ontology": "EFO:0004203"
+            },
+            "paired_end": false,
+            "provenance": {
+                "document_id": "3aece946-4be6-4a0c-af23-ac884a87bcbb",
+                "submission_date": "2018-09-05T12:11:53.105Z",
+                "update_date": "2018-09-05T12:16:50.390Z"
+            }
+        },
+        "specimen_from_organism_0.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "H1_pancreas",
+                "biomaterial_name": "Pancreas from donor H1",
+                "biomaterial_description": "Pancreas from normal donor H1",
+                "ncbi_taxon_id": [
+                    9606
+                ]
+            },
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606"
+                }
+            ],
+            "organ": {
+                "text": "pancreas",
+                "ontology": "UBERON:0001264"
+            },
+            "organ_part": {
+                "text": "islet of Langerhans",
+                "ontology": "UBERON:0000006"
+            },
+            "purchased_specimen": {
+                "manufacturer": "Prodo Laboratories Inc (Irvine, CA, USA) "
+            },
+            "provenance": {
+                "document_id": "38002d8f-eac5-4ee4-8290-03d323bf780e",
+                "submission_date": "2018-09-05T12:09:41.800Z",
+                "update_date": "2018-09-05T12:14:29.994Z"
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json
deleted file mode 100644
index 49f7df9e8..000000000
--- a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json	
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-        "sha1": "01074ce8f1d3edbe942659731663c7e12d0128cf",
-        "sha256": "ff9a4518c41f837b295a3beb44f2ad1bd0bb1a47cb3ddd92bb1edb192320239c",
-        "s3_etag": "322aeb89c995b0657e33b085b8b1f7aa",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "project_0.json",
-        "size": 5090,
-        "uuid": "372f77fe-9a81-483c-8d13-4e2d059bfda6",
-        "version": "1"
-    },
-    {
-        "crc32c": "3D02CDD9",
-        "sha1": "b2dad8a028624c456ba43f1f97ac20bba430af74",
-        "sha256": "730386f5383a1c82f114ba6cc9ff381f2c47872d6edc4f1342b0b9df9a282795",
-        "s3_etag": "5a43cfafe8d19b34b73ec4561653e517",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "sequence_file_0.json",
-        "size": 514,
-        "uuid": "e6f7823c-73c2-4484-b3b8-07aad4008dc1",
-        "version": "1"
-    },
-    {
-        "crc32c": "3D02CDD9",
-        "sha1": "b2dad8a028624c456ba43f1f97ac20bba430af74",
-        "sha256": "730386f5383a1c82f114ba6cc9ff381f2c47872d6edc4f1342b0b9df9a282795",
-        "s3_etag": "5a43cfafe8d19b34b73ec4561653e517",
-        "content-type": "application/octet-stream",
-        "indexed": false,
-        "name": "AZ_B8.fastq.gz",
-        "size": 514,
-        "uuid": "32d60a94-9f0f-44e3-83c6-eb2d1c1177bd",
-        "version": "1"
-    },
-    {
-        "crc32c": "D1ED7790",
-        "sha1": "b6347439cabfd949d62ea9bd4583668e4dae9ae3",
-        "sha256": "8b07de467f9656adfa2c17403be4969329592833e2582acd6e7b90764bad3c94",
-        "s3_etag": "71de6f17e7bd1a32cf38026269c9c548",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "sequencing_protocol_0.json",
-        "size": 928,
-        "uuid": "06e8f95d-bdfb-4b72-84e9-160eab21e059",
-        "version": "1"
-    },
-    {
-        "crc32c": "DAA2F138",
-        "sha1": "299ee695490d80e71963e51190f95808b79e0042",
-        "sha256": "6d5703145464fd2a53adcc79c2c3339dfec0e04cf1a463c078678ada7f79f374",
-        "s3_etag": "9b8fb5f7d54ef2b22a14abdaef88a677",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "specimen_from_organism_0.json",
-        "size": 1011,
-        "uuid": "888e84a3-26e0-4f46-983d-91014e7c60a3",
-        "version": "1"
-    }
-]
diff --git a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
deleted file mode 100644
index 50470a2e5..000000000
--- a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json	
+++ /dev/null
@@ -1,403 +0,0 @@
-{
-    "cell_suspension_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "AZ_B8",
-            "biomaterial_name": "AZ_B8 cell",
-            "biomaterial_description": "AZ_B8 cell",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "insdc_biomaterial": "ERS1348492",
-            "biosd_biomaterial": "SAMEA4437043"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "total_estimated_cells": 1,
-        "plate_based_sequencing": {
-            "plate_id": "AZ",
-            "well_id": "B8",
-            "cell_quality": "OK"
-        },
-        "provenance": {
-            "document_id": "1200f5bf-7d45-4f26-865e-b560797f1808",
-            "submission_date": "2018-09-05T12:09:41.946Z",
-            "update_date": "2018-09-05T12:21:55.818Z"
-        }
-    },
-    "dissociation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "dissociation_protocol_1",
-            "protocol_name": "Single cell dissociation",
-            "protocol_description": "Islets were dissociated into single-cell suspension and viable individual cells were distributed by FACS into 384-well plates containing lysis buffer.",
-            "publication_doi": "10.1016/j.cmet.2016.08.020"
-        },
-        "dissociation_method": {
-            "text": "fluorescence-activated cell sorting",
-            "ontology": "EFO:0009108"
-        },
-        "provenance": {
-            "document_id": "6029a289-861c-4349-9614-4c244103be21",
-            "submission_date": "2018-09-05T12:11:53.063Z",
-            "update_date": "2018-09-05T12:17:49.721Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "H1",
-            "biomaterial_name": "Normal Donor 1",
-            "biomaterial_description": "Normal Donor 1",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "is_living": "no",
-        "sex": "male",
-        "medical_history": {
-            "test_results": "HbA1c 5.0%"
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461"
-            }
-        ],
-        "development_stage": {
-            "text": "adult",
-            "ontology": "EFO:0001272"
-        },
-        "organism_age": "43",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036"
-        },
-        "human_specific": {
-            "body_mass_index": 30.8
-        },
-        "provenance": {
-            "document_id": "8bb4258a-90c7-4af6-8a1b-c4ab6c5483e2",
-            "submission_date": "2018-09-05T12:09:41.702Z",
-            "update_date": "2018-09-05T12:14:26.204Z"
-        }
-    },
-    "library_preparation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/4.3.2/library_preparation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "library_preparation_protocol_1",
-            "protocol_name": "Library preparation for sequencing",
-            "protocol_description": "Single-cell RNA-seq libraries were generated as described in Picelli et al., 2014, Full-length RNA-seq from single cells using Smart-seq2, Nature Protocols.",
-            "publication_doi": "10.1038/nprot.2014.006"
-        },
-        "library_construction_approach": {
-            "text": "Smart-seq2",
-            "ontology": "EFO:0008931"
-        },
-        "nucleic_acid_source": "single cell",
-        "end_bias": "full length",
-        "primer": "poly-dT",
-        "strand": "unstranded",
-        "input_nucleic_acid_molecule": {
-            "text": "polyA RNA",
-            "ontology": "OBI:0000869"
-        },
-        "spike_in_dilution": 40000,
-        "spike_in_kit": {
-            "retail_name": "External RNA Controls Consortium (ERCC)",
-            "manufacturer": "Ambion, Life Technologies"
-        },
-        "provenance": {
-            "document_id": "079bc155-71c9-45ab-bd12-cab025890d82",
-            "submission_date": "2018-09-05T12:11:53.080Z",
-            "update_date": "2018-09-05T12:17:48.051Z"
-        }
-    },
-    "links.json": {
-        "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
-        "schema_type": "link_bundle",
-        "schema_version": "1.1.1",
-        "links": [
-            {
-                "process": "aa67d2ed-e4ea-4cdf-92ed-7d5e6dc1f6fa",
-                "inputs": [
-                    "1200f5bf-7d45-4f26-865e-b560797f1808"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "60471337-a47b-4b9c-95e7-4a19349a5e05"
-                ],
-                "output_type": "file",
-                "protocols": [
-                    {
-                        "protocol_type": "library_preparation_protocol",
-                        "protocol_id": "079bc155-71c9-45ab-bd12-cab025890d82"
-                    },
-                    {
-                        "protocol_type": "sequencing_protocol",
-                        "protocol_id": "3aece946-4be6-4a0c-af23-ac884a87bcbb"
-                    }
-                ]
-            },
-            {
-                "process": "443b4672-3f14-4f1e-b7be-862ae02493dc",
-                "inputs": [
-                    "38002d8f-eac5-4ee4-8290-03d323bf780e"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "1200f5bf-7d45-4f26-865e-b560797f1808"
-                ],
-                "output_type": "biomaterial",
-                "protocols": [
-                    {
-                        "protocol_type": "dissociation_protocol",
-                        "protocol_id": "6029a289-861c-4349-9614-4c244103be21"
-                    }
-                ]
-            },
-            {
-                "process": "738243c5-e336-4c55-a8b6-b192b6f98fe7",
-                "inputs": [
-                    "8bb4258a-90c7-4af6-8a1b-c4ab6c5483e2"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "38002d8f-eac5-4ee4-8290-03d323bf780e"
-                ],
-                "output_type": "biomaterial",
-                "protocols": []
-            }
-        ]
-    },
-    "process_0.json": {
-        "insdc_experiment": {
-            "insdc_experiment": "ERX1700368"
-        },
-        "process_core": {
-            "process_id": "process_id_3526"
-        },
-        "schema_type": "process",
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
-        "provenance": {
-            "document_id": "aa67d2ed-e4ea-4cdf-92ed-7d5e6dc1f6fa",
-            "submission_date": "2018-09-05T12:13:16.786Z",
-            "update_date": "2018-09-05T12:26:35.419Z"
-        }
-    },
-    "process_1.json": {
-        "process_core": {
-            "process_id": "process_id_12"
-        },
-        "schema_type": "process",
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
-        "provenance": {
-            "document_id": "443b4672-3f14-4f1e-b7be-862ae02493dc",
-            "submission_date": "2018-09-05T12:11:53.403Z",
-            "update_date": "2018-09-05T12:25:01.078Z"
-        }
-    },
-    "process_2.json": {
-        "process_core": {
-            "process_id": "process_id_1"
-        },
-        "schema_type": "process",
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
-        "provenance": {
-            "document_id": "738243c5-e336-4c55-a8b6-b192b6f98fe7",
-            "submission_date": "2018-09-05T12:11:53.128Z",
-            "update_date": "2018-09-05T12:25:00.908Z"
-        }
-    },
-    "project_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/project/9.0.2/project",
-        "schema_type": "project",
-        "project_core": {
-            "project_short_name": "Healthy and type 2 diabetes pancreas",
-            "project_title": "Single-cell RNA-seq analysis of human pancreas from healthy individuals and type 2 diabetes patients",
-            "project_description": "We used single-cell RNA-sequencing to generate transcriptional profiles of endocrine and exocrine cell types of the human pancreas. Pancreatic tissue and islets were obtained from six healthy and four T2D cadaveric donors. Islets were cultured and dissociated into single-cell suspension. Viable individual cells were distributed via fluorescence-activated cell sorted (FACS) into 384-well plates containing lysis buffer. Single-cell cDNA libraries were generated using the Smart-seq2 protocol. Gene expression was quantified as reads per kilobase transcript and per million mapped reads (RPKM) using rpkmforgenes. Bioinformatics analysis was used to classify cells into cell types without knowledge of cell types or prior purification of cell populations. We revealed subpopulations in endocrine and exocrine cell types, identified genes with interesting correlations to body mass index (BMI) in specific cell types and found transcriptional alterations in T2D.  Complementary whole-islet RNA-seq data have also been deposited at ArrayExpress under accession number E-MTAB-5060 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5060)."
-        },
-        "insdc_project": "ERP017126",
-        "array_express_investigation": "E-MTAB-5061",
-        "insdc_study": "PRJEB15401",
-        "supplementary_links": [
-            "https://www.ebi.ac.uk/gxa/sc/experiments/E-MTAB-5061/Results"
-        ],
-        "contributors": [
-            {
-                "contact_name": "Athanasia,,Palasantza",
-                "email": "Athanasia.Palasantza@ki.se",
-                "institution": "Karolinska Institutet",
-                "laboratory": "Department of Cell and Molecular Biology (CMB)",
-                "address": "Nobels vag 3, 171 77, Stockholm",
-                "country": "Sweden",
-                "corresponding_contributor": false
-            },
-            {
-                "contact_name": "Rickard,,Sandberg",
-                "email": "Rickard.Sandberg@ki.se",
-                "institution": "Karolinska Institutet",
-                "laboratory": "Department of Cell and Molecular Biology (CMB)",
-                "address": "Nobels vag 3, 171 77, Stockholm",
-                "country": "Sweden",
-                "orcid_id": "0000-0001-6473-1740",
-                "corresponding_contributor": true
-            },
-            {
-                "contact_name": "Asa,,Segerstolpe",
-                "email": "Asa.Segerstolpe@ki.se",
-                "institution": "Karolinska Institutet",
-                "laboratory": "Department of Cell and Molecular Biology (CMB)",
-                "address": "Nobels vag 3, 171 77, Stockholm",
-                "country": "Sweden",
-                "corresponding_contributor": false
-            },
-            {
-                "contact_name": "Mallory,Ann,Freeberg",
-                "email": "mfreeberg@ebi.ac.uk",
-                "institution": "EMBL-EBI",
-                "laboratory": "Human Cell Atlas Data Coordination Platform",
-                "address": "Wellcome Trust Genome Campus, Cambridge",
-                "country": "UK",
-                "project_role": "Human Cell Atlas wrangler",
-                "orcid_id": "0000-0003-2949-3921",
-                "corresponding_contributor": false
-            },
-            {
-                "contact_name": "Laura,,Huerta",
-                "email": "lauhuema@ebi.ac.uk",
-                "institution": "EMBL-EBI",
-                "laboratory": "Molecular Atlas",
-                "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                "country": "UK",
-                "project_role": "external curator",
-                "orcid_id": "0000-0002-8748-599X",
-                "corresponding_contributor": false
-            }
-        ],
-        "funders": [
-            {
-                "grant_id": "648842",
-                "funder_name": "European Research Council"
-            },
-            {
-                "funder_name": "Swedish Research Council"
-            },
-            {
-                "funder_name": "Swedish Foundation for Strategic Research"
-            },
-            {
-                "funder_name": "Swedish Cancer Society"
-            },
-            {
-                "funder_name": "Center for Innovative Medicine"
-            }
-        ],
-        "publications": [
-            {
-                "authors": [
-                    "Segerstolpe A, Palasantza A, Eliasson P, Andersson EM, Andreasson AC, Sun X, Picelli S, Sabirsh A, Clausen M, Bjursell MK, Smith DM, Kasper M, Ammala C, Sandberg R"
-                ],
-                "publication_title": "Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes",
-                "doi": "10.1016/j.cmet.2016.08.020",
-                "pmid": 27667667,
-                "publication_url": "https://europepmc.org/abstract/MED/27667667"
-            }
-        ],
-        "provenance": {
-            "document_id": "6751cc10-8cc3-452f-929c-4dcb98ee1435",
-            "submission_date": "2018-09-05T12:09:41.693Z",
-            "update_date": "2018-09-05T12:14:26.167Z"
-        }
-    },
-    "sequence_file_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/6.5.2/sequence_file",
-        "schema_type": "file",
-        "file_core": {
-            "file_name": "AZ_B8.fastq.gz",
-            "file_format": "fastq.gz"
-        },
-        "read_index": "read1",
-        "read_length": 43,
-        "insdc_run": [
-            "ERR1630035"
-        ],
-        "provenance": {
-            "document_id": "60471337-a47b-4b9c-95e7-4a19349a5e05",
-            "submission_date": "2018-09-05T12:10:45.476Z",
-            "update_date": "2018-09-05T12:27:42.525Z"
-        }
-    },
-    "sequencing_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "sequencing_protocol_1",
-            "protocol_name": "SmartSeq2 single cell sequencing",
-            "protocol_description": "Libraries were sequenced on an Illumina HiSeq 2000, generating 43 bp single-end reads.",
-            "publication_doi": "10.1038/nprot.2014.006"
-        },
-        "sequencing_approach": {
-            "text": "full length single cell RNA sequencing",
-            "ontology": "EFO:0008441"
-        },
-        "instrument_manufacturer_model": {
-            "text": "Illumina HiSeq 2000",
-            "ontology": "EFO:0004203"
-        },
-        "paired_end": false,
-        "provenance": {
-            "document_id": "3aece946-4be6-4a0c-af23-ac884a87bcbb",
-            "submission_date": "2018-09-05T12:11:53.105Z",
-            "update_date": "2018-09-05T12:16:50.390Z"
-        }
-    },
-    "specimen_from_organism_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "H1_pancreas",
-            "biomaterial_name": "Pancreas from donor H1",
-            "biomaterial_description": "Pancreas from normal donor H1",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "organ": {
-            "text": "pancreas",
-            "ontology": "UBERON:0001264"
-        },
-        "organ_part": {
-            "text": "islet of Langerhans",
-            "ontology": "UBERON:0000006"
-        },
-        "purchased_specimen": {
-            "manufacturer": "Prodo Laboratories Inc (Irvine, CA, USA) "
-        },
-        "provenance": {
-            "document_id": "38002d8f-eac5-4ee4-8290-03d323bf780e",
-            "submission_date": "2018-09-05T12:09:41.800Z",
-            "update_date": "2018-09-05T12:14:29.994Z"
-        }
-    }
-}
diff --git a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
new file mode 100644
index 000000000..5c0f7246f
--- /dev/null
+++ b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -0,0 +1,592 @@
+{
+    "manifest": [
+        {
+            "crc32c": "EDCBEB27",
+            "sha1": "ec22573ee712d628ae8c89a857d46c36647d3840",
+            "sha256": "506ad9058ab7fd6cf9dfacd45f889df49db48c04f83a513c8c15c9ba64c48e94",
+            "s3_etag": "0476f6b3f19520e728aa2081b03cab12",
+            "content-type": "application/json; dcp-type=\"metadata/json\"",
+            "indexed": true,
+            "name": "cell_suspension_0.json",
+            "size": 902,
+            "uuid": "2636529a-872c-4174-a80f-7ecffb4de952",
+            "version": "1"
+        },
+        {
+            "crc32c": "ABC55204",
+            "sha1": "c217b4f309d6b37729a62e7d98d73e33d3077335",
+            "sha256": "02426b5f54d0e45cb4447d89f4ef165b0f7e460988ce1673a9c837651a1d18ac",
+            "s3_etag": "4ec906c1695ed9f4eabe1e875d88bfb4",
+            "content-type": "application/json; dcp-type=\"metadata/json\"",
+            "indexed": true,
+            "name": "dissociation_protocol_0.json",
+            "size": 670,
+            "uuid": "750baef6-9002-4527-a02c-526481add5dd",
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+                "document_id": "b93897c4-0681-407a-bc0c-fb791b919fa4",
+                "submission_date": "2018-09-04T12:47:44.261Z",
+                "update_date": "2018-09-04T13:20:33.745Z"
+            }
+        },
+        "sequencing_protocol_0.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "SmartSeq2_sequencing_protocol",
+                "protocol_name": "Sequencing SmartSeq2 cells"
+            },
+            "instrument_manufacturer_model": {
+                "text": "Illumina HiSeq 2500",
+                "ontology": "EFO:0008567"
+            },
+            "paired_end": true,
+            "sequencing_approach": {
+                "text": "Smart-seq2",
+                "ontology": "EFO:0008931"
+            },
+            "provenance": {
+                "document_id": "2c530a47-d87a-4d50-bfb9-74d15fdb1fd9",
+                "submission_date": "2018-09-04T12:53:51.118Z",
+                "update_date": "2018-09-04T12:57:59.862Z"
+            }
+        },
+        "specimen_from_organism_0.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "1131_LN",
+                "biomaterial_name": "Mouse_day8_LN_rep10",
+                "ncbi_taxon_id": [
+                    10090
+                ]
+            },
+            "genus_species": [
+                {
+                    "text": "Mus musculus",
+                    "ontology": "NCBITaxon:10090"
+                }
+            ],
+            "organ": {
+                "text": "lymph node",
+                "ontology": "UBERON:0000029"
+            },
+            "provenance": {
+                "document_id": "6dc01fb6-6aba-432e-828e-ae3045914f34",
+                "submission_date": "2018-09-04T12:44:38.074Z",
+                "update_date": "2018-09-04T13:10:12.581Z"
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json
deleted file mode 100644
index b52254881..000000000
--- a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json	
+++ /dev/null
@@ -1,170 +0,0 @@
-[
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-        "sha1": "ec22573ee712d628ae8c89a857d46c36647d3840",
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-        "indexed": true,
-        "name": "enrichment_protocol_0.json",
-        "size": 648,
-        "uuid": "a9a602bc-9333-43d5-897b-d41990b71d6c",
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-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "process_0.json",
-        "size": 385,
-        "uuid": "7581cfb0-451c-4195-bb36-5ce58ed6223e",
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-        "uuid": "f4ad3ffa-4fb9-4a5e-9657-d8358234570f",
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-        "content-type": "application/json; dcp-type=\"metadata/json\"",
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-        "size": 472,
-        "uuid": "5d5d99b1-ff9a-4c32-a33a-c71bb503ff51",
-        "version": "1"
-    },
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-        "crc32c": "4AEB011B",
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-        "uuid": "b2b4819a-e22d-4ed4-a5c8-c04a1dec79eb",
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-        "indexed": true,
-        "name": "sequencing_protocol_0.json",
-        "size": 726,
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-        "version": "1"
-    },
-    {
-        "crc32c": "600533E8",
-        "sha1": "54cd7297973e55ff746ba4fa0ef2e891a1b3c23a",
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-        "s3_etag": "94d2fa6136032ca63a8b1291853da5db",
-        "content-type": "application/json; dcp-type=\"metadata/json\"",
-        "indexed": true,
-        "name": "specimen_from_organism_0.json",
-        "size": 734,
-        "uuid": "2d1d1d4e-4ef7-4c51-aad5-f1f388f706f6",
-        "version": "1"
-    }
-]
diff --git a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
deleted file mode 100644
index 2f6cd47a8..000000000
--- a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json	
+++ /dev/null
@@ -1,420 +0,0 @@
-{
-    "cell_suspension_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "21784_6#10",
-            "ncbi_taxon_id": [
-                10090
-            ],
-            "supplementary_files": [
-                "FACS_sorting_markers.pdf"
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Mus musculus",
-                "ontology": "NCBITaxon:10090"
-            }
-        ],
-        "selected_cell_type": [
-            {
-                "text": "CD11b+ Macrophages/monocytes"
-            }
-        ],
-        "total_estimated_cells": 1,
-        "plate_based_sequencing": {
-            "plate_id": "607",
-            "well_id": "A05"
-        },
-        "provenance": {
-            "document_id": "1446ca36-ba75-45ea-b6ab-a80641a88812",
-            "submission_date": "2018-09-04T12:44:38.405Z",
-            "update_date": "2018-09-04T13:12:52.699Z"
-        }
-    },
-    "dissociation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "tissue_dissociation_protocol",
-            "protocol_name": "Extracting cells from lymph nodes",
-            "document": "TissueDissociationProtocol.pdf"
-        },
-        "dissociation_method": {
-            "text": "mechanical dissociation",
-            "ontology": "EFO:0009129"
-        },
-        "provenance": {
-            "document_id": "7142ed25-3237-4156-b10d-0aa74b2c37b3",
-            "submission_date": "2018-09-04T12:53:50.982Z",
-            "update_date": "2018-09-04T12:58:01.497Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "1131",
-            "biomaterial_name": "Mouse_day8_rep10",
-            "ncbi_taxon_id": [
-                10090
-            ]
-        },
-        "mouse_specific": {
-            "strain": [
-                {
-                    "text": "C57BL/6",
-                    "ontology": "EFO:0004472"
-                }
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Mus musculus",
-                "ontology": "NCBITaxon:10090"
-            }
-        ],
-        "organism_age": "6-12",
-        "organism_age_unit": {
-            "text": "week",
-            "ontology": "UO:0000034"
-        },
-        "diseases": [
-            {
-                "text": "subcutaneous melanoma",
-                "ontology": "MONDO:0005105"
-            }
-        ],
-        "is_living": "no",
-        "sex": "female",
-        "provenance": {
-            "document_id": "b56697f5-d350-4e1d-93b2-72eee68c972e",
-            "submission_date": "2018-09-04T12:44:37.445Z",
-            "update_date": "2018-09-04T13:08:09.637Z"
-        }
-    },
-    "enrichment_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "FACS3",
-            "protocol_name": "FACS sorting cells by surface markers"
-        },
-        "enrichment_method": {
-            "text": "fluorescence-activated cell sorting",
-            "ontology": "EFO:0009108"
-        },
-        "markers": "CD45+ CD3e- B220- CD11b+",
-        "provenance": {
-            "document_id": "4a19c599-e429-4eda-9644-3a46c1202c7f",
-            "submission_date": "2018-09-04T12:53:51.016Z",
-            "update_date": "2018-09-04T12:57:51.962Z"
-        }
-    },
-    "library_preparation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/4.3.2/library_preparation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "SmartSeq2_RTPCR_protocol",
-            "protocol_name": "Make/amplify cDNA for each cell",
-            "document": "SmartSeq2_RTPCR_protocol.pdf"
-        },
-        "nucleic_acid_source": "single cell",
-        "input_nucleic_acid_molecule": {
-            "text": "polyA RNA",
-            "ontology": "OBI:0000869"
-        },
-        "library_construction_approach": {
-            "text": "Smart-seq2",
-            "ontology": "EFO:0008931"
-        },
-        "end_bias": "full length",
-        "primer": "poly-dT",
-        "strand": "unstranded",
-        "umi_barcode": {
-            "barcode_read": "Read 1",
-            "barcode_offset": 0,
-            "barcode_length": 16
-        },
-        "provenance": {
-            "document_id": "38e07040-6198-4a46-b195-88c0680ef283",
-            "submission_date": "2018-09-04T12:53:51.109Z",
-            "update_date": "2018-09-04T12:55:56.069Z"
-        }
-    },
-    "links.json": {
-        "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
-        "schema_type": "link_bundle",
-        "schema_version": "1.1.1",
-        "links": [
-            {
-                "process": "e9c888db-256a-4c78-af5d-2977fa6bc22c",
-                "inputs": [
-                    "1446ca36-ba75-45ea-b6ab-a80641a88812"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "b93897c4-0681-407a-bc0c-fb791b919fa4"
-                ],
-                "output_type": "file",
-                "protocols": [
-                    {
-                        "protocol_type": "library_preparation_protocol",
-                        "protocol_id": "38e07040-6198-4a46-b195-88c0680ef283"
-                    },
-                    {
-                        "protocol_type": "sequencing_protocol",
-                        "protocol_id": "2c530a47-d87a-4d50-bfb9-74d15fdb1fd9"
-                    }
-                ]
-            },
-            {
-                "process": "3c85210e-6554-450c-88fb-c5d5035cf134",
-                "inputs": [
-                    "6dc01fb6-6aba-432e-828e-ae3045914f34"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "1446ca36-ba75-45ea-b6ab-a80641a88812"
-                ],
-                "output_type": "biomaterial",
-                "protocols": [
-                    {
-                        "protocol_type": "dissociation_protocol",
-                        "protocol_id": "7142ed25-3237-4156-b10d-0aa74b2c37b3"
-                    },
-                    {
-                        "protocol_type": "enrichment_protocol",
-                        "protocol_id": "4a19c599-e429-4eda-9644-3a46c1202c7f"
-                    }
-                ]
-            },
-            {
-                "process": "ab9f0b8f-3195-4ccd-8bdf-52d91a2c9029",
-                "inputs": [
-                    "b56697f5-d350-4e1d-93b2-72eee68c972e"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "6dc01fb6-6aba-432e-828e-ae3045914f34"
-                ],
-                "output_type": "biomaterial",
-                "protocols": []
-            }
-        ]
-    },
-    "process_0.json": {
-        "process_core": {
-            "process_id": "process_id_55"
-        },
-        "schema_type": "process",
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
-        "provenance": {
-            "document_id": "3c85210e-6554-450c-88fb-c5d5035cf134",
-            "submission_date": "2018-09-04T12:53:53.002Z",
-            "update_date": "2018-09-04T13:23:54.508Z"
-        }
-    },
-    "process_1.json": {
-        "process_core": {
-            "process_id": "process_id_28"
-        },
-        "schema_type": "process",
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
-        "provenance": {
-            "document_id": "ab9f0b8f-3195-4ccd-8bdf-52d91a2c9029",
-            "submission_date": "2018-09-04T12:53:52.144Z",
-            "update_date": "2018-09-04T13:23:54.228Z"
-        }
-    },
-    "process_2.json": {
-        "process_core": {
-            "process_id": "process_id_6694"
-        },
-        "schema_type": "process",
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
-        "provenance": {
-            "document_id": "e9c888db-256a-4c78-af5d-2977fa6bc22c",
-            "submission_date": "2018-09-04T12:59:17.940Z",
-            "update_date": "2018-09-04T13:27:57.677Z"
-        }
-    },
-    "project_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/project/9.0.2/project",
-        "schema_type": "project",
-        "project_core": {
-            "project_short_name": "Mouse Melanoma",
-            "project_title": "Melanoma infiltration of stromal and immune cells",
-            "project_description": "The cancer microenvironment is a complex ecosystem characterized by dynamic interactions between diverse cell types, including malignant, immune and stromal cells. Here, we performed single-cell RNA sequencing on CD45+ and CD45- cells isolated from tumour and lymph nodes during a mouse model of melanoma. The transcriptional profiles of these individual cells taken at different time points coupled with assembled T cell receptor sequences, allowed us to identify distinct immune subpopulations and delineate their developmental trajectory. Our study provides insights into the complex interplay among cells within the tumour microenvironment and presents a valuable resource for future translational applications."
-        },
-        "contributors": [
-            {
-                "contact_name": "Sarah,A,Teichmann",
-                "email": "st9@sanger.ac.uk",
-                "institution": "Wellcome Trust Sanger Institute",
-                "laboratory": "Sarah Teichmann",
-                "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Mirjana,,Efremova",
-                "email": "me5@sanger.ac.uk",
-                "institution": "Wellcome Trust Sanger Institute",
-                "laboratory": "Sarah Teichmann",
-                "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Bidesh,,Mahata",
-                "email": "bm11@sanger.ac.uk",
-                "institution": "Wellcome Trust Sanger Institute",
-                "laboratory": "Sarah Teichmann",
-                "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Jacqueline,D,Shields",
-                "email": "JS970@MRCCU.cam.ac.uk",
-                "institution": "University of Cambridge",
-                "laboratory": "MRC Cancer Unit",
-                "address": "Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Sarah,,Davidson",
-                "email": "SED49@MRCCU.cam.ac.uk",
-                "institution": "University of Cambridge",
-                "laboratory": "MRC Cancer Unit",
-                "address": "Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Angela,,Riedel",
-                "email": "a.riedel@dkfz-heidelberg.de",
-                "institution": "DKFZ German Cancer Research Center",
-                "country": "Germany"
-            },
-            {
-                "contact_name": "Roser,,Vento-Tormo",
-                "email": "rv4@sanger.ac.uk",
-                "institution": "Wellcome Trust Sanger Institute",
-                "laboratory": "Sarah Teichmann",
-                "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Jhuma,,Pramanik",
-                "email": "jp19@sanger.ac.uk",
-                "institution": "Wellcome Trust Sanger Institute",
-                "laboratory": "Sarah Teichmann",
-                "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Gozde,,Kar",
-                "email": "gkar@ebi.ac.uk",
-                "institution": "EMBL-EBI",
-                "laboratory": "Sarah Teichmann",
-                "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Jani,,Huuhtanen",
-                "email": "jani.huuhtanen@helsinki.fi",
-                "institution": "University of Helsinki",
-                "country": "Finland"
-            },
-            {
-                "contact_name": "Mallory,Ann,Freeberg",
-                "email": "mfreeberg@ebi.ac.uk",
-                "institution": "EMBL-EBI",
-                "laboratory": "Human Cell Atlas Data Coordination Platform",
-                "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                "country": "UK",
-                "project_role": "Human Cell Atlas wrangler",
-                "orcid_id": "0000-0003-2949-3921",
-                "corresponding_contributor": false
-            },
-            {
-                "contact_name": "Danielle,,Welter",
-                "email": "dwelter@ebi.ac.uk",
-                "institution": "EMBL-EBI",
-                "laboratory": "Human Cell Atlas Data Coordination Platform",
-                "address": "Wellcome Trust Genome Campus, Cambridge",
-                "country": "UK",
-                "project_role": "Human Cell Atlas wrangler",
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-        "protocol_core": {
-            "protocol_id": "SmartSeq2_sequencing_protocol",
-            "protocol_name": "Sequencing SmartSeq2 cells"
-        },
-        "instrument_manufacturer_model": {
-            "text": "Illumina HiSeq 2500",
-            "ontology": "EFO:0008567"
-        },
-        "paired_end": true,
-        "sequencing_approach": {
-            "text": "Smart-seq2",
-            "ontology": "EFO:0008931"
-        },
-        "provenance": {
-            "document_id": "2c530a47-d87a-4d50-bfb9-74d15fdb1fd9",
-            "submission_date": "2018-09-04T12:53:51.118Z",
-            "update_date": "2018-09-04T12:57:59.862Z"
-        }
-    },
-    "specimen_from_organism_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "1131_LN",
-            "biomaterial_name": "Mouse_day8_LN_rep10",
-            "ncbi_taxon_id": [
-                10090
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Mus musculus",
-                "ontology": "NCBITaxon:10090"
-            }
-        ],
-        "organ": {
-            "text": "lymph node",
-            "ontology": "UBERON:0000029"
-        },
-        "provenance": {
-            "document_id": "6dc01fb6-6aba-432e-828e-ae3045914f34",
-            "submission_date": "2018-09-04T12:44:38.074Z",
-            "update_date": "2018-09-04T13:10:12.581Z"
-        }
-    }
-}
diff --git a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
new file mode 100644
index 000000000..2acf73c7f
--- /dev/null
+++ b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
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+                    "outputs": [
+                        "07282a68-dca4-449e-81b6-7b0da34230df"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": []
+                }
+            ]
+        },
+        "process_0.json": {
+            "process_core": {
+                "process_id": "process_id_9"
+            },
+            "schema_type": "process",
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
+            "provenance": {
+                "document_id": "6c357ba8-bd9a-41cb-9d74-b9442efb7217",
+                "submission_date": "2018-09-06T14:18:32.012Z",
+                "update_date": "2018-09-06T14:31:09.024Z"
+            }
+        },
+        "process_1.json": {
+            "process_core": {
+                "process_id": "SRR3562210"
+            },
+            "schema_type": "process",
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
+            "provenance": {
+                "document_id": "5f868fc6-dc13-4f06-a82e-ff83497d03ee",
+                "submission_date": "2018-09-06T14:20:46.372Z",
+                "update_date": "2018-09-06T14:31:54.751Z"
+            }
+        },
+        "process_2.json": {
+            "process_core": {
+                "process_id": "process_id_4"
+            },
+            "schema_type": "process",
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
+            "provenance": {
+                "document_id": "0aede7bd-0a5d-4dc5-a8e8-2d4ad6d01bfb",
+                "submission_date": "2018-09-06T14:18:31.926Z",
+                "update_date": "2018-09-06T14:31:08.929Z"
+            }
+        },
+        "project_0.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/project/9.0.2/project",
+            "schema_type": "project",
+            "project_core": {
+                "project_short_name": "Single cell transcriptome analysis of human pancreas",
+                "project_title": "Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns.",
+                "project_description": "As organisms age, cells accumulate genetic and epigenetic changes that eventually lead to impaired organ function or catastrophic failure such as cancer. Here we describe a single-cell transcriptome analysis of 2544 human pancreas cells from donors, spanning six decades of life. We find that islet cells from older donors have increased levels of disorder as measured both by noise in the transcriptome and by the number of cells which display inappropriate hormone expression, revealing a transcriptional instability associated with aging. By analyzing the spectrum of somatic mutations in single cells from previously-healthy donors, we find a specific age-dependent mutational signature characterized by C to A and C to G transversions, indicators of oxidative stress, which is absent in single cells from human brain tissue or in a tumor cell line. Cells carrying a high load of such mutations also express higher levels of stress and senescence markers, including FOS, JUN, and the cytoplasmic superoxide dismutase SOD1, markers previously linked to pancreatic diseases with substantial age-dependent risk, such as type 2 diabetes mellitus and adenocarcinoma. Thus, our single-cell approach unveils gene expression changes and somatic mutations acquired in aging human tissue, and identifies molecular pathways induced by these genetic changes that could influence human disease. Also, our results demonstrate the feasibility of using single-cell RNA-seq data from primary cells to derive meaningful insights into the genetic processes that operate on aging human tissue and to determine which molecular mechanisms are coordinated with these processes. Examination of single cells from primary human pancreas tissue"
+            },
+            "supplementary_links": [
+                "https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-81547/Results"
+            ],
+            "contributors": [
+                {
+                    "contact_name": "Martin, Enge",
+                    "email": "martin.enge@gmail.com",
+                    "institution": "Stanford University",
+                    "address": "Bioengineering, Stanford University, James H. Clark Center, 318 Campus Drive,, Stanford, CA, USA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Laura,,Huerta",
+                    "email": "lauhuema@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "Molecular Atlas",
+                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
+                    "country": "UK",
+                    "project_role": "external curator",
+                    "orcid_id": "0000-0002-8748-599X",
+                    "corresponding_contributor": false
+                },
+                {
+                    "contact_name": "Matthew,,Green",
+                    "email": "hewgreen@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "HCA Data Coordination Platform",
+                    "address": "Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK",
+                    "project_role": "Human Cell Atlas wrangler",
+                    "orcid_id": "0000-0003-2771-9894"
+                }
+            ],
+            "provenance": {
+                "document_id": "05f74601-064c-4a8a-a9c1-a0b57c6c71a7",
+                "submission_date": "2018-09-06T14:14:54.609Z",
+                "update_date": "2018-09-06T14:23:05.636Z"
+            }
+        },
+        "sequence_file_0.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/6.5.2/sequence_file",
+            "schema_type": "file",
+            "file_core": {
+                "file_name": "SRR3562210_1.fastq.gz",
+                "file_format": "fastq.gz"
+            },
+            "read_index": "read1",
+            "read_length": 75,
+            "insdc_run": [
+                "SRR3562210"
+            ],
+            "provenance": {
+                "document_id": "baf745cd-9052-4a6c-8c1a-919390062c09",
+                "submission_date": "2018-09-06T14:16:32.925Z",
+                "update_date": "2018-09-06T14:29:33.854Z"
+            }
+        },
+        "sequence_file_1.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/6.5.2/sequence_file",
+            "schema_type": "file",
+            "file_core": {
+                "file_name": "SRR3562210_2.fastq.gz",
+                "file_format": "fastq.gz"
+            },
+            "read_index": "read2",
+            "read_length": 75,
+            "insdc_run": [
+                "SRR3562210"
+            ],
+            "provenance": {
+                "document_id": "0494ee09-b1e2-437a-986f-06d5df4a6858",
+                "submission_date": "2018-09-06T14:16:32.894Z",
+                "update_date": "2018-09-06T14:29:33.843Z"
+            }
+        },
+        "sequencing_protocol_0.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "sequencing_protocol_1"
+            },
+            "instrument_manufacturer_model": {
+                "text": "Illumina NextSeq 500",
+                "ontology": "EFO:0008566"
+            },
+            "paired_end": true,
+            "sequencing_approach": {
+                "text": "RNA-Seq"
+            },
+            "provenance": {
+                "document_id": "319dd8c8-e9d6-40df-bf72-e0423f4f5418",
+                "submission_date": "2018-09-06T14:18:31.870Z",
+                "update_date": "2018-09-06T14:18:35.890Z"
+            }
+        },
+        "specimen_from_organism_0.json": {
+            "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "DID_scRSq04_pancreas",
+                "ncbi_taxon_id": [
+                    9606
+                ]
+            },
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606"
+                }
+            ],
+            "organ": {
+                "text": "pancreas",
+                "ontology": "UBERON:0001264"
+            },
+            "organ_part": {
+                "text": "islet of Langerhans",
+                "ontology": "UBERON:0000006"
+            },
+            "diseases": [
+                {
+                    "text": "normal",
+                    "ontology": "PATO:0000461"
+                }
+            ],
+            "provenance": {
+                "document_id": "07282a68-dca4-449e-81b6-7b0da34230df",
+                "submission_date": "2018-09-06T14:14:54.969Z",
+                "update_date": "2018-09-06T14:24:20.677Z"
+            }
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json
deleted file mode 100644
index 3017ccd2d..000000000
--- a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/manifest.json	
+++ /dev/null
@@ -1,170 +0,0 @@
-[
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-]
diff --git a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
deleted file mode 100644
index d7df95026..000000000
--- a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json	
+++ /dev/null
@@ -1,326 +0,0 @@
-{
-    "cell_suspension_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "GSM2171880 1",
-            "biomaterial_description": "Single cell from human pancreas",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "insdc_biomaterial": "SRS1458605"
-        },
-        "selected_cell_type": [
-            {
-                "text": "pancreatic A cell",
-                "ontology": "CL:0000171"
-            }
-        ],
-        "total_estimated_cells": 1,
-        "provenance": {
-            "document_id": "c61125ab-d5e0-4d93-b0a7-2deac1729f65",
-            "submission_date": "2018-09-06T14:14:55.036Z",
-            "update_date": "2018-09-06T14:25:54.342Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "DID_scRSq04",
-            "ncbi_taxon_id": [
-                9696
-            ]
-        },
-        "human_specific": {
-            "body_mass_index": 28.4,
-            "ethnicity": [
-                {
-                    "text": "European",
-                    "ontology": "hancestro:0005"
-                }
-            ]
-        },
-        "death": {
-            "cause_of_death": "anoxia"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "organism_age": "21",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036"
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461"
-            }
-        ],
-        "is_living": "no",
-        "sex": "male",
-        "provenance": {
-            "document_id": "cd379b0c-7b23-4093-b0b0-65d592ab2839",
-            "submission_date": "2018-09-06T14:14:54.645Z",
-            "update_date": "2018-09-06T14:23:05.946Z"
-        }
-    },
-    "library_preparation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/4.3.2/library_preparation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "library_preparation_protocol_1"
-        },
-        "input_nucleic_acid_molecule": {
-            "text": "polyA RNA",
-            "ontology": "OBI:0000869"
-        },
-        "library_construction_approach": {
-            "text": "smart-seq2",
-            "ontology": "EFO:0008931"
-        },
-        "library_construction_kit": {
-            "retail_name": "Nextera XT kit",
-            "manufacturer": "Illumina"
-        },
-        "end_bias": "full length",
-        "primer": "poly-dT",
-        "strand": "unstranded",
-        "nucleic_acid_source": "single cell",
-        "provenance": {
-            "document_id": "34c6db60-ef27-4502-9191-102d1a235adc",
-            "submission_date": "2018-09-06T14:18:31.859Z",
-            "update_date": "2018-09-06T14:18:35.854Z"
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diff --git a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
new file mode 100644
index 000000000..6eea5c58b
--- /dev/null
+++ b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
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+}
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deleted file mode 100644
index 876ed60c1..000000000
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diff --git a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json
deleted file mode 100644
index c0e73bdfc..000000000
--- a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-08-03T082009.272868Z/metadata.json	
+++ /dev/null
@@ -1,538 +0,0 @@
-{
-    "cell_suspension_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "A1-Spl-0-TL5_cells",
-            "biomaterial_name": "cells from fresh spleen",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA1098924",
-            "insdc_biomaterial": "ERS2392443"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "total_estimated_cells": 1970,
-        "provenance": {
-            "document_id": "932dae75-ba79-42a6-915a-c6a67b39835c",
-            "submission_date": "2018-09-05T09:14:54.798Z",
-            "update_date": "2018-09-05T09:15:05.597Z"
-        }
-    },
-    "dissociation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "dissociation_protocol_1",
-            "protocol_name": "Dissociation of spleen tissue sample into cell suspension",
-            "document": "Human_spleen_dissociation_protocol.pdf"
-        },
-        "dissociation_method": {
-            "text": "mechanical",
-            "ontology": "EFO:0009129"
-        },
-        "provenance": {
-            "document_id": "f1f2f791-f5f0-4eaa-8a4d-d6de9cf6807b",
-            "submission_date": "2018-09-05T09:14:54.916Z",
-            "update_date": "2018-09-05T09:15:02.163Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "284C-A1",
-            "biomaterial_name": "284C-spleen",
-            "biomaterial_description": "Spleen",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "death": {
-            "cause_of_death": "Hypoxic brain damage",
-            "cold_perfused": true,
-            "organ_donation_death_type": "Donation after circulatory death (DCD)"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "is_living": "no",
-        "sex": "male",
-        "organism_age": "55-60",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036"
-        },
-        "development_stage": {
-            "text": "adult",
-            "ontology": "EFO:0001272"
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461"
-            }
-        ],
-        "height": "1.75-1.8",
-        "height_unit": {
-            "text": "meter",
-            "ontology": "UO:0000008"
-        },
-        "weight": "80-85",
-        "weight_unit": {
-            "text": "kilogram",
-            "ontology": "UO:0000009"
-        },
-        "medical_history": {
-            "alcohol_history": "3-6 units/day",
-            "smoking_history": "Smoker, 20/day for 25 years, stopped 2000"
-        },
-        "normothermic_regional_perfusion": "yes",
-        "provenance": {
-            "document_id": "8909e260-7472-4c95-a96e-05d53d3c9221",
-            "submission_date": "2018-09-05T09:14:54.658Z",
-            "update_date": "2018-09-05T09:15:03.935Z"
-        }
-    },
-    "enrichment_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "enrichment_protocol_1",
-            "protocol_name": "Enrichment for live cells",
-            "document": "Human_spleen_dissociation_protocol.pdf"
-        },
-        "enrichment_method": {
-            "text": "magnetic affinity cell sorting",
-            "ontology": "EFO:0009109"
-        },
-        "markers": "LiveCells",
-        "provenance": {
-            "document_id": "e8c1f3fe-d694-467c-a823-01426f44ed71",
-            "submission_date": "2018-09-05T09:14:54.896Z",
-            "update_date": "2018-09-05T09:15:02.160Z"
-        }
-    },
-    "library_preparation_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/4.3.2/library_preparation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "library_preparation_protocol_1",
-            "protocol_name": "Library preparation for 10x_v2 sequencing",
-            "protocol_description": "ChromiumTM Single Cell 3' Library & Gel Bead Kit v2",
-            "document": "10x_sequencing_protocol.pdf"
-        },
-        "cell_barcode": {
-            "barcode_read": "Read 1",
-            "barcode_offset": 0,
-            "barcode_length": 16
-        },
-        "input_nucleic_acid_molecule": {
-            "text": "polyA RNA",
-            "ontology": "OBI:0000869"
-        },
-        "library_construction_approach": {
-            "text": "10X sequencing",
-            "ontology": "EFO:0008995"
-        },
-        "nucleic_acid_source": "single cell",
-        "end_bias": "3 prime tag",
-        "strand": "second",
-        "umi_barcode": {
-            "barcode_read": "Read 1",
-            "barcode_offset": 16,
-            "barcode_length": 10
-        },
-        "provenance": {
-            "document_id": "cc50851b-4c12-463b-b527-60d1c8d5ef60",
-            "submission_date": "2018-09-05T09:14:54.945Z",
-            "update_date": "2018-09-05T09:15:02.223Z"
-        }
-    },
-    "links.json": {
-        "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
-        "schema_type": "link_bundle",
-        "schema_version": "1.1.1",
-        "links": [
-            {
-                "process": "8b006d76-80c0-4e2c-866a-01fa5e900ab5",
-                "inputs": [
-                    "932dae75-ba79-42a6-915a-c6a67b39835c"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "4d3839bf-e39f-4136-92a4-6f7009e88567"
-                ],
-                "output_type": "file",
-                "protocols": [
-                    {
-                        "protocol_type": "library_preparation_protocol",
-                        "protocol_id": "cc50851b-4c12-463b-b527-60d1c8d5ef60"
-                    },
-                    {
-                        "protocol_type": "sequencing_protocol",
-                        "protocol_id": "29150a65-718c-46bc-8a7f-11ac585bf959"
-                    }
-                ]
-            },
-            {
-                "process": "a85a679d-38f0-4eb2-bfce-ed0e621769c8",
-                "inputs": [
-                    "8909e260-7472-4c95-a96e-05d53d3c9221"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "932dae75-ba79-42a6-915a-c6a67b39835c"
-                ],
-                "output_type": "biomaterial",
-                "protocols": [
-                    {
-                        "protocol_type": "dissociation_protocol",
-                        "protocol_id": "f1f2f791-f5f0-4eaa-8a4d-d6de9cf6807b"
-                    },
-                    {
-                        "protocol_type": "enrichment_protocol",
-                        "protocol_id": "e8c1f3fe-d694-467c-a823-01426f44ed71"
-                    }
-                ]
-            }
-        ]
-    },
-    "process_0.json": {
-        "process_core": {
-            "process_id": "process_id_1"
-        },
-        "schema_type": "process",
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
-        "provenance": {
-            "document_id": "8b006d76-80c0-4e2c-866a-01fa5e900ab5",
-            "submission_date": "2018-09-05T09:14:54.996Z",
-            "update_date": "2018-09-05T09:15:03.169Z"
-        }
-    },
-    "process_1.json": {
-        "process_core": {
-            "process_id": "process_id_29"
-        },
-        "schema_type": "process",
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/process/6.0.2/process",
-        "provenance": {
-            "document_id": "a85a679d-38f0-4eb2-bfce-ed0e621769c8",
-            "submission_date": "2018-09-05T09:14:55.295Z",
-            "update_date": "2018-09-05T09:15:05.629Z"
-        }
-    },
-    "project_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/project/9.0.2/project",
-        "schema_type": "project",
-        "project_core": {
-            "project_short_name": "Tissue stability",
-            "project_title": "Ischaemic sensitivity of human tissue by single cell RNA seq",
-            "project_description": "Assessment of ischaemic sensitivity of human tissues using 10x 3' single cell RNA sequencing. Currently, this project contains data for spleen and oesophagus. Ultimately we aim to collect data from three tissues expected to have different sensitivity to ischaemia: spleen (expected least sensitive), oesophagus (in the middle), and lung. Samples will be collected fresh (i.e. as soon as possible) and at 12h, 24h, and 72h post onset of ischaemia in the donor. Single cell RNA sequencing data will be generated at each time point using the 10x genomics single cell 3' method."
-        },
-        "insdc_project": "ERP107913",
-        "insdc_study": "PRJEB25946",
-        "contributors": [
-            {
-                "contact_name": "Mike,,Stubbington",
-                "email": "ms31@sanger.ac.uk",
-                "phone": "44 (0)1223 834244",
-                "institution": "Wellcome Trust Sanger Institute",
-                "laboratory": "Human Cell Atlas (Mike Stubbington)",
-                "address": "Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge. CB10 1SA.",
-                "country": "UK",
-                "orcid_id": "0000-0001-5924-3566"
-            },
-            {
-                "contact_name": "Phillipa,,Harding",
-                "email": "ph11@sanger.ac.uk",
-                "phone": "44 (0)1223 834244",
-                "institution": "Wellcome Trust Sanger Institute",
-                "laboratory": "Human Cell Atlas (Mike Stubbington)",
-                "address": "Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge. CB10 1SA.",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Anna,,Wilbrey-Clark",
-                "email": "aw24@sanger.ac.uk",
-                "phone": "44 (0)1223 834244",
-                "institution": "Wellcome Trust Sanger Institute",
-                "laboratory": "Human Cell Atlas (Mike Stubbington)",
-                "address": "Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge. CB10 1SA.",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Krzysztof,,Polanski",
-                "email": "kp9@sanger.ac.uk",
-                "institution": "Wellcome Trust Sanger Institute",
-                "laboratory": "Human Cell Atlas (Mike Stubbington)",
-                "address": "Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge. CB10 1SA.",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Kevin,,Loudon",
-                "email": "kevinloudon@doctors.org.uk",
-                "institution": "University of Cambridge",
-                "laboratory": "Molecular Immunity Unit, Department of Medicine",
-                "address": "Cambridge CB2 0QQ",
-                "country": "UK"
-            },
-            {
-                "contact_name": "John,R,Ferdinand",
-                "email": "jrf58@cam.ac.uk",
-                "institution": "University of Cambridge",
-                "laboratory": "Molecular Immunity Unit, Department of Medicine",
-                "address": "Cambridge CB2 0QQ",
-                "country": "UK",
-                "orcid_id": "0000-0003-0936-0128"
-            },
-            {
-                "contact_name": "Krishnaa,,Mahbubani",
-                "email": "ktam2@cam.ac.uk",
-                "institution": "University of Cambridge",
-                "laboratory": "Cambridge Biorepository for Translational Medicine",
-                "address": "Cambridge CB2 0QQ",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Nikitas,,Georgakopoulos",
-                "email": "ng395@cam.ac.uk",
-                "institution": "University of Cambridge",
-                "laboratory": "Cambridge Biorepository for Translational Medicine",
-                "address": "Cambridge CB2 0QQ",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Kerstin,B,Meyer",
-                "email": "km16@sanger.ac.uk",
-                "institution": "Wellcome Trust Sanger Institute",
-                "address": "Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge. CB10 1SA.",
-                "country": "UK",
-                "corresponding_contributor": true
-            },
-            {
-                "contact_name": "Kourosh,,Saeb-Parsy",
-                "email": "ks10014@cam.ac.uk",
-                "institution": "University of Cambridge",
-                "address": "Cambridge CB2 0QQ",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Karol,,Nowicki-Osuch",
-                "email": "kpn25@mrc-cu.cam.ac.uk",
-                "institution": "MRC Cancer Unit",
-                "laboratory": "Rebecca Fitzgerald",
-                "address": "MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ.",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Rebecca,,Fitzgerald",
-                "email": "rcf29@mrc-cu.cam.ac.uk",
-                "institution": "MRC Cancer Unit",
-                "laboratory": "Rebecca Fitzgerald",
-                "address": "MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ.",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Ricardo,J,Miragaia",
-                "email": "rm13@sanger.ac.uk",
-                "institution": "Wellcome Trust Sanger Institute",
-                "laboratory": "Human Cell Atlas (Sarah Teichmann)",
-                "address": "Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge. CB10 1SA.",
-                "country": "UK"
-            },
-            {
-                "contact_name": "Mallory,Ann,Freeberg",
-                "email": "mfreeberg@ebi.ac.uk",
-                "institution": "EMBL-EBI",
-                "laboratory": "Human Cell Atlas Data Coordination Platform",
-                "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                "country": "UK",
-                "project_role": "Human Cell Atlas wrangler",
-                "orcid_id": "0000-0003-2949-3921",
-                "corresponding_contributor": false
-            },
-            {
-                "contact_name": "Danielle,,Welter",
-                "email": "dwelter@ebi.ac.uk",
-                "institution": "EMBL-EBI",
-                "laboratory": "Human Cell Atlas Data Coordination Platform",
-                "address": "Wellcome Trust Genome Campus, Cambridge",
-                "country": "UK",
-                "project_role": "Human Cell Atlas wrangler",
-                "orcid_id": "0000-0003-1058-2668",
-                "corresponding_contributor": false
-            }
-        ],
-        "provenance": {
-            "document_id": "e7043342-977a-4f43-b382-d2a4f0932b56",
-            "submission_date": "2018-09-05T09:14:54.288Z",
-            "update_date": "2018-09-05T09:15:01.681Z"
-        }
-    },
-    "sequence_file_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/6.5.2/sequence_file",
-        "schema_type": "file",
-        "file_core": {
-            "file_name": "HCATisStabAug177078016_S1_L001_I1_001.fastq.gz",
-            "file_format": "fastq.gz"
-        },
-        "read_index": "index1",
-        "lane_index": 1,
-        "insdc_run": [
-            "ERR2508319"
-        ],
-        "provenance": {
-            "document_id": "4d3839bf-e39f-4136-92a4-6f7009e88567",
-            "submission_date": "2018-09-05T09:14:54.400Z",
-            "update_date": "2018-09-05T09:14:56.841Z"
-        }
-    },
-    "sequencing_protocol_0.json": {
-        "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "sequencing_protocol_1",
-            "protocol_name": "10x_v2 sequencing",
-            "protocol_description": "ChromiumTM Single Cell 3' Library & Gel Bead Kit v2",
-            "document": "10x_sequencing_protocol.pdf"
-        },
-        "instrument_manufacturer_model": {
-            "text": "Illumina HiSeq 4000",
-            "ontology": "EFO:0008563"
-        },
-        "paired_end": true,
-        "sequencing_approach": {
-            "text": "tag based single cell RNA sequencing",
-            "ontology": "EFO:0008440"
-        },
-        "provenance": {
-            "document_id": "29150a65-718c-46bc-8a7f-11ac585bf959",
-            "submission_date": "2018-09-05T09:14:54.986Z",
-            "update_date": "2018-09-05T09:15:02.167Z"
-        }
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diff --git a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
new file mode 100644
index 000000000..bb2a50bf8
--- /dev/null
+++ b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
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+                    "contact_name": "Barbara,,Treutlein",
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+                },
+                {
+                    "contact_name": "Zhisong,,He",
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+                    "address": "Deutscher Pl. 6, 04103 Leipzig",
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+                "document_id": "baa3a061-534c-4b6e-8c51-a11a8307f537",
+                "submission_date": "2019-01-03T12:07:51.362Z",
+                "update_date": "2019-01-03T12:07:58.911Z"
+            }
+        },
+        "links.json": {
+            "describedBy": "https://schema.humancellatlas.org/system/1.1.4/links",
+            "schema_type": "link_bundle",
+            "schema_version": "1.1.4",
+            "links": [
+                {
+                    "process": "54438211-29fb-4e57-87f4-95412e5d8b15",
+                    "inputs": [
+                        "c2396f83-22e4-4a2d-8cce-a30feb533603"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "9c49bbf2-cf62-4f94-9b9d-a3da42e2d52a",
+                        "ac93d656-4aa5-4f6c-b273-dc1d8be1934c",
+                        "5989ca50-45b5-4834-bfde-d290a8dfa97e"
+                    ],
+                    "output_type": "file",
+                    "protocols": [
+                        {
+                            "protocol_type": "library_preparation_protocol",
+                            "protocol_id": "65ce5281-b07e-4b21-be8d-66ac5dea4d69"
+                        },
+                        {
+                            "protocol_type": "sequencing_protocol",
+                            "protocol_id": "1547584e-d9e4-4519-a72a-91db0d0fec3c"
+                        }
+                    ]
+                },
+                {
+                    "process": "7d683bc4-6e59-4c7e-bbc8-5dad46fe2684",
+                    "inputs": [
+                        "a690df06-cc52-4346-a926-fe5e5b3a7547",
+                        "f0b636ce-505c-4339-a69c-2305352b6796",
+                        "46e7ed04-5916-4c10-8a05-fe510eda819a",
+                        "d49998ff-c873-41fd-bb44-f221f89b8f15"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "c2396f83-22e4-4a2d-8cce-a30feb533603"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "dissociation_protocol",
+                            "protocol_id": "c23de226-536c-403d-a757-f4200cb1777b"
+                        }
+                    ]
+                },
+                {
+                    "process": "d1a9aae1-99dc-4b49-bee3-af685b7f013a",
+                    "inputs": [
+                        "a689172e-cae2-4e2c-b1d2-5aeff0a90171"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "a690df06-cc52-4346-a926-fe5e5b3a7547"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "differentiation_protocol",
+                            "protocol_id": "3ec905f4-5950-4cfa-bd0b-86cc0370fd47"
+                        }
+                    ]
+                },
+                {
+                    "process": "a02a2a59-cdb4-4261-b220-b0cfebaec5ac",
+                    "inputs": [
+                        "597b4050-0778-4a81-b882-e1704ab0b6ad"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "a689172e-cae2-4e2c-b1d2-5aeff0a90171"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "ipsc_induction_protocol",
+                            "protocol_id": "97a30135-246f-4c0d-aef8-4e33183d1ff7"
+                        }
+                    ]
+                },
+                {
+                    "process": "01e52705-77de-4715-b35f-442aff9312be",
+                    "inputs": [
+                        "4934d9c3-753b-47bc-b2d5-468ce255a139"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "597b4050-0778-4a81-b882-e1704ab0b6ad"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": []
+                },
+                {
+                    "process": "58a58315-2f03-4a36-9cea-dd306b609ba9",
+                    "inputs": [
+                        "37833da3-505d-4bb2-916e-26aa8985d183"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "f0b636ce-505c-4339-a69c-2305352b6796"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "differentiation_protocol",
+                            "protocol_id": "3ec905f4-5950-4cfa-bd0b-86cc0370fd47"
+                        }
+                    ]
+                },
+                {
+                    "process": "56c911d5-6b99-486c-9ce7-141ee41528eb",
+                    "inputs": [
+                        "1fc181fe-60c6-4b94-85c1-1f227be60658"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "37833da3-505d-4bb2-916e-26aa8985d183"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "ipsc_induction_protocol",
+                            "protocol_id": "97a30135-246f-4c0d-aef8-4e33183d1ff7"
+                        }
+                    ]
+                },
+                {
+                    "process": "23fe1739-6bbe-4a86-be96-bd75f19f8375",
+                    "inputs": [
+                        "7c3a6d87-9f43-4de5-b47d-6fa78a897624"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "1fc181fe-60c6-4b94-85c1-1f227be60658"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": []
+                },
+                {
+                    "process": "831dc734-9813-4c34-a163-16dd5b75d9a0",
+                    "inputs": [
+                        "d954547d-94bc-401d-bdff-ccd727251c74"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "46e7ed04-5916-4c10-8a05-fe510eda819a"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "differentiation_protocol",
+                            "protocol_id": "3ec905f4-5950-4cfa-bd0b-86cc0370fd47"
+                        }
+                    ]
+                },
+                {
+                    "process": "d8f1d436-6bc3-4638-9801-8a9241996d28",
+                    "inputs": [
+                        "ad702cb9-3b40-4f8f-b9a5-331eeb153d9b"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "d954547d-94bc-401d-bdff-ccd727251c74"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "ipsc_induction_protocol",
+                            "protocol_id": "97a30135-246f-4c0d-aef8-4e33183d1ff7"
+                        }
+                    ]
+                },
+                {
+                    "process": "a9a39b30-8243-4d08-8f36-8f2e1275e8d0",
+                    "inputs": [
+                        "3322ea3a-30ea-4e6e-b187-18525de4ee3e"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "ad702cb9-3b40-4f8f-b9a5-331eeb153d9b"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": []
+                },
+                {
+                    "process": "024c9f05-1743-4d66-83b7-134a31cd1c27",
+                    "inputs": [
+                        "95deef55-86e9-42be-9f82-3102b0d89dbe"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "d49998ff-c873-41fd-bb44-f221f89b8f15"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "differentiation_protocol",
+                            "protocol_id": "3ec905f4-5950-4cfa-bd0b-86cc0370fd47"
+                        }
+                    ]
+                },
+                {
+                    "process": "50d53f80-5e54-4cda-97f0-5acb4d686d3e",
+                    "inputs": [
+                        "2e32e319-53d4-4e69-af0f-c43e2b15a94f"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "95deef55-86e9-42be-9f82-3102b0d89dbe"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "ipsc_induction_protocol",
+                            "protocol_id": "97a30135-246f-4c0d-aef8-4e33183d1ff7"
+                        }
+                    ]
+                },
+                {
+                    "process": "baa3a061-534c-4b6e-8c51-a11a8307f537",
+                    "inputs": [
+                        "872169f4-8479-4476-9646-20b3997e1f01"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "2e32e319-53d4-4e69-af0f-c43e2b15a94f"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": []
+                }
+            ]
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000/2019-01-03T163633.780215Z/manifest.json b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000/2019-01-03T163633.780215Z/manifest.json
deleted file mode 100644
index 9583a9627..000000000
--- a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000/2019-01-03T163633.780215Z/manifest.json
+++ /dev/null
@@ -1,598 +0,0 @@
-[
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-        "uuid": "d2eedcf0-e06b-4975-99f8-f3c810ca1e39",
-        "version": "2019-01-03T163559.110502Z"
-    }
-]
diff --git a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000/2019-01-03T163633.780215Z/metadata.json b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000/2019-01-03T163633.780215Z/metadata.json
deleted file mode 100644
index 8af61d675..000000000
--- a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000/2019-01-03T163633.780215Z/metadata.json
+++ /dev/null
@@ -1,1449 +0,0 @@
-{
-    "cell_suspension_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.6.2/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI_organoids_pooled_2",
-            "biomaterial_name": "pooled cells from 4 dissociated organoids",
-            "biomaterial_description": "pooled cells from 4 dissociated organoids (wibj_2, kucg_2, hoik_1, sojd_3)",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "selected_cell_type": [
-            {
-                "text": "neural cell",
-                "ontology": "CL:0002319",
-                "ontology_label": "neural cell"
-            }
-        ],
-        "total_estimated_cells": 6210,
-        "provenance": {
-            "document_id": "c2396f83-22e4-4a2d-8cce-a30feb533603",
-            "submission_date": "2019-01-03T12:07:51.214Z",
-            "update_date": "2019-01-03T12:08:03.256Z"
-        }
-    },
-    "organoid_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.3.9/organoid",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "Org_HPSI0214i-wibj_2_2",
-            "biomaterial_name": "human cerebral organoid wibj_2",
-            "biomaterial_description": "human cerebral organoid wibj_2, 62d",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "model_for_organ": {
-            "text": "Brain",
-            "ontology": "UBERON:0000955",
-            "ontology_label": "brain"
-        },
-        "organoid_age": 62,
-        "organoid_age_unit": {
-            "text": "day",
-            "ontology": "UO:0000033",
-            "ontology_label": "day"
-        },
-        "organoid_type": "stem cell-derived",
-        "embedded_in_matrigel": true,
-        "organoid_growth_environment": "suspension",
-        "provenance": {
-            "document_id": "a690df06-cc52-4346-a926-fe5e5b3a7547",
-            "submission_date": "2019-01-03T12:07:51.090Z",
-            "update_date": "2019-01-03T12:08:02.342Z"
-        }
-    },
-    "organoid_1.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.3.9/organoid",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "Org_HPSI0214i-kucg_2_2",
-            "biomaterial_name": "human cerebral organoid kucg_2",
-            "biomaterial_description": "human cerebral organoid kucg_2, 62d",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "model_for_organ": {
-            "text": "Brain",
-            "ontology": "UBERON:0000955",
-            "ontology_label": "brain"
-        },
-        "organoid_age": 62,
-        "organoid_age_unit": {
-            "text": "day",
-            "ontology": "UO:0000033",
-            "ontology_label": "day"
-        },
-        "organoid_type": "stem cell-derived",
-        "embedded_in_matrigel": true,
-        "organoid_growth_environment": "suspension",
-        "provenance": {
-            "document_id": "f0b636ce-505c-4339-a69c-2305352b6796",
-            "submission_date": "2019-01-03T12:07:51.122Z",
-            "update_date": "2019-01-03T12:08:02.944Z"
-        }
-    },
-    "organoid_2.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.3.9/organoid",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "Org_HPSI0314i-hoik_1_2",
-            "biomaterial_name": "human cerebral organoid hoik_1",
-            "biomaterial_description": "human cerebral organoid hoik_1, 62d",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "model_for_organ": {
-            "text": "Brain",
-            "ontology": "UBERON:0000955",
-            "ontology_label": "brain"
-        },
-        "organoid_age": 62,
-        "organoid_age_unit": {
-            "text": "day",
-            "ontology": "UO:0000033",
-            "ontology_label": "day"
-        },
-        "organoid_type": "stem cell-derived",
-        "embedded_in_matrigel": true,
-        "organoid_growth_environment": "suspension",
-        "provenance": {
-            "document_id": "46e7ed04-5916-4c10-8a05-fe510eda819a",
-            "submission_date": "2019-01-03T12:07:51.151Z",
-            "update_date": "2019-01-03T12:08:02.497Z"
-        }
-    },
-    "organoid_3.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.3.9/organoid",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "Org_HPSI0314i-sojd_3_2",
-            "biomaterial_name": "human cerebral organoid sojd_3",
-            "biomaterial_description": "human cerebral organoid sojd_3, 62d",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "model_for_organ": {
-            "text": "Brain",
-            "ontology": "UBERON:0000955",
-            "ontology_label": "brain"
-        },
-        "organoid_age": 62,
-        "organoid_age_unit": {
-            "text": "day",
-            "ontology": "UO:0000033",
-            "ontology_label": "day"
-        },
-        "organoid_type": "stem cell-derived",
-        "embedded_in_matrigel": true,
-        "organoid_growth_environment": "suspension",
-        "provenance": {
-            "document_id": "d49998ff-c873-41fd-bb44-f221f89b8f15",
-            "submission_date": "2019-01-03T12:07:51.178Z",
-            "update_date": "2019-01-03T12:08:02.781Z"
-        }
-    },
-    "cell_line_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/9.0.1/cell_line",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0214i-wibj_2",
-            "biomaterial_name": "iPS cell line wibj_2",
-            "biomaterial_description": "iPS cell line wibj_2",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA2627567"
-        },
-        "disease": {
-            "text": "normal",
-            "ontology": "PATO:0000461",
-            "ontology_label": "normal"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "cell_type": {
-            "text": "pluripotent stem cell",
-            "ontology": "CL:0002248",
-            "ontology_label": "pluripotent stem cell"
-        },
-        "catalog_number": "77650057",
-        "catalog_url": "http://www.hipsci.org/lines/#/lines/HPSI0214i-wibj_2",
-        "cell_line_type": "induced pluripotent",
-        "cell_morphology": {
-            "cell_viability_method": "Growth to confluence post-thaw"
-        },
-        "growth_conditions": {
-            "passage_number": 32,
-            "growth_medium": "mTeSR1",
-            "feeder_layer_type": "feeder-free",
-            "drug_treatment": "Cells were cultured in presence of Penicillin and Streptomycin",
-            "mycoplasma_testing_method": "PCR",
-            "mycoplasma_testing_results": "pass"
-        },
-        "date_established": "2014-10-24T00:00:00Z",
-        "provenance": {
-            "document_id": "a689172e-cae2-4e2c-b1d2-5aeff0a90171",
-            "submission_date": "2019-01-03T12:07:51.043Z",
-            "update_date": "2019-01-03T12:08:03.319Z"
-        }
-    },
-    "specimen_from_organism_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/6.3.4/specimen_from_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0214i-wibj_skin",
-            "biomaterial_name": "Skin cells from HPSI0214i-wibj_skin",
-            "biomaterial_description": "Skin cells from HPSI0214i-wibj_skin",
-            "biosd_biomaterial": "SAMEA2397844",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "organ": {
-            "text": "skin of body",
-            "ontology": "UBERON:0002097",
-            "ontology_label": "skin of body"
-        },
-        "organ_part": {
-            "text": "skin epidermis",
-            "ontology": "UBERON:0001003",
-            "ontology_label": "skin epidermis"
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461",
-                "ontology_label": "normal"
-            }
-        ],
-        "provenance": {
-            "document_id": "597b4050-0778-4a81-b882-e1704ab0b6ad",
-            "submission_date": "2019-01-03T12:07:50.973Z",
-            "update_date": "2019-01-03T12:08:03.189Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.2.1/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0214i-wibj",
-            "biomaterial_name": "donor HPSI0214i-wibj",
-            "biomaterial_description": "donor HPSI0214i-wibj_2, iPSC, cell line, skin",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA2398911"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "sex": "female",
-        "organism_age": "55-59",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036",
-            "ontology_label": "year"
-        },
-        "human_specific": {
-            "ethnicity": [
-                {
-                    "text": "European, White, British",
-                    "ontology": "HANCESTRO:0462",
-                    "ontology_label": "British"
-                }
-            ]
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461",
-                "ontology_label": "normal"
-            }
-        ],
-        "is_living": "yes",
-        "provenance": {
-            "document_id": "4934d9c3-753b-47bc-b2d5-468ce255a139",
-            "submission_date": "2019-01-03T12:07:50.939Z",
-            "update_date": "2019-01-03T12:08:02.040Z"
-        }
-    },
-    "cell_line_1.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/9.0.1/cell_line",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0214i-kucg_2",
-            "biomaterial_name": "iPS cell line kucg_2",
-            "biomaterial_description": "iPS cell line kucg_2",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA2645814"
-        },
-        "disease": {
-            "text": "normal",
-            "ontology": "PATO:0000461",
-            "ontology_label": "normal"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "cell_type": {
-            "text": "pluripotent stem cell",
-            "ontology": "CL:0002248",
-            "ontology_label": "pluripotent stem cell"
-        },
-        "catalog_number": "77650065",
-        "catalog_url": "http://www.hipsci.org/lines/#/lines/HPSI0214i-kucg_2",
-        "cell_line_type": "induced pluripotent",
-        "cell_morphology": {
-            "cell_viability_method": "Growth to confluence post-thaw"
-        },
-        "growth_conditions": {
-            "passage_number": 36,
-            "growth_medium": "mTeSR1",
-            "feeder_layer_type": "feeder-free",
-            "drug_treatment": "Cells were cultured in presence of Penicillin and Streptomycin",
-            "mycoplasma_testing_method": "PCR",
-            "mycoplasma_testing_results": "pass"
-        },
-        "date_established": "2014-11-03T00:00:00Z",
-        "provenance": {
-            "document_id": "37833da3-505d-4bb2-916e-26aa8985d183",
-            "submission_date": "2019-01-03T12:07:51.052Z",
-            "update_date": "2019-01-03T12:08:03.268Z"
-        }
-    },
-    "specimen_from_organism_1.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/6.3.4/specimen_from_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0214i-kucg_skin",
-            "biomaterial_name": "Skin cells from HPSI0214i-kucg_skin",
-            "biomaterial_description": "Skin cells from HPSI0214i-kucg_skin",
-            "biosd_biomaterial": "SAMEA2398627",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "organ": {
-            "text": "skin of body",
-            "ontology": "UBERON:0002097",
-            "ontology_label": "skin of body"
-        },
-        "organ_part": {
-            "text": "skin epidermis",
-            "ontology": "UBERON:0001003",
-            "ontology_label": "skin epidermis"
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461",
-                "ontology_label": "normal"
-            }
-        ],
-        "provenance": {
-            "document_id": "1fc181fe-60c6-4b94-85c1-1f227be60658",
-            "submission_date": "2019-01-03T12:07:50.987Z",
-            "update_date": "2019-01-03T12:08:03.087Z"
-        }
-    },
-    "donor_organism_1.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.2.1/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0214i-kucg",
-            "biomaterial_name": "donor HPSI0214i-kucg",
-            "biomaterial_description": "donor HPSI0214i-kucg_2, iPSC, cell line, skin",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA2397923"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "sex": "male",
-        "organism_age": "65-69",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036",
-            "ontology_label": "year"
-        },
-        "human_specific": {
-            "ethnicity": [
-                {
-                    "text": "European, White, British",
-                    "ontology": "HANCESTRO:0462",
-                    "ontology_label": "British"
-                }
-            ]
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461",
-                "ontology_label": "normal"
-            }
-        ],
-        "is_living": "yes",
-        "provenance": {
-            "document_id": "7c3a6d87-9f43-4de5-b47d-6fa78a897624",
-            "submission_date": "2019-01-03T12:07:50.949Z",
-            "update_date": "2019-01-03T12:08:01.492Z"
-        }
-    },
-    "cell_line_2.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/9.0.1/cell_line",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0314i-hoik_1",
-            "biomaterial_name": "iPS cell line hoik_1",
-            "biomaterial_description": "iPS cell line hoik_1",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "biosd_biomaterial": "SAMEA2698315"
-        },
-        "disease": {
-            "text": "normal",
-            "ontology": "PATO:0000461",
-            "ontology_label": "normal"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "cell_type": {
-            "text": "pluripotent stem cell",
-            "ontology": "CL:0002248",
-            "ontology_label": "pluripotent stem cell"
-        },
-        "catalog_number": "77650129",
-        "catalog_url": "http://www.hipsci.org/lines/#/lines/HPSI0314i-hoik_1",
-        "cell_line_type": "induced pluripotent",
-        "cell_morphology": {
-            "cell_viability_method": "Growth to confluence post-thaw"
-        },
-        "growth_conditions": {
-            "passage_number": 28,
-            "growth_medium": "mTeSR1",
-            "feeder_layer_type": "feeder-free",
-            "drug_treatment": "Cells were cultured in presence of Penicillin and Streptomycin",
-            "mycoplasma_testing_method": "PCR",
-            "mycoplasma_testing_results": "pass"
-        },
-        "date_established": "2015-02-02T00:00:00Z",
-        "provenance": {
-            "document_id": "d954547d-94bc-401d-bdff-ccd727251c74",
-            "submission_date": "2019-01-03T12:07:51.061Z",
-            "update_date": "2019-01-03T12:08:03.322Z"
-        }
-    },
-    "specimen_from_organism_2.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/6.3.4/specimen_from_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0314i-hoik_skin",
-            "biomaterial_name": "Skin cells from HPSI0314i-hoik_skin",
-            "biomaterial_description": "Skin cells from HPSI0314i-hoik_skin",
-            "biosd_biomaterial": "SAMEA2399963",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "organ": {
-            "text": "skin of body",
-            "ontology": "UBERON:0002097",
-            "ontology_label": "skin of body"
-        },
-        "organ_part": {
-            "text": "skin epidermis",
-            "ontology": "UBERON:0001003",
-            "ontology_label": "skin epidermis"
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461",
-                "ontology_label": "normal"
-            }
-        ],
-        "provenance": {
-            "document_id": "ad702cb9-3b40-4f8f-b9a5-331eeb153d9b",
-            "submission_date": "2019-01-03T12:07:50.997Z",
-            "update_date": "2019-01-03T12:08:02.789Z"
-        }
-    },
-    "donor_organism_2.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.2.1/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "HPSI0314i-hoik",
-            "biomaterial_name": "donor HPSI0314i-hoik",
-            "biomaterial_description": "donor HPSI0314i-hoik_1, iPSC, cell line, skin",
-            "ncbi_taxon_id": [
-                9606
-            ],
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-                "contact_name": "Zhisong,,He",
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-                "address": "Deutscher Pl. 6, 04103 Leipzig",
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diff --git a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
new file mode 100644
index 000000000..8b58a1e79
--- /dev/null
+++ b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
@@ -0,0 +1,1072 @@
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+                "project_title": "Transcriptomic classification of human retinal cell types with single-nuclei RNA-seq.",
+                "project_description": "The human neural retina is a heterogenous tissue that is an ordered array of approximately 70 different types of neurons, each playing a unique role in processing the visual signal. Currently, the transcriptomic-level classification of human retinal cell types is still limited. Using single-nuclei RNA-seq, a comprehensive single-cell profiling study has been carried out for healthy human retina from four individual donors. With the transcriptomic profiles for a total of over 200K nuclei being generated, we aim at revealing the transcriptome profiles for most subtypes of the retinal cells. Comparison with previous published macaque and mice dataset indicates an overall good alignment among species. In addition, the gene expression profile that is unique to human has been discovered. Furthermore, over 200 genes associated with human retinal diseases are investigated in our dataset and are found to show both cell type and regional specificity. In summary, results from our study serves as not only a cell atlas reference but also the foundation for future studies of human retinal diseases."
+            },
+            "contributors": [
+                {
+                    "name": "Qingnan,,Liang",
+                    "email": "qingnan.liang@bcm.edu",
+                    "phone": "(+1)7137983610",
+                    "institution": "Baylor College of Medicine",
+                    "laboratory": "Human Genome Sequencing Center, Department of Molecular and Human Genetics,",
+                    "address": "One Baylor Plaza, Houston, Texas, 77054",
+                    "country": "USA",
+                    "corresponding_contributor": false,
+                    "project_role": {
+                        "text": "experimental scientist",
+                        "ontology": "EFO:0009741",
+                        "ontology_label": "experimental scientist"
+                    }
+                },
+                {
+                    "name": "Xuesen,,Cheng",
+                    "email": "xuesen.cheng@bcm.edu",
+                    "phone": "(+1)7137983654",
+                    "institution": "Baylor College of Medicine",
+                    "laboratory": "Human Genome Sequencing Center, Department of Molecular and Human Genetics,",
+                    "address": "One Baylor Plaza, Houston, Texas, 77054",
+                    "country": "USA",
+                    "corresponding_contributor": false,
+                    "project_role": {
+                        "text": "experimental scientist",
+                        "ontology": "EFO:0009741",
+                        "ontology_label": "experimental scientist"
+                    }
+                },
+                {
+                    "name": "Yumei,,Li",
+                    "email": "yumeil@bcm.edu",
+                    "phone": "(+1)7137987565",
+                    "institution": "Baylor College of Medicine",
+                    "laboratory": "Human Genome Sequencing Center, Department of Molecular and Human Genetics,",
+                    "address": "One Baylor Plaza, Houston, Texas, 77054",
+                    "country": "USA",
+                    "corresponding_contributor": false,
+                    "project_role": {
+                        "text": "experimental scientist",
+                        "ontology": "EFO:0009741",
+                        "ontology_label": "experimental scientist"
+                    }
+                },
+                {
+                    "name": "Leah,,Owen",
+                    "email": "leah.owen@hsc.utah.edu",
+                    "phone": "(+1)8015812352",
+                    "institution": "University of Utah",
+                    "laboratory": "Department of Ophthalmology and Visual Sciences",
+                    "address": "65 Mario Capecchi Drive, Salt Lake City, Utah, 84132",
+                    "country": "USA",
+                    "corresponding_contributor": false,
+                    "project_role": {
+                        "text": "experimental scientist",
+                        "ontology": "EFO:0009741",
+                        "ontology_label": "experimental scientist"
+                    }
+                },
+                {
+                    "name": "Denise,,Morgan",
+                    "email": "denisej.jones@hsc.utah.edu",
+                    "institution": "University of Utah",
+                    "laboratory": "Department of Ophthalmology and Visual Sciences",
+                    "address": "65 Mario Capecchi Drive, Salt Lake City, Utah, 84132",
+                    "country": "USA",
+                    "corresponding_contributor": false,
+                    "project_role": {
+                        "text": "experimental scientist",
+                        "ontology": "EFO:0009741",
+                        "ontology_label": "experimental scientist"
+                    }
+                },
+                {
+                    "name": "Sangbae,,Kim",
+                    "email": "sangbae.kim@bcm.edu",
+                    "phone": "(+1)7137983348",
+                    "institution": "Baylor College of Medicine",
+                    "laboratory": "Human Genome Sequencing Center, Department of Molecular and Human Genetics,",
+                    "address": "One Baylor Plaza, Houston, Texas, 77054",
+                    "country": "USA",
+                    "corresponding_contributor": false,
+                    "project_role": {
+                        "text": "experimental scientist",
+                        "ontology": "EFO:0009741",
+                        "ontology_label": "experimental scientist"
+                    }
+                },
+                {
+                    "name": "Albert,,Vitale",
+                    "email": "Albert.Vitale@hsc.utah.edu",
+                    "phone": "(+1)8015812352",
+                    "institution": "University of Utah",
+                    "laboratory": "Department of Ophthalmology and Visual Sciences",
+                    "address": "65 Mario Capecchi Drive, Salt Lake City, Utah, 84132",
+                    "country": "USA",
+                    "corresponding_contributor": false,
+                    "project_role": {
+                        "text": "experimental scientist",
+                        "ontology": "EFO:0009741",
+                        "ontology_label": "experimental scientist"
+                    }
+                },
+                {
+                    "name": "Ivana,,Kim",
+                    "email": "Ivana_Kim@meei.harvard.edu",
+                    "phone": "(+1)6175733367",
+                    "institution": "University of Utah",
+                    "laboratory": "Department of Ophthalmology and Visual Sciences",
+                    "address": "65 Mario Capecchi Drive, Salt Lake City, Utah, 84132",
+                    "country": "USA",
+                    "corresponding_contributor": false,
+                    "project_role": {
+                        "text": "experimental scientist",
+                        "ontology": "EFO:0009741",
+                        "ontology_label": "experimental scientist"
+                    }
+                },
+                {
+                    "name": "Akbar,,Shakoor",
+                    "email": "akbar.shakoor@hsc.utah.edu",
+                    "phone": "(+1)8015856701",
+                    "institution": "University of Utah",
+                    "laboratory": "Department of Ophthalmology and Visual Sciences",
+                    "address": "65 Mario Capecchi Drive, Salt Lake City, Utah, 84132",
+                    "country": "USA",
+                    "corresponding_contributor": false,
+                    "project_role": {
+                        "text": "experimental scientist",
+                        "ontology": "EFO:0009741",
+                        "ontology_label": "experimental scientist"
+                    }
+                },
+                {
+                    "name": "Margaret,,DeAngelis",
+                    "email": "margaret.deangelis@utah.edu",
+                    "phone": "(+1)8015812352",
+                    "institution": "University of Utah",
+                    "laboratory": "Department of Ophthalmology and Visual Sciences",
+                    "address": "65 Mario Capecchi Drive, Salt Lake City, Utah, 84132",
+                    "country": "USA",
+                    "corresponding_contributor": false,
+                    "project_role": {
+                        "text": "principal investigator",
+                        "ontology": "EFO:0009736",
+                        "ontology_label": "principal investigator"
+                    }
+                },
+                {
+                    "name": "Rui,,Chen",
+                    "email": "ruichen@bcm.edu",
+                    "phone": "(+1)7137985194",
+                    "institution": "Baylor College of Medicine",
+                    "laboratory": "Human Genome Sequencing Center, Department of Molecular and Human Genetics,",
+                    "address": "One Baylor Plaza, Houston, Texas, 77054",
+                    "country": "USA",
+                    "corresponding_contributor": true,
+                    "project_role": {
+                        "text": "principal investigator",
+                        "ontology": "EFO:0009736",
+                        "ontology_label": "principal investigator"
+                    }
+                },
+                {
+                    "name": "Zinaida,A,Perova",
+                    "email": "zina@ebi.ac.uk",
+                    "phone": "(+44) 01223494121",
+                    "institution": "EMBL-EBI",
+                    "address": "Wellcome Trust Genome Center, Hinxton, CB10 1SD",
+                    "country": "UK",
+                    "corresponding_contributor": false,
+                    "project_role": {
+                        "text": "HCA data wrangler",
+                        "ontology": "EFO:0009737",
+                        "ontology_label": "data curator"
+                    },
+                    "orcid_id": "0000-0001-9913-3249"
+                }
+            ],
+            "funders": [
+                {
+                    "grant_title": "Cell Atlas of the Neural Retina Seed Networks",
+                    "grant_id": "CZF2019-002425",
+                    "organization": "Chan Zuckerberg Foundation"
+                }
+            ],
+            "provenance": {
+                "document_id": "9c20a245-f2c0-43ae-82c9-2232ec6b594f",
+                "submission_date": "2019-09-20T08:29:51.843Z",
+                "update_date": "2019-09-20T08:29:55.163Z",
+                "schema_major_version": 14,
+                "schema_minor_version": 1
+            }
+        },
+        "library_preparation_protocol_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "standard_10x_library_preparation",
+                "protocol_name": "standard_10x_library_preparation",
+                "protocol_description": "This is a standard 10x genomics library preparation method",
+                "document": "standard_10x_library_preparation.pdf"
+            },
+            "cell_barcode": {
+                "barcode_read": "Read 1",
+                "barcode_offset": 0,
+                "barcode_length": 16
+            },
+            "input_nucleic_acid_molecule": {
+                "text": "polyA RNA",
+                "ontology": "OBI:0000869",
+                "ontology_label": "polyA RNA"
+            },
+            "nucleic_acid_source": "single nucleus",
+            "library_construction_method": {
+                "text": "10X 3' v3 sequencing",
+                "ontology": "EFO:0009922",
+                "ontology_label": "10x 3' v3 sequencing"
+            },
+            "end_bias": "3 prime tag",
+            "primer": "poly-dT",
+            "strand": "unstranded",
+            "umi_barcode": {
+                "barcode_read": "Read 1",
+                "barcode_offset": 16,
+                "barcode_length": 12
+            },
+            "library_preamplification_method": {
+                "text": "reverse transcription PCR",
+                "ontology": "OBI:0000552",
+                "ontology_label": "reverse transcription PCR"
+            },
+            "cdna_library_amplification_method": {
+                "text": "PCR",
+                "ontology": "OBI:0000415",
+                "ontology_label": "PCR"
+            },
+            "nominal_length": 150,
+            "provenance": {
+                "document_id": "6ce5a9c7-b4f7-41e5-a182-21e85627feee",
+                "submission_date": "2019-09-20T08:29:52.319Z",
+                "update_date": "2019-09-20T08:29:58.625Z",
+                "schema_major_version": 6,
+                "schema_minor_version": 2
+            }
+        },
+        "sequencing_protocol_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "seq_protocol",
+                "protocol_name": "seq_protocol",
+                "protocol_description": "a standard illumina sequencing protocol",
+                "document": "seq_protocol.pdf"
+            },
+            "instrument_manufacturer_model": {
+                "text": "Illumina Novaseq 6000",
+                "ontology": "EFO:0008637",
+                "ontology_label": "Illumina NovaSeq 6000"
+            },
+            "paired_end": false,
+            "method": {
+                "text": "tag based single cell RNA sequencing",
+                "ontology": "EFO:0008440",
+                "ontology_label": "tag based single cell RNA sequencing"
+            },
+            "10x": {
+                "fastq_method": "Cellranger mkfastq",
+                "fastq_method_version": "Cell Ranger 3.0.2",
+                "pooled_channels": 4.0
+            },
+            "provenance": {
+                "document_id": "e01aa420-488b-4189-a8c8-98ada395ee91",
+                "submission_date": "2019-09-20T08:29:52.324Z",
+                "update_date": "2019-09-20T08:29:58.905Z",
+                "schema_major_version": 10,
+                "schema_minor_version": 1
+            }
+        },
+        "dissociation_protocol_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "Single-nuclei-dissociation-protocol",
+                "protocol_name": "Single-nuclei-dissociation-protocol",
+                "document": "Single_nuclei_dissociation_protocol.pdf"
+            },
+            "method": {
+                "text": "sample dissociation",
+                "ontology": "EFO:0009091",
+                "ontology_label": "sample dissociation"
+            },
+            "provenance": {
+                "document_id": "a3623f22-83e7-4207-b204-34041abb54e2",
+                "submission_date": "2019-09-20T08:29:52.309Z",
+                "update_date": "2019-09-20T08:29:58.448Z",
+                "schema_major_version": 6,
+                "schema_minor_version": 2
+            }
+        },
+        "enrichment_protocol_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "NeuN-enrichment-protocol",
+                "protocol_name": "NeuN-enrichment-protocol",
+                "protocol_description": "Enrichment of the NeuN positive nuclei in the peripheral retina. The purpose is to enrich amacrine cells and retinal ganglion cells.",
+                "document": "NeuN_enrichment_protocol.pdf"
+            },
+            "method": {
+                "text": "antibody enrichment with FACS sorting",
+                "ontology": "EFO:0009108",
+                "ontology_label": "fluorescence-activated cell sorting"
+            },
+            "markers": "NeuN+",
+            "provenance": {
+                "document_id": "76f64d5b-fa01-4efe-ad4a-097d70311581",
+                "submission_date": "2019-09-20T08:29:52.314Z",
+                "update_date": "2019-09-20T08:29:58.761Z",
+                "schema_major_version": 3,
+                "schema_minor_version": 1
+            }
+        },
+        "collection_protocol_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "Retina_collection_protocol",
+                "protocol_name": "Retina_collection_protocol",
+                "protocol_description": "This is a standard protocol including post-mortem phenotyping (to make sure the donor does not have an retinal disease) and dissection of the eye.",
+                "publication_doi": "10.1167/iovs.18-24254"
+            },
+            "method": {
+                "text": "dissection",
+                "ontology": "EFO:0003856",
+                "ontology_label": "dissection"
+            },
+            "provenance": {
+                "document_id": "9a46c161-fb6e-4a4f-8c8d-a91a3c7b99c2",
+                "submission_date": "2019-09-20T08:29:52.304Z",
+                "update_date": "2019-09-20T08:29:58.737Z",
+                "schema_major_version": 9,
+                "schema_minor_version": 2
+            }
+        },
+        "process_0.json": {
+            "start_time": "2019/08/28",
+            "process_core": {
+                "process_id": "lib_prep10"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/9.2.0/process",
+            "provenance": {
+                "document_id": "a29d4d8a-e8bf-4e1a-aacc-eeea8f3b65d2",
+                "submission_date": "2019-09-20T08:29:52.505Z",
+                "update_date": "2019-09-20T08:29:59.338Z",
+                "schema_major_version": 9,
+                "schema_minor_version": 2
+            }
+        },
+        "process_1.json": {
+            "process_core": {
+                "process_id": "process_id_19"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/9.2.0/process",
+            "provenance": {
+                "document_id": "b6e09f03-0ddc-44ff-8cc9-7caf9eb70f57",
+                "submission_date": "2019-09-20T08:29:52.437Z",
+                "update_date": "2019-09-20T08:29:59.191Z",
+                "schema_major_version": 9,
+                "schema_minor_version": 2
+            }
+        },
+        "process_2.json": {
+            "process_core": {
+                "process_id": "process_id_7"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/9.2.0/process",
+            "provenance": {
+                "document_id": "b3cddf6f-65ee-4aa8-8682-60f00c55be73",
+                "submission_date": "2019-09-20T08:29:52.365Z",
+                "update_date": "2019-09-20T08:29:59.366Z",
+                "schema_major_version": 9,
+                "schema_minor_version": 2
+            }
+        },
+        "links.json": {
+            "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
+            "schema_type": "link_bundle",
+            "schema_version": "1.1.5",
+            "links": [
+                {
+                    "process": "a29d4d8a-e8bf-4e1a-aacc-eeea8f3b65d2",
+                    "inputs": [
+                        "eb27c398-f017-4ef1-acc8-3f51af87fe17"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "12484c33-24ec-4293-8f96-4cb1a43a6479",
+                        "f85b458b-b189-4ee7-939a-c905b70ae431",
+                        "18feeb7d-66ca-4ea4-a019-a10e5b762465"
+                    ],
+                    "output_type": "file",
+                    "protocols": [
+                        {
+                            "protocol_type": "library_preparation_protocol",
+                            "protocol_id": "6ce5a9c7-b4f7-41e5-a182-21e85627feee"
+                        },
+                        {
+                            "protocol_type": "sequencing_protocol",
+                            "protocol_id": "e01aa420-488b-4189-a8c8-98ada395ee91"
+                        }
+                    ]
+                },
+                {
+                    "process": "b6e09f03-0ddc-44ff-8cc9-7caf9eb70f57",
+                    "inputs": [
+                        "0a63e007-09d0-4330-989b-ca248f8b3c3c"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "eb27c398-f017-4ef1-acc8-3f51af87fe17"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "dissociation_protocol",
+                            "protocol_id": "a3623f22-83e7-4207-b204-34041abb54e2"
+                        },
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "76f64d5b-fa01-4efe-ad4a-097d70311581"
+                        }
+                    ]
+                },
+                {
+                    "process": "b3cddf6f-65ee-4aa8-8682-60f00c55be73",
+                    "inputs": [
+                        "fa1bd656-7f7b-4288-84c6-d511232cfe95"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "0a63e007-09d0-4330-989b-ca248f8b3c3c"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "collection_protocol",
+                            "protocol_id": "9a46c161-fb6e-4a4f-8c8d-a91a3c7b99c2"
+                        }
+                    ]
+                }
+            ]
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44/2019-09-20T103932.395795Z/manifest.json b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44/2019-09-20T103932.395795Z/manifest.json
deleted file mode 100644
index 481850e65..000000000
--- a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44/2019-09-20T103932.395795Z/manifest.json
+++ /dev/null
@@ -1,326 +0,0 @@
-[
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "27d5df55",
-        "indexed": true,
-        "name": "cell_suspension_0.json",
-        "s3_etag": "c2ae104c7e048e34f7e11c33d336ea76",
-        "sha1": "2d934a2d27629d3d0b1c146e9ebd8403f49f8bec",
-        "sha256": "2f9df9ebcdd0440e89070985d6d1868b5d9ab39b5ba6845afcb069f82e29e114",
-        "size": 1167,
-        "uuid": "eb27c398-f017-4ef1-acc8-3f51af87fe17",
-        "version": "2019-09-20T082959.187000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "5c140335",
-        "indexed": true,
-        "name": "specimen_from_organism_0.json",
-        "s3_etag": "a0bf601a253a5f851b45b9236af45064",
-        "sha1": "434291f6cc51414b40d886e46c3778be45beaa25",
-        "sha256": "24d0c61756a18088e1fb337b868ab636eae6dc2a0c3c0ea7e64da2dee72b16d5",
-        "size": 1095,
-        "uuid": "0a63e007-09d0-4330-989b-ca248f8b3c3c",
-        "version": "2019-09-20T082955.265000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "ec11426d",
-        "indexed": true,
-        "name": "donor_organism_0.json",
-        "s3_etag": "1c9ddd9f5a7b1e02e58b243561ec767a",
-        "sha1": "abf4c58394716263dffd188cf07555a5a73c948d",
-        "sha256": "83c0f4789214b4fd6419d8ee7d4c0ef7c3b46ce3df1dbc1856de85221316e182",
-        "size": 1762,
-        "uuid": "fa1bd656-7f7b-4288-84c6-d511232cfe95",
-        "version": "2019-09-20T082955.262000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "5523b822",
-        "indexed": true,
-        "name": "sequence_file_0.json",
-        "s3_etag": "dd9a989d9708f2c409f2eeaf758a682c",
-        "sha1": "cf0fa61520f7d160c5772da8e7b54eda67c2dfa5",
-        "sha256": "bd07544040ea5435e48e590e8647acf428011fcf987ef8f407c2a3bea57ea010",
-        "size": 770,
-        "uuid": "12484c33-24ec-4293-8f96-4cb1a43a6479",
-        "version": "2019-09-20T101335.720000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "68f76fda",
-        "indexed": true,
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diff --git a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44/2019-09-20T103932.395795Z/metadata.json b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44/2019-09-20T103932.395795Z/metadata.json
deleted file mode 100644
index 5d3ab627d..000000000
--- a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44/2019-09-20T103932.395795Z/metadata.json
+++ /dev/null
@@ -1,744 +0,0 @@
-{
-    "cell_suspension_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "19D015_NeuNT_nuclei",
-            "biomaterial_name": "19D015_NeuNT",
-            "biomaterial_description": "dissocitated nuclei of human retina (peripheral region), incubated with anti-NeuN antibody and FACS sorted (Nuclei with top 5% signal intensity)",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "selected_cell_types": [
-            {
-                "text": "NeuN-positive-nuclei in peripheral retina",
-                "ontology": "CL:0000540",
-                "ontology_label": "neuron"
-            }
-        ],
-        "estimated_cell_count": 24600,
-        "provenance": {
-            "document_id": "eb27c398-f017-4ef1-acc8-3f51af87fe17",
-            "submission_date": "2019-09-20T08:29:51.970Z",
-            "update_date": "2019-09-20T08:29:59.187Z",
-            "schema_major_version": 13,
-            "schema_minor_version": 3
-        }
-    },
-    "specimen_from_organism_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "19D015_per",
-            "biomaterial_name": "19D015_per",
-            "biomaterial_description": "retinal tissues from the donor body",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "organ": {
-            "text": "eye",
-            "ontology": "UBERON:0000970",
-            "ontology_label": "eye"
-        },
-        "organ_parts": [
-            {
-                "text": "retina",
-                "ontology": "UBERON:0000966",
-                "ontology_label": "retina"
-            }
-        ],
-        "provenance": {
-            "document_id": "0a63e007-09d0-4330-989b-ca248f8b3c3c",
-            "submission_date": "2019-09-20T08:29:51.904Z",
-            "update_date": "2019-09-20T08:29:55.265Z",
-            "schema_major_version": 10,
-            "schema_minor_version": 4
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "19D015",
-            "biomaterial_name": "Homo Sapiens",
-            "biomaterial_description": "postmortem human donor",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "human_specific": {
-            "ethnicity": [
-                {
-                    "text": "Caucasian",
-                    "ontology": "HANCESTRO:0005",
-                    "ontology_label": "European"
-                }
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "sex": "male",
-        "is_living": "no",
-        "organism_age": "73",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036",
-            "ontology_label": "year"
-        },
-        "development_stage": {
-            "text": "human adult",
-            "ontology": "HsapDv:0000087",
-            "ontology_label": "human adult stage"
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461",
-                "ontology_label": "normal"
-            }
-        ],
-        "death": {
-            "cause_of_death": "heart failure",
-            "cold_perfused": false,
-            "hardy_scale": 2,
-            "organ_donation_death_type": "Donation after brainstem death (DBD)",
-            "normothermic_regional_perfusion": "no"
-        },
-        "provenance": {
-            "document_id": "fa1bd656-7f7b-4288-84c6-d511232cfe95",
-            "submission_date": "2019-09-20T08:29:51.866Z",
-            "update_date": "2019-09-20T08:29:55.262Z",
-            "schema_major_version": 15,
-            "schema_minor_version": 5
-        }
-    },
-    "sequence_file_0.json": {
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-        "schema_type": "file",
-        "file_core": {
-            "file_name": "19D015_NeuNT_R1.fastq.gz",
-            "format": "fastq.gz",
-            "content_description": [
-                {
-                    "text": "DNA sequence",
-                    "ontology": "data:3494",
-                    "ontology_label": "DNA sequence"
-                }
-            ]
-        },
-        "read_index": "read1",
-        "read_length": 26,
-        "library_prep_id": "batch_1",
-        "provenance": {
-            "document_id": "12484c33-24ec-4293-8f96-4cb1a43a6479",
-            "submission_date": "2019-09-20T08:29:52.232Z",
-            "update_date": "2019-09-20T10:13:35.720Z",
-            "schema_major_version": 9,
-            "schema_minor_version": 2
-        }
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diff --git a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
new file mode 100644
index 000000000..9f0938781
--- /dev/null
+++ b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
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+                    "project_shortname": "Mouse Melanoma",
+                    "project_description": "The cancer microenvironment is a complex ecosystem characterized by dynamic interactions between diverse cell types, including malignant, immune and stromal cells. Here, we performed single-cell RNA sequencing on CD45+ and CD45- cells isolated from tumour and lymph nodes during a mouse model of melanoma. The transcriptional profiles of these individual cells taken at different time points coupled with assembled T cell receptor sequences, allowed us to identify distinct immune subpopulations and delineate their developmental trajectory. Our study provides insights into the complex interplay among cells within the tumour microenvironment and presents a valuable resource for future translational applications.",
+                    "project_title": "Melanoma infiltration of stromal and immune cells"
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+                        "country": "UK",
+                        "institution": "Wellcome Trust Sanger Institute",
+                        "address": "Wellcome Trust Genome Campus, Cambridge UK",
+                        "laboratory": "Sarah Teichmann",
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+                        "institution": "Wellcome Trust Sanger Institute",
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+                        "text": "CD11b+ Macrophages/monocytes"
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+                    "ncbi_taxon_id": [
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+                    "process_name": "Extracting cells from lymph nodes"
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+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:26.040Z",
+                "updateDate": "2018-03-28T14:45:43.500Z",
+                "document_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6"
+            }
+        },
+        "protocol_2.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_name": "Make/amplify cDNA for each cell",
+                    "document": "SmartSeq2_RTPCR_protocol.pdf",
+                    "protocol_id": "SmartSeq2_RTPCR_protocol"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "protocol_type": {
+                    "text": "Smart-seq2 protocol",
+                    "ontology": "EFO:0008442"
+                },
+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:26.044Z",
+                "updateDate": "2018-03-28T14:24:04.790Z",
+                "document_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643"
+            }
+        },
+        "protocol_3.json": {
+            "content": {
+                "protocol_core": {
+                    "protocol_name": "Sequencing SmartSeq2 cells",
+                    "protocol_id": "SmartSeq2_sequencing_protocol"
+                },
+                "describedBy": "https://schema.humancellatlas.org/type/protocol/5.1.0/protocol",
+                "schema_type": "protocol"
+            },
+            "hca_ingest": {
+                "accession": "",
+                "submissionDate": "2018-03-28T13:55:26.050Z",
+                "updateDate": "2018-03-28T14:30:39.321Z",
+                "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
+            }
+        },
+        "links.json": {
+            "links": [
+                {
+                    "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                    "source_type": "biomaterial",
+                    "destination_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                    "destination_type": "dissociation_process"
+                },
+                {
+                    "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                    "source_type": "dissociation_process",
+                    "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                    "destination_type": "biomaterial"
+                },
+                {
+                    "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                    "source_type": "dissociation_process",
+                    "destination_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127",
+                    "destination_type": "protocol"
+                },
+                {
+                    "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                    "source_type": "process",
+                    "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                    "destination_type": "biomaterial"
+                },
+                {
+                    "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
+                    "source_type": "biomaterial",
+                    "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                    "destination_type": "process"
+                },
+                {
+                    "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                    "source_type": "biomaterial",
+                    "destination_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
+                    "destination_type": "enrichment_process"
+                },
+                {
+                    "source_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
+                    "source_type": "enrichment_process",
+                    "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                    "destination_type": "biomaterial"
+                },
+                {
+                    "source_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
+                    "source_type": "enrichment_process",
+                    "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
+                    "destination_type": "protocol"
+                },
+                {
+                    "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                    "source_type": "process",
+                    "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                    "destination_type": "biomaterial"
+                },
+                {
+                    "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
+                    "source_type": "biomaterial",
+                    "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                    "destination_type": "process"
+                },
+                {
+                    "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                    "source_type": "biomaterial",
+                    "destination_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
+                    "destination_type": "enrichment_process"
+                },
+                {
+                    "source_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
+                    "source_type": "enrichment_process",
+                    "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                    "destination_type": "biomaterial"
+                },
+                {
+                    "source_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
+                    "source_type": "enrichment_process",
+                    "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
+                    "destination_type": "protocol"
+                },
+                {
+                    "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                    "source_type": "process",
+                    "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                    "destination_type": "biomaterial"
+                },
+                {
+                    "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
+                    "source_type": "biomaterial",
+                    "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                    "destination_type": "process"
+                },
+                {
+                    "source_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                    "source_type": "biomaterial",
+                    "destination_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                    "destination_type": "library_preparation_process"
+                },
+                {
+                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                    "source_type": "library_preparation_process",
+                    "destination_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1",
+                    "destination_type": "file"
+                },
+                {
+                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                    "source_type": "library_preparation_process",
+                    "destination_id": "aa662c76-d220-49f4-8316-f4af5820d60b",
+                    "destination_type": "file"
+                },
+                {
+                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                    "source_type": "library_preparation_process",
+                    "destination_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643",
+                    "destination_type": "protocol"
+                },
+                {
+                    "source_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                    "source_type": "biomaterial",
+                    "destination_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
+                    "destination_type": "sequencing_process"
+                },
+                {
+                    "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
+                    "source_type": "sequencing_process",
+                    "destination_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1",
+                    "destination_type": "file"
+                },
+                {
+                    "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
+                    "source_type": "sequencing_process",
+                    "destination_id": "aa662c76-d220-49f4-8316-f4af5820d60b",
+                    "destination_type": "file"
+                },
+                {
+                    "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
+                    "source_type": "sequencing_process",
+                    "destination_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9",
+                    "destination_type": "protocol"
+                }
+            ],
+            "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
+            "schema_version": "1.0.0",
+            "schema_type": "link_bundle"
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-03-29T142048.835519Z/manifest.json b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-03-29T142048.835519Z/manifest.json
deleted file mode 100644
index 445440e89..000000000
--- a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-03-29T142048.835519Z/manifest.json
+++ /dev/null
@@ -1,98 +0,0 @@
-[
-    {
-        "content-type": "application/json; dcp-type=\"metadata/project\"",
-        "crc32c": "aa2dfbb1",
-        "indexed": true,
-        "name": "project.json",
-        "s3_etag": "066f4af443f5db0e1d893bcee16db0e6",
-        "sha1": "fe667c736c9cbc5b129905cc04609d3f5b9a8caa",
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-        "crc32c": "85c42f70",
-        "indexed": true,
-        "name": "biomaterial.json",
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-        "crc32c": "02db8e33",
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-        "sha1": "ead8da55acf55d14f3205a5d1380f327d270f6d4",
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-        "version": "2018-03-29T142045.727350Z"
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-        "crc32c": "ef33a4cd",
-        "indexed": true,
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-        "version": "2018-03-29T142047.303889Z"
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-    {
-        "content-type": "application/json; dcp-type=\"metadata/links\"",
-        "crc32c": "4e6ce5dd",
-        "indexed": true,
-        "name": "links.json",
-        "s3_etag": "14c01392fd55df2b2cdbd08994009e24",
-        "sha1": "6ab7fdb229d9f0971a05e781ef52cbcfbf680e00",
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-]
diff --git a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-03-29T142048.835519Z/metadata.json b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-03-29T142048.835519Z/metadata.json
deleted file mode 100644
index 49a0fdfdd..000000000
--- a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953/2018-03-29T142048.835519Z/metadata.json
+++ /dev/null
@@ -1,578 +0,0 @@
-{
-    "project_0.json": {
-        "content": {
-            "describedBy": "https://schema.humancellatlas.org/type/project/5.1.0/project",
-            "project_core": {
-                "project_shortname": "Mouse Melanoma",
-                "project_description": "The cancer microenvironment is a complex ecosystem characterized by dynamic interactions between diverse cell types, including malignant, immune and stromal cells. Here, we performed single-cell RNA sequencing on CD45+ and CD45- cells isolated from tumour and lymph nodes during a mouse model of melanoma. The transcriptional profiles of these individual cells taken at different time points coupled with assembled T cell receptor sequences, allowed us to identify distinct immune subpopulations and delineate their developmental trajectory. Our study provides insights into the complex interplay among cells within the tumour microenvironment and presents a valuable resource for future translational applications.",
-                "project_title": "Melanoma infiltration of stromal and immune cells"
-            },
-            "publications": [],
-            "contributors": [
-                {
-                    "country": "UK",
-                    "institution": "Wellcome Trust Sanger Institute",
-                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                    "laboratory": "Sarah Teichmann",
-                    "contact_name": "Sarah,A,Teichmann",
-                    "email": "st9@sanger.ac.uk"
-                },
-                {
-                    "country": "UK",
-                    "institution": "Wellcome Trust Sanger Institute",
-                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                    "laboratory": "Sarah Teichmann",
-                    "contact_name": "Mirjana,,Efremova",
-                    "email": "me5@sanger.ac.uk"
-                },
-                {
-                    "country": "UK",
-                    "institution": "Wellcome Trust Sanger Institute",
-                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                    "laboratory": "Sarah Teichmann",
-                    "contact_name": "Bidesh,,Mahata",
-                    "email": "bm11@sanger.ac.uk"
-                },
-                {
-                    "country": "UK",
-                    "institution": "University of Cambridge",
-                    "address": "Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ",
-                    "laboratory": "MRC Cancer Unit",
-                    "contact_name": "Jacqueline,D,Shields",
-                    "email": "JS970@MRCCU.cam.ac.uk"
-                },
-                {
-                    "country": "UK",
-                    "institution": "University of Cambridge",
-                    "address": "Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ",
-                    "laboratory": "MRC Cancer Unit",
-                    "contact_name": "Sarah,,Davidson",
-                    "email": "SED49@MRCCU.cam.ac.uk"
-                },
-                {
-                    "country": "Germany",
-                    "contact_name": "Angela,,Riedel",
-                    "email": "a.riedel@dkfz-heidelberg.de",
-                    "institution": "DKFZ German Cancer Research Center"
-                },
-                {
-                    "country": "UK",
-                    "institution": "Wellcome Trust Sanger Institute",
-                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                    "laboratory": "Sarah Teichmann",
-                    "contact_name": "Roser,,Veno-Tormo",
-                    "email": "rv4@sanger.ac.uk"
-                },
-                {
-                    "country": "UK",
-                    "institution": "Wellcome Trust Sanger Institute",
-                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                    "laboratory": "Sarah Teichmann",
-                    "contact_name": "Jhuma,,Pramanik",
-                    "email": "jp19@sanger.ac.uk"
-                },
-                {
-                    "country": "UK",
-                    "institution": "EMBL-EBI",
-                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                    "laboratory": "Sarah Teichmann",
-                    "contact_name": "Gozde,,Kar",
-                    "email": "gkar@ebi.ac.uk"
-                },
-                {
-                    "country": "Finland",
-                    "contact_name": "Jani,,Huuhtanen",
-                    "email": "jani.huuhtanen@helsinki.fi",
-                    "institution": "University of Helsinki"
-                }
-            ],
-            "schema_type": "project"
-        },
-        "hca_ingest": {
-            "accession": "",
-            "submissionDate": "2018-03-28T13:55:26.025Z",
-            "updateDate": "2018-03-28T14:27:32.460Z",
-            "document_id": "93f6a42f-1790-4af4-b5d1-8c436cb6feae"
-        },
-        "describedBy": "https://schema.humancellatlas.org/bundle/5.1.0/project",
-        "schema_version": "5.1.0",
-        "schema_type": "project_bundle"
-    },
-    "cell_suspension_0.json": {
-        "content": {
-            "genus_species": [
-                {
-                    "text": "Mus musculus",
-                    "ontology": "NCBITaxon:10090"
-                }
-            ],
-            "total_estimated_cells": 1,
-            "target_cell_type": [
-                {
-                    "text": "CD11b+ Macrophages/monocytes"
-                }
-            ],
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "has_input_biomaterial": "1139_T",
-                "ncbi_taxon_id": [
-                    10090
-                ],
-                "biomaterial_id": "22011_1#268"
-            },
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/cell_suspension"
-        },
-        "hca_ingest": {
-            "accession": "",
-            "submissionDate": "2018-03-28T14:00:05.544Z",
-            "updateDate": "2018-03-28T14:39:28.596Z",
-            "document_id": "603a818f-dbe7-466a-8241-58b9c1618846"
-        }
-    },
-    "specimen_from_organism_1.json": {
-        "content": {
-            "biomaterial_core": {
-                "has_input_biomaterial": "1139",
-                "ncbi_taxon_id": [
-                    10090
-                ],
-                "biomaterial_id": "1139_T",
-                "supplementary_files": [
-                    "FACS_sorting_markers.pdf"
-                ],
-                "biomaterial_name": "Mouse_day11_T_rep5"
-            },
-            "genus_species": [
-                {
-                    "text": "Mus musculus",
-                    "ontology": "NCBITaxon:10090"
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/5.1.0/specimen_from_organism",
-            "organ": {
-                "text": "tumor"
-            },
-            "schema_type": "biomaterial"
-        },
-        "hca_ingest": {
-            "accession": "",
-            "submissionDate": "2018-03-28T13:55:31.072Z",
-            "updateDate": "2018-03-28T14:15:11.657Z",
-            "document_id": "4e41a067-dbb7-439f-b72f-80240ce858f6"
-        }
-    },
-    "donor_organism_2.json": {
-        "content": {
-            "is_living": false,
-            "mus_musculus_specific": {
-                "strain": [
-                    {
-                        "text": "C57BL/6"
-                    }
-                ]
-            },
-            "biological_sex": "female",
-            "genus_species": [
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diff --git a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
new file mode 100644
index 000000000..c8cc3a2b3
--- /dev/null
+++ b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
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+            "content-type": "application/json; dcp-type=\"metadata/process\"",
+            "crc32c": "ad459007",
+            "indexed": true,
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+            "sha1": "23ed66f1f47ecb29cf5354d6fb675784804df817",
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+            "uuid": "e521d67d-c134-4dbd-9555-29e23f0463c5",
+            "version": "2019-05-14T122720.135000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/process\"",
+            "crc32c": "4352f3bf",
+            "indexed": true,
+            "name": "process_2.json",
+            "s3_etag": "f94d4ee8d194714e8db01f7f1d9ad66e",
+            "sha1": "db413a2532ec0d9d235aa56fd69ba27fc96bc70d",
+            "sha256": "cf1d4be9c9a62590b38014d092b67a981ec516013af924d30870a18cd6a060ed",
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+            "uuid": "453a352c-94fb-4d3b-b609-df1e7abf8c09",
+            "version": "2019-05-14T122652.545000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/links\"",
+            "crc32c": "2c25a3c2",
+            "indexed": true,
+            "name": "links.json",
+            "s3_etag": "1f7c2cbccc797da2d885bb52de52232d",
+            "sha1": "39ba144902ba5d1095af5b8d5dace8dd19a4b08d",
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+            "size": 2083,
+            "uuid": "51168054-6dad-45aa-916a-ef71135651b2",
+            "version": "2019-05-16T015324.197421Z"
+        },
+        {
+            "content-type": "application/gzip; dcp-type=data",
+            "crc32c": "86192092",
+            "indexed": false,
+            "name": "21784_6#51_1.fastq.gz",
+            "s3_etag": "8ef4064fd5c94502b0d42c0dbecc74ca",
+            "sha1": "0c0a36b8e8e8bf53db8e5eed5688546f0d23f863",
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+            "uuid": "e4d9ebe5-2e62-47cf-bc35-1fb8ef7c1ef7",
+            "version": "2019-05-16T015324.490566Z"
+        },
+        {
+            "content-type": "application/pdf; dcp-type=data",
+            "crc32c": "847325b6",
+            "indexed": false,
+            "name": "TissueDissociationProtocol.pdf",
+            "s3_etag": "7e892bf8f6aa489ccb08a995c7f017e1",
+            "sha1": "f2237ad0a776fd7057eb3d3498114c85e2f521d7",
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+            "size": 32748,
+            "uuid": "6578c322-7060-4c82-8469-9e54100e6b44",
+            "version": "2019-05-16T015325.007527Z"
+        },
+        {
+            "content-type": "application/pdf; dcp-type=data",
+            "crc32c": "b9364bfa",
+            "indexed": false,
+            "name": "SmartSeq2_RTPCR_protocol.pdf",
+            "s3_etag": "846fd9e6b98041df46a1ddb94e85b6b9",
+            "sha1": "89d9eb3f1b94f78a33d46c0288c2e81d4002049b",
+            "sha256": "2f6866c4ede92123f90dd15fb180fac56e33309b8fd3f4f52f263ed2f8af2f16",
+            "size": 29230,
+            "uuid": "cd8e02d1-d0f9-4094-9a31-329931df60dc",
+            "version": "2019-05-16T015325.251968Z"
+        }
+    ],
+    "metadata": {
+        "cell_suspension_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.1.0/cell_suspension",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "21784_6#51",
+                "ncbi_taxon_id": [
+                    10090
+                ]
+            },
+            "provenance": {
+                "document_id": "01ba6be9-ed4b-4c6b-ae05-2e06aadc2019",
+                "submission_date": "2019-05-14T11:01:32.467Z",
+                "update_date": "2019-05-14T12:00:06.941Z"
+            }
+        },
+        "specimen_from_organism_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.2.0/specimen_from_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "1126_LN",
+                "ncbi_taxon_id": [
+                    10090
+                ]
+            },
+            "organ": {
+                "text": "lymph node"
+            },
+            "provenance": {
+                "document_id": "74eb3cb5-918a-49fc-9e15-3ac49fd54caf",
+                "submission_date": "2019-05-14T11:01:26.115Z",
+                "update_date": "2019-05-14T11:46:47.512Z"
+            }
+        },
+        "donor_organism_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.3.0/donor_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "1126",
+                "ncbi_taxon_id": [
+                    10090
+                ]
+            },
+            "genus_species": [
+                {
+                    "text": "Mus musculus"
+                }
+            ],
+            "is_living": "no",
+            "sex": "female",
+            "development_stage": {
+                "text": "adult"
+            },
+            "provenance": {
+                "document_id": "63818269-c4d9-429b-85a3-db39c0dd7fa0",
+                "submission_date": "2019-05-14T11:01:25.684Z",
+                "update_date": "2019-05-14T11:29:50.173Z"
+            }
+        },
+        "sequence_file_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/file/9.0.0/sequence_file",
+            "schema_type": "file",
+            "file_core": {
+                "file_name": "21784_6#51_1.fastq.gz",
+                "format": "fastq.gz"
+            },
+            "read_index": "read1",
+            "provenance": {
+                "document_id": "61fd5348-92c5-446b-a57a-746330cebf76",
+                "submission_date": "2019-05-14T10:52:59.245Z",
+                "update_date": "2019-05-14T11:21:17.762Z"
+            }
+        },
+        "supplementary_file_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/file/2.0.0/supplementary_file",
+            "schema_type": "file",
+            "file_core": {
+                "file_name": "TissueDissociationProtocol.pdf",
+                "format": "pdf"
+            },
+            "provenance": {
+                "document_id": "e738a267-87fc-4070-abc7-b3be6442c6d0",
+                "submission_date": "2019-05-14T10:52:33.892Z",
+                "update_date": "2019-05-14T11:01:15.816Z"
+            }
+        },
+        "supplementary_file_1.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/file/2.0.0/supplementary_file",
+            "schema_type": "file",
+            "file_core": {
+                "file_name": "SmartSeq2_RTPCR_protocol.pdf",
+                "format": "pdf"
+            },
+            "provenance": {
+                "document_id": "01a1d04b-05d0-4904-b627-68b0dc02bc17",
+                "submission_date": "2019-05-14T10:52:33.898Z",
+                "update_date": "2019-05-14T11:01:09.564Z"
+            }
+        },
+        "project_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/project/14.0.0/project",
+            "schema_type": "project",
+            "project_core": {
+                "project_short_name": "Mouse Melanoma",
+                "project_title": "Melanoma infiltration of stromal and immune cells",
+                "project_description": "The cancer microenvironment is a complex ecosystem characterized by dynamic interactions between diverse cell types, including malignant, immune and stromal cells. Here, we performed single-cell RNA sequencing on CD45+ and CD45- cells isolated from tumour and lymph nodes during a mouse model of melanoma. The transcriptional profiles of these individual cells taken at different time points coupled with assembled T cell receptor sequences, allowed us to identify distinct immune subpopulations and delineate their developmental trajectory. Our study provides insights into the complex interplay among cells within the tumour microenvironment and presents a valuable resource for future translational applications."
+            },
+            "funders": [],
+            "provenance": {
+                "document_id": "8c3c290d-dfff-4553-8868-54ce45f4ba7f",
+                "submission_date": "2019-05-14T10:52:33.885Z",
+                "update_date": "2019-05-14T11:20:51.382Z"
+            }
+        },
+        "process_0.json": {
+            "process_core": {
+                "process_id": "proc_21784_6#51"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/9.0.0/process",
+            "provenance": {
+                "document_id": "91f475ec-be51-4f1e-a904-74b10b7259f1",
+                "submission_date": "2019-05-14T11:06:54.971Z",
+                "update_date": "2019-05-14T12:10:53.274Z"
+            }
+        },
+        "process_1.json": {
+            "process_core": {
+                "process_id": "process_id_366"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/9.0.0/process",
+            "provenance": {
+                "document_id": "e521d67d-c134-4dbd-9555-29e23f0463c5",
+                "submission_date": "2019-05-14T11:12:40.680Z",
+                "update_date": "2019-05-14T12:27:20.135Z"
+            }
+        },
+        "process_2.json": {
+            "process_core": {
+                "process_id": "process_id_24"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/9.0.0/process",
+            "provenance": {
+                "document_id": "453a352c-94fb-4d3b-b609-df1e7abf8c09",
+                "submission_date": "2019-05-14T11:12:15.946Z",
+                "update_date": "2019-05-14T12:26:52.545Z"
+            }
+        },
+        "links.json": {
+            "describedBy": "https://schema.humancellatlas.org/system/2.0.0/links",
+            "schema_type": "link_bundle",
+            "schema_version": "2.0.0",
+            "links": [
+                {
+                    "link_type": "process_link",
+                    "process_id": "91f475ec-be51-4f1e-a904-74b10b7259f1",
+                    "process_type": "process",
+                    "inputs": [
+                        {
+                            "input_type": "cell_suspension",
+                            "input_id": "01ba6be9-ed4b-4c6b-ae05-2e06aadc2019"
+                        }
+                    ],
+                    "outputs": [
+                        {
+                            "output_type": "sequence_file",
+                            "output_id": "61fd5348-92c5-446b-a57a-746330cebf76"
+                        }
+                    ],
+                    "protocols": []
+                },
+                {
+                    "link_type": "process_link",
+                    "process_id": "e521d67d-c134-4dbd-9555-29e23f0463c5",
+                    "process_type": "process",
+                    "inputs": [
+                        {
+                            "input_type": "specimen_from_organism",
+                            "input_id": "74eb3cb5-918a-49fc-9e15-3ac49fd54caf"
+                        }
+                    ],
+                    "outputs": [
+                        {
+                            "output_type": "cell_suspension",
+                            "output_id": "01ba6be9-ed4b-4c6b-ae05-2e06aadc2019"
+                        }
+                    ],
+                    "protocols": []
+                },
+                {
+                    "link_type": "process_link",
+                    "process_id": "453a352c-94fb-4d3b-b609-df1e7abf8c09",
+                    "process_type": "process",
+                    "inputs": [
+                        {
+                            "input_type": "donor_organism",
+                            "input_id": "63818269-c4d9-429b-85a3-db39c0dd7fa0"
+                        }
+                    ],
+                    "outputs": [
+                        {
+                            "output_type": "specimen_from_organism",
+                            "output_id": "74eb3cb5-918a-49fc-9e15-3ac49fd54caf"
+                        }
+                    ],
+                    "protocols": []
+                },
+                {
+                    "link_type": "supplementary_file_link",
+                    "entity": {
+                        "entity_type": "project",
+                        "entity_id": "8c3c290d-dfff-4553-8868-54ce45f4ba7f"
+                    },
+                    "files": [
+                        {
+                            "file_id": "e738a267-87fc-4070-abc7-b3be6442c6d0",
+                            "file_type": "supplementary_file"
+                        },
+                        {
+                            "file_id": "01a1d04b-05d0-4904-b627-68b0dc02bc17",
+                            "file_type": "supplementary_file"
+                        }
+                    ]
+                }
+            ]
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439/2019-05-15T222432.561000Z/manifest.json b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439/2019-05-15T222432.561000Z/manifest.json
deleted file mode 100644
index 24e16c231..000000000
--- a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439/2019-05-15T222432.561000Z/manifest.json
+++ /dev/null
@@ -1,170 +0,0 @@
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-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "0300a92e",
-        "indexed": true,
-        "name": "cell_suspension_0.json",
-        "s3_etag": "4f3859e7778d1818bcf4120b76a1ffa6",
-        "sha1": "505038762f830ae810e7a63eea87ca72fc90196b",
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-        "version": "2019-05-14T120006.941000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "7158fd43",
-        "indexed": true,
-        "name": "specimen_from_organism_0.json",
-        "s3_etag": "676e573bec1eb8fe9d7b9888ece979e7",
-        "sha1": "04c71e27a86ea91ee260df9feab594517cf9c5cd",
-        "sha256": "37eb5a18c9be2be0c452aecbf2d7cf50ec9af68e0379f6647c7aedf5372b9833",
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-        "uuid": "74eb3cb5-918a-49fc-9e15-3ac49fd54caf",
-        "version": "2019-05-14T114647.512000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "833cd7f3",
-        "indexed": true,
-        "name": "donor_organism_0.json",
-        "s3_etag": "15380716b8a9c7a78f33a6051a1a477d",
-        "sha1": "657c0e467fb61ee80819f31f86369c2227220307",
-        "sha256": "33e5ecaf9d039b5a41718eb2e38a0d66d15a701eaca7fdbebc9f2b5f46561ee1",
-        "size": 1749,
-        "uuid": "63818269-c4d9-429b-85a3-db39c0dd7fa0",
-        "version": "2019-05-14T112950.173000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "02c57821",
-        "indexed": true,
-        "name": "sequence_file_0.json",
-        "s3_etag": "608e74f1bf465c2d5e4951fab48b349b",
-        "sha1": "b885e81fd0ce11e170176535536a45299e1eed3a",
-        "sha256": "e497c5c87514a04bf398d95c60884bfdf10bc084c75d413ff2d308cb22326b94",
-        "size": 459,
-        "uuid": "61fd5348-92c5-446b-a57a-746330cebf76",
-        "version": "2019-05-14T112117.762000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "61502b5b",
-        "indexed": true,
-        "name": "supplementary_file_0.json",
-        "s3_etag": "b9789082b025294c44dce46ddd22b7aa",
-        "sha1": "daa76ae1d2af21871d8180006b066f56cdf7594f",
-        "sha256": "069391131baa61584a57a5fd9ec9633b6224722c783faf269db28d76d6133c79",
-        "size": 481,
-        "uuid": "e738a267-87fc-4070-abc7-b3be6442c6d0",
-        "version": "2019-05-14T110115.816000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "030e888d",
-        "indexed": true,
-        "name": "supplementary_file_1.json",
-        "s3_etag": "0dc591fd5db04fbb770de26ae5419037",
-        "sha1": "48b75f01afaee3ca9f04510725c4c3b0c536f8b0",
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-        "size": 477,
-        "uuid": "01a1d04b-05d0-4904-b627-68b0dc02bc17",
-        "version": "2019-05-14T110109.564000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/project\"",
-        "crc32c": "ef3ef012",
-        "indexed": true,
-        "name": "project_0.json",
-        "s3_etag": "308189c7eab62a35a894125efbe76558",
-        "sha1": "9da3dba1ec159439071d6390a25ab9110be95f86",
-        "sha256": "2e2f330270644222106b2a8f648733cbd7609c283e29f1ee07363be32c223a9b",
-        "size": 8464,
-        "uuid": "8c3c290d-dfff-4553-8868-54ce45f4ba7f",
-        "version": "2019-05-14T112051.382000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/process\"",
-        "crc32c": "57699965",
-        "indexed": true,
-        "name": "process_0.json",
-        "s3_etag": "fdc514845934d034918521bb96f1ee24",
-        "sha1": "ba3c05024bdd18dd054ef07cbd2c6594fe64e168",
-        "sha256": "2ff1fab2dac6ac35b866a437f7bd720066212998432ab8eb05f6039b748c5225",
-        "size": 379,
-        "uuid": "91f475ec-be51-4f1e-a904-74b10b7259f1",
-        "version": "2019-05-14T121053.274000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/process\"",
-        "crc32c": "ad459007",
-        "indexed": true,
-        "name": "process_1.json",
-        "s3_etag": "b067d9b22cf3d999069bdc42a56fabbe",
-        "sha1": "23ed66f1f47ecb29cf5354d6fb675784804df817",
-        "sha256": "a3948a06685954b8f5d21113621e53cea384aea12aa07d9bb19796ccf4e7300d",
-        "size": 378,
-        "uuid": "e521d67d-c134-4dbd-9555-29e23f0463c5",
-        "version": "2019-05-14T122720.135000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/process\"",
-        "crc32c": "4352f3bf",
-        "indexed": true,
-        "name": "process_2.json",
-        "s3_etag": "f94d4ee8d194714e8db01f7f1d9ad66e",
-        "sha1": "db413a2532ec0d9d235aa56fd69ba27fc96bc70d",
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-        "version": "2019-05-14T122652.545000Z"
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-    {
-        "content-type": "application/json; dcp-type=\"metadata/links\"",
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-        "indexed": true,
-        "name": "links.json",
-        "s3_etag": "1f7c2cbccc797da2d885bb52de52232d",
-        "sha1": "39ba144902ba5d1095af5b8d5dace8dd19a4b08d",
-        "sha256": "33052247612f39f6ea48568a12c761842af30030e1242943bb2c5eb238722488",
-        "size": 2083,
-        "uuid": "51168054-6dad-45aa-916a-ef71135651b2",
-        "version": "2019-05-16T015324.197421Z"
-    },
-    {
-        "content-type": "application/gzip; dcp-type=data",
-        "crc32c": "86192092",
-        "indexed": false,
-        "name": "21784_6#51_1.fastq.gz",
-        "s3_etag": "8ef4064fd5c94502b0d42c0dbecc74ca",
-        "sha1": "0c0a36b8e8e8bf53db8e5eed5688546f0d23f863",
-        "sha256": "1975336c7071ac70caef3ff833089b0dc26962b4d6fc5159aece28eaa4324052",
-        "size": 7591723,
-        "uuid": "e4d9ebe5-2e62-47cf-bc35-1fb8ef7c1ef7",
-        "version": "2019-05-16T015324.490566Z"
-    },
-    {
-        "content-type": "application/pdf; dcp-type=data",
-        "crc32c": "847325b6",
-        "indexed": false,
-        "name": "TissueDissociationProtocol.pdf",
-        "s3_etag": "7e892bf8f6aa489ccb08a995c7f017e1",
-        "sha1": "f2237ad0a776fd7057eb3d3498114c85e2f521d7",
-        "sha256": "6929799f227ae5f0b3e0167a6cf2bd683db097848af6ccde6329185212598779",
-        "size": 32748,
-        "uuid": "6578c322-7060-4c82-8469-9e54100e6b44",
-        "version": "2019-05-16T015325.007527Z"
-    },
-    {
-        "content-type": "application/pdf; dcp-type=data",
-        "crc32c": "b9364bfa",
-        "indexed": false,
-        "name": "SmartSeq2_RTPCR_protocol.pdf",
-        "s3_etag": "846fd9e6b98041df46a1ddb94e85b6b9",
-        "sha1": "89d9eb3f1b94f78a33d46c0288c2e81d4002049b",
-        "sha256": "2f6866c4ede92123f90dd15fb180fac56e33309b8fd3f4f52f263ed2f8af2f16",
-        "size": 29230,
-        "uuid": "cd8e02d1-d0f9-4094-9a31-329931df60dc",
-        "version": "2019-05-16T015325.251968Z"
-    }
-]
diff --git a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439/2019-05-15T222432.561000Z/metadata.json b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439/2019-05-15T222432.561000Z/metadata.json
deleted file mode 100644
index b7c2fea82..000000000
--- a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439/2019-05-15T222432.561000Z/metadata.json
+++ /dev/null
@@ -1,233 +0,0 @@
-{
-    "cell_suspension_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.1.0/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "21784_6#51",
-            "ncbi_taxon_id": [
-                10090
-            ]
-        },
-        "provenance": {
-            "document_id": "01ba6be9-ed4b-4c6b-ae05-2e06aadc2019",
-            "submission_date": "2019-05-14T11:01:32.467Z",
-            "update_date": "2019-05-14T12:00:06.941Z"
-        }
-    },
-    "specimen_from_organism_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.2.0/specimen_from_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "1126_LN",
-            "ncbi_taxon_id": [
-                10090
-            ]
-        },
-        "organ": {
-            "text": "lymph node"
-        },
-        "provenance": {
-            "document_id": "74eb3cb5-918a-49fc-9e15-3ac49fd54caf",
-            "submission_date": "2019-05-14T11:01:26.115Z",
-            "update_date": "2019-05-14T11:46:47.512Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.3.0/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "1126",
-            "ncbi_taxon_id": [
-                10090
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Mus musculus"
-            }
-        ],
-        "is_living": "no",
-        "sex": "female",
-        "development_stage": {
-            "text": "adult"
-        },
-        "provenance": {
-            "document_id": "63818269-c4d9-429b-85a3-db39c0dd7fa0",
-            "submission_date": "2019-05-14T11:01:25.684Z",
-            "update_date": "2019-05-14T11:29:50.173Z"
-        }
-    },
-    "sequence_file_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/file/9.0.0/sequence_file",
-        "schema_type": "file",
-        "file_core": {
-            "file_name": "21784_6#51_1.fastq.gz",
-            "format": "fastq.gz"
-        },
-        "read_index": "read1",
-        "provenance": {
-            "document_id": "61fd5348-92c5-446b-a57a-746330cebf76",
-            "submission_date": "2019-05-14T10:52:59.245Z",
-            "update_date": "2019-05-14T11:21:17.762Z"
-        }
-    },
-    "supplementary_file_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/file/2.0.0/supplementary_file",
-        "schema_type": "file",
-        "file_core": {
-            "file_name": "TissueDissociationProtocol.pdf",
-            "format": "pdf"
-        },
-        "provenance": {
-            "document_id": "e738a267-87fc-4070-abc7-b3be6442c6d0",
-            "submission_date": "2019-05-14T10:52:33.892Z",
-            "update_date": "2019-05-14T11:01:15.816Z"
-        }
-    },
-    "supplementary_file_1.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/file/2.0.0/supplementary_file",
-        "schema_type": "file",
-        "file_core": {
-            "file_name": "SmartSeq2_RTPCR_protocol.pdf",
-            "format": "pdf"
-        },
-        "provenance": {
-            "document_id": "01a1d04b-05d0-4904-b627-68b0dc02bc17",
-            "submission_date": "2019-05-14T10:52:33.898Z",
-            "update_date": "2019-05-14T11:01:09.564Z"
-        }
-    },
-    "project_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/project/14.0.0/project",
-        "schema_type": "project",
-        "project_core": {
-            "project_short_name": "Mouse Melanoma",
-            "project_title": "Melanoma infiltration of stromal and immune cells",
-            "project_description": "The cancer microenvironment is a complex ecosystem characterized by dynamic interactions between diverse cell types, including malignant, immune and stromal cells. Here, we performed single-cell RNA sequencing on CD45+ and CD45- cells isolated from tumour and lymph nodes during a mouse model of melanoma. The transcriptional profiles of these individual cells taken at different time points coupled with assembled T cell receptor sequences, allowed us to identify distinct immune subpopulations and delineate their developmental trajectory. Our study provides insights into the complex interplay among cells within the tumour microenvironment and presents a valuable resource for future translational applications."
-        },
-        "funders": [
-        ],
-        "provenance": {
-            "document_id": "8c3c290d-dfff-4553-8868-54ce45f4ba7f",
-            "submission_date": "2019-05-14T10:52:33.885Z",
-            "update_date": "2019-05-14T11:20:51.382Z"
-        }
-    },
-    "process_0.json": {
-        "process_core": {
-            "process_id": "proc_21784_6#51"
-        },
-        "schema_type": "process",
-        "describedBy": "https://schema.humancellatlas.org/type/process/9.0.0/process",
-        "provenance": {
-            "document_id": "91f475ec-be51-4f1e-a904-74b10b7259f1",
-            "submission_date": "2019-05-14T11:06:54.971Z",
-            "update_date": "2019-05-14T12:10:53.274Z"
-        }
-    },
-    "process_1.json": {
-        "process_core": {
-            "process_id": "process_id_366"
-        },
-        "schema_type": "process",
-        "describedBy": "https://schema.humancellatlas.org/type/process/9.0.0/process",
-        "provenance": {
-            "document_id": "e521d67d-c134-4dbd-9555-29e23f0463c5",
-            "submission_date": "2019-05-14T11:12:40.680Z",
-            "update_date": "2019-05-14T12:27:20.135Z"
-        }
-    },
-    "process_2.json": {
-        "process_core": {
-            "process_id": "process_id_24"
-        },
-        "schema_type": "process",
-        "describedBy": "https://schema.humancellatlas.org/type/process/9.0.0/process",
-        "provenance": {
-            "document_id": "453a352c-94fb-4d3b-b609-df1e7abf8c09",
-            "submission_date": "2019-05-14T11:12:15.946Z",
-            "update_date": "2019-05-14T12:26:52.545Z"
-        }
-    },
-    "links.json": {
-        "describedBy": "https://schema.humancellatlas.org/system/2.0.0/links",
-        "schema_type": "link_bundle",
-        "schema_version": "2.0.0",
-        "links": [
-            {
-                "link_type": "process_link",
-                "process_id": "91f475ec-be51-4f1e-a904-74b10b7259f1",
-                "process_type": "process",
-                "inputs": [
-                    {
-                        "input_type": "cell_suspension",
-                        "input_id": "01ba6be9-ed4b-4c6b-ae05-2e06aadc2019"
-                    }
-                ],
-                "outputs": [
-                    {
-                        "output_type": "sequence_file",
-                        "output_id": "61fd5348-92c5-446b-a57a-746330cebf76"
-                    }
-                ],
-                "protocols": [
-                ]
-            },
-            {
-                "link_type": "process_link",
-                "process_id": "e521d67d-c134-4dbd-9555-29e23f0463c5",
-                "process_type": "process",
-                "inputs": [
-                    {
-                        "input_type": "specimen_from_organism",
-                        "input_id": "74eb3cb5-918a-49fc-9e15-3ac49fd54caf"
-                    }
-                ],
-                "outputs": [
-                    {
-                        "output_type": "cell_suspension",
-                        "output_id": "01ba6be9-ed4b-4c6b-ae05-2e06aadc2019"
-                    }
-                ],
-                "protocols": [
-                ]
-            },
-            {
-                "link_type": "process_link",
-                "process_id": "453a352c-94fb-4d3b-b609-df1e7abf8c09",
-                "process_type": "process",
-                "inputs": [
-                    {
-                        "input_type": "donor_organism",
-                        "input_id": "63818269-c4d9-429b-85a3-db39c0dd7fa0"
-                    }
-                ],
-                "outputs": [
-                    {
-                        "output_type": "specimen_from_organism",
-                        "output_id": "74eb3cb5-918a-49fc-9e15-3ac49fd54caf"
-                    }
-                ],
-                "protocols": [
-                ]
-            },
-            {
-                "link_type": "supplementary_file_link",
-                "entity": {
-                    "entity_type": "project",
-                    "entity_id": "8c3c290d-dfff-4553-8868-54ce45f4ba7f"
-                },
-                "files": [
-                    {
-                        "file_id": "e738a267-87fc-4070-abc7-b3be6442c6d0",
-                        "file_type": "supplementary_file"
-                    },
-                    {
-                        "file_id": "01a1d04b-05d0-4904-b627-68b0dc02bc17",
-                        "file_type": "supplementary_file"
-                    }
-                ]
-            }
-        ]
-    }
-}
diff --git a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
new file mode 100644
index 000000000..dfb5dc797
--- /dev/null
+++ b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
@@ -0,0 +1,933 @@
+{
+    "manifest": [
+        {
+            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
+            "crc32c": "31fb9874",
+            "indexed": true,
+            "name": "cell_suspension_0.json",
+            "s3_etag": "d35373d17f0b8d6e0adbcf2635e90927",
+            "sha1": "542fb7cc2aa70950b6d0519ec72cb4a4fcfa0595",
+            "sha256": "6d123df0dc62444d9d1e7945c6285483b3e73f38d359bb811f2035c04ddffc5d",
+            "size": 1189,
+            "uuid": "e4c205cd-746f-4665-8c29-149c6e109e9d",
+            "version": "2019-04-17T165831.889000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
+            "crc32c": "13330aa8",
+            "indexed": true,
+            "name": "cell_line_0.json",
+            "s3_etag": "4f6c406d38126638b2efe099e34e5132",
+            "sha1": "6fb2de1be0ccd64fed8dc3bf739d645dcd797b99",
+            "sha256": "afb44a026bc584d5901a9257010c7722599517719e361dd417e0c64aa824cb11",
+            "size": 2169,
+            "uuid": "961092cd-dcff-4b59-a0d2-ceeef0aece74",
+            "version": "2019-04-17T165709.605000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
+            "crc32c": "87a10080",
+            "indexed": true,
+            "name": "specimen_from_organism_0.json",
+            "s3_etag": "d44942d408351ec1a2eec5a908fc3978",
+            "sha1": "55a7dfa2d545c65419127276eb810812edb29883",
+            "sha256": "f0945852b9635aaee40b6b3afd42f91618f7e8345c75834bb078464c5d9bede6",
+            "size": 1210,
+            "uuid": "a72a2ac2-c91b-406a-968c-28c8e15a2eaf",
+            "version": "2019-04-17T165513.039000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
+            "crc32c": "2055f28f",
+            "indexed": true,
+            "name": "donor_organism_0.json",
+            "s3_etag": "cf706b33e8e38dc192bec6b8feb4c64d",
+            "sha1": "91ab9faf48683e414b291c8007a9da3ff05e6e3b",
+            "sha256": "6df293d1672526cd59c8b61e93b4cddf556fe186ec0d92499afebd8663b4dea2",
+            "size": 1085,
+            "uuid": "6c6973d5-9b4a-426d-9d88-825b464500f8",
+            "version": "2019-04-17T165512.518000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/file\"",
+            "crc32c": "bdbe85cf",
+            "indexed": true,
+            "name": "sequence_file_0.json",
+            "s3_etag": "114003372a3fed68b887c22dd5177b44",
+            "sha1": "95e4b3ce1514b715662b02bf097d10e0a886a083",
+            "sha256": "92e5489e8f70036e9a8e146a3bfb380b9f692ac635874668f0f5c3f7bcf7fb88",
+            "size": 443,
+            "uuid": "a31d51c9-7354-4c8c-91e6-a9d2a2e10616",
+            "version": "2019-04-17T172747.623000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/file\"",
+            "crc32c": "62bec389",
+            "indexed": true,
+            "name": "sequence_file_1.json",
+            "s3_etag": "707774c897974c0cfa870bfdc3d598c7",
+            "sha1": "9d53052507f196999b68af4395966266bd497990",
+            "sha256": "ca24c3513ffe9d8c70a0ff0b0fff137d55dfbb262052f3ea5d3a172043a3e31d",
+            "size": 443,
+            "uuid": "a2db643f-decd-426d-94db-13c3279ea80a",
+            "version": "2019-04-17T172746.767000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/project\"",
+            "crc32c": "8602077b",
+            "indexed": true,
+            "name": "project_0.json",
+            "s3_etag": "6aa786f7908881fb0701ed835f751a3d",
+            "sha1": "346aca51dc29e1f5b472cc484930c373c7403c75",
+            "sha256": "11623355930046c0f06c6654b8e366c503843cbcd58de4b29e81ab38a58f4998",
+            "size": 10546,
+            "uuid": "b6dc9b93-929a-45d0-beb2-5cf8e64872fe",
+            "version": "2019-04-17T165512.490000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
+            "crc32c": "46d2028e",
+            "indexed": true,
+            "name": "library_preparation_protocol_0.json",
+            "s3_etag": "8cad7b7082191b96c773ea1583a9dd96",
+            "sha1": "e455fbd5a9ccdab87a0c731f15a232c4a4e27fd8",
+            "sha256": "dfeab0c917b6dcdf69573c4fa45a24e16f1edb7c16bb09c508780363728a2f74",
+            "size": 1472,
+            "uuid": "60085aee-e5a6-40ac-bda1-855c052550b5",
+            "version": "2019-04-17T165216.679000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
+            "crc32c": "f807f58c",
+            "indexed": true,
+            "name": "sequencing_protocol_0.json",
+            "s3_etag": "bc3691263c280e45fc928b49fcf67a05",
+            "sha1": "bff9c6d8a621aa6dd50f34601fe5a3b4b128f7ac",
+            "sha256": "b490ddfb2a22e5c022e5d7e007ca65fc36da6413144e0b2ddea6c80f01839134",
+            "size": 1081,
+            "uuid": "9ccabcf3-7203-4f07-837f-6dde903d4cec",
+            "version": "2019-04-17T165216.627000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
+            "crc32c": "82a95038",
+            "indexed": true,
+            "name": "differentiation_protocol_0.json",
+            "s3_etag": "5e4f3feb3b7ba30579ebcb1b76d0c00f",
+            "sha1": "a0c737ad1c9b1e370a6fd6858da4b7c11da37328",
+            "sha256": "13abe058727b856ab001f64ebd5efcfa383c36c16a454b1508aed03f3026eca2",
+            "size": 1104,
+            "uuid": "348b04e9-d131-4d45-b198-0c75300ee4a3",
+            "version": "2019-04-17T165216.700000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
+            "crc32c": "bb48168a",
+            "indexed": true,
+            "name": "dissociation_protocol_0.json",
+            "s3_etag": "2ae5313e657058a1c3f9c49710f9c98f",
+            "sha1": "da6e31409943f151904e2b5dfff64370227d88d4",
+            "sha256": "3e0a21aee2833f42b26cabe78d6626ee3943aa0b0515114ac78c1a0da79b46ea",
+            "size": 1551,
+            "uuid": "31b89ceb-0625-4f88-9623-85a18bbb84ee",
+            "version": "2019-04-17T165216.668000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
+            "crc32c": "cc1373d7",
+            "indexed": true,
+            "name": "enrichment_protocol_0.json",
+            "s3_etag": "9946569b542b61802a615ee8478e709f",
+            "sha1": "9eee2e73dc4118c34b76d746707fb2fb6bd6d3cf",
+            "sha256": "6c71b70f8800205976c11891d1a36c3d542bd45cd295ea459478ec247259e2b0",
+            "size": 1301,
+            "uuid": "958d38c4-fd0a-4352-9b1d-d95e28e2085e",
+            "version": "2019-04-17T165216.605000Z"
+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/process\"",
+            "crc32c": "1cc89bf5",
+            "indexed": true,
+            "name": "process_0.json",
+            "s3_etag": "b02ca14e2cb05eca02851ac75c375a42",
+            "sha1": "51d86aaa2854a8ac7321e3f11db1f2d185223710",
+            "sha256": "ea90ac5cf595ce7a6ac86543fb7ceaf6303ca7c050b2a25780b46378278d05c0",
+            "size": 374,
+            "uuid": "3d88118e-44df-4c1a-a364-bf92ff2ca0e6",
+            "version": "2019-04-17T170201.452000Z"
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+                    "Close JL",
+                    "Yao Z",
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+                    "Ting JT",
+                    "Wall A",
+                    "Krostag AR",
+                    "Thomsen ER",
+                    "Nelson AM",
+                    "Mich JK",
+                    "Hodge RD",
+                    "Shehata SI",
+                    "Glass IA",
+                    "Bort S",
+                    "Shapovalova NV",
+                    "Ngo NK",
+                    "Grimley JS",
+                    "Phillips JW",
+                    "Thompson CL",
+                    "Ramanathan S",
+                    "Lein E"
+                ],
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+                "doi": "10.1016/j.neuron.2017.02.014",
+                "pmid": 28279351,
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+                "project_short_name": "Single cell RNAseq characterization of cell types produced over time in an in vitro model of human inhibitory interneuron differentiation.",
+                "project_title": "Single-cell RNA-seq analysis  throughout a 125-day differentiation protocol that converted H1 human embryonic stem cells to a variety of ventrally-derived cell types.",
+                "project_description": "Diverse cell types are produced from dorsal and ventral regions of the developing neural tube. In this study we describe a system for generating human inhibitory interneurons by ventralizing human embryonic stem cells in vitro and characterizing the gene expression of the cell types produced over time. We engineered a DCX-Citrine/Y hESC line to sort and characterize progenitor and neuron transcriptomics separately at both the subpopulation and single cell level. The cells generated in vitro were compared to similar populations present in human fetal brain samples by mapping gene expression data from human fetal cells onto the principal component analysis (PCA) space of in vitro-derived populations. Weighted gene co-expression network analysis (WGCNA) was used to determine the discreet cell types present at D24, D54, D100 and D125 of culture, and describe the gene expression changes that occur in progenitor and neuron populations over time. Immature lateral ganglionic eminence and medial ganglionic eminence cells are present at early timepoints, along with MGE-like and dorsal pallium-like neuronal progenitors. At later timepoints we observe the emergence of SST-expressing interneurons, as well as oligodendrocyte and astrocyte progenitors. We also identified genes that were upregulated in somatostatin-expressing interneurons as they mature. The transcriptomes of 1732 ventralized single cells were profiled by SmartSeq2 at different timepoints throughout a 125-day differentiation protocol that converted H1 human embryonic stem cells to a variety of ventrally-derived cell types."
+            },
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+                "SRP096727"
+            ],
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+                "GSE93593"
+            ],
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+                "PRJNA361254"
+            ],
+            "supplementary_links": [
+                "https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-93593/Results"
+            ],
+            "array_express_accessions": [
+                "E-GEOD-93593"
+            ],
+            "contributors": [
+                {
+                    "contact_name": "Jennie,,Close",
+                    "email": "jenniec@alleninstitute.org",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Zizhen,,Yao",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Boaz,,Levi",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Jeremy,,Miller",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Trygve,,Bakken",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Vilas,,Menon",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Jonathan,,Ting",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Abigail,,Wall",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Anne-Rachel,,Krogstag",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Elliot,,Thomsen",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Angel,,Nelson",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "John,,Mich",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Rebecca,,Hodge",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Soraya,,Shehata",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Ian,,Glass",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Susan,,Bort",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Nadiya,,Shapovalova",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Olivia,,Fong",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Kiet,,Ngo",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Joshua,,Grimley",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "John,,Phillips",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Carol,,Thompson",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Sharad,,Ramanathan",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Ed,,Lein",
+                    "institution": "The Allen Institute for Brain Science",
+                    "address": "615 Westlake Ave N, Seattle, WA",
+                    "country": "USA"
+                },
+                {
+                    "contact_name": "Laura,,Huerta",
+                    "email": "lauhuema@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "Molecular Atlas",
+                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
+                    "country": "UK",
+                    "project_role": "external curator",
+                    "orcid_id": "0000-0002-8748-599X",
+                    "corresponding_contributor": false
+                },
+                {
+                    "contact_name": "Matthew,,Green",
+                    "email": "hewgreen@ebi.ac.uk",
+                    "phone": "(+44) 122-349-4444",
+                    "institution": "EMBL-EBI European Bioinformatics Institute",
+                    "laboratory": "Human Cell Atlas Data Coordination Platform",
+                    "address": "Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD",
+                    "country": "UK",
+                    "project_role": "Human Cell Atlas wrangler",
+                    "orcid_id": "0000-0003-2771-9894",
+                    "corresponding_contributor": false
+                }
+            ],
+            "funders": [
+                {
+                    "grant_title": "Directors Pioneer Award",
+                    "grant_id": "5DP1MH099906-03",
+                    "organization": "National Institute of Health"
+                },
+                {
+                    "grant_title": "National Science Foundation grant",
+                    "grant_id": "PHY-0952766",
+                    "organization": "National Science Foundation"
+                }
+            ],
+            "publications": [
+                {
+                    "authors": [
+                        "Close JL",
+                        "Yao Z",
+                        "Levi BP",
+                        "Miller JA",
+                        "Bakken TE",
+                        "Menon V",
+                        "Ting JT",
+                        "Wall A",
+                        "Krostag AR",
+                        "Thomsen ER",
+                        "Nelson AM",
+                        "Mich JK",
+                        "Hodge RD",
+                        "Shehata SI",
+                        "Glass IA",
+                        "Bort S",
+                        "Shapovalova NV",
+                        "Ngo NK",
+                        "Grimley JS",
+                        "Phillips JW",
+                        "Thompson CL",
+                        "Ramanathan S",
+                        "Lein E"
+                    ],
+                    "publication_title": "Single-Cell Profiling of an In\u00a0Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation.",
+                    "doi": "10.1016/j.neuron.2017.02.014",
+                    "pmid": 28279351,
+                    "publication_url": "https://europepmc.org/abstract/MED/28279351"
+                }
+            ],
+            "provenance": {
+                "document_id": "b6dc9b93-929a-45d0-beb2-5cf8e64872fe",
+                "submission_date": "2019-04-17T16:51:35.026Z",
+                "update_date": "2019-04-17T16:55:12.490Z"
+            }
+        },
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+            "protocol_core": {
+                "protocol_id": "P-GSE93593-3",
+                "protocol_name": "single cell library construction protocol",
+                "protocol_description": "Cells were prepared for single-cell transcriptomics using SmartSeq2 (Picelli et al., 2014). After reverse transcription and template switching, we amplified cDNA with KAPA HotStart HIFI 2\u00d7 ReadyMix (Kapa Biosystems) for 22 cycles for RNA from single primary cortical cells. We purified PCR products using Ampure XP beads (Beckman Coulter). We quantified cDNA using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 or with the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher) on an Enspire plate reader (PerkinElmer)."
+            },
+            "nucleic_acid_source": "single cell",
+            "input_nucleic_acid_molecule": {
+                "text": "polyA RNA",
+                "ontology": "OBI:0000869",
+                "ontology_label": "polyA RNA"
+            },
+            "library_construction_method": {
+                "text": "Smart-seq2",
+                "ontology": "EFO:0008931",
+                "ontology_label": "Smart-seq2"
+            },
+            "end_bias": "full length",
+            "primer": "poly-dT",
+            "strand": "unstranded",
+            "provenance": {
+                "document_id": "60085aee-e5a6-40ac-bda1-855c052550b5",
+                "submission_date": "2019-04-17T16:52:10.952Z",
+                "update_date": "2019-04-17T16:52:16.679Z"
+            }
+        },
+        "sequencing_protocol_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.0.0/sequencing_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "P-GSE93593-4",
+                "protocol_name": "single cell sequencing protocol",
+                "protocol_description": "We used 1 ng of cDNA to generate RNA-Seq libraries using the Nextera XT library prep system (Illumina). We carried out sequencing of human cortical cells the on Illumina HiSeq using 50 base paired-end reads"
+            },
+            "instrument_manufacturer_model": {
+                "text": "Illumina HiSeq 2500",
+                "ontology": "EFO:0008565",
+                "ontology_label": "Illumina HiSeq 2500"
+            },
+            "paired_end": true,
+            "method": {
+                "text": "full length single cell RNA sequencing",
+                "ontology": "EFO:0008441",
+                "ontology_label": "full length single cell RNA sequencing"
+            },
+            "provenance": {
+                "document_id": "9ccabcf3-7203-4f07-837f-6dde903d4cec",
+                "submission_date": "2019-04-17T16:52:11.186Z",
+                "update_date": "2019-04-17T16:52:16.627Z"
+            }
+        },
+        "differentiation_protocol_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/1.3.3/differentiation_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "P-GSE93593-1",
+                "protocol_name": "growth protocol",
+                "protocol_description": "We constructed an hESC line with Citrine (Cit) fused to the endogenous copy of the DCX gene in the H1 parent line (WAe001-A RRID:CVCL_9771) to allow us to profile neurons (Cit+) and progenitors (Cit\u2212) (Yao et al., 2017). hESCs were seeded for a 10-day cortical induction phase in NIMX media with SMAD inhibitors; reseeded for the ventralization phase at D10 in culture media containing Shh and purmorphamine, and finally at D24 for neural differentiation with neurogenic/neurotrophic factors BDNF, GDNF, NT3, and cAMP. The protocol was ended at D125."
+            },
+            "differentiation_method": "cell suspension",
+            "provenance": {
+                "document_id": "348b04e9-d131-4d45-b198-0c75300ee4a3",
+                "submission_date": "2019-04-17T16:52:10.815Z",
+                "update_date": "2019-04-17T16:52:16.700Z"
+            }
+        },
+        "dissociation_protocol_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.0.0/dissociation_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "P-GSE93593-2",
+                "protocol_name": "single cell isolation protocol",
+                "protocol_description": "To generate single cell suspensions, hESC-derived cultures were dissociated from plates using Accutase (ThermoFisher) at 37C. Light trituration using a P1000 pipette was done every 5 min until nearly all clumps had been dissociated (up to 1 h). Cell suspension was washed and filtered through a 40 um cell strainer. Cells were washed in PBS with 1% FBS and stained with 0.5-1 ug/mL DAPI. Single-cell suspensions were loaded onto a FACSAria II SORP (Becton Dickinson) and sorted directly into PCR strip tubes or plates held in chilled aluminium blocks. Doublets and dead cells were excluded based on forward scatter, side scatter and DAPI fluorescence. Sorting was done using the 130 um nozzle with the sort mode set to single cell. Accuracy of single-cell sorts was confirmed by sorting DAPI-stained fixed cells onto a dry well of a 96-well plate and analyzing by fluorescence microscopy."
+            },
+            "method": {
+                "text": "enzymatic dissociation",
+                "ontology": "EFO:0009128",
+                "ontology_label": "enzymatic dissociation"
+            },
+            "provenance": {
+                "document_id": "31b89ceb-0625-4f88-9623-85a18bbb84ee",
+                "submission_date": "2019-04-17T16:52:10.865Z",
+                "update_date": "2019-04-17T16:52:16.668Z"
+            }
+        },
+        "enrichment_protocol_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/2.2.9/enrichment_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "FACS_enrichment_protocol",
+                "protocol_name": "FACS enrichment for single, live cells.",
+                "protocol_description": "Single-cell suspensions were loaded onto  a  FACSAria  II  SORP  (Becton  Dickinson)  and  sorted  directly  into  PCR  strip  tubes  or  plates  held  in  chilled aluminum  blocks.    Doublets  and  dead  cells  were  excluded  based  on  forward  scatter,  side  scatter  and  DAPI fluorescence. Sorting was done using the 130  \u03bcm nozzle with the sort mode set to single cell. Accuracy of single-cell  sorts  was  confirmed  by  sorting  DAPI-stained  fixed  cells  onto  a  dry  well  of  a  96-well  plate  and  analyzing  by fluorescence microscopy."
+            },
+            "enrichment_method": {
+                "text": "fluorescence-activated cell sorting",
+                "ontology": "EFO:0009108",
+                "ontology_label": "fluorescence-activated cell sorting"
+            },
+            "markers": "DAPI",
+            "provenance": {
+                "document_id": "958d38c4-fd0a-4352-9b1d-d95e28e2085e",
+                "submission_date": "2019-04-17T16:52:10.900Z",
+                "update_date": "2019-04-17T16:52:16.605Z"
+            }
+        },
+        "process_0.json": {
+            "process_core": {
+                "process_id": "D54Dn15E01"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/7.0.0/process",
+            "provenance": {
+                "document_id": "3d88118e-44df-4c1a-a364-bf92ff2ca0e6",
+                "submission_date": "2019-04-17T16:54:54.638Z",
+                "update_date": "2019-04-17T17:02:01.452Z"
+            }
+        },
+        "process_1.json": {
+            "process_core": {
+                "process_id": "process_id_601"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/7.0.0/process",
+            "provenance": {
+                "document_id": "2fbc1012-55ae-4fde-9069-fbf5376ca535",
+                "submission_date": "2019-04-17T16:53:46.016Z",
+                "update_date": "2019-04-17T17:00:21.013Z"
+            }
+        },
+        "process_2.json": {
+            "process_core": {
+                "process_id": "process_id_4"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/7.0.0/process",
+            "provenance": {
+                "document_id": "466050f5-213c-4554-939e-4bb8298130dd",
+                "submission_date": "2019-04-17T16:53:30.594Z",
+                "update_date": "2019-04-17T16:59:59.704Z"
+            }
+        },
+        "process_3.json": {
+            "process_core": {
+                "process_id": "process_id_1"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/7.0.0/process",
+            "provenance": {
+                "document_id": "4276c1dd-50aa-4ffa-a618-dee757bff479",
+                "submission_date": "2019-04-17T16:53:30.570Z",
+                "update_date": "2019-04-17T16:59:59.680Z"
+            }
+        },
+        "links.json": {
+            "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
+            "schema_type": "link_bundle",
+            "schema_version": "1.1.5",
+            "links": [
+                {
+                    "process": "3d88118e-44df-4c1a-a364-bf92ff2ca0e6",
+                    "inputs": [
+                        "e4c205cd-746f-4665-8c29-149c6e109e9d"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "a31d51c9-7354-4c8c-91e6-a9d2a2e10616",
+                        "a2db643f-decd-426d-94db-13c3279ea80a"
+                    ],
+                    "output_type": "file",
+                    "protocols": [
+                        {
+                            "protocol_type": "library_preparation_protocol",
+                            "protocol_id": "60085aee-e5a6-40ac-bda1-855c052550b5"
+                        },
+                        {
+                            "protocol_type": "sequencing_protocol",
+                            "protocol_id": "9ccabcf3-7203-4f07-837f-6dde903d4cec"
+                        }
+                    ]
+                },
+                {
+                    "process": "2fbc1012-55ae-4fde-9069-fbf5376ca535",
+                    "inputs": [
+                        "961092cd-dcff-4b59-a0d2-ceeef0aece74"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "e4c205cd-746f-4665-8c29-149c6e109e9d"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "differentiation_protocol",
+                            "protocol_id": "348b04e9-d131-4d45-b198-0c75300ee4a3"
+                        },
+                        {
+                            "protocol_type": "dissociation_protocol",
+                            "protocol_id": "31b89ceb-0625-4f88-9623-85a18bbb84ee"
+                        },
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "958d38c4-fd0a-4352-9b1d-d95e28e2085e"
+                        }
+                    ]
+                },
+                {
+                    "process": "466050f5-213c-4554-939e-4bb8298130dd",
+                    "inputs": [
+                        "a72a2ac2-c91b-406a-968c-28c8e15a2eaf"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "961092cd-dcff-4b59-a0d2-ceeef0aece74"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": []
+                },
+                {
+                    "process": "4276c1dd-50aa-4ffa-a618-dee757bff479",
+                    "inputs": [
+                        "6c6973d5-9b4a-426d-9d88-825b464500f8"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "a72a2ac2-c91b-406a-968c-28c8e15a2eaf"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": []
+                }
+            ]
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe/2019-04-17T175706.867000Z/manifest.json b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe/2019-04-17T175706.867000Z/manifest.json
deleted file mode 100644
index 7406d4ba5..000000000
--- a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe/2019-04-17T175706.867000Z/manifest.json
+++ /dev/null
@@ -1,230 +0,0 @@
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-        "content-type": "application/json; dcp-type=\"metadata/file\"",
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\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe/2019-04-17T175706.867000Z/metadata.json b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe/2019-04-17T175706.867000Z/metadata.json
deleted file mode 100644
index 77de5eeec..000000000
--- a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe/2019-04-17T175706.867000Z/metadata.json
+++ /dev/null
@@ -1,701 +0,0 @@
-{
-    "cell_suspension_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/11.0.0/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "D54Dn15E01",
-            "biomaterial_name": "hESC-derived inhibitory interneurons",
-            "biomaterial_description": "hESC-derived inhibitory interneurons at day 54",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "genotype": "DCX-Citrine"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "selected_cell_type": [
-            {
-                "text": "inhibitory interneurons",
-                "ontology": "CL:0000498",
-                "ontology_label": "inhibitory interneuron"
-            }
-        ],
-        "timecourse": {
-            "value": "54",
-            "unit": {
-                "text": "day",
-                "ontology_label": "day",
-                "ontology": "UO:0000627"
-            }
-        },
-        "provenance": {
-            "document_id": "e4c205cd-746f-4665-8c29-149c6e109e9d",
-            "submission_date": "2019-04-17T16:51:39.733Z",
-            "update_date": "2019-04-17T16:58:31.889Z"
-        }
-    },
-    "cell_line_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/11.0.0/cell_line",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "cell_line_at_day_54",
-            "biomaterial_name": "cell_line_at_day_54",
-            "biomaterial_description": "hESC-derived inhibitory interneurons at day 54",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "genotype": "DCX-Citrine"
-        },
-        "cell_line_type": "stem cell-derived",
-        "cell_type": {
-            "text": "interneuron",
-            "ontology": "CL:0000099",
-            "ontology_label": "interneuron"
-        },
-        "disease": {
-            "text": "normal",
-            "ontology": "PATO:0000461",
-            "ontology_label": "normal"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "publication": {
-            "authors": [
-                "Close JL",
-                "Yao Z",
-                "Levi BP",
-                "Miller JA",
-                "Bakken TE",
-                "Menon V",
-                "Ting JT",
-                "Wall A",
-                "Krostag AR",
-                "Thomsen ER",
-                "Nelson AM",
-                "Mich JK",
-                "Hodge RD",
-                "Shehata SI",
-                "Glass IA",
-                "Bort S",
-                "Shapovalova NV",
-                "Ngo NK",
-                "Grimley JS",
-                "Phillips JW",
-                "Thompson CL",
-                "Ramanathan S",
-                "Lein E"
-            ],
-            "publication_title": "Single-Cell Profiling of an In\u00a0Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation.",
-            "doi": "10.1016/j.neuron.2017.02.014",
-            "pmid": 28279351,
-            "publication_url": "https://europepmc.org/abstract/MED/28279351"
-        },
-        "model_organ": {
-            "text": "brain",
-            "ontology": "UBERON_0000955",
-            "ontology_label": "brain"
-        },
-        "provenance": {
-            "document_id": "961092cd-dcff-4b59-a0d2-ceeef0aece74",
-            "submission_date": "2019-04-17T16:51:35.053Z",
-            "update_date": "2019-04-17T16:57:09.605Z"
-        }
-    },
-    "specimen_from_organism_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/9.0.0/specimen_from_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "embryo_WAe001-A",
-            "biomaterial_name": "human embryo",
-            "biomaterial_description": "human embryo",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "genotype": "DCX-Citrine"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "organ": {
-            "text": "embryo",
-            "ontology": "UBERON:0000922",
-            "ontology_label": "embryo"
-        },
-        "organ_parts": [
-            {
-                "text": "blastocyst",
-                "ontology": "UBERON:0000358",
-                "ontology_label": "blastocyst"
-            }
-        ],
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461",
-                "ontology_label": "normal"
-            }
-        ],
-        "provenance": {
-            "document_id": "a72a2ac2-c91b-406a-968c-28c8e15a2eaf",
-            "submission_date": "2019-04-17T16:51:35.037Z",
-            "update_date": "2019-04-17T16:55:13.039Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/14.0.7/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "donor_WAe001-A",
-            "biomaterial_name": "human embryo",
-            "biomaterial_description": "human embryo",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "development_stage": {
-            "text": "human embryonic stage",
-            "ontology": "HsapDv:0000002",
-            "ontology_label": "human embryonic stage"
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461",
-                "ontology_label": "normal"
-            }
-        ],
-        "is_living": "yes",
-        "sex": "male",
-        "provenance": {
-            "document_id": "6c6973d5-9b4a-426d-9d88-825b464500f8",
-            "submission_date": "2019-04-17T16:51:35.032Z",
-            "update_date": "2019-04-17T16:55:12.518Z"
-        }
-    },
-    "sequence_file_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/file/8.0.0/sequence_file",
-        "schema_type": "file",
-        "file_core": {
-            "file_name": "SRR5174359_2.fastq.gz",
-            "file_format": "fastq.gz"
-        },
-        "read_index": "read2",
-        "provenance": {
-            "document_id": "a31d51c9-7354-4c8c-91e6-a9d2a2e10616",
-            "submission_date": "2019-04-17T16:53:04.375Z",
-            "update_date": "2019-04-17T17:27:47.623Z"
-        }
-    },
-    "sequence_file_1.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/file/8.0.0/sequence_file",
-        "schema_type": "file",
-        "file_core": {
-            "file_name": "SRR5174359_1.fastq.gz",
-            "file_format": "fastq.gz"
-        },
-        "read_index": "read1",
-        "provenance": {
-            "document_id": "a2db643f-decd-426d-94db-13c3279ea80a",
-            "submission_date": "2019-04-17T16:53:04.385Z",
-            "update_date": "2019-04-17T17:27:46.767Z"
-        }
-    },
-    "project_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/project/11.1.0/project",
-        "schema_type": "project",
-        "project_core": {
-            "project_short_name": "Single cell RNAseq characterization of cell types produced over time in an in vitro model of human inhibitory interneuron differentiation.",
-            "project_title": "Single-cell RNA-seq analysis  throughout a 125-day differentiation protocol that converted H1 human embryonic stem cells to a variety of ventrally-derived cell types.",
-            "project_description": "Diverse cell types are produced from dorsal and ventral regions of the developing neural tube. In this study we describe a system for generating human inhibitory interneurons by ventralizing human embryonic stem cells in vitro and characterizing the gene expression of the cell types produced over time. We engineered a DCX-Citrine/Y hESC line to sort and characterize progenitor and neuron transcriptomics separately at both the subpopulation and single cell level. The cells generated in vitro were compared to similar populations present in human fetal brain samples by mapping gene expression data from human fetal cells onto the principal component analysis (PCA) space of in vitro-derived populations. Weighted gene co-expression network analysis (WGCNA) was used to determine the discreet cell types present at D24, D54, D100 and D125 of culture, and describe the gene expression changes that occur in progenitor and neuron populations over time. Immature lateral ganglionic eminence and medial ganglionic eminence cells are present at early timepoints, along with MGE-like and dorsal pallium-like neuronal progenitors. At later timepoints we observe the emergence of SST-expressing interneurons, as well as oligodendrocyte and astrocyte progenitors. We also identified genes that were upregulated in somatostatin-expressing interneurons as they mature. The transcriptomes of 1732 ventralized single cells were profiled by SmartSeq2 at different timepoints throughout a 125-day differentiation protocol that converted H1 human embryonic stem cells to a variety of ventrally-derived cell types."
-        },
-        "insdc_project_accessions": [
-            "SRP096727"
-        ],
-        "geo_series_accessions": [
-            "GSE93593"
-        ],
-        "insdc_study_accessions": [
-            "PRJNA361254"
-        ],
-        "supplementary_links": [
-            "https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-93593/Results"
-        ],
-        "array_express_accessions": [
-            "E-GEOD-93593"
-        ],
-        "contributors": [
-            {
-                "contact_name": "Jennie,,Close",
-                "email": "jenniec@alleninstitute.org",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Zizhen,,Yao",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Boaz,,Levi",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Jeremy,,Miller",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Trygve,,Bakken",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Vilas,,Menon",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Jonathan,,Ting",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Abigail,,Wall",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Anne-Rachel,,Krogstag",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Elliot,,Thomsen",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Angel,,Nelson",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "John,,Mich",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Rebecca,,Hodge",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Soraya,,Shehata",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Ian,,Glass",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Susan,,Bort",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Nadiya,,Shapovalova",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Olivia,,Fong",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Kiet,,Ngo",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Joshua,,Grimley",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "John,,Phillips",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Carol,,Thompson",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Sharad,,Ramanathan",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Ed,,Lein",
-                "institution": "The Allen Institute for Brain Science",
-                "address": "615 Westlake Ave N, Seattle, WA",
-                "country": "USA"
-            },
-            {
-                "contact_name": "Laura,,Huerta",
-                "email": "lauhuema@ebi.ac.uk",
-                "institution": "EMBL-EBI",
-                "laboratory": "Molecular Atlas",
-                "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                "country": "UK",
-                "project_role": "external curator",
-                "orcid_id": "0000-0002-8748-599X",
-                "corresponding_contributor": false
-            },
-            {
-                "contact_name": "Matthew,,Green",
-                "email": "hewgreen@ebi.ac.uk",
-                "phone": "(+44) 122-349-4444",
-                "institution": "EMBL-EBI European Bioinformatics Institute",
-                "laboratory": "Human Cell Atlas Data Coordination Platform",
-                "address": "Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD",
-                "country": "UK",
-                "project_role": "Human Cell Atlas wrangler",
-                "orcid_id": "0000-0003-2771-9894",
-                "corresponding_contributor": false
-            }
-        ],
-        "funders": [
-            {
-                "grant_title": "Directors Pioneer Award",
-                "grant_id": "5DP1MH099906-03",
-                "organization": "National Institute of Health"
-            },
-            {
-                "grant_title": "National Science Foundation grant",
-                "grant_id": "PHY-0952766",
-                "organization": "National Science Foundation"
-            }
-        ],
-        "publications": [
-            {
-                "authors": [
-                    "Close JL",
-                    "Yao Z",
-                    "Levi BP",
-                    "Miller JA",
-                    "Bakken TE",
-                    "Menon V",
-                    "Ting JT",
-                    "Wall A",
-                    "Krostag AR",
-                    "Thomsen ER",
-                    "Nelson AM",
-                    "Mich JK",
-                    "Hodge RD",
-                    "Shehata SI",
-                    "Glass IA",
-                    "Bort S",
-                    "Shapovalova NV",
-                    "Ngo NK",
-                    "Grimley JS",
-                    "Phillips JW",
-                    "Thompson CL",
-                    "Ramanathan S",
-                    "Lein E"
-                ],
-                "publication_title": "Single-Cell Profiling of an In\u00a0Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation.",
-                "doi": "10.1016/j.neuron.2017.02.014",
-                "pmid": 28279351,
-                "publication_url": "https://europepmc.org/abstract/MED/28279351"
-            }
-        ],
-        "provenance": {
-            "document_id": "b6dc9b93-929a-45d0-beb2-5cf8e64872fe",
-            "submission_date": "2019-04-17T16:51:35.026Z",
-            "update_date": "2019-04-17T16:55:12.490Z"
-        }
-    },
-    "library_preparation_protocol_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.0.0/library_preparation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "P-GSE93593-3",
-            "protocol_name": "single cell library construction protocol",
-            "protocol_description": "Cells were prepared for single-cell transcriptomics using SmartSeq2 (Picelli et al., 2014). After reverse transcription and template switching, we amplified cDNA with KAPA HotStart HIFI 2\u00d7 ReadyMix (Kapa Biosystems) for 22 cycles for RNA from single primary cortical cells. We purified PCR products using Ampure XP beads (Beckman Coulter). We quantified cDNA using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 or with the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher) on an Enspire plate reader (PerkinElmer)."
-        },
-        "nucleic_acid_source": "single cell",
-        "input_nucleic_acid_molecule": {
-            "text": "polyA RNA",
-            "ontology": "OBI:0000869",
-            "ontology_label": "polyA RNA"
-        },
-        "library_construction_method": {
-            "text": "Smart-seq2",
-            "ontology": "EFO:0008931",
-            "ontology_label": "Smart-seq2"
-        },
-        "end_bias": "full length",
-        "primer": "poly-dT",
-        "strand": "unstranded",
-        "provenance": {
-            "document_id": "60085aee-e5a6-40ac-bda1-855c052550b5",
-            "submission_date": "2019-04-17T16:52:10.952Z",
-            "update_date": "2019-04-17T16:52:16.679Z"
-        }
-    },
-    "sequencing_protocol_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.0.0/sequencing_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "P-GSE93593-4",
-            "protocol_name": "single cell sequencing protocol",
-            "protocol_description": "We used 1 ng of cDNA to generate RNA-Seq libraries using the Nextera XT library prep system (Illumina). We carried out sequencing of human cortical cells the on Illumina HiSeq using 50 base paired-end reads"
-        },
-        "instrument_manufacturer_model": {
-            "text": "Illumina HiSeq 2500",
-            "ontology": "EFO:0008565",
-            "ontology_label": "Illumina HiSeq 2500"
-        },
-        "paired_end": true,
-        "method": {
-            "text": "full length single cell RNA sequencing",
-            "ontology": "EFO:0008441",
-            "ontology_label": "full length single cell RNA sequencing"
-        },
-        "provenance": {
-            "document_id": "9ccabcf3-7203-4f07-837f-6dde903d4cec",
-            "submission_date": "2019-04-17T16:52:11.186Z",
-            "update_date": "2019-04-17T16:52:16.627Z"
-        }
-    },
-    "differentiation_protocol_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/1.3.3/differentiation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "P-GSE93593-1",
-            "protocol_name": "growth protocol",
-            "protocol_description": "We constructed an hESC line with Citrine (Cit) fused to the endogenous copy of the DCX gene in the H1 parent line (WAe001-A RRID:CVCL_9771) to allow us to profile neurons (Cit+) and progenitors (Cit\u2212) (Yao et al., 2017). hESCs were seeded for a 10-day cortical induction phase in NIMX media with SMAD inhibitors; reseeded for the ventralization phase at D10 in culture media containing Shh and purmorphamine, and finally at D24 for neural differentiation with neurogenic/neurotrophic factors BDNF, GDNF, NT3, and cAMP. The protocol was ended at D125."
-        },
-        "differentiation_method": "cell suspension",
-        "provenance": {
-            "document_id": "348b04e9-d131-4d45-b198-0c75300ee4a3",
-            "submission_date": "2019-04-17T16:52:10.815Z",
-            "update_date": "2019-04-17T16:52:16.700Z"
-        }
-    },
-    "dissociation_protocol_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.0.0/dissociation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "P-GSE93593-2",
-            "protocol_name": "single cell isolation protocol",
-            "protocol_description": "To generate single cell suspensions, hESC-derived cultures were dissociated from plates using Accutase (ThermoFisher) at 37C. Light trituration using a P1000 pipette was done every 5 min until nearly all clumps had been dissociated (up to 1 h). Cell suspension was washed and filtered through a 40 um cell strainer. Cells were washed in PBS with 1% FBS and stained with 0.5-1 ug/mL DAPI. Single-cell suspensions were loaded onto a FACSAria II SORP (Becton Dickinson) and sorted directly into PCR strip tubes or plates held in chilled aluminium blocks. Doublets and dead cells were excluded based on forward scatter, side scatter and DAPI fluorescence. Sorting was done using the 130 um nozzle with the sort mode set to single cell. Accuracy of single-cell sorts was confirmed by sorting DAPI-stained fixed cells onto a dry well of a 96-well plate and analyzing by fluorescence microscopy."
-        },
-        "method": {
-            "text": "enzymatic dissociation",
-            "ontology": "EFO:0009128",
-            "ontology_label": "enzymatic dissociation"
-        },
-        "provenance": {
-            "document_id": "31b89ceb-0625-4f88-9623-85a18bbb84ee",
-            "submission_date": "2019-04-17T16:52:10.865Z",
-            "update_date": "2019-04-17T16:52:16.668Z"
-        }
-    },
-    "enrichment_protocol_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/2.2.9/enrichment_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "FACS_enrichment_protocol",
-            "protocol_name": "FACS enrichment for single, live cells.",
-            "protocol_description": "Single-cell suspensions were loaded onto  a  FACSAria  II  SORP  (Becton  Dickinson)  and  sorted  directly  into  PCR  strip  tubes  or  plates  held  in  chilled aluminum  blocks.    Doublets  and  dead  cells  were  excluded  based  on  forward  scatter,  side  scatter  and  DAPI fluorescence. Sorting was done using the 130  \u03bcm nozzle with the sort mode set to single cell. Accuracy of single-cell  sorts  was  confirmed  by  sorting  DAPI-stained  fixed  cells  onto  a  dry  well  of  a  96-well  plate  and  analyzing  by fluorescence microscopy."
-        },
-        "enrichment_method": {
-            "text": "fluorescence-activated cell sorting",
-            "ontology": "EFO:0009108",
-            "ontology_label": "fluorescence-activated cell sorting"
-        },
-        "markers": "DAPI",
-        "provenance": {
-            "document_id": "958d38c4-fd0a-4352-9b1d-d95e28e2085e",
-            "submission_date": "2019-04-17T16:52:10.900Z",
-            "update_date": "2019-04-17T16:52:16.605Z"
-        }
-    },
-    "process_0.json": {
-        "process_core": {
-            "process_id": "D54Dn15E01"
-        },
-        "schema_type": "process",
-        "describedBy": "https://schema.humancellatlas.org/type/process/7.0.0/process",
-        "provenance": {
-            "document_id": "3d88118e-44df-4c1a-a364-bf92ff2ca0e6",
-            "submission_date": "2019-04-17T16:54:54.638Z",
-            "update_date": "2019-04-17T17:02:01.452Z"
-        }
-    },
-    "process_1.json": {
-        "process_core": {
-            "process_id": "process_id_601"
-        },
-        "schema_type": "process",
-        "describedBy": "https://schema.humancellatlas.org/type/process/7.0.0/process",
-        "provenance": {
-            "document_id": "2fbc1012-55ae-4fde-9069-fbf5376ca535",
-            "submission_date": "2019-04-17T16:53:46.016Z",
-            "update_date": "2019-04-17T17:00:21.013Z"
-        }
-    },
-    "process_2.json": {
-        "process_core": {
-            "process_id": "process_id_4"
-        },
-        "schema_type": "process",
-        "describedBy": "https://schema.humancellatlas.org/type/process/7.0.0/process",
-        "provenance": {
-            "document_id": "466050f5-213c-4554-939e-4bb8298130dd",
-            "submission_date": "2019-04-17T16:53:30.594Z",
-            "update_date": "2019-04-17T16:59:59.704Z"
-        }
-    },
-    "process_3.json": {
-        "process_core": {
-            "process_id": "process_id_1"
-        },
-        "schema_type": "process",
-        "describedBy": "https://schema.humancellatlas.org/type/process/7.0.0/process",
-        "provenance": {
-            "document_id": "4276c1dd-50aa-4ffa-a618-dee757bff479",
-            "submission_date": "2019-04-17T16:53:30.570Z",
-            "update_date": "2019-04-17T16:59:59.680Z"
-        }
-    },
-    "links.json": {
-        "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
-        "schema_type": "link_bundle",
-        "schema_version": "1.1.5",
-        "links": [
-            {
-                "process": "3d88118e-44df-4c1a-a364-bf92ff2ca0e6",
-                "inputs": [
-                    "e4c205cd-746f-4665-8c29-149c6e109e9d"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "a31d51c9-7354-4c8c-91e6-a9d2a2e10616",
-                    "a2db643f-decd-426d-94db-13c3279ea80a"
-                ],
-                "output_type": "file",
-                "protocols": [
-                    {
-                        "protocol_type": "library_preparation_protocol",
-                        "protocol_id": "60085aee-e5a6-40ac-bda1-855c052550b5"
-                    },
-                    {
-                        "protocol_type": "sequencing_protocol",
-                        "protocol_id": "9ccabcf3-7203-4f07-837f-6dde903d4cec"
-                    }
-                ]
-            },
-            {
-                "process": "2fbc1012-55ae-4fde-9069-fbf5376ca535",
-                "inputs": [
-                    "961092cd-dcff-4b59-a0d2-ceeef0aece74"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "e4c205cd-746f-4665-8c29-149c6e109e9d"
-                ],
-                "output_type": "biomaterial",
-                "protocols": [
-                    {
-                        "protocol_type": "differentiation_protocol",
-                        "protocol_id": "348b04e9-d131-4d45-b198-0c75300ee4a3"
-                    },
-                    {
-                        "protocol_type": "dissociation_protocol",
-                        "protocol_id": "31b89ceb-0625-4f88-9623-85a18bbb84ee"
-                    },
-                    {
-                        "protocol_type": "enrichment_protocol",
-                        "protocol_id": "958d38c4-fd0a-4352-9b1d-d95e28e2085e"
-                    }
-                ]
-            },
-            {
-                "process": "466050f5-213c-4554-939e-4bb8298130dd",
-                "inputs": [
-                    "a72a2ac2-c91b-406a-968c-28c8e15a2eaf"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "961092cd-dcff-4b59-a0d2-ceeef0aece74"
-                ],
-                "output_type": "biomaterial",
-                "protocols": []
-            },
-            {
-                "process": "4276c1dd-50aa-4ffa-a618-dee757bff479",
-                "inputs": [
-                    "6c6973d5-9b4a-426d-9d88-825b464500f8"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "a72a2ac2-c91b-406a-968c-28c8e15a2eaf"
-                ],
-                "output_type": "biomaterial",
-                "protocols": []
-            }
-        ]
-    }
-}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
new file mode 100644
index 000000000..b1eeeff62
--- /dev/null
+++ b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
@@ -0,0 +1,2704 @@
+{
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+        {
+            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
+            "crc32c": "395b270f",
+            "indexed": true,
+            "name": "specimen_from_organism_0.json",
+            "s3_etag": "9ce845764eade1bba05960e960702af4",
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+                "project_title": "Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics",
+                "project_description": "During early human pregnancy the uterine mucosa transforms into the decidua, into which the fetal placenta implants and where placental trophoblast cells intermingle and communicate with maternal cells. Trophoblast\u2013decidual interactions underlie common diseases of pregnancy, including pre-eclampsia and stillbirth. Here we profile the transcriptomes of about 70,000 single cells from first-trimester placentas with matched maternal blood and decidual cells. The cellular composition of human decidua reveals subsets of perivascular and stromal cells that are located in distinct decidual layers. There are three major subsets of decidual natural killer cells that have distinctive immunomodulatory and chemokine profiles. We develop a repository of ligand\u2013receptor complexes and a statistical tool to predict the cell-type specificity of cell\u2013cell communication via these molecular interactions. Our data identify many regulatory interactions that prevent harmful innate or adaptive immune responses in this environment. Our single-cell atlas of the maternal\u2013fetal interface reveals the cellular organization of the decidua and placenta, and the interactions that are critical for placentation and reproductive success."
+            },
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+                "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6678/",
+                "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-6701/",
+                "https://www.ebi.ac.uk/ena/data/view/PRJEB25794",
+                "https://www.ebi.ac.uk/ena/data/view/PRJEB28266"
+            ],
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+                {
+                    "contact_name": "Johan,,Henriksson",
+                    "email": "mahogny@areta.org",
+                    "institution": "Wellcome Trust Sanger Institute",
+                    "address": "Wellcome Trust Genome Campus, Cambridge",
+                    "country": "UK",
+                    "corresponding_contributor": false
+                },
+                {
+                    "contact_name": "Mirjana,,Efremova",
+                    "email": "me5@sanger.ac.uk",
+                    "institution": "Wellcome Trust Sanger Institute",
+                    "address": "Wellcome Trust Genome Campus, Cambridge",
+                    "country": "UK",
+                    "corresponding_contributor": true
+                },
+                {
+                    "contact_name": "Roser,,Vento-Tormo",
+                    "email": "rv4@sanger.ac.uk",
+                    "institution": "Wellcome Trust Sanger Institute",
+                    "address": "Wellcome Trust Genome Campus, Cambridge",
+                    "country": "UK",
+                    "corresponding_contributor": true
+                },
+                {
+                    "contact_name": "Muzlifah,,Haniffa",
+                    "email": "m.a.haniffa@ncl.ac.uk",
+                    "institution": "Newcastle University",
+                    "laboratory": "Institute of Cellular Medicine",
+                    "address": "Newcastle upon Tyne, NE2 4HH",
+                    "country": "UK",
+                    "corresponding_contributor": true
+                },
+                {
+                    "contact_name": "Ashley,,Moffett",
+                    "email": "am485@cam.ac.uk",
+                    "institution": "University of Cambridge",
+                    "laboratory": "Centre for Trophoblast Research",
+                    "address": "Cambridge, CB2 3EG",
+                    "country": "UK",
+                    "corresponding_contributor": true
+                },
+                {
+                    "contact_name": "Sarah,A,Teichmann",
+                    "email": "st9@sanger.ac.uk",
+                    "institution": "Wellcome Trust Sanger Institute",
+                    "address": "Wellcome Trust Genome Campus, Cambridge",
+                    "country": "UK",
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+                },
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+                    "contact_name": "Mallory,Ann,Freeberg",
+                    "email": "mfreeberg@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "Human Cell Atlas Data Coordination Platform",
+                    "address": "Wellcome Trust Genome Campus, Cambridge",
+                    "country": "UK",
+                    "project_role": "Human Cell Atlas wrangler",
+                    "orcid_id": "0000-0003-2949-3921",
+                    "corresponding_contributor": false
+                },
+                {
+                    "contact_name": "Zinaida, A, Perova",
+                    "email": "zina@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "Human Cell Atlas Data Coordination Platform",
+                    "address": "Wellcome Trust Genome Campus, Cambridge",
+                    "country": "UK",
+                    "project_role": "Human Cell Atlas wrangler",
+                    "orcid_id": "0000-0001-9913-3249",
+                    "corresponding_contributor": false
+                },
+                {
+                    "contact_name": "Anja,,Fullgrabe",
+                    "email": "anjaf@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "ArrayExpress ",
+                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
+                    "country": "UK",
+                    "project_role": "external curator",
+                    "orcid_id": "0000-0002-8674-0039",
+                    "corresponding_contributor": false
+                }
+            ],
+            "funders": [
+                {
+                    "funder_name": "Swedish Research Council"
+                },
+                {
+                    "grant_id": "099175/Z/12/Z",
+                    "funder_name": "Medical Research Council / Wellcome Trust"
+                },
+                {
+                    "grant_id": "WT107931/Z/15/Z",
+                    "funder_name": "Wellcome Trust"
+                },
+                {
+                    "funder_name": "EMBO Long-Term Fellowship"
+                },
+                {
+                    "funder_name": "Human Frontier Science Program Long-Term Fellowship"
+                },
+                {
+                    "funder_name": "Royal Society Dorothy Hodgkin Fellowship"
+                },
+                {
+                    "funder_name": "The Lister Institute for Preventive Medicine"
+                },
+                {
+                    "funder_name": "National Institute for Health Research"
+                },
+                {
+                    "funder_name": "Newcastle Biomedical Research Centre"
+                },
+                {
+                    "grant_id": "ThDEFINE, ThSWITCH",
+                    "funder_name": "ERC"
+                },
+                {
+                    "grant_id": "MRG-GRAMMAR no. 664918",
+                    "funder_name": "EU FET-OPEN"
+                },
+                {
+                    "grant_id": "Investigator award",
+                    "funder_name": "Wellcome Trust"
+                },
+                {
+                    "grant_id": "WT206194",
+                    "funder_name": "Wellcome Sanger core funding"
+                }
+            ],
+            "publications": [
+                {
+                    "authors": [
+                        "Vento-Tormo R",
+                        "Efremova M",
+                        "Botting RA",
+                        "Turco MY",
+                        "Vento-Tormo M",
+                        "Meyer KB",
+                        "Park J",
+                        "Stephenson E",
+                        "Polanski K",
+                        "Payne RP",
+                        "Goncalves A",
+                        "Zou A",
+                        "Henriksson J",
+                        "Wood L",
+                        "Lisgo S",
+                        "Filby A",
+                        "Wright GJ",
+                        "Stubbington MJ",
+                        "Haniffa M",
+                        "Moffett A",
+                        "Teichmann SA"
+                    ],
+                    "publication_title": "Reconstructing the human first trimester fetal-maternal interface using single cell transcriptomics",
+                    "doi": "10.1101/429589",
+                    "publication_url": "https://www.biorxiv.org/content/early/2018/09/29/429589"
+                },
+                {
+                    "authors": [
+                        "Vento-Tormo R",
+                        "Efremova M",
+                        "Botting RA",
+                        "Turco MY",
+                        "Vento-Tormo M",
+                        "Meyer KB",
+                        "Park J",
+                        "Stephenson E",
+                        "Polanski K",
+                        "Goncalves A",
+                        "Gardner L",
+                        "Holmqvist S",
+                        "Henriksson J",
+                        "Zou A",
+                        "Sharkey A",
+                        "Millar B",
+                        "Innes B",
+                        "Wood L",
+                        "Wilbrey-Clark A",
+                        "Payne RP",
+                        "Ivarsson M",
+                        "Lisgo S",
+                        "Filby A",
+                        "Rowitch D",
+                        "Bulmer J",
+                        "Wright GJ",
+                        "Stubbington MJ",
+                        "Haniffa M",
+                        "Moffett A",
+                        "Teichmann SA"
+                    ],
+                    "publication_title": "Single-cell reconstruction of the early maternal\u2013fetal interface in humans",
+                    "doi": "10.1038/s41586-018-0698-6",
+                    "pmid": 30429548,
+                    "publication_url": "https://www.nature.com/articles/s41586-018-0698-6#Sec35"
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+                "publication_doi": "10.1038/nprot.2014.006"
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+                "protocol_description": "Libraries were sequenced on the Illumina HiSeq 2000 platform to obtain 75-bp paired-end reads."
+            },
+            "sequencing_approach": {
+                "text": "full length single cell RNA sequencing",
+                "ontology": "EFO:0008441",
+                "ontology_label": "full length single cell RNA sequencing"
+            },
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+                "ontology_label": "Illumina HiSeq 2000"
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+                "submission_date": "2019-01-23T10:33:59.865Z",
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+                    "docker_image": "quay.io/humancellatlas/secondary-analysis-picard:v0.2.2-2.10.10",
+                    "log_err": "gs://hca-dcp-pipelines-prod-cromwell-execution/caas-cromwell-executions/AdapterSmartSeq2SingleCell/e39de6d0-0ba4-4c92-bd96-f4b1117ca390/call-analysis/ss2.SmartSeq2SingleCell/1a5b6337-c719-4dc7-9014-e7cb7f739e22/call-CollectRnaMetrics/stderr",
+                    "log_out": "gs://hca-dcp-pipelines-prod-cromwell-execution/caas-cromwell-executions/AdapterSmartSeq2SingleCell/e39de6d0-0ba4-4c92-bd96-f4b1117ca390/call-analysis/ss2.SmartSeq2SingleCell/1a5b6337-c719-4dc7-9014-e7cb7f739e22/call-CollectRnaMetrics/stdout",
+                    "memory": "3.5 GB",
+                    "start_time": "2019-02-02T06:17:07.504Z",
+                    "stop_time": "2019-02-02T06:30:57.010Z",
+                    "task_name": "CollectRnaMetrics",
+                    "zone": "us-central1-b"
+                },
+                {
+                    "cpus": 1,
+                    "disk_size": "local-disk 20 HDD",
+                    "docker_image": "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.0",
+                    "log_err": "gs://hca-dcp-pipelines-prod-cromwell-execution/caas-cromwell-executions/AdapterSmartSeq2SingleCell/e39de6d0-0ba4-4c92-bd96-f4b1117ca390/call-analysis/ss2.SmartSeq2SingleCell/1a5b6337-c719-4dc7-9014-e7cb7f739e22/call-GroupQCOutputs/stderr",
+                    "log_out": "gs://hca-dcp-pipelines-prod-cromwell-execution/caas-cromwell-executions/AdapterSmartSeq2SingleCell/e39de6d0-0ba4-4c92-bd96-f4b1117ca390/call-analysis/ss2.SmartSeq2SingleCell/1a5b6337-c719-4dc7-9014-e7cb7f739e22/call-GroupQCOutputs/stdout",
+                    "memory": "2 GB",
+                    "start_time": "2019-02-02T06:30:58.954Z",
+                    "stop_time": "2019-02-02T06:36:21.014Z",
+                    "task_name": "GroupQCOutputs",
+                    "zone": "us-central1-b"
+                },
+                {
+                    "cpus": 4,
+                    "disk_size": "local-disk 23 HDD",
+                    "docker_image": "quay.io/humancellatlas/secondary-analysis-hisat2:v0.2.2-2-2.1.0",
+                    "log_err": "gs://hca-dcp-pipelines-prod-cromwell-execution/caas-cromwell-executions/AdapterSmartSeq2SingleCell/e39de6d0-0ba4-4c92-bd96-f4b1117ca390/call-analysis/ss2.SmartSeq2SingleCell/1a5b6337-c719-4dc7-9014-e7cb7f739e22/call-HISAT2PairedEnd/stderr",
+                    "log_out": "gs://hca-dcp-pipelines-prod-cromwell-execution/caas-cromwell-executions/AdapterSmartSeq2SingleCell/e39de6d0-0ba4-4c92-bd96-f4b1117ca390/call-analysis/ss2.SmartSeq2SingleCell/1a5b6337-c719-4dc7-9014-e7cb7f739e22/call-HISAT2PairedEnd/stdout",
+                    "memory": "15 GB",
+                    "start_time": "2019-02-02T06:09:49.934Z",
+                    "stop_time": "2019-02-02T06:17:06.009Z",
+                    "task_name": "HISAT2PairedEnd",
+                    "zone": "us-central1-b"
+                },
+                {
+                    "cpus": 4,
+                    "disk_size": "local-disk 14 HDD",
+                    "docker_image": "quay.io/humancellatlas/secondary-analysis-hisat2:v0.2.2-2-2.1.0",
+                    "log_err": "gs://hca-dcp-pipelines-prod-cromwell-execution/caas-cromwell-executions/AdapterSmartSeq2SingleCell/e39de6d0-0ba4-4c92-bd96-f4b1117ca390/call-analysis/ss2.SmartSeq2SingleCell/1a5b6337-c719-4dc7-9014-e7cb7f739e22/call-HISAT2Transcriptome/stderr",
+                    "log_out": "gs://hca-dcp-pipelines-prod-cromwell-execution/caas-cromwell-executions/AdapterSmartSeq2SingleCell/e39de6d0-0ba4-4c92-bd96-f4b1117ca390/call-analysis/ss2.SmartSeq2SingleCell/1a5b6337-c719-4dc7-9014-e7cb7f739e22/call-HISAT2Transcriptome/stdout",
+                    "memory": "15 GB",
+                    "start_time": "2019-02-02T06:09:49.935Z",
+                    "stop_time": "2019-02-02T06:13:12.013Z",
+                    "task_name": "HISAT2Transcriptome",
+                    "zone": "us-central1-b"
+                },
+                {
+                    "cpus": 4,
+                    "disk_size": "local-disk 22 HDD",
+                    "docker_image": "quay.io/humancellatlas/secondary-analysis-rsem:v0.2.2-1.3.0",
+                    "log_err": "gs://hca-dcp-pipelines-prod-cromwell-execution/caas-cromwell-executions/AdapterSmartSeq2SingleCell/e39de6d0-0ba4-4c92-bd96-f4b1117ca390/call-analysis/ss2.SmartSeq2SingleCell/1a5b6337-c719-4dc7-9014-e7cb7f739e22/call-RSEMExpression/stderr",
+                    "log_out": "gs://hca-dcp-pipelines-prod-cromwell-execution/caas-cromwell-executions/AdapterSmartSeq2SingleCell/e39de6d0-0ba4-4c92-bd96-f4b1117ca390/call-analysis/ss2.SmartSeq2SingleCell/1a5b6337-c719-4dc7-9014-e7cb7f739e22/call-RSEMExpression/stdout",
+                    "memory": "3.5 GB",
+                    "start_time": "2019-02-02T06:13:13.934Z",
+                    "stop_time": "2019-02-02T06:18:24.008Z",
+                    "task_name": "RSEMExpression",
+                    "zone": "us-central1-b"
+                },
+                {
+                    "cpus": 4,
+                    "disk_size": "local-disk 100 HDD",
+                    "docker_image": "quay.io/humancellatlas/secondary-analysis-python3-scientific:0.1.7",
+                    "log_err": "gs://hca-dcp-pipelines-prod-cromwell-execution/caas-cromwell-executions/AdapterSmartSeq2SingleCell/e39de6d0-0ba4-4c92-bd96-f4b1117ca390/call-analysis/ss2.SmartSeq2SingleCell/1a5b6337-c719-4dc7-9014-e7cb7f739e22/call-SmartSeq2ZarrConversion/stderr",
+                    "log_out": "gs://hca-dcp-pipelines-prod-cromwell-execution/caas-cromwell-executions/AdapterSmartSeq2SingleCell/e39de6d0-0ba4-4c92-bd96-f4b1117ca390/call-analysis/ss2.SmartSeq2SingleCell/1a5b6337-c719-4dc7-9014-e7cb7f739e22/call-SmartSeq2ZarrConversion/stdout",
+                    "memory": "16 GB",
+                    "start_time": "2019-02-02T06:36:22.504Z",
+                    "stop_time": "2019-02-02T06:39:18.012Z",
+                    "task_name": "SmartSeq2ZarrConversion",
+                    "zone": "us-central1-b"
+                }
+            ],
+            "timestamp_start_utc": "2019-02-02T06:09:46.854Z",
+            "timestamp_stop_utc": "2019-02-02T06:39:21.010Z",
+            "provenance": {
+                "document_id": "d6c56c65-bed0-4d6e-bf89-7e0d71bd3026",
+                "submission_date": "2019-02-02T06:44:59.796Z",
+                "update_date": "2019-02-02T06:45:04.794Z"
+            }
+        },
+        "process_0.json": {
+            "insdc_experiment": {
+                "insdc_experiment": "ERX2481489"
+            },
+            "process_core": {
+                "process_id": "24088_4_92"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/6.0.6/process",
+            "provenance": {
+                "document_id": "55faef19-0c09-41ef-b21c-ad25a89ea2e3",
+                "submission_date": "2019-01-23T10:40:00.000Z",
+                "update_date": "2019-01-23T11:19:16.982Z"
+            }
+        },
+        "process_1.json": {
+            "process_core": {
+                "process_id": "process_id_5845"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/6.0.6/process",
+            "provenance": {
+                "document_id": "e84cac5b-1467-4055-a029-48d67a5505d6",
+                "submission_date": "2019-01-23T10:36:29.102Z",
+                "update_date": "2019-01-23T11:10:57.210Z"
+            }
+        },
+        "process_2.json": {
+            "process_core": {
+                "process_id": "process_id_21"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/6.0.6/process",
+            "provenance": {
+                "document_id": "832b39e3-ebba-4686-a724-52babb96056f",
+                "submission_date": "2019-01-23T10:34:00.619Z",
+                "update_date": "2019-01-23T11:05:44.002Z"
+            }
+        },
+        "links.json": {
+            "describedBy": "https://schema.humancellatlas.org/system/1.1.4/links",
+            "schema_type": "link_bundle",
+            "schema_version": "1.1.4",
+            "links": [
+                {
+                    "process": "d6c56c65-bed0-4d6e-bf89-7e0d71bd3026",
+                    "inputs": [
+                        "c15ee840-4702-45f7-bb19-693de19a742a",
+                        "5f5d9c84-3565-4398-886c-2e50ad4c3964"
+                    ],
+                    "input_type": "file",
+                    "outputs": [
+                        "b91aca7b-e71b-4014-ab09-5d87e52bc305",
+                        "34e92010-0e2d-49af-b4b7-bed7a2c9e490",
+                        "3db4d80f-cbd5-45da-9048-6fe8e2e4d0d2",
+                        "ed37a61e-4449-4bce-a774-7cbd732781c8",
+                        "b70e4907-383c-4466-a244-3e7ce9890dae",
+                        "7ee496ab-286c-4962-919a-70244090e315",
+                        "c15427d1-e5b7-4bee-91fe-d98b04dc6a01",
+                        "b11e96c4-2472-4317-b45b-5bc1c9b55704",
+                        "828d7e40-4f6b-42e1-8cd2-6ddccb5b0e6c",
+                        "6804b943-fda7-4e8f-bfba-23e368843e63",
+                        "aeb5aebe-9e45-4c9d-931a-883f8fa71225",
+                        "7c5a87c1-e3b6-42aa-8d68-0f534ded7d2d",
+                        "87bd704c-3d36-4620-bdf2-5ad28c5a3d56",
+                        "0aa4b2f3-b969-40d7-97f9-f33af0088915",
+                        "697a869d-079b-48d4-9a7d-c04cf05dd0a9",
+                        "6d928f58-2e83-46a0-84a2-d08744a42abd",
+                        "cc958050-fd69-4919-8529-6f91552ce0ea",
+                        "0a5730dc-eeeb-4f25-bcc7-24cb7d15ac01",
+                        "42fffad8-d47d-4da5-8318-45b0f5577c08",
+                        "2842a995-c205-4d80-959f-fcb9ff8719ee",
+                        "90d148ed-a6eb-44c3-a398-df29459943ff",
+                        "269a143b-a2c2-40cd-9394-41a13321581d",
+                        "1dda8255-de1c-4bfa-aa79-dbc501d3a112",
+                        "d76f404c-d294-49f2-bfd5-d475e08fa783",
+                        "3f672b26-ea2f-4e94-ba77-f463c3cb7c38",
+                        "4bc5b41c-9fea-4baa-9bf9-75fa4f4a9818",
+                        "3e44e8f9-e76d-4158-a7af-eeb9602cf8cc",
+                        "3fe1e9e8-1b0f-4683-a402-ae970b33f144",
+                        "e53c14f5-1a4f-44d6-9773-53faac32233b",
+                        "7a26e63d-fcf2-419a-a945-bca9e539480f",
+                        "644b261b-450e-453c-bb5e-0498a1cf5804",
+                        "b367129a-e83f-4a2b-9278-b5f7930ad457",
+                        "6d4785d0-bd42-4f98-8f7a-ab9ca8fcab39"
+                    ],
+                    "output_type": "file",
+                    "protocols": [
+                        {
+                            "protocol_type": "analysis_protocol",
+                            "protocol_id": "bb17ee61-193e-4ae1-a014-4f1b1c19b8b7"
+                        }
+                    ]
+                },
+                {
+                    "process": "55faef19-0c09-41ef-b21c-ad25a89ea2e3",
+                    "inputs": [
+                        "9ea49dd1-7511-48f8-be12-237e3d0690c0"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "c15ee840-4702-45f7-bb19-693de19a742a",
+                        "5f5d9c84-3565-4398-886c-2e50ad4c3964"
+                    ],
+                    "output_type": "file",
+                    "protocols": [
+                        {
+                            "protocol_type": "library_preparation_protocol",
+                            "protocol_id": "edda2708-1172-47f0-9c8b-b6771f463db1"
+                        },
+                        {
+                            "protocol_type": "sequencing_protocol",
+                            "protocol_id": "46f58d61-c784-47fb-9c75-7af37871810e"
+                        }
+                    ]
+                },
+                {
+                    "process": "e84cac5b-1467-4055-a029-48d67a5505d6",
+                    "inputs": [
+                        "e7049663-aa57-4001-8bb4-870e341b4f0b"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "9ea49dd1-7511-48f8-be12-237e3d0690c0"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "dcfe8429-af02-491e-96e9-4ac0569cd5d1"
+                        },
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "55dd1cfc-cc9c-4a03-aa43-2cb92b843253"
+                        },
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "3d2707fa-83ad-472b-8282-7b6191f96bc2"
+                        },
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "88bd21a4-8d6c-48ce-ab57-8b5e0b582cca"
+                        }
+                    ]
+                },
+                {
+                    "process": "832b39e3-ebba-4686-a724-52babb96056f",
+                    "inputs": [
+                        "a879fffa-3b98-4204-ae5a-603180007ca0"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "e7049663-aa57-4001-8bb4-870e341b4f0b"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "collection_protocol",
+                            "protocol_id": "477b201f-67f0-4f97-86d5-de32a7afc267"
+                        }
+                    ]
+                },
+                {
+                    "process": "55faef19-0c09-41ef-b21c-ad25a89ea2e3",
+                    "inputs": [
+                        "9ea49dd1-7511-48f8-be12-237e3d0690c0"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "c15ee840-4702-45f7-bb19-693de19a742a",
+                        "5f5d9c84-3565-4398-886c-2e50ad4c3964"
+                    ],
+                    "output_type": "file",
+                    "protocols": [
+                        {
+                            "protocol_type": "library_preparation_protocol",
+                            "protocol_id": "edda2708-1172-47f0-9c8b-b6771f463db1"
+                        },
+                        {
+                            "protocol_type": "sequencing_protocol",
+                            "protocol_id": "46f58d61-c784-47fb-9c75-7af37871810e"
+                        }
+                    ]
+                },
+                {
+                    "process": "e84cac5b-1467-4055-a029-48d67a5505d6",
+                    "inputs": [
+                        "e7049663-aa57-4001-8bb4-870e341b4f0b"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "9ea49dd1-7511-48f8-be12-237e3d0690c0"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "dcfe8429-af02-491e-96e9-4ac0569cd5d1"
+                        },
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "55dd1cfc-cc9c-4a03-aa43-2cb92b843253"
+                        },
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "3d2707fa-83ad-472b-8282-7b6191f96bc2"
+                        },
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "88bd21a4-8d6c-48ce-ab57-8b5e0b582cca"
+                        }
+                    ]
+                },
+                {
+                    "process": "832b39e3-ebba-4686-a724-52babb96056f",
+                    "inputs": [
+                        "a879fffa-3b98-4204-ae5a-603180007ca0"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "e7049663-aa57-4001-8bb4-870e341b4f0b"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "collection_protocol",
+                            "protocol_id": "477b201f-67f0-4f97-86d5-de32a7afc267"
+                        }
+                    ]
+                }
+            ]
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e/2019-02-02T065454.662896Z/manifest.json b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e/2019-02-02T065454.662896Z/manifest.json
deleted file mode 100644
index 53e464737..000000000
--- a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e/2019-02-02T065454.662896Z/manifest.json
+++ /dev/null
@@ -1,1046 +0,0 @@
-[
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "a3819d97",
-        "indexed": true,
-        "name": "cell_suspension_0.json",
-        "s3_etag": "9eb9b583cc0632a1c3bb8361cec98265",
-        "sha1": "32466a72fafb78ddb4b0dc460ccb9f34f671f642",
-        "sha256": "d55ea6bdacfa2fa1048fbdc84a180744e5ddd953ccb15fbcc5aa5a342f6645bf",
-        "size": 1071,
-        "uuid": "9ea49dd1-7511-48f8-be12-237e3d0690c0",
-        "version": "2019-01-23T110124.376000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "395b270f",
-        "indexed": true,
-        "name": "specimen_from_organism_0.json",
-        "s3_etag": "9ce845764eade1bba05960e960702af4",
-        "sha1": "165fcda6a5633c42c9501c687c71aacfdcabd20e",
-        "sha256": "0d708f8d888e952a2ce0a7f1b08c83e2b4614a8712c792fb2a7f53d9fa52ca96",
-        "size": 1137,
-        "uuid": "e7049663-aa57-4001-8bb4-870e341b4f0b",
-        "version": "2019-01-23T105557.143000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "c72cf496",
-        "indexed": true,
-        "name": "donor_organism_0.json",
-        "s3_etag": "7c211658b06ab28a84fb002c343fefb0",
-        "sha1": "40d7d6817fe781b0bd0d7443a43890d120c83e3e",
-        "sha256": "0a8c089566f7416e06465a1f11a819c7a6b1af85ce6306fcae70712366314d00",
-        "size": 1051,
-        "uuid": "a879fffa-3b98-4204-ae5a-603180007ca0",
-        "version": "2019-01-23T104040.695000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "bc395265",
-        "indexed": true,
-        "name": "analysis_file_0.json",
-        "s3_etag": "52496571a574b30bd7bd87139c38891c",
-        "sha1": "8c35a49b5873ef29fee2037e38871f09a321654d",
-        "sha256": "48d46c5d1c970fef0da0db25b570e3e0bf61f6adf3f37b6339f21469d79aced8",
-        "size": 459,
-        "uuid": "b91aca7b-e71b-4014-ab09-5d87e52bc305",
-        "version": "2019-02-02T064943.861000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "b2177c37",
-        "indexed": true,
-        "name": "analysis_file_1.json",
-        "s3_etag": "c25537e11b224072d5715789b641aaaf",
-        "sha1": "77d3839cfd011df3c32b33c618a077bdb6698f4d",
-        "sha256": "ba8af5feaa7df65888217075a28ca8ae2fb0c461884e702e372fdb3828e8b992",
-        "size": 453,
-        "uuid": "34e92010-0e2d-49af-b4b7-bed7a2c9e490",
-        "version": "2019-02-02T064937.893000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "f1394c2a",
-        "indexed": true,
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\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e/2019-02-02T065454.662896Z/metadata.json b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e/2019-02-02T065454.662896Z/metadata.json
deleted file mode 100644
index 6377fb91d..000000000
--- a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e/2019-02-02T065454.662896Z/metadata.json
+++ /dev/null
@@ -1,1656 +0,0 @@
-{
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-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "24088_4_92",
-            "biomaterial_name": "T cell from blood",
-            "biomaterial_description": "=",
-            "ncbi_taxon_id": [
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-            "insdc_biomaterial": "ERS2335002",
-            "biosd_biomaterial": "SAMEA1015535"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "selected_cell_type": [
-            {
-                "text": "T cell",
-                "ontology": "CL:0000084",
-                "ontology_label": "T cell"
-            }
-        ],
-        "total_estimated_cells": 1,
-        "plate_based_sequencing": {
-            "plate_id": "not provided"
-        },
-        "provenance": {
-            "document_id": "9ea49dd1-7511-48f8-be12-237e3d0690c0",
-            "submission_date": "2019-01-23T10:27:50.080Z",
-            "update_date": "2019-01-23T11:01:24.376Z"
-        }
-    },
-    "specimen_from_organism_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/6.3.8/specimen_from_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "blood_from_donor_D4",
-            "biomaterial_name": "Peripheral blood sample 1",
-            "biomaterial_description": "Blood from early pregnancy (6- 14 weeks gestation)",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
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-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "organ": {
-            "text": "blood",
-            "ontology": "UBERON:0000178",
-            "ontology_label": "blood"
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461",
-                "ontology_label": "normal"
-            }
-        ],
-        "preservation_storage": {
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-        "provenance": {
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-            "submission_date": "2019-01-23T10:25:32.280Z",
-            "update_date": "2019-01-23T10:55:57.143Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "https://schema.humancellatlas.org/type/biomaterial/12.0.5/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "D4",
-            "biomaterial_name": "Donor 4",
-            "biomaterial_description": "Donor 4, 6-14 weeks pregnant",
-            "ncbi_taxon_id": [
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-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "is_living": "yes",
-        "sex": "female",
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461",
-                "ontology_label": "normal"
-            }
-        ],
-        "development_stage": {
-            "text": "adult",
-            "ontology": "EFO:0001272",
-            "ontology_label": "adult"
-        },
-        "provenance": {
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-            "submission_date": "2019-01-23T10:25:32.001Z",
-            "update_date": "2019-01-23T10:40:40.695Z"
-        }
-    },
-    "analysis_file_0.json": {
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-        "schema_type": "file",
-        "file_core": {
-            "file_name": "9ea49dd1-7511-48f8-be12-237e3d0690c0_qc.bait_bias_summary_metrics.txt",
-            "file_format": "txt"
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-            "submission_date": "2019-02-02T06:45:00.418Z",
-            "update_date": "2019-02-02T06:49:43.861Z"
-        }
-    },
-    "analysis_file_1.json": {
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-        "schema_type": "file",
-        "file_core": {
-            "file_name": "9ea49dd1-7511-48f8-be12-237e3d0690c0_qc.insert_size_metrics.txt",
-            "file_format": "txt"
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-        "provenance": {
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-            "submission_date": "2019-02-02T06:45:00.594Z",
-            "update_date": "2019-02-02T06:49:37.893Z"
-        }
-    },
-    "analysis_file_2.json": {
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-        "schema_type": "file",
-        "file_core": {
-            "file_name": "9ea49dd1-7511-48f8-be12-237e3d0690c0_qc.quality_by_cycle_metrics.txt",
-            "file_format": "txt"
-        },
-        "provenance": {
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-            "submission_date": "2019-02-02T06:45:00.770Z",
-            "update_date": "2019-02-02T06:49:40.900Z"
-        }
-    },
-    "analysis_file_3.json": {
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-        "schema_type": "file",
-        "file_core": {
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-            "file_format": "txt"
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-            "submission_date": "2019-02-02T06:45:00.949Z",
-            "update_date": "2019-02-02T06:49:40.853Z"
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-                    "c15ee840-4702-45f7-bb19-693de19a742a",
-                    "5f5d9c84-3565-4398-886c-2e50ad4c3964"
-                ],
-                "output_type": "file",
-                "protocols": [
-                    {
-                        "protocol_type": "library_preparation_protocol",
-                        "protocol_id": "edda2708-1172-47f0-9c8b-b6771f463db1"
-                    },
-                    {
-                        "protocol_type": "sequencing_protocol",
-                        "protocol_id": "46f58d61-c784-47fb-9c75-7af37871810e"
-                    }
-                ]
-            },
-            {
-                "process": "e84cac5b-1467-4055-a029-48d67a5505d6",
-                "inputs": [
-                    "e7049663-aa57-4001-8bb4-870e341b4f0b"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "9ea49dd1-7511-48f8-be12-237e3d0690c0"
-                ],
-                "output_type": "biomaterial",
-                "protocols": [
-                    {
-                        "protocol_type": "enrichment_protocol",
-                        "protocol_id": "dcfe8429-af02-491e-96e9-4ac0569cd5d1"
-                    },
-                    {
-                        "protocol_type": "enrichment_protocol",
-                        "protocol_id": "55dd1cfc-cc9c-4a03-aa43-2cb92b843253"
-                    },
-                    {
-                        "protocol_type": "enrichment_protocol",
-                        "protocol_id": "3d2707fa-83ad-472b-8282-7b6191f96bc2"
-                    },
-                    {
-                        "protocol_type": "enrichment_protocol",
-                        "protocol_id": "88bd21a4-8d6c-48ce-ab57-8b5e0b582cca"
-                    }
-                ]
-            },
-            {
-                "process": "832b39e3-ebba-4686-a724-52babb96056f",
-                "inputs": [
-                    "a879fffa-3b98-4204-ae5a-603180007ca0"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "e7049663-aa57-4001-8bb4-870e341b4f0b"
-                ],
-                "output_type": "biomaterial",
-                "protocols": [
-                    {
-                        "protocol_type": "collection_protocol",
-                        "protocol_id": "477b201f-67f0-4f97-86d5-de32a7afc267"
-                    }
-                ]
-            },
-            {
-                "process": "55faef19-0c09-41ef-b21c-ad25a89ea2e3",
-                "inputs": [
-                    "9ea49dd1-7511-48f8-be12-237e3d0690c0"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "c15ee840-4702-45f7-bb19-693de19a742a",
-                    "5f5d9c84-3565-4398-886c-2e50ad4c3964"
-                ],
-                "output_type": "file",
-                "protocols": [
-                    {
-                        "protocol_type": "library_preparation_protocol",
-                        "protocol_id": "edda2708-1172-47f0-9c8b-b6771f463db1"
-                    },
-                    {
-                        "protocol_type": "sequencing_protocol",
-                        "protocol_id": "46f58d61-c784-47fb-9c75-7af37871810e"
-                    }
-                ]
-            },
-            {
-                "process": "e84cac5b-1467-4055-a029-48d67a5505d6",
-                "inputs": [
-                    "e7049663-aa57-4001-8bb4-870e341b4f0b"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "9ea49dd1-7511-48f8-be12-237e3d0690c0"
-                ],
-                "output_type": "biomaterial",
-                "protocols": [
-                    {
-                        "protocol_type": "enrichment_protocol",
-                        "protocol_id": "dcfe8429-af02-491e-96e9-4ac0569cd5d1"
-                    },
-                    {
-                        "protocol_type": "enrichment_protocol",
-                        "protocol_id": "55dd1cfc-cc9c-4a03-aa43-2cb92b843253"
-                    },
-                    {
-                        "protocol_type": "enrichment_protocol",
-                        "protocol_id": "3d2707fa-83ad-472b-8282-7b6191f96bc2"
-                    },
-                    {
-                        "protocol_type": "enrichment_protocol",
-                        "protocol_id": "88bd21a4-8d6c-48ce-ab57-8b5e0b582cca"
-                    }
-                ]
-            },
-            {
-                "process": "832b39e3-ebba-4686-a724-52babb96056f",
-                "inputs": [
-                    "a879fffa-3b98-4204-ae5a-603180007ca0"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "e7049663-aa57-4001-8bb4-870e341b4f0b"
-                ],
-                "output_type": "biomaterial",
-                "protocols": [
-                    {
-                        "protocol_type": "collection_protocol",
-                        "protocol_id": "477b201f-67f0-4f97-86d5-de32a7afc267"
-                    }
-                ]
-            }
-        ]
-    }
-}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
new file mode 100644
index 000000000..c301e8a49
--- /dev/null
+++ b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
@@ -0,0 +1,672 @@
+{
+    "manifest": [
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+            "crc32c": "092b0c23",
+            "indexed": true,
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+            "sha1": "ad19c4ec4b4cbc6efc2a381ac7a0d5f063d6f13d",
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+            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
+            "crc32c": "ac85eb5f",
+            "indexed": true,
+            "name": "specimen_from_organism_0.json",
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+            "indexed": true,
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+        {
+            "content-type": "application/json; dcp-type=\"metadata/file\"",
+            "crc32c": "cbad3ef1",
+            "indexed": true,
+            "name": "sequence_file_0.json",
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+            "crc32c": "0c8996e6",
+            "indexed": true,
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+        {
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+            "crc32c": "b7b8f50f",
+            "indexed": true,
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+            "crc32c": "1649738e",
+            "indexed": true,
+            "name": "enrichment_protocol_0.json",
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+            "version": "2018-10-07T115850.413000Z"
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+        {
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+            "crc32c": "076cf3c4",
+            "indexed": true,
+            "name": "collection_protocol_0.json",
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+            "indexed": true,
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+            "indexed": true,
+            "name": "process_1.json",
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+            "sha1": "11a2ba86e5e6b994a993451cf54964c27c9edcce",
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+        },
+        {
+            "content-type": "application/json; dcp-type=\"metadata/process\"",
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+            "indexed": true,
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+            "sha1": "bbef6705b342d6be7b5b7860ee57a68c7524c769",
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+            "version": "2018-10-07T120517.018000Z"
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+        {
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+            "indexed": true,
+            "name": "links.json",
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+            "uuid": "a1681a39-e8d2-43f7-8781-ac4edab527fe",
+            "version": "2018-10-07T130110.624725Z"
+        },
+        {
+            "content-type": "application/gzip; dcp-type=data",
+            "crc32c": "a3f89844",
+            "indexed": false,
+            "name": "SRR6260013.fastq.gz",
+            "s3_etag": "8c9bb4704875cbe67cfc12abb0c66d57",
+            "sha1": "ee681bf47c0b7fbad663b20704ddb45d632709ed",
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+            "version": "2018-10-07T130110.968810Z"
+        }
+    ],
+    "metadata": {
+        "cell_suspension_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "Single-cell_RNA-seq_Subject9_TEMRA_Cell030",
+                "biomaterial_name": "Single-cell_RNA-seq_Subject9_TEMRA_Cell030",
+                "biomaterial_description": "Single-cell_RNA-seq_Subject9_TEMRA_Cell030",
+                "ncbi_taxon_id": [
+                    9606
+                ],
+                "insdc_biomaterial": "SRS2664188"
+            },
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606"
+                }
+            ],
+            "selected_cell_type": [
+                {
+                    "text": "TEMRA",
+                    "ontology": "CL:0000625"
+                }
+            ],
+            "total_estimated_cells": 1,
+            "plate_based_sequencing": {
+                "plate_id": "subject9-10_batch1",
+                "cell_quality": "OK"
+            },
+            "provenance": {
+                "document_id": "ef97eef1-a436-4462-a152-1a2b86ee8831",
+                "submission_date": "2018-10-07T11:57:52.282Z",
+                "update_date": "2018-10-07T12:04:46.292Z"
+            }
+        },
+        "specimen_from_organism_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "Subject9_DENV negative_PBMC_TEMRA",
+                "biomaterial_name": "Subject9_DENV negative_PBMC_TEMRA",
+                "biomaterial_description": "Subject9_DENV negative_PBMC_TEMRA",
+                "ncbi_taxon_id": [
+                    9606
+                ]
+            },
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606"
+                }
+            ],
+            "organ": {
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+                "ontology": "UBERON:0000178"
+            },
+            "organ_part": {
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+                "ontology": "CL:2000001"
+            },
+            "preservation_storage": {
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+                "storage_method": "frozen, liquid nitrogen"
+            },
+            "provenance": {
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+                "submission_date": "2018-10-07T11:56:59.350Z",
+                "update_date": "2018-10-07T12:01:39.672Z"
+            }
+        },
+        "donor_organism_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "Subject9",
+                "biomaterial_name": "Subject9",
+                "biomaterial_description": "Subject9",
+                "ncbi_taxon_id": [
+                    9606
+                ],
+                "genotype": "not provided"
+            },
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606"
+                }
+            ],
+            "is_living": "yes",
+            "sex": "unknown",
+            "medical_history": {
+                "test_results": "dengue virus negative"
+            },
+            "diseases": [
+                {
+                    "text": "normal",
+                    "ontology": "PATO:0000461"
+                }
+            ],
+            "development_stage": {
+                "text": "adult",
+                "ontology": "EFO:0001272"
+            },
+            "organism_age": "18-60",
+            "organism_age_unit": {
+                "text": "year",
+                "ontology": "UO:0000036"
+            },
+            "provenance": {
+                "document_id": "6c992ba4-c132-4dd3-840e-13cf3f38243e",
+                "submission_date": "2018-10-07T11:56:59.023Z",
+                "update_date": "2018-10-07T12:00:40.749Z"
+            }
+        },
+        "sequence_file_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/6.5.2/sequence_file",
+            "schema_type": "file",
+            "file_core": {
+                "file_name": "SRR6260013.fastq.gz",
+                "file_format": "fastq.gz"
+            },
+            "read_index": "read1",
+            "read_length": 50,
+            "insdc_run": [
+                "SRR6260013"
+            ],
+            "provenance": {
+                "document_id": "f3d5c7cb-7ab4-4903-8e0e-dc942121fe27",
+                "submission_date": "2018-10-07T11:58:46.814Z",
+                "update_date": "2018-10-07T12:08:49.204Z"
+            }
+        },
+        "project_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/project/9.0.3/project",
+            "schema_type": "project",
+            "project_core": {
+                "project_short_name": "CD4+ cytotoxic T lymphocytes",
+                "project_title": "Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis",
+                "project_description": "CD4+ cytotoxic T lymphocytes (CD4-CTLs) have been reported to play a protective role in several viral infections. However, little is known in humans about the biology of CD4-CTL generation, their functional properties, heterogeneity and clonal diversity, especially in relation to other well-described CD4+ memory T cell subsets. We performed single-cell RNA-seq in over 9000 cells to unravel CD4-CTL heterogeneity, transcriptional profile and clonality in humans. The single-cell differential gene expression analysis, revealed a spectrum of known transcripts, including several linked to cytotoxic and co-stimulatory function, and transcripts of unknown cytotoxicity-related function that are expressed at higher levels in the TEMRA subset, which is highly enriched for CD4-CTLs, compared to cells in the central and effector memory subsets (TCM, TEM). Simultaneous T cells antigen receptor (TCR) analysis in single-cells and bulk subsets revealed that CD4-TEMRA cells show marked clonal expansion compared to TCM and TEM cells and that the majority of CD4-TEMRA were dengue virus (DENV)-specific in subjects with previous DENV infection. The profile of CD4-TEMRA was highly heterogeneous across subjects, with four distinct clusters identified by the single-cell analysis. Most importantly, we identified distinct clusters of CD4-CTL effector and precursor cells in the TEMRA subset; the precursor cells shared TCR clonotypes with CD4-CTL effectors and were distinguished by high expression of the interleukin-7 receptor. Our identification of a CD4-CTL precursor population may allow further investigation of how CD4-CTLs arise in humans and thus could provide insights into the mechanisms that may be utilized to generate durable and effective CD4-CTL immunity."
+            },
+            "insdc_project": "SRP124157",
+            "geo_series": "GSE106540",
+            "insdc_study": "PRJNA417191",
+            "supplementary_links": [
+                "https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-106540/Results"
+            ],
+            "contributors": [
+                {
+                    "contact_name": "Pandurangan,,Vijayanand",
+                    "email": "vijay@lji.org",
+                    "institution": "La Jolla Institute for Allergy and Immunology",
+                    "laboratory": "Division of Vaccine Discovery",
+                    "address": "La Jolla, CA 92037",
+                    "country": "USA",
+                    "corresponding_contributor": true
+                },
+                {
+                    "contact_name": "Mallory,Ann,Freeberg",
+                    "email": "mfreeberg@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "Human Cell Atlas Data Coordination Platform",
+                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
+                    "country": "UK",
+                    "project_role": "Human Cell Atlas wrangler",
+                    "orcid_id": "0000-0003-2949-3921",
+                    "corresponding_contributor": false
+                },
+                {
+                    "contact_name": "Laura,,Huerta",
+                    "email": "lauhuema@ebi.ac.uk",
+                    "institution": "EMBL-EBI",
+                    "laboratory": "Molecular Atlas",
+                    "address": "Wellcome Trust Genome Campus, Cambridge UK",
+                    "country": "UK",
+                    "project_role": "external curator",
+                    "orcid_id": "0000-0002-8748-599X",
+                    "corresponding_contributor": false
+                }
+            ],
+            "funders": [
+                {
+                    "grant_id": "U19AI118626",
+                    "funder_name": "National Institutes of Health (NIH)"
+                },
+                {
+                    "grant_id": "U19AI118610",
+                    "funder_name": "National Institutes of Health (NIH)"
+                },
+                {
+                    "grant_id": "R01HL114093",
+                    "funder_name": "National Institutes of Health (NIH)"
+                },
+                {
+                    "grant_id": "R24AI108564",
+                    "funder_name": "National Institutes of Health (NIH)"
+                },
+                {
+                    "funder_name": "William K. Bowes Jr. Foundation"
+                }
+            ],
+            "publications": [
+                {
+                    "authors": [
+                        "Patil VS",
+                        "Madrigal A",
+                        "Schmiedel BJ",
+                        "Clarke J",
+                        "ORourke P",
+                        "Harris E",
+                        "de Silva AD",
+                        "Harris E",
+                        "Peters B",
+                        "Seumois G",
+                        "Weiskopf D",
+                        "Sette A",
+                        "Vijayanand P"
+                    ],
+                    "publication_title": "Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis.",
+                    "doi": "10.1126/sciimmunol.aan8664",
+                    "pmid": 29352091,
+                    "publication_url": "http://immunology.sciencemag.org/content/3/19/eaan8664.long"
+                }
+            ],
+            "provenance": {
+                "document_id": "519b58ef-6462-4ed3-8c0d-375b54f53c31",
+                "submission_date": "2018-10-07T11:56:58.869Z",
+                "update_date": "2018-10-07T12:00:40.290Z"
+            }
+        },
+        "library_preparation_protocol_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/4.3.3/library_preparation_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "library_preparation_protocol_1",
+                "protocol_name": "Preparation of mRNAs for single cell SmartSeq2 sequencing",
+                "protocol_description": "Single cell RNAseq was performed as described in Picelli et al.Nat Protoc. 2014, PMID:24385147. We performed 23 cycles of amplification. Barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina) were prepared as following manufacturers protocol.",
+                "publication_doi": "10.1038/nprot.2014.006"
+            },
+            "library_construction_approach": {
+                "text": "Smart-seq2",
+                "ontology": "EFO:0008931"
+            },
+            "nucleic_acid_source": "single cell",
+            "end_bias": "full length",
+            "primer": "poly-dT",
+            "strand": "unstranded",
+            "input_nucleic_acid_molecule": {
+                "text": "polyA RNA",
+                "ontology": "OBI:0000869"
+            },
+            "library_construction_kit": {
+                "retail_name": "Nextera XT library preparation kit",
+                "manufacturer": "Illumina"
+            },
+            "library_preamplification_method": {
+                "text": "PCR",
+                "ontology": "OBI:0000415"
+            },
+            "provenance": {
+                "document_id": "5f82b9c4-f3d7-410c-b843-0e5cdec9efa5",
+                "submission_date": "2018-10-07T11:58:47.200Z",
+                "update_date": "2018-10-07T11:58:50.532Z"
+            }
+        },
+        "sequencing_protocol_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "sequencing_protocol_1",
+                "protocol_name": "SmartSeq 2 single cell sequencing",
+                "protocol_description": "Libraries were sequenced on the Illumina HiSeq 2500 platform to obtain 50-bp single end reads (barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina))."
+            },
+            "sequencing_approach": {
+                "text": "full length single cell RNA sequencing",
+                "ontology": "EFO:0008441"
+            },
+            "instrument_manufacturer_model": {
+                "text": "Illumina HiSeq 2500",
+                "ontology": "EFO:0008565"
+            },
+            "paired_end": false,
+            "provenance": {
+                "document_id": "d678165b-2753-4393-bf3b-5e2a09ba892c",
+                "submission_date": "2018-10-07T11:58:47.211Z",
+                "update_date": "2018-10-07T11:58:50.511Z"
+            }
+        },
+        "dissociation_protocol_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "dissociation_protocol_1",
+                "protocol_name": "Dissociation by FACS into single cells",
+                "protocol_description": "Dissociation by FACS into single cells",
+                "publication_doi": "10.1126/sciimmunol.aan8664"
+            },
+            "dissociation_method": {
+                "text": "fluorescence-activated cell sorting",
+                "ontology": "EFO:0009108"
+            },
+            "provenance": {
+                "document_id": "920078d0-b17e-4f23-8cf6-0674b19e7bec",
+                "submission_date": "2018-10-07T11:58:47.100Z",
+                "update_date": "2018-10-07T11:58:50.432Z"
+            }
+        },
+        "enrichment_protocol_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "enrichment_protocol_2",
+                "protocol_name": "TEMRA Enrichment",
+                "protocol_description": "For single-cell RNA-seq experiments, live and singlet gated cells were further gated to sort 1) TCM; CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA-CCR7+, 2) TEM; CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA-CCR7-, 3) TEMRA; CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA+CCR7-, 4) IL-7Rhigh TEMRA (CD4-CTL precursors); CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA+CCR7-CD127high, 5) IL-7R- TEMRA (CD4-CTL effectors); CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA+CCR7- CD127-. Single cells were directly sorted into 96 well plate with lysis buffer for downstream processing using Smart-seq2 method",
+                "publication_doi": "10.1126/sciimmunol.aan8664"
+            },
+            "enrichment_method": {
+                "text": "fluorescence-activated cell sorting",
+                "ontology": "EFO:0009108"
+            },
+            "markers": "CD3+ CD4+ CD8alpha/CD14/CD19- CD45RA+ CCR7-",
+            "provenance": {
+                "document_id": "644c5f2d-33c8-4bf4-b411-b2dbec8b8227",
+                "submission_date": "2018-10-07T11:58:47.120Z",
+                "update_date": "2018-10-07T11:58:50.413Z"
+            }
+        },
+        "collection_protocol_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/8.2.6/collection_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "collection_protocol_2",
+                "protocol_name": "Blood sample collection",
+                "protocol_description": "Blood sample collection by blood draw",
+                "publication_doi": "10.1126/sciimmunol.aan8664"
+            },
+            "collection_method": {
+                "text": "blood draw",
+                "ontology": "EFO:0009121"
+            },
+            "provenance": {
+                "document_id": "403b586f-fd8d-45f2-a431-4bb6cc33d7d4",
+                "submission_date": "2018-10-07T11:58:47.087Z",
+                "update_date": "2018-10-07T11:58:50.563Z"
+            }
+        },
+        "enrichment_protocol_1.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "enrichment_protocol_1",
+                "protocol_name": "PBMC Enrichment",
+                "protocol_description": "Enrichment for peripheral blood mononuclear cells",
+                "publication_doi": "10.1073/pnas.1305227110"
+            },
+            "enrichment_method": {
+                "text": "Ficoll-Hypaque method",
+                "ontology": "EFO:0009110"
+            },
+            "provenance": {
+                "document_id": "9ab53e6a-464e-44b1-aa24-12daca989969",
+                "submission_date": "2018-10-07T11:58:47.110Z",
+                "update_date": "2018-10-07T11:58:50.474Z"
+            }
+        },
+        "process_0.json": {
+            "insdc_experiment": {
+                "insdc_experiment": "SRX3366459"
+            },
+            "process_core": {
+                "process_id": "process_id_4499"
+            },
+            "schema_type": "process",
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/process/6.0.2/process",
+            "provenance": {
+                "document_id": "18d49b08-d095-4371-bb34-151037f9f461",
+                "submission_date": "2018-10-07T12:00:39.740Z",
+                "update_date": "2018-10-07T12:08:28.754Z"
+            }
+        },
+        "process_1.json": {
+            "process_core": {
+                "process_id": "process_id_2255"
+            },
+            "schema_type": "process",
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/process/6.0.2/process",
+            "provenance": {
+                "document_id": "d13a5a85-b8c7-4a07-9c0c-9180bd0a78eb",
+                "submission_date": "2018-10-07T11:59:45.914Z",
+                "update_date": "2018-10-07T12:06:52.636Z"
+            }
+        },
+        "process_2.json": {
+            "process_core": {
+                "process_location": "Sri Lanka",
+                "process_id": "process_id_15"
+            },
+            "schema_type": "process",
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/process/6.0.2/process",
+            "provenance": {
+                "document_id": "5a15ed38-5e37-44ff-ba35-0d17bb8564bd",
+                "submission_date": "2018-10-07T11:58:47.999Z",
+                "update_date": "2018-10-07T12:05:17.018Z"
+            }
+        },
+        "links.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.3/links",
+            "schema_type": "link_bundle",
+            "schema_version": "1.1.3",
+            "links": [
+                {
+                    "process": "18d49b08-d095-4371-bb34-151037f9f461",
+                    "inputs": [
+                        "ef97eef1-a436-4462-a152-1a2b86ee8831"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "f3d5c7cb-7ab4-4903-8e0e-dc942121fe27"
+                    ],
+                    "output_type": "file",
+                    "protocols": [
+                        {
+                            "protocol_type": "library_preparation_protocol",
+                            "protocol_id": "5f82b9c4-f3d7-410c-b843-0e5cdec9efa5"
+                        },
+                        {
+                            "protocol_type": "sequencing_protocol",
+                            "protocol_id": "d678165b-2753-4393-bf3b-5e2a09ba892c"
+                        }
+                    ]
+                },
+                {
+                    "process": "d13a5a85-b8c7-4a07-9c0c-9180bd0a78eb",
+                    "inputs": [
+                        "80cb479b-dcb4-4dbb-a75d-0249a964bb70"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "ef97eef1-a436-4462-a152-1a2b86ee8831"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "dissociation_protocol",
+                            "protocol_id": "920078d0-b17e-4f23-8cf6-0674b19e7bec"
+                        },
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "644c5f2d-33c8-4bf4-b411-b2dbec8b8227"
+                        }
+                    ]
+                },
+                {
+                    "process": "5a15ed38-5e37-44ff-ba35-0d17bb8564bd",
+                    "inputs": [
+                        "6c992ba4-c132-4dd3-840e-13cf3f38243e"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "80cb479b-dcb4-4dbb-a75d-0249a964bb70"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "collection_protocol",
+                            "protocol_id": "403b586f-fd8d-45f2-a431-4bb6cc33d7d4"
+                        },
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "9ab53e6a-464e-44b1-aa24-12daca989969"
+                        }
+                    ]
+                }
+            ]
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018/2018-10-07T130111.835234Z/manifest.json b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018/2018-10-07T130111.835234Z/manifest.json
deleted file mode 100644
index 278d9f55b..000000000
--- a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018/2018-10-07T130111.835234Z/manifest.json
+++ /dev/null
@@ -1,194 +0,0 @@
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-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "092b0c23",
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-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "84b139be",
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-        "content-type": "application/json; dcp-type=\"metadata/file\"",
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-        "version": "2018-10-07T120849.204000Z"
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-    {
-        "content-type": "application/json; dcp-type=\"metadata/project\"",
-        "crc32c": "1b63912f",
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-        "name": "project_0.json",
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-    {
-        "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-        "crc32c": "b7b8f50f",
-        "indexed": true,
-        "name": "dissociation_protocol_0.json",
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-        "uuid": "644c5f2d-33c8-4bf4-b411-b2dbec8b8227",
-        "version": "2018-10-07T115850.413000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-        "crc32c": "076cf3c4",
-        "indexed": true,
-        "name": "collection_protocol_0.json",
-        "s3_etag": "4851e0601f479550bb68e6c1f92b15ce",
-        "sha1": "e3b0565d7dca00a513b607d8218f511ee27691c8",
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-        "size": 716,
-        "uuid": "403b586f-fd8d-45f2-a431-4bb6cc33d7d4",
-        "version": "2018-10-07T115850.563000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-        "crc32c": "51f9d7f0",
-        "indexed": true,
-        "name": "enrichment_protocol_1.json",
-        "s3_etag": "055a83f481596882b8798897ee50d781",
-        "sha1": "9aa0c45b79a32c98ab6ea18b463d505662389a92",
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-        "uuid": "9ab53e6a-464e-44b1-aa24-12daca989969",
-        "version": "2018-10-07T115850.474000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/process\"",
-        "crc32c": "bec07d53",
-        "indexed": true,
-        "name": "process_0.json",
-        "s3_etag": "feed82fc2af4e32d7f91b029109d7860",
-        "sha1": "ab75c100a5336e0d69966303b88185008be48963",
-        "sha256": "75270eceb8c411a386f9793196cb96a23d9e644bb53a3925f863b475956e862a",
-        "size": 465,
-        "uuid": "18d49b08-d095-4371-bb34-151037f9f461",
-        "version": "2018-10-07T120828.754000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/process\"",
-        "crc32c": "5e38608b",
-        "indexed": true,
-        "name": "process_1.json",
-        "s3_etag": "c1b135ffd9ea0c6d0c8c70b3ad808ec3",
-        "sha1": "11a2ba86e5e6b994a993451cf54964c27c9edcce",
-        "sha256": "2e58428d74c3e07db41cbe954630ceb2e2840d822ba09ac7245b8ae8186dc482",
-        "size": 391,
-        "uuid": "d13a5a85-b8c7-4a07-9c0c-9180bd0a78eb",
-        "version": "2018-10-07T120652.636000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/process\"",
-        "crc32c": "078475f9",
-        "indexed": true,
-        "name": "process_2.json",
-        "s3_etag": "1c0345db2437b44dc1fcb017929e0461",
-        "sha1": "bbef6705b342d6be7b5b7860ee57a68c7524c769",
-        "sha256": "70a79f92be2a19ddd63fc4369c79770808072151396c3b88abbcfaa9edef50f8",
-        "size": 430,
-        "uuid": "5a15ed38-5e37-44ff-ba35-0d17bb8564bd",
-        "version": "2018-10-07T120517.018000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/links\"",
-        "crc32c": "56d56718",
-        "indexed": true,
-        "name": "links.json",
-        "s3_etag": "70623328382d0927e3242efc726fe29d",
-        "sha1": "a947b0283b948cf08e1197064506bfa2491d8b3a",
-        "sha256": "0bc6c6fa6a9093caddd8a4921826cd47c6a0773312cc62f51abcd55f93e52ecb",
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-        "uuid": "a1681a39-e8d2-43f7-8781-ac4edab527fe",
-        "version": "2018-10-07T130110.624725Z"
-    },
-    {
-        "content-type": "application/gzip; dcp-type=data",
-        "crc32c": "a3f89844",
-        "indexed": false,
-        "name": "SRR6260013.fastq.gz",
-        "s3_etag": "8c9bb4704875cbe67cfc12abb0c66d57",
-        "sha1": "ee681bf47c0b7fbad663b20704ddb45d632709ed",
-        "sha256": "3f50829dc75cbb1e5a95403fe59e1f3bc4e897e5fbf1bb3c5861854eafa5b84c",
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-        "uuid": "9dee7111-d743-43a1-b768-118614bf7987",
-        "version": "2018-10-07T130110.968810Z"
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-]
diff --git a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018/2018-10-07T130111.835234Z/metadata.json b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018/2018-10-07T130111.835234Z/metadata.json
deleted file mode 100644
index c3c7e596c..000000000
--- a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018/2018-10-07T130111.835234Z/metadata.json
+++ /dev/null
@@ -1,476 +0,0 @@
-{
-    "cell_suspension_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "Single-cell_RNA-seq_Subject9_TEMRA_Cell030",
-            "biomaterial_name": "Single-cell_RNA-seq_Subject9_TEMRA_Cell030",
-            "biomaterial_description": "Single-cell_RNA-seq_Subject9_TEMRA_Cell030",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "insdc_biomaterial": "SRS2664188"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "selected_cell_type": [
-            {
-                "text": "TEMRA",
-                "ontology": "CL:0000625"
-            }
-        ],
-        "total_estimated_cells": 1,
-        "plate_based_sequencing": {
-            "plate_id": "subject9-10_batch1",
-            "cell_quality": "OK"
-        },
-        "provenance": {
-            "document_id": "ef97eef1-a436-4462-a152-1a2b86ee8831",
-            "submission_date": "2018-10-07T11:57:52.282Z",
-            "update_date": "2018-10-07T12:04:46.292Z"
-        }
-    },
-    "specimen_from_organism_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "Subject9_DENV negative_PBMC_TEMRA",
-            "biomaterial_name": "Subject9_DENV negative_PBMC_TEMRA",
-            "biomaterial_description": "Subject9_DENV negative_PBMC_TEMRA",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "organ": {
-            "text": "blood",
-            "ontology": "UBERON:0000178"
-        },
-        "organ_part": {
-            "text": "peripheral blood mononuclear cell",
-            "ontology": "CL:2000001"
-        },
-        "preservation_storage": {
-            "preservation_method": "cryopreservation, other",
-            "storage_method": "frozen, liquid nitrogen"
-        },
-        "provenance": {
-            "document_id": "80cb479b-dcb4-4dbb-a75d-0249a964bb70",
-            "submission_date": "2018-10-07T11:56:59.350Z",
-            "update_date": "2018-10-07T12:01:39.672Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "Subject9",
-            "biomaterial_name": "Subject9",
-            "biomaterial_description": "Subject9",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "genotype": "not provided"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606"
-            }
-        ],
-        "is_living": "yes",
-        "sex": "unknown",
-        "medical_history": {
-            "test_results": "dengue virus negative"
-        },
-        "diseases": [
-            {
-                "text": "normal",
-                "ontology": "PATO:0000461"
-            }
-        ],
-        "development_stage": {
-            "text": "adult",
-            "ontology": "EFO:0001272"
-        },
-        "organism_age": "18-60",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036"
-        },
-        "provenance": {
-            "document_id": "6c992ba4-c132-4dd3-840e-13cf3f38243e",
-            "submission_date": "2018-10-07T11:56:59.023Z",
-            "update_date": "2018-10-07T12:00:40.749Z"
-        }
-    },
-    "sequence_file_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/6.5.2/sequence_file",
-        "schema_type": "file",
-        "file_core": {
-            "file_name": "SRR6260013.fastq.gz",
-            "file_format": "fastq.gz"
-        },
-        "read_index": "read1",
-        "read_length": 50,
-        "insdc_run": [
-            "SRR6260013"
-        ],
-        "provenance": {
-            "document_id": "f3d5c7cb-7ab4-4903-8e0e-dc942121fe27",
-            "submission_date": "2018-10-07T11:58:46.814Z",
-            "update_date": "2018-10-07T12:08:49.204Z"
-        }
-    },
-    "project_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/project/9.0.3/project",
-        "schema_type": "project",
-        "project_core": {
-            "project_short_name": "CD4+ cytotoxic T lymphocytes",
-            "project_title": "Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis",
-            "project_description": "CD4+ cytotoxic T lymphocytes (CD4-CTLs) have been reported to play a protective role in several viral infections. However, little is known in humans about the biology of CD4-CTL generation, their functional properties, heterogeneity and clonal diversity, especially in relation to other well-described CD4+ memory T cell subsets. We performed single-cell RNA-seq in over 9000 cells to unravel CD4-CTL heterogeneity, transcriptional profile and clonality in humans. The single-cell differential gene expression analysis, revealed a spectrum of known transcripts, including several linked to cytotoxic and co-stimulatory function, and transcripts of unknown cytotoxicity-related function that are expressed at higher levels in the TEMRA subset, which is highly enriched for CD4-CTLs, compared to cells in the central and effector memory subsets (TCM, TEM). Simultaneous T cells antigen receptor (TCR) analysis in single-cells and bulk subsets revealed that CD4-TEMRA cells show marked clonal expansion compared to TCM and TEM cells and that the majority of CD4-TEMRA were dengue virus (DENV)-specific in subjects with previous DENV infection. The profile of CD4-TEMRA was highly heterogeneous across subjects, with four distinct clusters identified by the single-cell analysis. Most importantly, we identified distinct clusters of CD4-CTL effector and precursor cells in the TEMRA subset; the precursor cells shared TCR clonotypes with CD4-CTL effectors and were distinguished by high expression of the interleukin-7 receptor. Our identification of a CD4-CTL precursor population may allow further investigation of how CD4-CTLs arise in humans and thus could provide insights into the mechanisms that may be utilized to generate durable and effective CD4-CTL immunity."
-        },
-        "insdc_project": "SRP124157",
-        "geo_series": "GSE106540",
-        "insdc_study": "PRJNA417191",
-        "supplementary_links": [
-            "https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-106540/Results"
-        ],
-        "contributors": [
-            {
-                "contact_name": "Pandurangan,,Vijayanand",
-                "email": "vijay@lji.org",
-                "institution": "La Jolla Institute for Allergy and Immunology",
-                "laboratory": "Division of Vaccine Discovery",
-                "address": "La Jolla, CA 92037",
-                "country": "USA",
-                "corresponding_contributor": true
-            },
-            {
-                "contact_name": "Mallory,Ann,Freeberg",
-                "email": "mfreeberg@ebi.ac.uk",
-                "institution": "EMBL-EBI",
-                "laboratory": "Human Cell Atlas Data Coordination Platform",
-                "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                "country": "UK",
-                "project_role": "Human Cell Atlas wrangler",
-                "orcid_id": "0000-0003-2949-3921",
-                "corresponding_contributor": false
-            },
-            {
-                "contact_name": "Laura,,Huerta",
-                "email": "lauhuema@ebi.ac.uk",
-                "institution": "EMBL-EBI",
-                "laboratory": "Molecular Atlas",
-                "address": "Wellcome Trust Genome Campus, Cambridge UK",
-                "country": "UK",
-                "project_role": "external curator",
-                "orcid_id": "0000-0002-8748-599X",
-                "corresponding_contributor": false
-            }
-        ],
-        "funders": [
-            {
-                "grant_id": "U19AI118626",
-                "funder_name": "National Institutes of Health (NIH)"
-            },
-            {
-                "grant_id": "U19AI118610",
-                "funder_name": "National Institutes of Health (NIH)"
-            },
-            {
-                "grant_id": "R01HL114093",
-                "funder_name": "National Institutes of Health (NIH)"
-            },
-            {
-                "grant_id": "R24AI108564",
-                "funder_name": "National Institutes of Health (NIH)"
-            },
-            {
-                "funder_name": "William K. Bowes Jr. Foundation"
-            }
-        ],
-        "publications": [
-            {
-                "authors": [
-                    "Patil VS",
-                    "Madrigal A",
-                    "Schmiedel BJ",
-                    "Clarke J",
-                    "ORourke P",
-                    "Harris E",
-                    "de Silva AD",
-                    "Harris E",
-                    "Peters B",
-                    "Seumois G",
-                    "Weiskopf D",
-                    "Sette A",
-                    "Vijayanand P"
-                ],
-                "publication_title": "Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis.",
-                "doi": "10.1126/sciimmunol.aan8664",
-                "pmid": 29352091,
-                "publication_url": "http://immunology.sciencemag.org/content/3/19/eaan8664.long"
-            }
-        ],
-        "provenance": {
-            "document_id": "519b58ef-6462-4ed3-8c0d-375b54f53c31",
-            "submission_date": "2018-10-07T11:56:58.869Z",
-            "update_date": "2018-10-07T12:00:40.290Z"
-        }
-    },
-    "library_preparation_protocol_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/4.3.3/library_preparation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "library_preparation_protocol_1",
-            "protocol_name": "Preparation of mRNAs for single cell SmartSeq2 sequencing",
-            "protocol_description": "Single cell RNAseq was performed as described in Picelli et al.Nat Protoc. 2014, PMID:24385147. We performed 23 cycles of amplification. Barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina) were prepared as following manufacturers protocol.",
-            "publication_doi": "10.1038/nprot.2014.006"
-        },
-        "library_construction_approach": {
-            "text": "Smart-seq2",
-            "ontology": "EFO:0008931"
-        },
-        "nucleic_acid_source": "single cell",
-        "end_bias": "full length",
-        "primer": "poly-dT",
-        "strand": "unstranded",
-        "input_nucleic_acid_molecule": {
-            "text": "polyA RNA",
-            "ontology": "OBI:0000869"
-        },
-        "library_construction_kit": {
-            "retail_name": "Nextera XT library preparation kit",
-            "manufacturer": "Illumina"
-        },
-        "library_preamplification_method": {
-            "text": "PCR",
-            "ontology": "OBI:0000415"
-        },
-        "provenance": {
-            "document_id": "5f82b9c4-f3d7-410c-b843-0e5cdec9efa5",
-            "submission_date": "2018-10-07T11:58:47.200Z",
-            "update_date": "2018-10-07T11:58:50.532Z"
-        }
-    },
-    "sequencing_protocol_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "sequencing_protocol_1",
-            "protocol_name": "SmartSeq 2 single cell sequencing",
-            "protocol_description": "Libraries were sequenced on the Illumina HiSeq 2500 platform to obtain 50-bp single end reads (barcoded Illumina sequencing libraries (Nextera XT library preparation kit, Illumina))."
-        },
-        "sequencing_approach": {
-            "text": "full length single cell RNA sequencing",
-            "ontology": "EFO:0008441"
-        },
-        "instrument_manufacturer_model": {
-            "text": "Illumina HiSeq 2500",
-            "ontology": "EFO:0008565"
-        },
-        "paired_end": false,
-        "provenance": {
-            "document_id": "d678165b-2753-4393-bf3b-5e2a09ba892c",
-            "submission_date": "2018-10-07T11:58:47.211Z",
-            "update_date": "2018-10-07T11:58:50.511Z"
-        }
-    },
-    "dissociation_protocol_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "dissociation_protocol_1",
-            "protocol_name": "Dissociation by FACS into single cells",
-            "protocol_description": "Dissociation by FACS into single cells",
-            "publication_doi": "10.1126/sciimmunol.aan8664"
-        },
-        "dissociation_method": {
-            "text": "fluorescence-activated cell sorting",
-            "ontology": "EFO:0009108"
-        },
-        "provenance": {
-            "document_id": "920078d0-b17e-4f23-8cf6-0674b19e7bec",
-            "submission_date": "2018-10-07T11:58:47.100Z",
-            "update_date": "2018-10-07T11:58:50.432Z"
-        }
-    },
-    "enrichment_protocol_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "enrichment_protocol_2",
-            "protocol_name": "TEMRA Enrichment",
-            "protocol_description": "For single-cell RNA-seq experiments, live and singlet gated cells were further gated to sort 1) TCM; CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA-CCR7+, 2) TEM; CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA-CCR7-, 3) TEMRA; CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA+CCR7-, 4) IL-7Rhigh TEMRA (CD4-CTL precursors); CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA+CCR7-CD127high, 5) IL-7R- TEMRA (CD4-CTL effectors); CD3+CD4+CD8\u03b1/CD14/CD19-CD45RA+CCR7- CD127-. Single cells were directly sorted into 96 well plate with lysis buffer for downstream processing using Smart-seq2 method",
-            "publication_doi": "10.1126/sciimmunol.aan8664"
-        },
-        "enrichment_method": {
-            "text": "fluorescence-activated cell sorting",
-            "ontology": "EFO:0009108"
-        },
-        "markers": "CD3+ CD4+ CD8alpha/CD14/CD19- CD45RA+ CCR7-",
-        "provenance": {
-            "document_id": "644c5f2d-33c8-4bf4-b411-b2dbec8b8227",
-            "submission_date": "2018-10-07T11:58:47.120Z",
-            "update_date": "2018-10-07T11:58:50.413Z"
-        }
-    },
-    "collection_protocol_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/8.2.6/collection_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "collection_protocol_2",
-            "protocol_name": "Blood sample collection",
-            "protocol_description": "Blood sample collection by blood draw",
-            "publication_doi": "10.1126/sciimmunol.aan8664"
-        },
-        "collection_method": {
-            "text": "blood draw",
-            "ontology": "EFO:0009121"
-        },
-        "provenance": {
-            "document_id": "403b586f-fd8d-45f2-a431-4bb6cc33d7d4",
-            "submission_date": "2018-10-07T11:58:47.087Z",
-            "update_date": "2018-10-07T11:58:50.563Z"
-        }
-    },
-    "enrichment_protocol_1.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "enrichment_protocol_1",
-            "protocol_name": "PBMC Enrichment",
-            "protocol_description": "Enrichment for peripheral blood mononuclear cells",
-            "publication_doi": "10.1073/pnas.1305227110"
-        },
-        "enrichment_method": {
-            "text": "Ficoll-Hypaque method",
-            "ontology": "EFO:0009110"
-        },
-        "provenance": {
-            "document_id": "9ab53e6a-464e-44b1-aa24-12daca989969",
-            "submission_date": "2018-10-07T11:58:47.110Z",
-            "update_date": "2018-10-07T11:58:50.474Z"
-        }
-    },
-    "process_0.json": {
-        "insdc_experiment": {
-            "insdc_experiment": "SRX3366459"
-        },
-        "process_core": {
-            "process_id": "process_id_4499"
-        },
-        "schema_type": "process",
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/process/6.0.2/process",
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diff --git a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
new file mode 100644
index 000000000..15a52e8e6
--- /dev/null
+++ b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
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+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "Q4_DEMO-cellsus_SAMN02797092",
+                "ncbi_taxon_id": [
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+                ]
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+        },
+        "specimen_from_organism_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.2.7/specimen_from_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "Q4_DEMO-sample_SAMN02797092",
+                "biomaterial_name": "Q4_DEMO-Single cell mRNA-seq_MGH30_A01",
+                "ncbi_taxon_id": [
+                    9606
+                ],
+                "supplementary_files": [
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+                ]
+            },
+            "genus_species": [
+                {
+                    "text": "Homo sapiens"
+                }
+            ],
+            "organ": {
+                "text": "brain",
+                "ontology": "UBERON:0000955"
+            },
+            "organ_part": {
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+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "Q4_DEMO-donor_MGH30",
+                "biomaterial_name": "Q4 DEMO donor MGH30",
+                "ncbi_taxon_id": [
+                    9606
+                ]
+            },
+            "medical_history": {
+                "smoking_history": "yes"
+            },
+            "genus_species": [
+                {
+                    "text": "Homo sapiens"
+                }
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+            "sex": "unknown",
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+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/6.5.0/sequence_file",
+            "schema_type": "file",
+            "file_core": {
+                "file_name": "R2.fastq.gz",
+                "file_format": "fastq.gz"
+            },
+            "read_index": "read2",
+            "lane_index": 1,
+            "provenance": {
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+                "submission_date": "2018-09-05T18:24:05.995Z",
+                "update_date": "2018-09-05T18:25:10.316Z"
+            }
+        },
+        "project_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/project/9.0.0/project",
+            "schema_type": "project",
+            "project_core": {
+                "project_short_name": "integration/Smart-seq2/2018-09-05T18:24:03Z",
+                "project_title": "Q4_DEMO-Single cell RNA-seq of primary human glioblastomas",
+                "project_description": "Q4_DEMO-We report transcriptomes from 430 single glioblastoma cells isolated from 5 individual tumors and 102 single cells from gliomasphere cells lines generated using SMART-seq. In addition, we report population RNA-seq from the five tumors as well as RNA-seq from cell lines derived from 3 tumors (MGH26, MGH28, MGH31) cultured under serum free (GSC) and differentiated (DGC) conditions. This dataset highlights intratumoral heterogeneity with regards to the expression of de novo derived transcriptional modules and established subtype classifiers. Overall design: Operative specimens from five glioblastoma patients (MGH26, MGH28, MGH29, MGH30, MGH31) were acutely dissociated, depleted for CD45+ inflammatory cells and then sorted as single cells (576 samples). Population controls for each tumor were isolated by sorting 2000-10000 cells and processed in parallel (5 population control samples). Single cells from two established cell lines, GBM6 and GBM8, were also sorted as single cells (192 samples). SMART-seq protocol was implemented to generate single cell full length transcriptomes (modified from Shalek, et al Nature 2013) and sequenced using 25 bp paired end reads. Single cell cDNA libraries for MGH30 were resequenced using 100 bp paired end reads to allow for isoform and splice junction reconstruction (96 samples, annotated MGH30L). Cells were also cultured in serum free conditions to generate gliomasphere cell lines for MGH26, MGH28, and MGH31 (GSC) which were then differentiated using 10% serum (DGC). Population RNA-seq was performed on these samples (3 GSC, 3 DGC, 6 total). The initial dataset included 875 RNA-seq libraries (576 single glioblastoma cells, 96 resequenced MGH30L, 192 single gliomasphere cells, 5 tumor population controls, 6 population libraries from GSC and DGC samples). Data was processed as described below using RSEM for quantification of gene expression. 5,948 genes with the highest composite expression either across all single cells combined (average log2(TPM)>4.5) or within a single tumor (average log2(TPM)>6 in at least one tumor) were included. Cells expressing less than 2,000 of these 5,948 genes were excluded. The final processed dataset then included 430 primary single cell glioblastoma transcriptomes, 102 single cell transcriptomes from cell lines(GBM6,GBM8), 5 population controls (1 for each tumor), and 6 population libraries from cell lines derived from the tumors (GSC and DGC for MGH26, MGH28 and MGH31). The final matrix (GBM_data_matrix.txt) therefore contains 5948 rows (genes) quantified in 543 samples (columns). Please note that the samples which are not included in the data processing are indicated in the sample description field."
+            },
+            "contributors": [
+                {
+                    "contact_name": "Q4_DEMO-MintTeam",
+                    "email": "dummy@email.com",
+                    "institution": "Fake Institution"
+                }
+            ],
+            "provenance": {
+                "document_id": "bedfd14f-cc98-4142-b627-d44dfec5aced",
+                "submission_date": "2018-09-05T18:24:05.880Z",
+                "update_date": "2018-09-05T18:24:10.105Z"
+            }
+        },
+        "library_preparation_protocol_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/4.3.0/library_preparation_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "preparation1"
+            },
+            "input_nucleic_acid_molecule": {
+                "text": "polyA RNA"
+            },
+            "library_construction_approach": {
+                "text": "Smart-seq2",
+                "ontology": "EFO:0008931"
+            },
+            "nucleic_acid_source": "single cell",
+            "end_bias": "5 prime end bias",
+            "primer": "poly-dT",
+            "strand": "unstranded",
+            "provenance": {
+                "document_id": "f77e65be-ca7a-4711-a7a9-701ad372901a",
+                "submission_date": "2018-09-05T18:24:06.041Z",
+                "update_date": "2018-09-05T18:24:09.959Z"
+            }
+        },
+        "sequencing_protocol_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/9.0.0/sequencing_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "assay_1"
+            },
+            "instrument_manufacturer_model": {
+                "text": "Illumina HiSeq 2500"
+            },
+            "paired_end": true,
+            "sequencing_approach": {
+                "text": "full length single cell RNA sequencing",
+                "ontology": "EFO:0008441"
+            },
+            "provenance": {
+                "document_id": "9d3c0c92-2716-410b-85c6-963a29c24fe0",
+                "submission_date": "2018-09-05T18:24:06.050Z",
+                "update_date": "2018-09-05T18:24:09.960Z"
+            }
+        },
+        "dissociation_protocol_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.1/dissociation_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "dissociation_1",
+                "protocol_name": "a FACS method to separate cells"
+            },
+            "dissociation_method": {
+                "text": "fluorescence-activated cell sorting",
+                "ontology": "EFO:0009108"
+            },
+            "provenance": {
+                "document_id": "d08422cf-7d04-46cd-9452-394bb2864ba7",
+                "submission_date": "2018-09-05T18:24:06.024Z",
+                "update_date": "2018-09-05T18:24:10.036Z"
+            }
+        },
+        "enrichment_protocol_0.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.3/enrichment_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "enrichment1"
+            },
+            "enrichment_method": {
+                "text": "fluorescence-activated cell sorting",
+                "ontology": "EFO:0009108"
+            },
+            "provenance": {
+                "document_id": "f3304cfe-c133-444c-a2db-92294d3f6a4d",
+                "submission_date": "2018-09-05T18:24:06.033Z",
+                "update_date": "2018-09-05T18:24:09.887Z"
+            }
+        },
+        "process_0.json": {
+            "process_core": {
+                "process_id": "sequence_process_file_1"
+            },
+            "schema_type": "process",
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/process/6.0.0/process",
+            "provenance": {
+                "document_id": "bf7360ae-511e-4803-821e-c03167107588",
+                "submission_date": "2018-09-05T18:24:06.090Z",
+                "update_date": "2018-09-05T18:24:09.872Z"
+            }
+        },
+        "process_1.json": {
+            "process_core": {
+                "process_id": "process_id_2"
+            },
+            "schema_type": "process",
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/process/6.0.0/process",
+            "provenance": {
+                "document_id": "b78f4279-9c6f-49da-890f-98499d8fb84a",
+                "submission_date": "2018-09-05T18:24:06.079Z",
+                "update_date": "2018-09-05T18:24:09.856Z"
+            }
+        },
+        "process_2.json": {
+            "process_core": {
+                "process_id": "process_id_1"
+            },
+            "schema_type": "process",
+            "describedBy": "http://schema.staging.data.humancellatlas.org/type/process/6.0.0/process",
+            "provenance": {
+                "document_id": "6284381f-de72-4015-ae51-fa17e13677f8",
+                "submission_date": "2018-09-05T18:24:06.058Z",
+                "update_date": "2018-09-05T18:24:09.861Z"
+            }
+        },
+        "links.json": {
+            "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.1/links",
+            "schema_type": "link_bundle",
+            "schema_version": "1.1.1",
+            "links": [
+                {
+                    "process": "bf7360ae-511e-4803-821e-c03167107588",
+                    "inputs": [
+                        "a31a0e93-5be4-44b8-b152-9e25b066e1e5"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "20474552-c0a3-471e-8fa0-d3c5aa05c017",
+                        "177a9d2c-99d4-4fb6-aab7-5869923e9d6a"
+                    ],
+                    "output_type": "file",
+                    "protocols": [
+                        {
+                            "protocol_type": "library_preparation_protocol",
+                            "protocol_id": "f77e65be-ca7a-4711-a7a9-701ad372901a"
+                        },
+                        {
+                            "protocol_type": "sequencing_protocol",
+                            "protocol_id": "9d3c0c92-2716-410b-85c6-963a29c24fe0"
+                        }
+                    ]
+                },
+                {
+                    "process": "b78f4279-9c6f-49da-890f-98499d8fb84a",
+                    "inputs": [
+                        "e964f81f-54d9-4600-a9e9-981b1f1a6ca2"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "a31a0e93-5be4-44b8-b152-9e25b066e1e5"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "dissociation_protocol",
+                            "protocol_id": "d08422cf-7d04-46cd-9452-394bb2864ba7"
+                        },
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "f3304cfe-c133-444c-a2db-92294d3f6a4d"
+                        }
+                    ]
+                },
+                {
+                    "process": "6284381f-de72-4015-ae51-fa17e13677f8",
+                    "inputs": [
+                        "c6001597-990c-4753-80bb-c5a01c9dda0d"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "e964f81f-54d9-4600-a9e9-981b1f1a6ca2"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": []
+                }
+            ]
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab/2018-09-05T182535.846470Z/manifest.json b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab/2018-09-05T182535.846470Z/manifest.json
deleted file mode 100644
index 781d94c59..000000000
--- a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab/2018-09-05T182535.846470Z/manifest.json
+++ /dev/null
@@ -1,194 +0,0 @@
-[
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "d4f5cd12",
-        "indexed": true,
-        "name": "cell_suspension_0.json",
-        "s3_etag": "5e8254dfdffffd29565733dd2cfffcaa",
-        "sha1": "0781fe1a5664f0c551a2f1abb2405b42e545ba2f",
-        "sha256": "18a711089e7e7521167480ff618cbe359a3ead6acfb9042e95345c7d4e361330",
-        "size": 483,
-        "uuid": "a31a0e93-5be4-44b8-b152-9e25b066e1e5",
-        "version": "2018-09-05T182529.829436Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "3a5dcf9f",
-        "indexed": true,
-        "name": "specimen_from_organism_0.json",
-        "s3_etag": "bab34095b45b908e90af42b38a100610",
-        "sha1": "351a584cf4b86f310e342e4b1aee46ee9c7ed4ee",
-        "sha256": "fc5db431a010774ea3f44b550f40d2506cbef3333234a6f97925d3fa06856152",
-        "size": 979,
-        "uuid": "e964f81f-54d9-4600-a9e9-981b1f1a6ca2",
-        "version": "2018-09-05T182530.509615Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "b2a8ddd4",
-        "indexed": true,
-        "name": "donor_organism_0.json",
-        "s3_etag": "64a3df1095f7ad856316df6a7cc3769b",
-        "sha1": "0c5fdd8242ca2b47ab6b45588499756b3792adcd",
-        "sha256": "4e37a6623bf54545f79e81c1f00138b097f1bf9effff5b8779cc7aab05a90172",
-        "size": 720,
-        "uuid": "c6001597-990c-4753-80bb-c5a01c9dda0d",
-        "version": "2018-09-05T182530.753141Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "07762f9b",
-        "indexed": true,
-        "name": "sequence_file_0.json",
-        "s3_etag": "e080db2a9bad61cc224b431bc19d6ee1",
-        "sha1": "50acb0b71506f7d33e21a569a8c948de0d2ffa0d",
-        "sha256": "6d85b91099ccf7cc0885b7768a4ad0bba1976142607febeae3a126fb3f49d822",
-        "size": 466,
-        "uuid": "20474552-c0a3-471e-8fa0-d3c5aa05c017",
-        "version": "2018-09-05T182531.434373Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "a48d67f8",
-        "indexed": true,
-        "name": "sequence_file_1.json",
-        "s3_etag": "42558005fcec60f60eba431070911579",
-        "sha1": "74b69311babd0340193b2a7badf95933da48ed13",
-        "sha256": "ae586e31de46482795e445d86b72a64445dffbda6caf63eee9f030e0fbbc42e4",
-        "size": 466,
-        "uuid": "177a9d2c-99d4-4fb6-aab7-5869923e9d6a",
-        "version": "2018-09-05T182531.758479Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/project\"",
-        "crc32c": "cb5778fc",
-        "indexed": true,
-        "name": "project_0.json",
-        "s3_etag": "59ff33c4be479e7d1e533f4226eee790",
-        "sha1": "773758a3ad93e4739b8b2b95d62dfaa2f34b96b1",
-        "sha256": "13b631dd0391b76855ab62813b9b89ff266505c1a32d3fd25b37f6b863696331",
-        "size": 3447,
-        "uuid": "bedfd14f-cc98-4142-b627-d44dfec5aced",
-        "version": "2018-09-05T182532.053288Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-        "crc32c": "7991780e",
-        "indexed": true,
-        "name": "library_preparation_protocol_0.json",
-        "s3_etag": "971b2da85e96e0e0c97c32961e5a7759",
-        "sha1": "7b28867a79c2ebee2d65c36e25b7ea2fc1e2f184",
-        "sha256": "26f468e4b48171408932bedeba4d566ad0f90bce485e901f979056231f99da78",
-        "size": 737,
-        "uuid": "f77e65be-ca7a-4711-a7a9-701ad372901a",
-        "version": "2018-09-05T182532.367703Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-        "crc32c": "8f1349fc",
-        "indexed": true,
-        "name": "sequencing_protocol_0.json",
-        "s3_etag": "0580202fa550118fbf296ff1e7be07c7",
-        "sha1": "c61aea8b5343c254384ecc8c2e1068ba03f5c68d",
-        "sha256": "35be2f7be3b0f668fbf6266670659a56c438fb3c92321647c177f62a3ebb8ee3",
-        "size": 646,
-        "uuid": "9d3c0c92-2716-410b-85c6-963a29c24fe0",
-        "version": "2018-09-05T182532.806226Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-        "crc32c": "9d493dd1",
-        "indexed": true,
-        "name": "dissociation_protocol_0.json",
-        "s3_etag": "fe728c06f0155a281a7cd7c262e67576",
-        "sha1": "a887d082c83bbebfd86921ecbc3d0fcdc5cdf938",
-        "sha256": "cdf539ca7aa9daf909e1aaeec294da31d4cb9180db3f3a6a91ba8089701b2fab",
-        "size": 616,
-        "uuid": "d08422cf-7d04-46cd-9452-394bb2864ba7",
-        "version": "2018-09-05T182533.118298Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-        "crc32c": "87ed3a2e",
-        "indexed": true,
-        "name": "enrichment_protocol_0.json",
-        "s3_etag": "cba92494442a5fed8fe32c90c007845d",
-        "sha1": "798f4e6b3408538d1d6fb34a39cbcff5e3652634",
-        "sha256": "d7489161783fbb31702e8b42d00e9783cdf89f879d3606a48d9fca668c382ea2",
-        "size": 549,
-        "uuid": "f3304cfe-c133-444c-a2db-92294d3f6a4d",
-        "version": "2018-09-05T182533.623990Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/process\"",
-        "crc32c": "7e86bd3e",
-        "indexed": true,
-        "name": "process_0.json",
-        "s3_etag": "cde6f57b10bbf2fd2ef0d113b1f1ba46",
-        "sha1": "04e75ecff86fd496a46893fca40a94f69ca08ab0",
-        "sha256": "ca18f50c068bf1e4dccc425eb04396f2f3970e5ae45de5d90339bb1fdd961e71",
-        "size": 399,
-        "uuid": "bf7360ae-511e-4803-821e-c03167107588",
-        "version": "2018-09-05T182533.917284Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/process\"",
-        "crc32c": "b4aa6e39",
-        "indexed": true,
-        "name": "process_1.json",
-        "s3_etag": "2346a2c4650ff05cd589aa7c0ece8684",
-        "sha1": "e41eeef27f8064a47fb575a2e367cf2a23075069",
-        "sha256": "d8681a89bfd3d0a4491e4bed969683f7bf69868d1fd132afdb4d109812455ca9",
-        "size": 388,
-        "uuid": "b78f4279-9c6f-49da-890f-98499d8fb84a",
-        "version": "2018-09-05T182534.250294Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/process\"",
-        "crc32c": "51ee448d",
-        "indexed": true,
-        "name": "process_2.json",
-        "s3_etag": "636cdff0ff32a4802c1a553fc8eae22b",
-        "sha1": "818b0e257652e179fe023945117b89e16b3ba807",
-        "sha256": "faaeaab765ff6dd7cfbfb42bd4b276f85222bd635c595429ec6ab9c5f4efbdf1",
-        "size": 388,
-        "uuid": "6284381f-de72-4015-ae51-fa17e13677f8",
-        "version": "2018-09-05T182534.886667Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/links\"",
-        "crc32c": "ac18a06b",
-        "indexed": true,
-        "name": "links.json",
-        "s3_etag": "46cce577c8cfc281c8e33233f0366f99",
-        "sha1": "da4381b79641d4de4fe15ff2e7385aa75b79d79f",
-        "sha256": "0d881b169fbc809219d9eaf6b1c77349b9bbd298ac5c7ce9714517f01ca47a0b",
-        "size": 2095,
-        "uuid": "d33848ba-a9f8-4aa9-a72c-26755f0273d1",
-        "version": "2018-09-05T182535.148513Z"
-    },
-    {
-        "content-type": "application/gzip; dcp-type=data",
-        "crc32c": "4ef74578",
-        "indexed": false,
-        "name": "R1.fastq.gz",
-        "s3_etag": "c7bbee4c46bbf29432862e05830c8f39",
-        "sha1": "17f8b4be0cc6e8281a402bb365b1283b458906a3",
-        "sha256": "fe6d4fdfea2ff1df97500dcfe7085ac3abfb760026bff75a34c20fb97a4b2b29",
-        "size": 125191,
-        "uuid": "2580e8f2-f2f8-4292-b14d-c9ae8bd25a4e",
-        "version": "2018-09-05T182535.418417Z"
-    },
-    {
-        "content-type": "application/gzip; dcp-type=data",
-        "crc32c": "69987b3e",
-        "indexed": false,
-        "name": "R2.fastq.gz",
-        "s3_etag": "a3a9f23d07cfc5e40a4c3a8adf3903ae",
-        "sha1": "f166b6952e30a41e1409e7fb0cb0fb1ad93f3f21",
-        "sha256": "c305bee37b3c3735585e11306272b6ab085f04cd22ea8703957b4503488cfeba",
-        "size": 130024,
-        "uuid": "a53ef014-85f1-4ea8-b24a-454328724e77",
-        "version": "2018-09-05T182535.627826Z"
-    }
-]
diff --git a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab/2018-09-05T182535.846470Z/metadata.json b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab/2018-09-05T182535.846470Z/metadata.json
deleted file mode 100644
index 5d79269d7..000000000
--- a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab/2018-09-05T182535.846470Z/metadata.json
+++ /dev/null
@@ -1,305 +0,0 @@
-{
-    "cell_suspension_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.4.0/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "Q4_DEMO-cellsus_SAMN02797092",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "provenance": {
-            "document_id": "a31a0e93-5be4-44b8-b152-9e25b066e1e5",
-            "submission_date": "2018-09-05T18:24:05.915Z",
-            "update_date": "2018-09-05T18:24:09.865Z"
-        }
-    },
-    "specimen_from_organism_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.2.7/specimen_from_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "Q4_DEMO-sample_SAMN02797092",
-            "biomaterial_name": "Q4_DEMO-Single cell mRNA-seq_MGH30_A01",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "supplementary_files": [
-                "Q4_DEMO-protocol"
-            ]
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens"
-            }
-        ],
-        "organ": {
-            "text": "brain",
-            "ontology": "UBERON:0000955"
-        },
-        "organ_part": {
-            "text": "temporal lobe",
-            "ontology": "UBERON:0001871"
-        },
-        "disease": [
-            {
-                "text": "glioblastoma"
-            }
-        ],
-        "provenance": {
-            "document_id": "e964f81f-54d9-4600-a9e9-981b1f1a6ca2",
-            "submission_date": "2018-09-05T18:24:05.907Z",
-            "update_date": "2018-09-05T18:24:10.111Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.0.0/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "Q4_DEMO-donor_MGH30",
-            "biomaterial_name": "Q4 DEMO donor MGH30",
-            "ncbi_taxon_id": [
-                9606
-            ]
-        },
-        "medical_history": {
-            "smoking_history": "yes"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens"
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-        "is_living": "no",
-        "sex": "unknown",
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-            "update_date": "2018-09-05T18:24:09.957Z"
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-        "schema_type": "file",
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-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/6.5.0/sequence_file",
-        "schema_type": "file",
-        "file_core": {
-            "file_name": "R2.fastq.gz",
-            "file_format": "fastq.gz"
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-            "document_id": "177a9d2c-99d4-4fb6-aab7-5869923e9d6a",
-            "submission_date": "2018-09-05T18:24:05.995Z",
-            "update_date": "2018-09-05T18:25:10.316Z"
-        }
-    },
-    "project_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/project/9.0.0/project",
-        "schema_type": "project",
-        "project_core": {
-            "project_short_name": "integration/Smart-seq2/2018-09-05T18:24:03Z",
-            "project_title": "Q4_DEMO-Single cell RNA-seq of primary human glioblastomas",
-            "project_description": "Q4_DEMO-We report transcriptomes from 430 single glioblastoma cells isolated from 5 individual tumors and 102 single cells from gliomasphere cells lines generated using SMART-seq. In addition, we report population RNA-seq from the five tumors as well as RNA-seq from cell lines derived from 3 tumors (MGH26, MGH28, MGH31) cultured under serum free (GSC) and differentiated (DGC) conditions. This dataset highlights intratumoral heterogeneity with regards to the expression of de novo derived transcriptional modules and established subtype classifiers. Overall design: Operative specimens from five glioblastoma patients (MGH26, MGH28, MGH29, MGH30, MGH31) were acutely dissociated, depleted for CD45+ inflammatory cells and then sorted as single cells (576 samples). Population controls for each tumor were isolated by sorting 2000-10000 cells and processed in parallel (5 population control samples). Single cells from two established cell lines, GBM6 and GBM8, were also sorted as single cells (192 samples). SMART-seq protocol was implemented to generate single cell full length transcriptomes (modified from Shalek, et al Nature 2013) and sequenced using 25 bp paired end reads. Single cell cDNA libraries for MGH30 were resequenced using 100 bp paired end reads to allow for isoform and splice junction reconstruction (96 samples, annotated MGH30L). Cells were also cultured in serum free conditions to generate gliomasphere cell lines for MGH26, MGH28, and MGH31 (GSC) which were then differentiated using 10% serum (DGC). Population RNA-seq was performed on these samples (3 GSC, 3 DGC, 6 total). The initial dataset included 875 RNA-seq libraries (576 single glioblastoma cells, 96 resequenced MGH30L, 192 single gliomasphere cells, 5 tumor population controls, 6 population libraries from GSC and DGC samples). Data was processed as described below using RSEM for quantification of gene expression. 5,948 genes with the highest composite expression either across all single cells combined (average log2(TPM)>4.5) or within a single tumor (average log2(TPM)>6 in at least one tumor) were included. Cells expressing less than 2,000 of these 5,948 genes were excluded. The final processed dataset then included 430 primary single cell glioblastoma transcriptomes, 102 single cell transcriptomes from cell lines(GBM6,GBM8), 5 population controls (1 for each tumor), and 6 population libraries from cell lines derived from the tumors (GSC and DGC for MGH26, MGH28 and MGH31). The final matrix (GBM_data_matrix.txt) therefore contains 5948 rows (genes) quantified in 543 samples (columns). Please note that the samples which are not included in the data processing are indicated in the sample description field."
-        },
-        "contributors": [
-            {
-                "contact_name": "Q4_DEMO-MintTeam",
-                "email": "dummy@email.com",
-                "institution": "Fake Institution"
-            }
-        ],
-        "provenance": {
-            "document_id": "bedfd14f-cc98-4142-b627-d44dfec5aced",
-            "submission_date": "2018-09-05T18:24:05.880Z",
-            "update_date": "2018-09-05T18:24:10.105Z"
-        }
-    },
-    "library_preparation_protocol_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/4.3.0/library_preparation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "preparation1"
-        },
-        "input_nucleic_acid_molecule": {
-            "text": "polyA RNA"
-        },
-        "library_construction_approach": {
-            "text": "Smart-seq2",
-            "ontology": "EFO:0008931"
-        },
-        "nucleic_acid_source": "single cell",
-        "end_bias": "5 prime end bias",
-        "primer": "poly-dT",
-        "strand": "unstranded",
-        "provenance": {
-            "document_id": "f77e65be-ca7a-4711-a7a9-701ad372901a",
-            "submission_date": "2018-09-05T18:24:06.041Z",
-            "update_date": "2018-09-05T18:24:09.959Z"
-        }
-    },
-    "sequencing_protocol_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/9.0.0/sequencing_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "assay_1"
-        },
-        "instrument_manufacturer_model": {
-            "text": "Illumina HiSeq 2500"
-        },
-        "paired_end": true,
-        "sequencing_approach": {
-            "text": "full length single cell RNA sequencing",
-            "ontology": "EFO:0008441"
-        },
-        "provenance": {
-            "document_id": "9d3c0c92-2716-410b-85c6-963a29c24fe0",
-            "submission_date": "2018-09-05T18:24:06.050Z",
-            "update_date": "2018-09-05T18:24:09.960Z"
-        }
-    },
-    "dissociation_protocol_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.1/dissociation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "dissociation_1",
-            "protocol_name": "a FACS method to separate cells"
-        },
-        "dissociation_method": {
-            "text": "fluorescence-activated cell sorting",
-            "ontology": "EFO:0009108"
-        },
-        "provenance": {
-            "document_id": "d08422cf-7d04-46cd-9452-394bb2864ba7",
-            "submission_date": "2018-09-05T18:24:06.024Z",
-            "update_date": "2018-09-05T18:24:10.036Z"
-        }
-    },
-    "enrichment_protocol_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.3/enrichment_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "enrichment1"
-        },
-        "enrichment_method": {
-            "text": "fluorescence-activated cell sorting",
-            "ontology": "EFO:0009108"
-        },
-        "provenance": {
-            "document_id": "f3304cfe-c133-444c-a2db-92294d3f6a4d",
-            "submission_date": "2018-09-05T18:24:06.033Z",
-            "update_date": "2018-09-05T18:24:09.887Z"
-        }
-    },
-    "process_0.json": {
-        "process_core": {
-            "process_id": "sequence_process_file_1"
-        },
-        "schema_type": "process",
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/process/6.0.0/process",
-        "provenance": {
-            "document_id": "bf7360ae-511e-4803-821e-c03167107588",
-            "submission_date": "2018-09-05T18:24:06.090Z",
-            "update_date": "2018-09-05T18:24:09.872Z"
-        }
-    },
-    "process_1.json": {
-        "process_core": {
-            "process_id": "process_id_2"
-        },
-        "schema_type": "process",
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/process/6.0.0/process",
-        "provenance": {
-            "document_id": "b78f4279-9c6f-49da-890f-98499d8fb84a",
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-            "update_date": "2018-09-05T18:24:09.856Z"
-        }
-    },
-    "process_2.json": {
-        "process_core": {
-            "process_id": "process_id_1"
-        },
-        "schema_type": "process",
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/process/6.0.0/process",
-        "provenance": {
-            "document_id": "6284381f-de72-4015-ae51-fa17e13677f8",
-            "submission_date": "2018-09-05T18:24:06.058Z",
-            "update_date": "2018-09-05T18:24:09.861Z"
-        }
-    },
-    "links.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.1/links",
-        "schema_type": "link_bundle",
-        "schema_version": "1.1.1",
-        "links": [
-            {
-                "process": "bf7360ae-511e-4803-821e-c03167107588",
-                "inputs": [
-                    "a31a0e93-5be4-44b8-b152-9e25b066e1e5"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "20474552-c0a3-471e-8fa0-d3c5aa05c017",
-                    "177a9d2c-99d4-4fb6-aab7-5869923e9d6a"
-                ],
-                "output_type": "file",
-                "protocols": [
-                    {
-                        "protocol_type": "library_preparation_protocol",
-                        "protocol_id": "f77e65be-ca7a-4711-a7a9-701ad372901a"
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-                        "protocol_type": "sequencing_protocol",
-                        "protocol_id": "9d3c0c92-2716-410b-85c6-963a29c24fe0"
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-                    "e964f81f-54d9-4600-a9e9-981b1f1a6ca2"
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-                "input_type": "biomaterial",
-                "outputs": [
-                    "a31a0e93-5be4-44b8-b152-9e25b066e1e5"
-                ],
-                "output_type": "biomaterial",
-                "protocols": [
-                    {
-                        "protocol_type": "dissociation_protocol",
-                        "protocol_id": "d08422cf-7d04-46cd-9452-394bb2864ba7"
-                    },
-                    {
-                        "protocol_type": "enrichment_protocol",
-                        "protocol_id": "f3304cfe-c133-444c-a2db-92294d3f6a4d"
-                    }
-                ]
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-            {
-                "process": "6284381f-de72-4015-ae51-fa17e13677f8",
-                "inputs": [
-                    "c6001597-990c-4753-80bb-c5a01c9dda0d"
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-                "input_type": "biomaterial",
-                "outputs": [
-                    "e964f81f-54d9-4600-a9e9-981b1f1a6ca2"
-                ],
-                "output_type": "biomaterial",
-                "protocols": []
-            }
-        ]
-    }
-}
diff --git a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
new file mode 100644
index 000000000..6072f329f
--- /dev/null
+++ b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
@@ -0,0 +1,11982 @@
+{
+    "manifest": [
+        {
+            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
+            "crc32c": "8079eb90",
+            "indexed": true,
+            "name": "imaged_specimen_0.json",
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+            "sha1": "a5d1b0e5457d029d0fe0f2c19c0c2b2f45c67083",
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+            "crc32c": "d46a73e9",
+            "indexed": true,
+            "name": "specimen_from_organism_0.json",
+            "s3_etag": "889570fe22be551b40a308389b62aef7",
+            "sha1": "f2b51ec11480e4b8613d1adef1beb5850847f57c",
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+            "describedBy": "https://schema.staging.data.humancellatlas.org/type/project/11.0.1/project",
+            "schema_type": "project",
+            "project_core": {
+                "project_short_name": "barista_seq",
+                "project_title": "1 FOV BaristaSeq mouse SpaceTx dataset",
+                "project_description": "1 FOV BaristaSeq mouse SpaceTx dataset"
+            },
+            "supplementary_links": [
+                "https://github.com/spacetx"
+            ],
+            "funders": [
+                {
+                    "grant_title": "grant",
+                    "grant_id": "1",
+                    "organization": "funder"
+                }
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+                "protocol_id": "zador_singlerolseq_1"
+            },
+            "microscope_setup_description": "PerkinElmer Ultraview Vox Spinning disk (Nikon Ti-E, Yokogawa CSU-X1, Hamamatsu orca-R2, ASI MS-2000 xyz stage, Nikon Plan Apo 10x 0.45 and Nikon Plan Apo 20x 0.75)",
+            "microscopy_technique": {
+                "text": "spinning disk confocal"
+            },
+            "magnification": "20x",
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+            "immersion_medium_type": "air",
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+                {
+                    "molecule_name": "Ank1",
+                    "molecule_id": "NM_001277289",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ggcccacactcattccagagaaggatcaccaccatccaaggg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
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+                    "molecule_id": "NM_001277289",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
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+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ank1",
+                    "molecule_id": "NM_001277289",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "agcagcgagttcacgcccgaatcacagactcaccctcagtgag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Kcnmb2",
+                    "molecule_id": "NM_028231",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gtgggagacaaagctggtgagatcactcccagtaaactgactgg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Kcnmb2",
+                    "molecule_id": "NM_028231",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
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+                    "probe_sequence": "cctgaccaaactctacagctccaatgtgctgttccattctctct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
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+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Kcnmb2",
+                    "molecule_id": "NM_028231",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ttcagctgtgggcccgactgttggaagctctctcagtacccttg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ankrd55",
+                    "molecule_id": "NM_001168404",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "agggcccgtccattatcaactacgacgacgagagtgggaaga",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ankrd55",
+                    "molecule_id": "NM_001168404",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgcagagcctgatgtgaggctcctcatagtcctgctgcagca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ankrd55",
+                    "molecule_id": "NM_001168404",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgtgtgagtctgctcagaaacggtgccaagcacaacatcccag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Slc32a1",
+                    "molecule_id": "NM_009508",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tcttcacgctgctcatggccatctacgtgccacacttcgcgct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Slc32a1",
+                    "molecule_id": "NM_009508",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tatccgttgcccttcttcgcggccgtcgaagtgctggagaagt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Slc32a1",
+                    "molecule_id": "NM_009508",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tcaacatcctggtcatcgcttactgtctctctcgcgcgcgtgatt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Btbd11",
+                    "molecule_id": "NM_001017525",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgagatcatggagcttctgtctgctgctaaatttttccagctggag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Btbd11",
+                    "molecule_id": "NM_001017525",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cgtgaagtatcccatcttccagctcgtcatgcagtatctctactac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Btbd11",
+                    "molecule_id": "NM_001017525",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctcttgttcacagcctctcccaggttcaaggccctcctctcca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Arx",
+                    "molecule_id": "NM_001305940",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "agcattttggcgctctatgttgatttaagcgcggcccggctaaa",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Arx",
+                    "molecule_id": "NM_001305940",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "caaggcagttcttggcgctaaaggatgtggcacctcctccact",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Arx",
+                    "molecule_id": "NM_001305940",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "atggaaacagaggaccagctcactcccaagaaggcacagacag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Dlx1",
+                    "molecule_id": "NM_010053",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctgtaaacatgttgcacaagcttagcctctttccgttctgttgtg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Dlx1",
+                    "molecule_id": "NM_010053",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "taagacacaagcagcggctcgaccacagaacacaagtcatcaccct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Dlx1",
+                    "molecule_id": "NM_010053",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gcacagtaacttttgtacttggctgaaatgcagaaagggaaaac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Gad2",
+                    "molecule_id": "NM_008078",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aaaggtggcgccagtgattaaagccagaatgatggagtatggg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Gad2",
+                    "molecule_id": "NM_008078",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "agtgttcagctctcctggttagagaggagggactgatgcagagct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Gad2",
+                    "molecule_id": "NM_008078",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tactgatgtcccggaaacacaagtggaagctgagtggagtagaga",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Pvalb",
+                    "molecule_id": "NM_013645",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctgcttggtactgagtgctcatgtgggccacctcgttcaatc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Pvalb",
+                    "molecule_id": "NM_013645",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ggagaaacaataaaggctgtaccaatcggacaccacctgtaggg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Pvalb",
+                    "molecule_id": "NM_013645",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctcctcagatgccagagacttgtctgctaaagaaacaaagacgc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Pdgfra",
+                    "molecule_id": "NM_001083316",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgggcaagaggaacagacacagctcacagacttcggaagagag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Pdgfra",
+                    "molecule_id": "NM_001083316",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gaaaagattcacctggacttcctaaagagtgaccatccggccgt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Pdgfra",
+                    "molecule_id": "NM_001083316",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "agtgagcccgagaagagaccctccttctaccacctcagcgagata",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nxph4",
+                    "molecule_id": "NM_183297",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aattgccacgtggaatatgagaagacaaaccgcgctcgcaag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nxph4",
+                    "molecule_id": "NM_183297",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cacaattcgtccagcctgggtaacctaagcgtcagtatcgtgc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nxph4",
+                    "molecule_id": "NM_183297",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgtgcataccctcaagttctcgctgttggtgaccggcaagatc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Car3",
+                    "molecule_id": "NM_007606",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cattgtgtggctgctgctcaaagagcccatgactgtgagctc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Car3",
+                    "molecule_id": "NM_007606",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "catcatgcctgttccctgcttgccgggactattggacctatc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Car3",
+                    "molecule_id": "NM_007606",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gggagaaaggcgagttccagattcttcttgatgccctggacaaa",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Slc17a8",
+                    "molecule_id": "NM_001310710",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gaactcaaccacgagactttcgtaagtcccagaaagaagatgtct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Slc17a8",
+                    "molecule_id": "NM_001310710",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ggctttgctatttcaggcttcaatgtcaaccacctggacattgc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Slc17a8",
+                    "molecule_id": "NM_001310710",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgctcctggtggttggattttcccataccaaaggagtggctatc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Syt6",
+                    "molecule_id": "NM_001276679",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cgagacgctgattgtgcgcatcctgaaggcctttgacctccct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Syt6",
+                    "molecule_id": "NM_001276679",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "agatgcatgtctccagcgtggactatggcaatgagctgccgc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Syt6",
+                    "molecule_id": "NM_001276679",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "acaaagctgcagcgacagaccacagagccagcatcctccacca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Rspo1",
+                    "molecule_id": "NM_138683",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aagaagaggaagctgtgcggtttccggaagggatcggaagag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Rspo1",
+                    "molecule_id": "NM_138683",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gtgtcaggagggcttgtacttacacaagggccgctgctatcca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Rspo1",
+                    "molecule_id": "NM_138683",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cccaagctcttcattctgctggagaggaacgacatccgccaggt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Fam84b",
+                    "molecule_id": "NM_001162926",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gcctggaggacttgatcatggagaagcggcgcaacgaccagat",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Fam84b",
+                    "molecule_id": "NM_001162926",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aacgatctgtatcgctacaagccactgagccctagcgctgtagt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Fam84b",
+                    "molecule_id": "NM_001162926",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aacaagtgcagtccgggtgacctggtggagtttgtatcgcaggc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Deptor",
+                    "molecule_id": "NM_001037937",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctcaggagacgcatgacagtcccttctgtctgaggaagcagag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Deptor",
+                    "molecule_id": "NM_001037937",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gcaacctcctctaccagttcagaatgaacttccgtcggaggcgga",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Deptor",
+                    "molecule_id": "NM_001037937",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aagaggcagagcagctttgccaccggcttatggaccatgggatc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ndnf",
+                    "molecule_id": "NM_172399",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "caccagaaagaaatcagagaaggtcctttgcaaatacttccacag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ndnf",
+                    "molecule_id": "NM_172399",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "agcttttgacaagctacgtacctgctcttcagttacggtggcat",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ndnf",
+                    "molecule_id": "NM_172399",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aggcaacaggaaaggagcatcaaagctgaaaatactggcgacca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Chrna2",
+                    "molecule_id": "NM_144803",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aagcactagaaggtgtacactacattgctgaccacctgaggtct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Chrna2",
+                    "molecule_id": "NM_144803",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tcattggctggagaccaacatggatgctgaagaaagggaggag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Chrna2",
+                    "molecule_id": "NM_144803",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgtcttcctgctgctcatcacagaaattatcccatccacctcac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Calb1",
+                    "molecule_id": "NM_009788",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cacccaaagcacctctgtgctgcttctatctggcggaagggat",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Calb1",
+                    "molecule_id": "NM_009788",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cgaacagaccttgctcttattctttctgctggagacaactagagtt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Calb1",
+                    "molecule_id": "NM_009788",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctgcgaggaattcatgaagacttggagaaagtatgatactgaccac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Sncg",
+                    "molecule_id": "NM_011430",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gttgcccaagttctctgtccctagcccagtgccacaagtcca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Sncg",
+                    "molecule_id": "NM_011430",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gagaatgaagaggccaagagtggagaagactagaaggctgccag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Sncg",
+                    "molecule_id": "NM_011430",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tggtcagcagcgtcaacacagtggccaacaagaccgtggagga",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Th",
+                    "molecule_id": "NM_009377",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gacaagctcaggaactatgcctctcgtatccagcgcccattctc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Th",
+                    "molecule_id": "NM_009377",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgggacacgtacccatgttggctgaccgcacatttgcccagtt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Th",
+                    "molecule_id": "NM_009377",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gtttcagtgcacacagtacatccgtcatgcctcctcacctatgc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Gad1",
+                    "molecule_id": "NM_001312900",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgatcgctccaccaaggttctggatttccaccacccacacca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Gad1",
+                    "molecule_id": "NM_001312900",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tccaagaacctgctttcctgtgaaaacagtgaccagggtgccc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Gad1",
+                    "molecule_id": "NM_001312900",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tctgtggcttcttacaaaggaccaatagcctggaagagaagagtcg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Slc17a7",
+                    "molecule_id": "NM_182993",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "atcgctgactttttgcgcagtcgtcacataatgtccactaccaa",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Slc17a7",
+                    "molecule_id": "NM_182993",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "caccctggaggcgcttctttacgtccatgcccgtctatgccat",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Slc17a7",
+                    "molecule_id": "NM_182993",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tatggcagcttcgggatcttttggtacctgttctggttgcttgtct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Neurod1",
+                    "molecule_id": "NM_010894",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gatcctgcgctcaggcaaaagccctgatctggtctccttcgta",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Neurod1",
+                    "molecule_id": "NM_010894",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cttgctactccaagacccagaaactgtctaaaatagagacactgcg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Neurod1",
+                    "molecule_id": "NM_010894",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gcgcgcctagaacgttttaaattaaggcgcatgaaggccaacg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Rorb",
+                    "molecule_id": "NM_146095",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctttgcgaagaatctgtgttccttgcagctgactgaggaagagat",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Rorb",
+                    "molecule_id": "NM_146095",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ccacacctacgaggaaatcaaggcgtatcaaagcaagtccaggga",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Rorb",
+                    "molecule_id": "NM_146095",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgcacagaacatcattaagtcccatttggagacatgtcagtacac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Fezf2",
+                    "molecule_id": "NM_080433",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gctttcaccaaaaagggaactacaagaatcacaagctcacccaca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Fezf2",
+                    "molecule_id": "NM_080433",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ttcaatcgcagctccacgctcaacacgcacatccgcatccac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Fezf2",
+                    "molecule_id": "NM_080433",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "agctagaccgtttgtgtgcaaagtctgtggcaaaggcttccg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Adarb2",
+                    "molecule_id": "NM_001289530",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ataccgacaaaacaggcctctccttagtggcgtgagtcacgca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Adarb2",
+                    "molecule_id": "NM_001289530",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "atcgagcctgtgtacctccacagcatcattgtgggcagcctgca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Adarb2",
+                    "molecule_id": "NM_001289530",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cagacttgaacagcagcaaacacatcgtcaggaagttccgaggg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Lamp5",
+                    "molecule_id": "NM_029530",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctgactttgtcttcagtgaagaacataaatgtccagtggatgagc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Lamp5",
+                    "molecule_id": "NM_029530",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tttctctggcctccagtgaccctcagaagactgtcaccatgatcct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Lamp5",
+                    "molecule_id": "NM_029530",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctcagaatgctctttgtaaaggaaagtcacaacacttccaaagg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Vip",
+                    "molecule_id": "NM_001313969",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gggtcagatttctgccaaaaaataccttgagtcactcattggcaa",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Vip",
+                    "molecule_id": "NM_001313969",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gcagaaaatggcacaccctattatgatgtgtcaagaaatgccaggc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Vip",
+                    "molecule_id": "NM_001313969",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ccttctgtagtgagtaggctggatgacaggatgccgtttgaagg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Lhx6",
+                    "molecule_id": "NM_001083127",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cgcatccattacgacaccatgatcgagaacctcaagagggcc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Lhx6",
+                    "molecule_id": "NM_001083127",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctggcatgtttcgcctgcttttcctgcaagcgccagctatcca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Lhx6",
+                    "molecule_id": "NM_001083127",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "atttggaaccaagtgcgcccggtgcggcagacaaatctatgcc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Chodl",
+                    "molecule_id": "NM_139134",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ggtgcaacatgaagcacaattacatctgcaagtatgaaccagaga",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Chodl",
+                    "molecule_id": "NM_139134",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aatgtgtagtcatgtaccaccaaccaactgccaatcctggccta",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Chodl",
+                    "molecule_id": "NM_139134",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aaacatcgggtgcctgcccagatctctaccagtggtctgatggaag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Fa2h",
+                    "molecule_id": "NM_178086",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tacctgcacttcggctctccacacaagggctcctacctgtacaac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Fa2h",
+                    "molecule_id": "NM_178086",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gattgccttcttctatgtgttcctgcggctcattctgcctgaga",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Fa2h",
+                    "molecule_id": "NM_178086",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gccattacctcatcatgttgcattttgtcatgcacggccagcac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ly86",
+                    "molecule_id": "NM_010745",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ggcttggaagtagtctaccagagctgtgatcccttacaggattttg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ly86",
+                    "molecule_id": "NM_010745",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "attctgacttctccgagcagcagtgaccatggcagcgaaaatg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ly86",
+                    "molecule_id": "NM_010745",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "atggcaaaaggctcttctattctgaactactcctatcccctttg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Dcn",
+                    "molecule_id": "NM_007833",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "caggtcgtctaccttcacaacaacaacatctccgcagttgggcaaa",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Dcn",
+                    "molecule_id": "NM_007833",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tctcactgaagtgcatctagatggcaacaagatcaccaaggttgat",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Dcn",
+                    "molecule_id": "NM_007833",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "agggactgaagagtctctcatacattcgcatctcagacaccaacat",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Fgfr3",
+                    "molecule_id": "NM_001163216",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cctcactgtgacatcaaccgacgagtacttggacctctccgt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Fgfr3",
+                    "molecule_id": "NM_001163216",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctgtacatgatcatgcgggaatgttggcatgcggtgccttcacag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Fgfr3",
+                    "molecule_id": "NM_001163216",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgctggtggagtacgcagccaagggcaatctccgggagttcctt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Map3k7cl",
+                    "molecule_id": "NM_144854",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aagctacctatcgttcagacacaccgttgagtgaatgcagaattag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Map3k7cl",
+                    "molecule_id": "NM_144854",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cctttgtgttagcacacagtggtcacatttgccttggccgtgtg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Map3k7cl",
+                    "molecule_id": "NM_144854",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gagcctaaatgctttcttgtgaaaatatcagcaggcgtgtgtcc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nxph1",
+                    "molecule_id": "NM_008751",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gattccaagtccttcaactgtcgcattgagtatgagaaggttgac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nxph1",
+                    "molecule_id": "NM_008751",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tctgggactggctgaggaactccacagatcttcaggagcctcg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nxph1",
+                    "molecule_id": "NM_008751",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gtcggctcctctcacagactttccgtggtaaagaaaatgacac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Pcp4",
+                    "molecule_id": "NM_008791",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "agaagaaaaaggcaggatcacagtcctagtggtgaagctgcttc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Pcp4",
+                    "molecule_id": "NM_008791",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ggcagaagaaagtccaagaagaatttgatatcgacatggatgcacc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Pcp4",
+                    "molecule_id": "NM_008791",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tagctgcggagtcaggccaacatgagtgagagacaaagtgccgg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Neurod6",
+                    "molecule_id": "NM_009717",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ccaactacaaacttggtggcaggctgcttacagctcaacgcca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Neurod6",
+                    "molecule_id": "NM_009717",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ttacatctgggcactttctgaaattctgaggattggcaagagacc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Neurod6",
+                    "molecule_id": "NM_009717",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ggtcaagttcaggagacaggaagctaatgcgcgcgagaggaa",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nrn1",
+                    "molecule_id": "NM_153529",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "actcacccacactcacaccatgctcccggaaatcgagaggaata",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nrn1",
+                    "molecule_id": "NM_153529",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "accgtgtgcacatactgggaggatttccacagctgcacggtc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nrn1",
+                    "molecule_id": "NM_153529",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cttttcagactgtttgctcaagctgggcgacagcatggccaacta",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nrgn",
+                    "molecule_id": "NM_022029",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ttctttgtttatgcaaaagcctcctgagcgcctggaggctcc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nrgn",
+                    "molecule_id": "NM_022029",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctcccgctcttctttgtttatgcaaaagcctcctgagcgcctgga",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nrgn",
+                    "molecule_id": "NM_022029",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ccaagccagacgacgatattcttgacatcccgctggatgatcc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ptn",
+                    "molecule_id": "NM_008973",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "caatgctgactgtcagaaaactgtcaccatctccaagccctgtg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ptn",
+                    "molecule_id": "NM_008973",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ccttcctggcattgattttcatcttggcagctgtggacactgct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ptn",
+                    "molecule_id": "NM_008973",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aaaggcagccagctagtcagcgaggacctctgcaagccaaaaaatg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cck",
+                    "molecule_id": "NM_031161",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgccgaggactacgaatacccatcgtagtgggccagcgtctt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cck",
+                    "molecule_id": "NM_031161",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tacatccagcaggtccgcaaagctccttctggccgcatgtccgtt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cck",
+                    "molecule_id": "NM_031161",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aagagcggcgtatgtctgtgcgtggtgatggcagtcctagctgct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Synpr",
+                    "molecule_id": "NM_001163032",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgatgtcagcttgcaagcagccttccaacaagtgcatggctg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Synpr",
+                    "molecule_id": "NM_001163032",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gactttatcgtcactgtagtcttttcattcttgtggctggtgg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Synpr",
+                    "molecule_id": "NM_001163032",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tttctctactccctggctgccacggtcgtgtacattttcttccag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Slc6a1",
+                    "molecule_id": "NM_178703",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "catcattgtggcgggcgtgtttctcttcagtgctgtgcagatg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Slc6a1",
+                    "molecule_id": "NM_178703",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgtcaaccggttctatgacaacatccaggagatggttggctcca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Slc6a1",
+                    "molecule_id": "NM_178703",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctcttcattgctgccgtgtgcatcgtgtcctacctgattggc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Dlx6",
+                    "molecule_id": "NM_010057",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cacaccaggacaccatgcagagaccacagatgatgtgacttctc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Dlx6",
+                    "molecule_id": "NM_010057",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgtcaccacgatcaccagccctgcctccagtgtgggacgtttct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Dlx6",
+                    "molecule_id": "NM_010057",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ccatcgctttcagcagactcaatacctggcccttcccgagaga",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Atp1a3",
+                    "molecule_id": "NM_001290469",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "actgggatgatcgcactgtcaatgacctagaagacagttatggg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Atp1a3",
+                    "molecule_id": "NM_001290469",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cccacgcacagacaaactggtcaacgaaaggctcatcagcatg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Atp1a3",
+                    "molecule_id": "NM_001290469",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cctgagatcacacccttcctgctcttcatcatggctaacatccc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Arpp19",
+                    "molecule_id": "NM_021548",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "caatgcatctccaccatttgatatgcaataggacactgcctgt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Arpp19",
+                    "molecule_id": "NM_021548",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gcccactgtaagcacttcacttacattttctaaagcaccgtcttg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Arpp19",
+                    "molecule_id": "NM_021548",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aagcaggtagcctctgggaagagctattctgatggttaccaagg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cxcl14",
+                    "molecule_id": "NM_019568",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "acagcactgttctctgagttaggatgttaggacgatcctgcgcc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cxcl14",
+                    "molecule_id": "NM_019568",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aagggaagatgcaggattagatgcaggacacacagccagagcta",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cxcl14",
+                    "molecule_id": "NM_019568",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tactgctccgctccaggcttacaaagcttccgctcagagagcct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Rab3b",
+                    "molecule_id": "NM_023537",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cttttccaataagtgtgatcccgtcgcttggaatcctgcccaag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Rab3b",
+                    "molecule_id": "NM_023537",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gctggtatcaggcccagtgatcaaatgaaagggccaaatagag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Rab3b",
+                    "molecule_id": "NM_023537",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aggtaaagggagctctatagggaagcaggctcaggctgtagtg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cryab",
+                    "molecule_id": "NM_001289785",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aaacaggtgtctggccctgagcgcaccattcccatcacccgtgaa",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cryab",
+                    "molecule_id": "NM_001289785",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ggcttcatctccagggagttccacaggaagtaccggatccca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cryab",
+                    "molecule_id": "NM_001289785",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gatgcgtttggagaaggacagattctctgtgaatctggacgtgaa",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Penk",
+                    "molecule_id": "NM_001002927",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gctgaaagagctactgggaacgggagacaaccgtgcgaaagac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Penk",
+                    "molecule_id": "NM_001002927",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ggtacggaggcttcatgaagaagatggacgagctatatcccatg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Penk",
+                    "molecule_id": "NM_001002927",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "acatcgacatgtacaaagacagcagcaaacaggatgagagccac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Crh",
+                    "molecule_id": "NM_205769",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gcaagctcacagcaacaggaaactgatggagattatcgggaaa",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Crh",
+                    "molecule_id": "NM_205769",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cgcccatctctctggatctcaccttccaccttctgcgggaagt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Crh",
+                    "molecule_id": "NM_205769",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aaacctgcaggaggcatcctgagagaagtccctctgcagaggca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Caln1",
+                    "molecule_id": "NM_021371",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tccatcccgcaccagcatcttggaatctgcagagagcctggct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Caln1",
+                    "molecule_id": "NM_021371",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gccacctctatccatgacccaattctttcaacccagggaccc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Caln1",
+                    "molecule_id": "NM_021371",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctgctttcttttcgtcttggaattccagtagccatccagatagca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Kcnip1",
+                    "molecule_id": "NM_027398",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gatcatgtgcaaatggtacttccagacagcacctcttttctaat",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Kcnip1",
+                    "molecule_id": "NM_027398",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctctatggctcaggagaggcaagttgtgacaaagggtggttagt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Kcnip1",
+                    "molecule_id": "NM_027398",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ccaaatgtgcaccatcctccgatggcctcccaagccaatgtg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Gm11549",
+                    "molecule_id": "NR_040411",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aactcagacatccgcctgcctctgcctcctgagtgctgggatta",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Gm11549",
+                    "molecule_id": "NR_040411",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ggctattgtatgtacagttcacaccattctcgtgtgtgtgtgt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Gm11549",
+                    "molecule_id": "NR_040411",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "acagcctacgtactggccaagccgagggagaagaaacacttcc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ctxn1",
+                    "molecule_id": "NM_183315",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gactcacattggacgctgcctacctataatgcacggtacagtt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ctxn1",
+                    "molecule_id": "NM_183315",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "agggcgttcggagaagtccagtccttacctaccttagctacccat",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ctxn1",
+                    "molecule_id": "NM_183315",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgttcgccttcgtgctctgcctgctcgtggtgttggttctgtt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Car4",
+                    "molecule_id": "NM_007607",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aacttcctccagtaatggcccacttctggatatctgacctctga",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Car4",
+                    "molecule_id": "NM_007607",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gaaggacaagtttgcagtgctggcatttatgattgaggtaggag",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Car4",
+                    "molecule_id": "NM_007607",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gaatgacaacggttcagagcacagtattgatgggagacactttgc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nfib",
+                    "molecule_id": "NM_008687",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "atgacatgaactctggtgtgaacctgcagaggtcgctgtcttct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nfib",
+                    "molecule_id": "NM_008687",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gagtatccagaacacccataacccagggaactggagtcaacttcc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Nfib",
+                    "molecule_id": "NM_008687",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "acaatcaggaagtccaagccacagtgatcctgccaagaatcctc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Id2",
+                    "molecule_id": "NM_010496",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aaggaattgcccaatgtaagcagactttgccttttcacaaaggtgg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Id2",
+                    "molecule_id": "NM_010496",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gcggaaggaaaactaaggatgatcgtcttgcccaggtgtcgttct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Id2",
+                    "molecule_id": "NM_010496",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "acccgatgagtctgctctacaacatgaacgactgctactccaagc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Igfbp6",
+                    "molecule_id": "NM_008344",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gcctttgccagtgtctccagatggtcaaggaagcactcagtg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Igfbp6",
+                    "molecule_id": "NM_008344",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgggctctatgtgccaaactgtgacctcagaggcttctaccg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Igfbp6",
+                    "molecule_id": "NM_008344",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aggagtgtacagggcaaaaactctgaccatgacctgggatgggct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Itpka",
+                    "molecule_id": "NM_146125",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cttcgtgcatgaccattgccatcgtgctggtgtgtggctcatc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Itpka",
+                    "molecule_id": "NM_146125",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gcctacagcagatccgggataccctggagatctctgatttcttt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Itpka",
+                    "molecule_id": "NM_146125",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "acgaagccgagagcaagtgacccgtgtctttgaggagttcatgca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ptprd",
+                    "molecule_id": "NM_001352630",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ccgccttgttaatattatgccatatgaatccacaagggtgtgcc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ptprd",
+                    "molecule_id": "NM_001352630",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "atccatgatgcactgttagaagcagtgacatgtggaaataccgaa",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Ptprd",
+                    "molecule_id": "NM_001352630",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aatcctccagatgcagggccaatggtggtacactgcagtgctggt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Sv2b",
+                    "molecule_id": "NM_001109753",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tttggcaacagcgagtctgcgatgatcggctggcaatgcctgtt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Sv2b",
+                    "molecule_id": "NM_001109753",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gctcatggacagaattggaagactcaagatgattggcggctccat",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Sv2b",
+                    "molecule_id": "NM_001109753",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ggactttgaagaggacaatgattttctgatttacctcgtcagct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Vxn",
+                    "molecule_id": "NM_178399",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ctgagcatctgaccctcatgtccaaacatagtctggacacttgg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Vxn",
+                    "molecule_id": "NM_178399",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "acatggcggtaagtcaaacccagacttccaggctcttgcctt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Vxn",
+                    "molecule_id": "NM_178399",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgaactgtttgggtatcaggcttgcttctgctgttctgtggattct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Reln",
+                    "molecule_id": "NM_001310464",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aggagttctactgcgctggtggcagccacgccacaatggaaca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Reln",
+                    "molecule_id": "NM_001310464",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "atcacctggcacgtcatcgctcagcaccagccgaaggacttcaca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Reln",
+                    "molecule_id": "NM_001310464",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cactcgagcaagcaaaattatgtttgtcttgcaaattgggagcc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Rprml",
+                    "molecule_id": "NM_001033212",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aacgaagtacctcgcaccacccgggtctggacaccataggact",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Rprml",
+                    "molecule_id": "NM_001033212",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "cttgccagagttgaagcaccgcgaggaagagactacggagcct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Rprml",
+                    "molecule_id": "NM_001033212",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tcaagtccgagagcatgatcaactttctgatgcaggagcgcagg",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cnr1",
+                    "molecule_id": "NM_007726",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gagacatgctttccgcagcatgttcccttcatgtgaaggcact",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cnr1",
+                    "molecule_id": "NM_007726",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgaacaagcttatcaagacggtgtttgccttctgtagtatgctct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cnr1",
+                    "molecule_id": "NM_007726",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "atccagcgtggaacccagaaaagcatcatcattcacacctcaga",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cacna2d3",
+                    "molecule_id": "NM_009785",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gaatcccttaagtgtgaacggttaaaggctcagaagatcagacgac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cacna2d3",
+                    "molecule_id": "NM_009785",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tggtggtggacagtagctgtctctgtgagtccgtggctcctata",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Cacna2d3",
+                    "molecule_id": "NM_009785",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "agaccacagggaacattgcttgcgaagactgctccaagtcct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Plpp4",
+                    "molecule_id": "NM_001080963",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "gaggagtgattggcctcatttttgcctatatttgctacagacaac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Plpp4",
+                    "molecule_id": "NM_001080963",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "tgctgccatcttgcccttgtactgtgccatgatgatcgccct",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Plpp4",
+                    "molecule_id": "NM_001080963",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "ttctcgggcctcggtttcacaacattctacctggctggcaagc",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Adcy2",
+                    "molecule_id": "NM_153534",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "caataagcactccttcaacgacttcaaacttcgagtgggtatcaac",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Adcy2",
+                    "molecule_id": "NM_153534",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "atacatggcagccacgggtctgagtgctgtacccagtcaggagca",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Adcy2",
+                    "molecule_id": "NM_153534",
+                    "subcellular_structure": {
+                        "text": "cytoplasmic"
+                    },
+                    "probe_sequence": "aggagttgtaccaccagtcctacgattgtgtctgtgtcatgtt",
+                    "assay_type": {
+                        "text": "in situ sequencing"
+                    },
+                    "multiplexed": "yes"
+                },
+                {
+                    "molecule_name": "Kcnip4",
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+                        "b69a349b-0e07-4fbe-9e3b-9f2cea828b96",
+                        "753c2a57-b5f1-4984-b874-b2b10d582847",
+                        "e0b93b3d-075b-482b-838a-e36d8849607b",
+                        "96c8ed8d-8bd6-49f3-b97b-025b0d6bc9ec",
+                        "c647964a-7796-4dd2-9fa8-b23f012ac14e",
+                        "87a63649-9834-49b8-89a0-310211c1b5b3",
+                        "b2eb5b20-fd1a-403c-8b55-9eec5972d482",
+                        "4b3b36cb-cd90-4526-978d-2e7e8f7add39",
+                        "cdc774f8-3310-4f1f-8c67-03579c253640",
+                        "607370e0-7e7e-4d25-ba5c-957c00a73ac1",
+                        "3240d7ab-568b-4be5-adba-3178b3e8f85e",
+                        "c0b6ee98-677a-41d9-9d80-9ac63d251b08",
+                        "f34c01ec-06df-49e6-bc2f-c50c7f398851",
+                        "2047311b-f3ee-4137-8338-a45166e01d53",
+                        "44ea335a-1991-4504-be12-04f1a332ddfb",
+                        "59f3d0ab-1fe1-4cc8-b343-c12b520d769d",
+                        "58f9fb1a-b6be-42c4-98ed-a5c091a3c716",
+                        "6af3cb41-9e64-4b11-b272-be87adf0fa94",
+                        "7541d176-dfba-4e05-ba45-0c6964271dff",
+                        "8ee1e829-a507-40a5-87ac-7fd8379b87ce",
+                        "8e57554a-abb2-4664-87b6-a397f4da6555",
+                        "88fa5ec5-db7d-49bf-8c7e-86f348fbc84c",
+                        "a2b4ab97-84bd-4808-884d-bd8cc5e7b922",
+                        "56c83f8e-3ef2-4a3a-b808-52cc1e96ac8e",
+                        "8af22b64-2c3f-4aad-a2d5-5d9b122a7b1c",
+                        "f0cb4244-e19a-46a0-89f1-04143548872d",
+                        "73074f55-d009-41a2-929e-6fd9949bb1dd",
+                        "0c2a3965-fbd7-4dc2-bcf0-9c51650a7331",
+                        "3774ecbd-d397-4b46-ba08-a7cbc6da0c07",
+                        "146231bb-1b13-4db5-8157-9d9962cc3a3a",
+                        "1d1b3f27-4f67-4338-bb36-173fd6ecf14b",
+                        "7fe17380-3090-4fc3-9504-02b3f8ed95b6",
+                        "fc405b01-60ca-436f-a06c-2f38f7156a87",
+                        "bae92b53-c6c7-4712-865e-6cff3cba506e",
+                        "83662ec5-a202-42ab-9a47-a701d4f19de3",
+                        "a04957c6-8ce8-4fa6-950d-71812ff3d698",
+                        "9284d3a4-73bd-4aa0-847c-ab273d14185a",
+                        "4d664562-c333-4aaf-bb8b-641e0568733e",
+                        "b533685d-3c60-4483-841b-a054f0a69fec",
+                        "3f14c88e-58db-4f76-b6e0-4b483ded1ca3",
+                        "32d0b267-f399-408a-b35f-f1ebc7d0fc1f",
+                        "3e8510c9-7e31-49bd-bb90-cb55577c2f25",
+                        "463aff9a-ec7e-40d0-be42-c6686af9130d",
+                        "02ddb50f-4a97-4fbc-ac08-32cd5f0fb319",
+                        "868efb99-df36-462b-91a2-bb6ca27e842a",
+                        "dd124d84-cb44-42e6-88d8-0d97fcb2c0f1",
+                        "36ded48a-869f-4fa8-971f-56bc28298276",
+                        "b62567c9-27d5-49b9-aa2e-7e9e1513dcb4",
+                        "e72742a4-23ba-4e5d-a29b-ad449abe8101",
+                        "cd6e1096-f8c3-4eda-957d-b09741d60901",
+                        "903ea376-5153-4fb8-8ffa-e2948951409c",
+                        "89c5fc1e-9d18-4a6b-9025-ea0b75d01adb",
+                        "8381d167-c4dd-49a2-b5df-1ae815bbe42e",
+                        "9be80be6-ee45-49d5-8d3d-a6df8f0383f6",
+                        "cf305c60-bb2c-41af-82bf-0631c2a7b0be",
+                        "074290a9-35e1-422f-a3af-e5ed58781b4d",
+                        "0c49b3ca-bb47-41d9-a58c-e5ea79f673c3",
+                        "783c4def-7dc3-40a6-aa9e-a3f92a2dffba",
+                        "5165cc56-ff89-42bf-b000-fec4bd57176e",
+                        "545be634-5893-45e0-93b2-dd4ea93e00db",
+                        "2d2e58c6-7c24-4089-bbe9-d47b7482be46",
+                        "e4ce035a-f9e2-459f-8ecf-ce138ea00b34",
+                        "81214e49-318f-4221-bf2c-4ef00cfa916b",
+                        "7fc97754-1121-468b-b1e4-839bde86b6c8",
+                        "7d70d44c-b5d7-47be-9687-e9a775e86251",
+                        "ddb4f9d4-f2a1-42a5-87fa-e818071a5b33",
+                        "b7607809-e975-4c32-bff7-375cb2d8276f",
+                        "b8a6c863-626d-4fbf-863b-610cffaac37d",
+                        "45077a5c-ee96-47c0-a84f-9d46cf799338",
+                        "49d82b74-6f1a-415c-93ab-958c60f083b6",
+                        "753b51b7-a909-44e7-bb21-cf2cd18328f8",
+                        "c7ab6349-b2bb-4ba3-9c9b-27d270550052",
+                        "7be770fc-4a56-4f82-a4cf-3cf908d54dca",
+                        "3f5f8537-c1af-4d2e-a732-53b6d4275588",
+                        "3820feac-72c4-49c5-a5a0-773f4e5ee3c1",
+                        "f986c2c2-2823-45a0-80cf-5e6f67958afb",
+                        "7d17d6d6-d038-40c6-b965-6de41ce9c931",
+                        "3d208b38-62c8-492d-9434-21bb66ead16e",
+                        "9a982898-77c6-4a56-8e54-9cb83ff0b235",
+                        "1bdd91d7-0a1a-488d-ab9c-78eba7a6daa3",
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+                        "ec1d0987-fb49-48b8-aaeb-321c659fb67f",
+                        "e756ce65-ad72-42e6-a8cc-9c1bac781ce5",
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+                        "c225fa8c-e8c8-46a4-bf23-720e2cf1c9ac",
+                        "aa6fca0d-6a70-4016-a0e4-307878e9ff45",
+                        "ee62cd8d-fb93-4082-980b-213c7a8a0c47",
+                        "bbd60a79-3572-42c0-8e53-b0c566a72f06",
+                        "bf585666-2fb4-4ad5-a9b3-b268a9953ed9",
+                        "52548ff8-5bbd-4b1c-9c52-4e5d82f846e2",
+                        "240a67cc-e827-41bf-8ac8-a66bc2797f13",
+                        "7a9b6534-fa1d-4282-a064-11e60e57a322",
+                        "b0af6371-4379-45f0-8c09-f6610833fc46",
+                        "f5ce7a96-cfc0-42c4-852b-386f9a27111d",
+                        "8bc05db7-bd23-4a10-9761-96be7b8ef9ee",
+                        "3dff4add-7d6f-418c-afba-e46864af51d2",
+                        "ab2b7c67-8f13-4388-acd7-e2abb0091f30",
+                        "d9912d93-3d92-48d2-9f75-826fbba3d94e",
+                        "8b37aba2-be5e-4963-8e6f-51a2df8e143e",
+                        "81c0e4e2-9021-4c4d-9876-1ed5b78ca7a7",
+                        "2d7e88dd-bddd-4289-9556-27d301be0b83",
+                        "0c1c578d-d4cc-40bb-a54d-d1d4d004373f",
+                        "9dc0ead3-f17a-4bb8-88e2-87f779029ff8",
+                        "f618a8bc-5e07-477f-a6d3-1b0af8c81ff0",
+                        "e834d3df-8432-40ba-b67d-c7cd0bd7328d",
+                        "d8908d6d-5daa-454d-9082-726054cfddc1",
+                        "c5a7142e-4702-4e84-b7aa-239df2a71ba8",
+                        "f69e44ef-cf23-4571-8dad-e44222697974",
+                        "ea72f81c-2c58-43e2-acca-294254f470f7",
+                        "89d1d2b5-81d3-487d-9fc1-d8b1d8ac34ab",
+                        "6928ac1b-fd1d-436c-bfc6-4087c65809d7",
+                        "07a7b938-435b-4804-b140-c255957b6532",
+                        "3d532a7b-55e7-4461-afbc-65ef76403384",
+                        "bab40245-28bd-49a2-8be0-ba109fe41c91",
+                        "9d577bd4-3a27-48be-ad7c-8c44cf803cda",
+                        "c4de7605-fec5-4389-bb9e-f2ea0c41cdef",
+                        "21a043b6-6dde-41b9-b20e-74b961da8b88",
+                        "11280200-1803-4110-aa84-2808776c2d50",
+                        "86df5269-576b-4d18-a0ce-6e2b2a36d51b",
+                        "e524ff4e-95fa-4561-bfd3-276cba79e664",
+                        "3d5737da-b1ab-48cb-a26f-d420e53edccd",
+                        "44cf15ec-3d4e-4698-bb14-107c34891191",
+                        "6242cdf3-fd6d-4479-a08a-1747818fd978",
+                        "bc60bbd4-8b09-425c-b507-9da24a84f412",
+                        "1f054ccf-f8dd-4127-a6f8-c577d7dd93dc",
+                        "9954cb4b-b0a4-4479-b31d-0bee1e75d9c7",
+                        "5f67c32c-a154-4620-8603-0b64979b04a4",
+                        "7d5bffb2-8bf9-4366-a8b2-762ebb4d6c5d",
+                        "dcee6df0-9e87-4935-8873-f8d30d449d76",
+                        "7d6bdde6-523f-46cb-bed5-d6cfa8fea80c",
+                        "e6d00b0c-3641-4ec4-a553-8fd742193dba",
+                        "e5034863-0528-4f55-be95-c8501c29f9fe",
+                        "cc61b14a-59d9-477b-8cb1-43c4ee4cf434",
+                        "33d332c9-aefe-4db5-8830-b8daddaed0d2",
+                        "bb3b6fc7-0902-432d-bad1-6b3f61951314",
+                        "2b734e88-3a33-4c73-92bb-82e0b8f8c13b"
+                    ],
+                    "output_type": "file",
+                    "protocols": [
+                        {
+                            "protocol_type": "imaging_protocol",
+                            "protocol_id": "96ecb94d-e848-4d7b-8df9-f19af6ab17b8"
+                        }
+                    ]
+                },
+                {
+                    "process": "07acb7d0-3f1c-47f7-9ef9-851c4f1caaec",
+                    "inputs": [
+                        "edd1d525-a6ae-4658-a6bf-6c31d7ab6948"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "87f58f88-ef8b-4323-bd19-cde1a2497b59"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "imaging_preparation_protocol",
+                            "protocol_id": "a6d431b0-4373-4eaf-a3af-8c3fe461ab38"
+                        }
+                    ]
+                },
+                {
+                    "process": "fee8a188-5783-44cd-a1c1-ed9d5d7c32a9",
+                    "inputs": [
+                        "6cb9fc09-7755-4a35-b6b1-0d6fe696b2d4"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "edd1d525-a6ae-4658-a6bf-6c31d7ab6948"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "collection_protocol",
+                            "protocol_id": "caf94c25-8327-4379-b88e-2a6642cd7513"
+                        }
+                    ]
+                }
+            ]
+        }
+    }
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c/2019-04-03T103426.471000Z/manifest.json b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c/2019-04-03T103426.471000Z/manifest.json
deleted file mode 100644
index 65a9ac759..000000000
--- a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c/2019-04-03T103426.471000Z/manifest.json
+++ /dev/null
@@ -1,5582 +0,0 @@
-[
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "8079eb90",
-        "indexed": true,
-        "name": "imaged_specimen_0.json",
-        "s3_etag": "038fab03a6a415e07fa01214f058cb01",
-        "sha1": "a5d1b0e5457d029d0fe0f2c19c0c2b2f45c67083",
-        "sha256": "dcabfb5b083bb3ec5ef482c6266aa46617da50712520f911542d7428228e315d",
-        "size": 896,
-        "uuid": "87f58f88-ef8b-4323-bd19-cde1a2497b59",
-        "version": "2019-04-03T101350.866000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "d46a73e9",
-        "indexed": true,
-        "name": "specimen_from_organism_0.json",
-        "s3_etag": "889570fe22be551b40a308389b62aef7",
-        "sha1": "f2b51ec11480e4b8613d1adef1beb5850847f57c",
-        "sha256": "86b0f47a079ed4226c6297c02196c0d9ac3b75666790a0bfa2aed117c158883c",
-        "size": 1006,
-        "uuid": "edd1d525-a6ae-4658-a6bf-6c31d7ab6948",
-        "version": "2019-04-03T101345.512000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "387a6170",
-        "indexed": true,
-        "name": "donor_organism_0.json",
-        "s3_etag": "3ed8a682ec9b84753e948b05aa7b50d3",
-        "sha1": "c054bb3fdbe4a5c87b2cbbf8af58c9e32445b9af",
-        "sha256": "3bcd6249e1982a1400a67330c8eb6c72c1c2a6bb94e3f27df9abbd75a2cd4fca",
-        "size": 1461,
-        "uuid": "6cb9fc09-7755-4a35-b6b1-0d6fe696b2d4",
-        "version": "2019-04-03T101345.427000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "15c0476b",
-        "indexed": true,
-        "name": "image_file_0.json",
-        "s3_etag": "78969f572594bd6ec8db29581fc3fc49",
-        "sha1": "821bcb53fadcf5a54df2b80912509394bcf85251",
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-        "uuid": "6baa3aff-b2a5-4e49-82f7-25c108a6107a",
-        "version": "2019-04-03T101544.995000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "b2bc1297",
-        "indexed": true,
-        "name": "image_file_1.json",
-        "s3_etag": "352bd9b676d359440b0ab6610d82f880",
-        "sha1": "92ace2e3683c59df707f6c2cea97a245211b29e4",
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-        "uuid": "06dcfc33-21da-485f-8e50-49d294713a9e",
-        "version": "2019-04-03T101544.993000Z"
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-        "crc32c": "e80dc77a",
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diff --git a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c/2019-04-03T103426.471000Z/metadata.json b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c/2019-04-03T103426.471000Z/metadata.json
deleted file mode 100644
index 41b547638..000000000
--- a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c/2019-04-03T103426.471000Z/metadata.json
+++ /dev/null
@@ -1,6398 +0,0 @@
-{
-    "imaged_specimen_0.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/2.0.7/imaged_specimen",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "420508-10-1",
-            "biomaterial_name": "420508 coronal sections slice 10-1",
-            "biomaterial_description": "mouse brain coronal section 20um",
-            "ncbi_taxon_id": [
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-            ],
-            "supplementary_files": [
-                "point1nissl10x.tar.gz"
-            ]
-        },
-        "slice_thickness": 20.0,
-        "internal_anatomical_structures": [
-            {
-                "text": "V1, Provided files are Neurotrace stain and DIC images of the half brain slice imaged at 10x"
-            }
-        ],
-        "provenance": {
-            "document_id": "87f58f88-ef8b-4323-bd19-cde1a2497b59",
-            "submission_date": "2019-04-03T10:13:40.000Z",
-            "update_date": "2019-04-03T10:13:50.866Z"
-        }
-    },
-    "specimen_from_organism_0.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/specimen_from_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "420508_specimen",
-            "biomaterial_name": "fresh frozen brain",
-            "ncbi_taxon_id": [
-                10090
-            ],
-            "genotype": "wt"
-        },
-        "genus_species": [
-            {
-                "text": "Mus musculus",
-                "ontology": "NCBITaxon:10090",
-                "ontology_label": "Mus musculus"
-            }
-        ],
-        "organ": {
-            "text": "brain",
-            "ontology": "UBERON:0000955",
-            "ontology_label": "brain"
-        },
-        "preservation_storage": {
-            "storage_method": "fresh",
-            "preservation_method": "fresh"
-        },
-        "collection_time": "2018-09-18T10:00:00Z",
-        "provenance": {
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-            "submission_date": "2019-04-03T10:13:39.992Z",
-            "update_date": "2019-04-03T10:13:45.512Z"
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-    },
-    "donor_organism_0.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/14.0.7/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "420508",
-            "biomaterial_name": "C57BL6J-420508",
-            "ncbi_taxon_id": [
-                10090
-            ],
-            "genotype": "wt"
-        },
-        "mouse_specific": {
-            "strain": [
-                {
-                    "text": "C57BL6J",
-                    "ontology": "EFO:0000606",
-                    "ontology_label": "C57BL/6J"
-                }
-            ]
-        },
-        "death": {
-            "cause_of_death": "euthanasia under anesthesia",
-            "cold_perfused": false,
-            "days_on_ventilator": 0.0,
-            "hardy_scale": 1,
-            "time_of_death": "2018-09-18T10:00:00Z"
-        },
-        "genus_species": [
-            {
-                "text": "Mus musculus",
-                "ontology": "NCBITaxon:10090",
-                "ontology_label": "Mus musculus"
-            }
-        ],
-        "organism_age": "56",
-        "organism_age_unit": {
-            "text": "days",
-            "ontology": "UO:0000033",
-            "ontology_label": "day"
-        },
-        "development_stage": {
-            "text": "adult",
-            "ontology": "EFO:0001272",
-            "ontology_label": "adult"
-        },
-        "is_living": "no",
-        "sex": "male",
-        "provenance": {
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-            "submission_date": "2019-04-03T10:13:39.984Z",
-            "update_date": "2019-04-03T10:13:45.427Z"
-        }
-    },
-    "image_file_0.json": {
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-        "schema_type": "file",
-        "file_core": {
-            "file_name": "codebook.json",
-            "file_format": "json"
-        },
-        "provenance": {
-            "document_id": "6baa3aff-b2a5-4e49-82f7-25c108a6107a",
-            "submission_date": "2019-04-03T10:13:40.056Z",
-            "update_date": "2019-04-03T10:15:44.995Z"
-        }
-    },
-    "image_file_1.json": {
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-        "schema_type": "file",
-        "file_core": {
-            "file_name": "experiment.json",
-            "file_format": "json"
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-            "submission_date": "2019-04-03T10:13:40.066Z",
-            "update_date": "2019-04-03T10:15:44.993Z"
-        }
-    },
-    "image_file_2.json": {
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-        "schema_type": "file",
-        "file_core": {
-            "file_name": "nuclei-fov_000-Z0-H0-C0.tiff",
-            "file_format": "tiff"
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-            "submission_date": "2019-04-03T10:13:40.076Z",
-            "update_date": "2019-04-03T10:15:51.032Z"
-        }
-    },
-    "image_file_3.json": {
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-        "schema_type": "file",
-        "file_core": {
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-            "update_date": "2019-04-03T10:15:47.812Z"
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-        "schema_type": "file",
-        "file_core": {
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-    "image_file_5.json": {
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-        "schema_type": "file",
-        "file_core": {
-            "file_name": "nuclei-fov_000-Z11-H0-C0.tiff",
-            "file_format": "tiff"
-        },
-        "provenance": {
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-            "submission_date": "2019-04-03T10:13:40.102Z",
-            "update_date": "2019-04-03T10:15:54.073Z"
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-    },
-    "image_file_6.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
-        "schema_type": "file",
-        "file_core": {
-            "file_name": "nuclei-fov_000-Z12-H0-C0.tiff",
-            "file_format": "tiff"
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-        "provenance": {
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-            "submission_date": "2019-04-03T10:13:40.111Z",
-            "update_date": "2019-04-03T10:15:51.125Z"
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-    "image_file_7.json": {
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-        "file_core": {
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-            "update_date": "2019-04-03T10:15:50.982Z"
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-                "molecule_id": "NM_138683",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aagaagaggaagctgtgcggtttccggaagggatcggaagag",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Rspo1",
-                "molecule_id": "NM_138683",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gtgtcaggagggcttgtacttacacaagggccgctgctatcca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Rspo1",
-                "molecule_id": "NM_138683",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cccaagctcttcattctgctggagaggaacgacatccgccaggt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Fam84b",
-                "molecule_id": "NM_001162926",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gcctggaggacttgatcatggagaagcggcgcaacgaccagat",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Fam84b",
-                "molecule_id": "NM_001162926",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aacgatctgtatcgctacaagccactgagccctagcgctgtagt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Fam84b",
-                "molecule_id": "NM_001162926",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aacaagtgcagtccgggtgacctggtggagtttgtatcgcaggc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Deptor",
-                "molecule_id": "NM_001037937",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ctcaggagacgcatgacagtcccttctgtctgaggaagcagag",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Deptor",
-                "molecule_id": "NM_001037937",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gcaacctcctctaccagttcagaatgaacttccgtcggaggcgga",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Deptor",
-                "molecule_id": "NM_001037937",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aagaggcagagcagctttgccaccggcttatggaccatgggatc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ndnf",
-                "molecule_id": "NM_172399",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "caccagaaagaaatcagagaaggtcctttgcaaatacttccacag",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ndnf",
-                "molecule_id": "NM_172399",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "agcttttgacaagctacgtacctgctcttcagttacggtggcat",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ndnf",
-                "molecule_id": "NM_172399",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aggcaacaggaaaggagcatcaaagctgaaaatactggcgacca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Chrna2",
-                "molecule_id": "NM_144803",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aagcactagaaggtgtacactacattgctgaccacctgaggtct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Chrna2",
-                "molecule_id": "NM_144803",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tcattggctggagaccaacatggatgctgaagaaagggaggag",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Chrna2",
-                "molecule_id": "NM_144803",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgtcttcctgctgctcatcacagaaattatcccatccacctcac",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Calb1",
-                "molecule_id": "NM_009788",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cacccaaagcacctctgtgctgcttctatctggcggaagggat",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Calb1",
-                "molecule_id": "NM_009788",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cgaacagaccttgctcttattctttctgctggagacaactagagtt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Calb1",
-                "molecule_id": "NM_009788",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ctgcgaggaattcatgaagacttggagaaagtatgatactgaccac",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Sncg",
-                "molecule_id": "NM_011430",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gttgcccaagttctctgtccctagcccagtgccacaagtcca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Sncg",
-                "molecule_id": "NM_011430",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gagaatgaagaggccaagagtggagaagactagaaggctgccag",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Sncg",
-                "molecule_id": "NM_011430",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tggtcagcagcgtcaacacagtggccaacaagaccgtggagga",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Th",
-                "molecule_id": "NM_009377",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gacaagctcaggaactatgcctctcgtatccagcgcccattctc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Th",
-                "molecule_id": "NM_009377",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgggacacgtacccatgttggctgaccgcacatttgcccagtt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Th",
-                "molecule_id": "NM_009377",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gtttcagtgcacacagtacatccgtcatgcctcctcacctatgc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Gad1",
-                "molecule_id": "NM_001312900",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgatcgctccaccaaggttctggatttccaccacccacacca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Gad1",
-                "molecule_id": "NM_001312900",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tccaagaacctgctttcctgtgaaaacagtgaccagggtgccc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Gad1",
-                "molecule_id": "NM_001312900",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tctgtggcttcttacaaaggaccaatagcctggaagagaagagtcg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Slc17a7",
-                "molecule_id": "NM_182993",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "atcgctgactttttgcgcagtcgtcacataatgtccactaccaa",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Slc17a7",
-                "molecule_id": "NM_182993",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "caccctggaggcgcttctttacgtccatgcccgtctatgccat",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Slc17a7",
-                "molecule_id": "NM_182993",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tatggcagcttcgggatcttttggtacctgttctggttgcttgtct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Neurod1",
-                "molecule_id": "NM_010894",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gatcctgcgctcaggcaaaagccctgatctggtctccttcgta",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Neurod1",
-                "molecule_id": "NM_010894",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cttgctactccaagacccagaaactgtctaaaatagagacactgcg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Neurod1",
-                "molecule_id": "NM_010894",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gcgcgcctagaacgttttaaattaaggcgcatgaaggccaacg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Rorb",
-                "molecule_id": "NM_146095",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ctttgcgaagaatctgtgttccttgcagctgactgaggaagagat",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Rorb",
-                "molecule_id": "NM_146095",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ccacacctacgaggaaatcaaggcgtatcaaagcaagtccaggga",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Rorb",
-                "molecule_id": "NM_146095",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgcacagaacatcattaagtcccatttggagacatgtcagtacac",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Fezf2",
-                "molecule_id": "NM_080433",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gctttcaccaaaaagggaactacaagaatcacaagctcacccaca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Fezf2",
-                "molecule_id": "NM_080433",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ttcaatcgcagctccacgctcaacacgcacatccgcatccac",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Fezf2",
-                "molecule_id": "NM_080433",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "agctagaccgtttgtgtgcaaagtctgtggcaaaggcttccg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Adarb2",
-                "molecule_id": "NM_001289530",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ataccgacaaaacaggcctctccttagtggcgtgagtcacgca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Adarb2",
-                "molecule_id": "NM_001289530",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "atcgagcctgtgtacctccacagcatcattgtgggcagcctgca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Adarb2",
-                "molecule_id": "NM_001289530",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cagacttgaacagcagcaaacacatcgtcaggaagttccgaggg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Lamp5",
-                "molecule_id": "NM_029530",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ctgactttgtcttcagtgaagaacataaatgtccagtggatgagc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Lamp5",
-                "molecule_id": "NM_029530",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tttctctggcctccagtgaccctcagaagactgtcaccatgatcct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Lamp5",
-                "molecule_id": "NM_029530",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ctcagaatgctctttgtaaaggaaagtcacaacacttccaaagg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Vip",
-                "molecule_id": "NM_001313969",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gggtcagatttctgccaaaaaataccttgagtcactcattggcaa",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Vip",
-                "molecule_id": "NM_001313969",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gcagaaaatggcacaccctattatgatgtgtcaagaaatgccaggc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Vip",
-                "molecule_id": "NM_001313969",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ccttctgtagtgagtaggctggatgacaggatgccgtttgaagg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Lhx6",
-                "molecule_id": "NM_001083127",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cgcatccattacgacaccatgatcgagaacctcaagagggcc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Lhx6",
-                "molecule_id": "NM_001083127",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ctggcatgtttcgcctgcttttcctgcaagcgccagctatcca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Lhx6",
-                "molecule_id": "NM_001083127",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "atttggaaccaagtgcgcccggtgcggcagacaaatctatgcc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Chodl",
-                "molecule_id": "NM_139134",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ggtgcaacatgaagcacaattacatctgcaagtatgaaccagaga",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Chodl",
-                "molecule_id": "NM_139134",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aatgtgtagtcatgtaccaccaaccaactgccaatcctggccta",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Chodl",
-                "molecule_id": "NM_139134",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aaacatcgggtgcctgcccagatctctaccagtggtctgatggaag",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Fa2h",
-                "molecule_id": "NM_178086",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tacctgcacttcggctctccacacaagggctcctacctgtacaac",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Fa2h",
-                "molecule_id": "NM_178086",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gattgccttcttctatgtgttcctgcggctcattctgcctgaga",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Fa2h",
-                "molecule_id": "NM_178086",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gccattacctcatcatgttgcattttgtcatgcacggccagcac",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ly86",
-                "molecule_id": "NM_010745",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ggcttggaagtagtctaccagagctgtgatcccttacaggattttg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ly86",
-                "molecule_id": "NM_010745",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "attctgacttctccgagcagcagtgaccatggcagcgaaaatg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ly86",
-                "molecule_id": "NM_010745",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "atggcaaaaggctcttctattctgaactactcctatcccctttg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Dcn",
-                "molecule_id": "NM_007833",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "caggtcgtctaccttcacaacaacaacatctccgcagttgggcaaa",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Dcn",
-                "molecule_id": "NM_007833",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tctcactgaagtgcatctagatggcaacaagatcaccaaggttgat",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Dcn",
-                "molecule_id": "NM_007833",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "agggactgaagagtctctcatacattcgcatctcagacaccaacat",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Fgfr3",
-                "molecule_id": "NM_001163216",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cctcactgtgacatcaaccgacgagtacttggacctctccgt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Fgfr3",
-                "molecule_id": "NM_001163216",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ctgtacatgatcatgcgggaatgttggcatgcggtgccttcacag",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Fgfr3",
-                "molecule_id": "NM_001163216",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgctggtggagtacgcagccaagggcaatctccgggagttcctt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Map3k7cl",
-                "molecule_id": "NM_144854",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aagctacctatcgttcagacacaccgttgagtgaatgcagaattag",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Map3k7cl",
-                "molecule_id": "NM_144854",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cctttgtgttagcacacagtggtcacatttgccttggccgtgtg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Map3k7cl",
-                "molecule_id": "NM_144854",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gagcctaaatgctttcttgtgaaaatatcagcaggcgtgtgtcc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Nxph1",
-                "molecule_id": "NM_008751",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gattccaagtccttcaactgtcgcattgagtatgagaaggttgac",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Nxph1",
-                "molecule_id": "NM_008751",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tctgggactggctgaggaactccacagatcttcaggagcctcg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Nxph1",
-                "molecule_id": "NM_008751",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gtcggctcctctcacagactttccgtggtaaagaaaatgacac",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Pcp4",
-                "molecule_id": "NM_008791",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "agaagaaaaaggcaggatcacagtcctagtggtgaagctgcttc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Pcp4",
-                "molecule_id": "NM_008791",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ggcagaagaaagtccaagaagaatttgatatcgacatggatgcacc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Pcp4",
-                "molecule_id": "NM_008791",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tagctgcggagtcaggccaacatgagtgagagacaaagtgccgg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Neurod6",
-                "molecule_id": "NM_009717",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ccaactacaaacttggtggcaggctgcttacagctcaacgcca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Neurod6",
-                "molecule_id": "NM_009717",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ttacatctgggcactttctgaaattctgaggattggcaagagacc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Neurod6",
-                "molecule_id": "NM_009717",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ggtcaagttcaggagacaggaagctaatgcgcgcgagaggaa",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Nrn1",
-                "molecule_id": "NM_153529",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "actcacccacactcacaccatgctcccggaaatcgagaggaata",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Nrn1",
-                "molecule_id": "NM_153529",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "accgtgtgcacatactgggaggatttccacagctgcacggtc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Nrn1",
-                "molecule_id": "NM_153529",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cttttcagactgtttgctcaagctgggcgacagcatggccaacta",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Nrgn",
-                "molecule_id": "NM_022029",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ttctttgtttatgcaaaagcctcctgagcgcctggaggctcc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Nrgn",
-                "molecule_id": "NM_022029",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ctcccgctcttctttgtttatgcaaaagcctcctgagcgcctgga",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Nrgn",
-                "molecule_id": "NM_022029",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ccaagccagacgacgatattcttgacatcccgctggatgatcc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ptn",
-                "molecule_id": "NM_008973",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "caatgctgactgtcagaaaactgtcaccatctccaagccctgtg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ptn",
-                "molecule_id": "NM_008973",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ccttcctggcattgattttcatcttggcagctgtggacactgct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ptn",
-                "molecule_id": "NM_008973",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aaaggcagccagctagtcagcgaggacctctgcaagccaaaaaatg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cck",
-                "molecule_id": "NM_031161",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgccgaggactacgaatacccatcgtagtgggccagcgtctt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cck",
-                "molecule_id": "NM_031161",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tacatccagcaggtccgcaaagctccttctggccgcatgtccgtt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cck",
-                "molecule_id": "NM_031161",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aagagcggcgtatgtctgtgcgtggtgatggcagtcctagctgct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Synpr",
-                "molecule_id": "NM_001163032",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgatgtcagcttgcaagcagccttccaacaagtgcatggctg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Synpr",
-                "molecule_id": "NM_001163032",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gactttatcgtcactgtagtcttttcattcttgtggctggtgg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Synpr",
-                "molecule_id": "NM_001163032",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tttctctactccctggctgccacggtcgtgtacattttcttccag",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Slc6a1",
-                "molecule_id": "NM_178703",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "catcattgtggcgggcgtgtttctcttcagtgctgtgcagatg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Slc6a1",
-                "molecule_id": "NM_178703",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgtcaaccggttctatgacaacatccaggagatggttggctcca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Slc6a1",
-                "molecule_id": "NM_178703",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ctcttcattgctgccgtgtgcatcgtgtcctacctgattggc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Dlx6",
-                "molecule_id": "NM_010057",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cacaccaggacaccatgcagagaccacagatgatgtgacttctc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Dlx6",
-                "molecule_id": "NM_010057",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgtcaccacgatcaccagccctgcctccagtgtgggacgtttct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Dlx6",
-                "molecule_id": "NM_010057",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ccatcgctttcagcagactcaatacctggcccttcccgagaga",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Atp1a3",
-                "molecule_id": "NM_001290469",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "actgggatgatcgcactgtcaatgacctagaagacagttatggg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Atp1a3",
-                "molecule_id": "NM_001290469",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cccacgcacagacaaactggtcaacgaaaggctcatcagcatg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Atp1a3",
-                "molecule_id": "NM_001290469",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cctgagatcacacccttcctgctcttcatcatggctaacatccc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Arpp19",
-                "molecule_id": "NM_021548",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "caatgcatctccaccatttgatatgcaataggacactgcctgt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Arpp19",
-                "molecule_id": "NM_021548",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gcccactgtaagcacttcacttacattttctaaagcaccgtcttg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Arpp19",
-                "molecule_id": "NM_021548",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aagcaggtagcctctgggaagagctattctgatggttaccaagg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cxcl14",
-                "molecule_id": "NM_019568",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "acagcactgttctctgagttaggatgttaggacgatcctgcgcc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cxcl14",
-                "molecule_id": "NM_019568",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aagggaagatgcaggattagatgcaggacacacagccagagcta",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cxcl14",
-                "molecule_id": "NM_019568",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tactgctccgctccaggcttacaaagcttccgctcagagagcct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Rab3b",
-                "molecule_id": "NM_023537",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cttttccaataagtgtgatcccgtcgcttggaatcctgcccaag",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Rab3b",
-                "molecule_id": "NM_023537",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gctggtatcaggcccagtgatcaaatgaaagggccaaatagag",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Rab3b",
-                "molecule_id": "NM_023537",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aggtaaagggagctctatagggaagcaggctcaggctgtagtg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cryab",
-                "molecule_id": "NM_001289785",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aaacaggtgtctggccctgagcgcaccattcccatcacccgtgaa",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cryab",
-                "molecule_id": "NM_001289785",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ggcttcatctccagggagttccacaggaagtaccggatccca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cryab",
-                "molecule_id": "NM_001289785",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gatgcgtttggagaaggacagattctctgtgaatctggacgtgaa",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Penk",
-                "molecule_id": "NM_001002927",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gctgaaagagctactgggaacgggagacaaccgtgcgaaagac",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Penk",
-                "molecule_id": "NM_001002927",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ggtacggaggcttcatgaagaagatggacgagctatatcccatg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Penk",
-                "molecule_id": "NM_001002927",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "acatcgacatgtacaaagacagcagcaaacaggatgagagccac",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Crh",
-                "molecule_id": "NM_205769",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gcaagctcacagcaacaggaaactgatggagattatcgggaaa",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Crh",
-                "molecule_id": "NM_205769",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cgcccatctctctggatctcaccttccaccttctgcgggaagt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Crh",
-                "molecule_id": "NM_205769",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aaacctgcaggaggcatcctgagagaagtccctctgcagaggca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Caln1",
-                "molecule_id": "NM_021371",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tccatcccgcaccagcatcttggaatctgcagagagcctggct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Caln1",
-                "molecule_id": "NM_021371",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gccacctctatccatgacccaattctttcaacccagggaccc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Caln1",
-                "molecule_id": "NM_021371",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ctgctttcttttcgtcttggaattccagtagccatccagatagca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Kcnip1",
-                "molecule_id": "NM_027398",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gatcatgtgcaaatggtacttccagacagcacctcttttctaat",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Kcnip1",
-                "molecule_id": "NM_027398",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ctctatggctcaggagaggcaagttgtgacaaagggtggttagt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Kcnip1",
-                "molecule_id": "NM_027398",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ccaaatgtgcaccatcctccgatggcctcccaagccaatgtg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Gm11549",
-                "molecule_id": "NR_040411",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aactcagacatccgcctgcctctgcctcctgagtgctgggatta",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Gm11549",
-                "molecule_id": "NR_040411",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ggctattgtatgtacagttcacaccattctcgtgtgtgtgtgt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Gm11549",
-                "molecule_id": "NR_040411",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "acagcctacgtactggccaagccgagggagaagaaacacttcc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ctxn1",
-                "molecule_id": "NM_183315",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gactcacattggacgctgcctacctataatgcacggtacagtt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ctxn1",
-                "molecule_id": "NM_183315",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "agggcgttcggagaagtccagtccttacctaccttagctacccat",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ctxn1",
-                "molecule_id": "NM_183315",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgttcgccttcgtgctctgcctgctcgtggtgttggttctgtt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Car4",
-                "molecule_id": "NM_007607",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aacttcctccagtaatggcccacttctggatatctgacctctga",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Car4",
-                "molecule_id": "NM_007607",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gaaggacaagtttgcagtgctggcatttatgattgaggtaggag",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Car4",
-                "molecule_id": "NM_007607",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gaatgacaacggttcagagcacagtattgatgggagacactttgc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Nfib",
-                "molecule_id": "NM_008687",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "atgacatgaactctggtgtgaacctgcagaggtcgctgtcttct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Nfib",
-                "molecule_id": "NM_008687",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gagtatccagaacacccataacccagggaactggagtcaacttcc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Nfib",
-                "molecule_id": "NM_008687",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "acaatcaggaagtccaagccacagtgatcctgccaagaatcctc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Id2",
-                "molecule_id": "NM_010496",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aaggaattgcccaatgtaagcagactttgccttttcacaaaggtgg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Id2",
-                "molecule_id": "NM_010496",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gcggaaggaaaactaaggatgatcgtcttgcccaggtgtcgttct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Id2",
-                "molecule_id": "NM_010496",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "acccgatgagtctgctctacaacatgaacgactgctactccaagc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Igfbp6",
-                "molecule_id": "NM_008344",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gcctttgccagtgtctccagatggtcaaggaagcactcagtg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Igfbp6",
-                "molecule_id": "NM_008344",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgggctctatgtgccaaactgtgacctcagaggcttctaccg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Igfbp6",
-                "molecule_id": "NM_008344",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aggagtgtacagggcaaaaactctgaccatgacctgggatgggct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Itpka",
-                "molecule_id": "NM_146125",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cttcgtgcatgaccattgccatcgtgctggtgtgtggctcatc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Itpka",
-                "molecule_id": "NM_146125",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gcctacagcagatccgggataccctggagatctctgatttcttt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Itpka",
-                "molecule_id": "NM_146125",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "acgaagccgagagcaagtgacccgtgtctttgaggagttcatgca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ptprd",
-                "molecule_id": "NM_001352630",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ccgccttgttaatattatgccatatgaatccacaagggtgtgcc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ptprd",
-                "molecule_id": "NM_001352630",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "atccatgatgcactgttagaagcagtgacatgtggaaataccgaa",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Ptprd",
-                "molecule_id": "NM_001352630",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aatcctccagatgcagggccaatggtggtacactgcagtgctggt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Sv2b",
-                "molecule_id": "NM_001109753",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tttggcaacagcgagtctgcgatgatcggctggcaatgcctgtt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Sv2b",
-                "molecule_id": "NM_001109753",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gctcatggacagaattggaagactcaagatgattggcggctccat",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Sv2b",
-                "molecule_id": "NM_001109753",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ggactttgaagaggacaatgattttctgatttacctcgtcagct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Vxn",
-                "molecule_id": "NM_178399",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "ctgagcatctgaccctcatgtccaaacatagtctggacacttgg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Vxn",
-                "molecule_id": "NM_178399",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "acatggcggtaagtcaaacccagacttccaggctcttgcctt",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Vxn",
-                "molecule_id": "NM_178399",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgaactgtttgggtatcaggcttgcttctgctgttctgtggattct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Reln",
-                "molecule_id": "NM_001310464",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aggagttctactgcgctggtggcagccacgccacaatggaaca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Reln",
-                "molecule_id": "NM_001310464",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "atcacctggcacgtcatcgctcagcaccagccgaaggacttcaca",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Reln",
-                "molecule_id": "NM_001310464",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cactcgagcaagcaaaattatgtttgtcttgcaaattgggagcc",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Rprml",
-                "molecule_id": "NM_001033212",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "aacgaagtacctcgcaccacccgggtctggacaccataggact",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Rprml",
-                "molecule_id": "NM_001033212",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "cttgccagagttgaagcaccgcgaggaagagactacggagcct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Rprml",
-                "molecule_id": "NM_001033212",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tcaagtccgagagcatgatcaactttctgatgcaggagcgcagg",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cnr1",
-                "molecule_id": "NM_007726",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gagacatgctttccgcagcatgttcccttcatgtgaaggcact",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cnr1",
-                "molecule_id": "NM_007726",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgaacaagcttatcaagacggtgtttgccttctgtagtatgctct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cnr1",
-                "molecule_id": "NM_007726",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "atccagcgtggaacccagaaaagcatcatcattcacacctcaga",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cacna2d3",
-                "molecule_id": "NM_009785",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gaatcccttaagtgtgaacggttaaaggctcagaagatcagacgac",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cacna2d3",
-                "molecule_id": "NM_009785",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tggtggtggacagtagctgtctctgtgagtccgtggctcctata",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Cacna2d3",
-                "molecule_id": "NM_009785",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "agaccacagggaacattgcttgcgaagactgctccaagtcct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Plpp4",
-                "molecule_id": "NM_001080963",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "gaggagtgattggcctcatttttgcctatatttgctacagacaac",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Plpp4",
-                "molecule_id": "NM_001080963",
-                "subcellular_structure": {
-                    "text": "cytoplasmic"
-                },
-                "probe_sequence": "tgctgccatcttgcccttgtactgtgccatgatgatcgccct",
-                "assay_type": {
-                    "text": "in situ sequencing"
-                },
-                "multiplexed": "yes"
-            },
-            {
-                "molecule_name": "Plpp4",
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diff --git a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
new file mode 100644
index 000000000..6b5bd4ff6
--- /dev/null
+++ b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
@@ -0,0 +1,790 @@
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+            "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.9/enrichment_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "enrichment_protocol_1",
+                "protocol_name": "an example enrichment protocol",
+                "protocol_description": "an example enrichemnt protocol description",
+                "publication_doi": "10.1101/193219",
+                "protocols_io_doi": "10.17504/protocols.io.mgjc3un",
+                "document": "my_cool_protocol.pdf"
+            },
+            "enrichment_method": {
+                "text": "fluorescence-activated cell sorting",
+                "ontology": "EFO:0009108",
+                "ontology_label": "fluorescence-activated cell sorting"
+            },
+            "markers": "CD4+ CD8-",
+            "min_size_selected": 70.0,
+            "max_size_selected": 90.0,
+            "provenance": {
+                "document_id": "df679627-ccb6-426d-a709-c259db607d84",
+                "submission_date": "2019-03-17T22:00:57.731Z",
+                "update_date": "2019-03-17T22:01:03.051Z"
+            }
+        },
+        "collection_protocol_0.json": {
+            "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/8.2.11/collection_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "collection_protocol_1",
+                "protocol_name": "A dummy collection protocol",
+                "protocol_description": "A dummy collection protocol description",
+                "publication_doi": "10.1101/193219",
+                "protocols_io_doi": "10.17504/protocols.io.mgjc3un",
+                "document": "my_cool_protocol.pdf"
+            },
+            "collection_method": {
+                "text": "organ extraction",
+                "ontology": "EFO:0009124",
+                "ontology_label": "organ extraction"
+            },
+            "protocol_reagents": [
+                {
+                    "retail_name": "SureCell WTA 3' Library Prep Kit",
+                    "catalog_number": "20014279",
+                    "manufacturer": "Illumina",
+                    "lot_number": "10001A",
+                    "expiry_date": "2018-01-31",
+                    "kit_titer": "Titer: Specification is 3.0x10^7"
+                }
+            ],
+            "provenance": {
+                "document_id": "c3dabd8c-6f32-4c0b-a13b-11bb71cc95de",
+                "submission_date": "2019-03-17T22:00:57.724Z",
+                "update_date": "2019-03-17T22:01:03.060Z"
+            }
+        },
+        "process_0.json": {
+            "process_core": {
+                "process_id": "bundle1"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/6.0.7/process",
+            "provenance": {
+                "document_id": "8a0879df-13e0-4dce-9776-20fb259796e9",
+                "submission_date": "2019-03-17T22:00:57.752Z",
+                "update_date": "2019-03-17T22:01:03.421Z"
+            }
+        },
+        "process_1.json": {
+            "process_core": {
+                "process_id": "process_id_2"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/6.0.7/process",
+            "provenance": {
+                "document_id": "b2e86d49-6874-4522-a68c-43166e858bdd",
+                "submission_date": "2019-03-17T22:00:57.748Z",
+                "update_date": "2019-03-17T22:01:03.392Z"
+            }
+        },
+        "process_2.json": {
+            "process_core": {
+                "process_id": "process_id_1"
+            },
+            "schema_type": "process",
+            "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/6.0.7/process",
+            "provenance": {
+                "document_id": "b147df84-443b-4dd2-8327-7ea42adcd151",
+                "submission_date": "2019-03-17T22:00:57.743Z",
+                "update_date": "2019-03-17T22:01:03.254Z"
+            }
+        },
+        "links.json": {
+            "describedBy": "https://schema.staging.data.humancellatlas.org/system/1.1.5/links",
+            "schema_type": "link_bundle",
+            "schema_version": "1.1.5",
+            "links": [
+                {
+                    "process": "8a0879df-13e0-4dce-9776-20fb259796e9",
+                    "inputs": [
+                        "74a06f8b-dff1-44d2-b1a6-99e3d14b69d1"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "6380c3bc-8bc3-459b-aea3-05dd6c0842ef",
+                        "ceb4dfaa-ecaf-4757-ae54-9d83707f66cc",
+                        "5201d410-d789-4df6-b3fd-9edac998e5f3"
+                    ],
+                    "output_type": "file",
+                    "protocols": [
+                        {
+                            "protocol_type": "library_preparation_protocol",
+                            "protocol_id": "aa7e9a08-2a0c-4575-a9a9-13cab4e96e73"
+                        },
+                        {
+                            "protocol_type": "sequencing_protocol",
+                            "protocol_id": "4bc436f7-e429-4355-8d6e-853d8e639b37"
+                        }
+                    ]
+                },
+                {
+                    "process": "b2e86d49-6874-4522-a68c-43166e858bdd",
+                    "inputs": [
+                        "f3531ee2-d408-4075-b63e-0d0e2b01116c"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "74a06f8b-dff1-44d2-b1a6-99e3d14b69d1"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "dissociation_protocol",
+                            "protocol_id": "1e9abdf3-54da-4c73-9e57-1297ceb39399"
+                        },
+                        {
+                            "protocol_type": "enrichment_protocol",
+                            "protocol_id": "df679627-ccb6-426d-a709-c259db607d84"
+                        }
+                    ]
+                },
+                {
+                    "process": "b147df84-443b-4dd2-8327-7ea42adcd151",
+                    "inputs": [
+                        "20db3238-9ce6-4820-8495-6753e4147d51"
+                    ],
+                    "input_type": "biomaterial",
+                    "outputs": [
+                        "f3531ee2-d408-4075-b63e-0d0e2b01116c"
+                    ],
+                    "output_type": "biomaterial",
+                    "protocols": [
+                        {
+                            "protocol_type": "collection_protocol",
+                            "protocol_id": "c3dabd8c-6f32-4c0b-a13b-11bb71cc95de"
+                        }
+                    ]
+                }
+            ]
+        }
+    }
+}
diff --git a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde/2019-03-17T220646.332108Z/manifest.json b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde/2019-03-17T220646.332108Z/manifest.json
deleted file mode 100644
index 21fe45282..000000000
--- a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde/2019-03-17T220646.332108Z/manifest.json
+++ /dev/null
@@ -1,230 +0,0 @@
-[
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "e4a41880",
-        "indexed": true,
-        "name": "cell_suspension_0.json",
-        "s3_etag": "771087082e3841e2d955d3a4738b6bf6",
-        "sha1": "88fbdf8c6792ef638696f520fbf7073ee77f8a70",
-        "sha256": "bba2d6251b3b95adf3aae07f6de78f6706186d8cf77e6b846004ba561607b952",
-        "size": 1695,
-        "uuid": "74a06f8b-dff1-44d2-b1a6-99e3d14b69d1",
-        "version": "2019-03-17T220103.482000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "ec0f9294",
-        "indexed": true,
-        "name": "specimen_from_organism_0.json",
-        "s3_etag": "ba64e0187f8e1acbb831501ca2d9c55d",
-        "sha1": "84c4b0e71fad61df1e0cab4e8578e8f26c572b3e",
-        "sha256": "e97c736042bb2352b33dd42286706391b1ea80de23fcb591364bbafec5491510",
-        "size": 1447,
-        "uuid": "f3531ee2-d408-4075-b63e-0d0e2b01116c",
-        "version": "2019-03-17T220103.535000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-        "crc32c": "ce292309",
-        "indexed": true,
-        "name": "donor_organism_0.json",
-        "s3_etag": "384f53dbf137044fc4846e2a4a0fc673",
-        "sha1": "fde9a6fbfb6d351d7ff8c2adbc26f8e14784dcc9",
-        "sha256": "ce49a3e318ffac754fd475c72a492e0061037be6131e620f7ac4a367932a66da",
-        "size": 2456,
-        "uuid": "20db3238-9ce6-4820-8495-6753e4147d51",
-        "version": "2019-03-17T220103.211000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "cd22b0a4",
-        "indexed": true,
-        "name": "sequence_file_0.json",
-        "s3_etag": "54153f330aa1b9fe000cb92ccf13909f",
-        "sha1": "a1b752760ef553d58a4d5cc6590ae905493ec9c9",
-        "sha256": "27e3670238f3e64d296b5a21f44a9e708eadc9d34434768fc2536bead22e9d5b",
-        "size": 616,
-        "uuid": "6380c3bc-8bc3-459b-aea3-05dd6c0842ef",
-        "version": "2019-03-17T220304.130000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "654ecf2b",
-        "indexed": true,
-        "name": "sequence_file_1.json",
-        "s3_etag": "53fdd0c163b64f32eb33c2d2f5e490a2",
-        "sha1": "e44596e5542317da3a6db9559cd8370bf8959bc4",
-        "sha256": "8457e0954e940e4915d0d07584b798d990823cb4ef606455f8abd17bf8310da5",
-        "size": 616,
-        "uuid": "ceb4dfaa-ecaf-4757-ae54-9d83707f66cc",
-        "version": "2019-03-17T220306.010000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/file\"",
-        "crc32c": "5c8d6472",
-        "indexed": true,
-        "name": "sequence_file_2.json",
-        "s3_etag": "b893d7fdf85cd6134a8eaf8947617743",
-        "sha1": "8cc158bbdf896bba39e94b264485c13aeefd06fa",
-        "sha256": "2baf9973d9760dafbe4d24e99886ba4131c31a98ef3f1f41392b104dce0db13e",
-        "size": 616,
-        "uuid": "5201d410-d789-4df6-b3fd-9edac998e5f3",
-        "version": "2019-03-17T220303.738000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/project\"",
-        "crc32c": "d5b43d3f",
-        "indexed": true,
-        "name": "project_0.json",
-        "s3_etag": "affb98ff4e5d2076c1b5d2c1fc2a1123",
-        "sha1": "ff8c83a24199185bc677f9aa5f5a7a9131a0162b",
-        "sha256": "4ac31750071a3f15a075178cdfb472aae4aa3c065289f401636aa7599255ce1e",
-        "size": 2455,
-        "uuid": "5014cd10-bbed-4e85-bc45-6fe3a8a0079b",
-        "version": "2019-03-17T220103.175000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-        "crc32c": "c4e3d5a5",
-        "indexed": true,
-        "name": "library_preparation_protocol_0.json",
-        "s3_etag": "3ef0fa45f8d083ea5b42e2b635205e79",
-        "sha1": "fc269fd520a49bf6d66b3b18d6638fbf55df1346",
-        "sha256": "81279b1c39714fa20eea17e18633108d39c648d91efd57efce632fe7c3a66ca1",
-        "size": 1440,
-        "uuid": "aa7e9a08-2a0c-4575-a9a9-13cab4e96e73",
-        "version": "2019-03-17T220103.138000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-        "crc32c": "76e3c622",
-        "indexed": true,
-        "name": "sequencing_protocol_0.json",
-        "s3_etag": "bcf4dcb6e3e3fcec70a3f89a60fc0090",
-        "sha1": "7856e3b6253a26a87e06b929884844ddbe69e737",
-        "sha256": "44379340e53ac31cb854837be33d070d6aa7de4fd012692cf83b5a8d5894b7fa",
-        "size": 1268,
-        "uuid": "4bc436f7-e429-4355-8d6e-853d8e639b37",
-        "version": "2019-03-17T220102.999000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-        "crc32c": "cbf4692f",
-        "indexed": true,
-        "name": "dissociation_protocol_0.json",
-        "s3_etag": "7e3594b3b69b41801e075805bbbdc8d1",
-        "sha1": "7835112e34c9cc1751723dd6fd52778f7d7ab9a4",
-        "sha256": "f08c780ee2d13a193634717c0b5c22f3e4a6b5457e7864681b5778fc4bf565e2",
-        "size": 922,
-        "uuid": "1e9abdf3-54da-4c73-9e57-1297ceb39399",
-        "version": "2019-03-17T220103.046000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-        "crc32c": "3833fa5f",
-        "indexed": true,
-        "name": "enrichment_protocol_0.json",
-        "s3_etag": "c7f29b7b9f36f2b122e80c6722a24b17",
-        "sha1": "8a09a92e0c280ed904bf6a7a5360b5e4f3994f62",
-        "sha256": "3733fb5a7e4c9a07eee111ce90cc8eed742004e1e059c58348663541230522cf",
-        "size": 1002,
-        "uuid": "df679627-ccb6-426d-a709-c259db607d84",
-        "version": "2019-03-17T220103.051000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-        "crc32c": "2aa8eec5",
-        "indexed": true,
-        "name": "collection_protocol_0.json",
-        "s3_etag": "e9f572d88d7ee22c0f3b92e228fb0129",
-        "sha1": "fc931acb005de2b533b03fc4cc8a44bdb702530f",
-        "sha256": "bcfba8a40f1dd713d575981f8d4eb9f30ce766f42c1dcadff830c776221a8eab",
-        "size": 1205,
-        "uuid": "c3dabd8c-6f32-4c0b-a13b-11bb71cc95de",
-        "version": "2019-03-17T220103.060000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/process\"",
-        "crc32c": "4fa2e0d6",
-        "indexed": true,
-        "name": "process_0.json",
-        "s3_etag": "7a351255d56c389e1e591bcadb0b3c64",
-        "sha1": "e3648ac0c76bc0999c2a45c6234008a8f5724616",
-        "sha256": "aa638f85b6c3e4ee2fe8acf38d377c0c4a854a0b1aa8fb6370bb822cf915f1d7",
-        "size": 384,
-        "uuid": "8a0879df-13e0-4dce-9776-20fb259796e9",
-        "version": "2019-03-17T220103.421000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/process\"",
-        "crc32c": "06ed887a",
-        "indexed": true,
-        "name": "process_1.json",
-        "s3_etag": "31100497d87e6b38004ec40da7db51ee",
-        "sha1": "366e43a7ddf7cca422ae0125fc07da1a6344b6ce",
-        "sha256": "8241f763f889193a253b134a9ef56950ee9a2dfe191b40c039465111a2bf1a4c",
-        "size": 389,
-        "uuid": "b2e86d49-6874-4522-a68c-43166e858bdd",
-        "version": "2019-03-17T220103.392000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/process\"",
-        "crc32c": "bb866e25",
-        "indexed": true,
-        "name": "process_2.json",
-        "s3_etag": "04b015a2e2204519c66c8a5dbcb63d1c",
-        "sha1": "205b1fe5aa068df2269a8b977dc27d3f191a0d0a",
-        "sha256": "e67a3ecd72b75d60c46db965836f0b4dc01e94485e1447928833f5304d2ee7f0",
-        "size": 389,
-        "uuid": "b147df84-443b-4dd2-8327-7ea42adcd151",
-        "version": "2019-03-17T220103.254000Z"
-    },
-    {
-        "content-type": "application/json; dcp-type=\"metadata/links\"",
-        "crc32c": "5356a6ba",
-        "indexed": true,
-        "name": "links.json",
-        "s3_etag": "9b3b812e32f35e5406449b2b4221da39",
-        "sha1": "0881415da33135bb54802129c3fec9b462035ab4",
-        "sha256": "82606b3dc782eeacdcc0d5a670d4e6bf5fc453998c63fc40a2f0318ac5dfc1ef",
-        "size": 2335,
-        "uuid": "feb61912-5a3c-4e12-a4ba-28a0207835fd",
-        "version": "2019-03-17T220643.786686Z"
-    },
-    {
-        "content-type": "application/gzip; dcp-type=data",
-        "crc32c": "da1a6040",
-        "indexed": false,
-        "name": "pbmc4k_1000_S1_L001_R1_001.fastq.gz",
-        "s3_etag": "eeaf6532a43b731e1ed9068bf32add47",
-        "sha1": "1e9baaa563f2559a6eb42f586730d1fc2aba6abc",
-        "sha256": "5e3f4a1a8cad609ab42b3c66c069fc29c2cfc3875f600e121aed3bde36b66fd1",
-        "size": 10287500,
-        "uuid": "46ab4893-bb4a-43fa-bc86-22f0d89fddf6",
-        "version": "2019-03-17T220644.137081Z"
-    },
-    {
-        "content-type": "application/gzip; dcp-type=data",
-        "crc32c": "0eee0a0a",
-        "indexed": false,
-        "name": "pbmc4k_1000_S1_L001_R2_001.fastq.gz",
-        "s3_etag": "891e3067ff772d599a5c424f5a93bfd5",
-        "sha1": "b866551f9f1b449039b4eeeda6c6b05bf3eee72b",
-        "sha256": "4718d026a1a2fdd13e6c9cb3bb92eb096f24478571cb6045cd3ce54f2623c2e1",
-        "size": 30926462,
-        "uuid": "2a2b38af-9776-41c8-b643-2e094ac1c58b",
-        "version": "2019-03-17T220644.507486Z"
-    },
-    {
-        "content-type": "application/gzip; dcp-type=data",
-        "crc32c": "51ffe105",
-        "indexed": false,
-        "name": "pbmc4k_1000_S1_L001_I1_001.fastq.gz",
-        "s3_etag": "3d252f83492bf030ddfd05a5a1411cdc",
-        "sha1": "02e40d38df063e54310edefe956fc9ed336c70fb",
-        "sha256": "7f11f8f3a5a8e879d3c7d612f4d37233ebfdd3e226406c013bc375403bae2137",
-        "size": 3454130,
-        "uuid": "04a1ab2c-e522-4d73-a881-effa1d9492d1",
-        "version": "2019-03-17T220644.766900Z"
-    }
-]
diff --git a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde/2019-03-17T220646.332108Z/metadata.json b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde/2019-03-17T220646.332108Z/metadata.json
deleted file mode 100644
index 7b2d26f70..000000000
--- a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde/2019-03-17T220646.332108Z/metadata.json
+++ /dev/null
@@ -1,558 +0,0 @@
-{
-    "cell_suspension_0.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_suspension",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "cell_ID_1",
-            "biomaterial_name": "This is a dummy cell",
-            "biomaterial_description": "This is a dummy donor cell",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "genotype": "DRB1 0401 protective allele",
-            "biosd_biomaterial": "SAMN00000000",
-            "insdc_biomaterial": "SRS0000000"
-        },
-        "cell_morphology": {
-            "cell_morphology": "adherent cells, form single layer colonies",
-            "cell_size": "20-30",
-            "cell_size_unit": {
-                "text": "nm",
-                "ontology": "UO:0000018",
-                "ontology_label": "nanometer"
-            },
-            "percent_cell_viability": 85.3,
-            "cell_viability_method": "Fluorescein diacetate hydrolysis assay",
-            "cell_viability_result": "pass",
-            "percent_necrosis": 10.0
-        },
-        "growth_conditions": {
-            "passage_number": 22,
-            "growth_medium": "lysogeny broth (LB) medium",
-            "mycoplasma_testing_results": "pass",
-            "drug_treatment": "100 ug/mL ampicillin",
-            "feeder_layer_type": "feeder-dependent, mouse embryonic fibroblast cells"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "estimated_cell_count": 10000,
-        "provenance": {
-            "document_id": "74a06f8b-dff1-44d2-b1a6-99e3d14b69d1",
-            "submission_date": "2019-03-17T22:00:57.699Z",
-            "update_date": "2019-03-17T22:01:03.482Z"
-        }
-    },
-    "specimen_from_organism_0.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/7.0.3/specimen_from_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "specimen_ID_1",
-            "biomaterial_name": "This is a dummy specimen",
-            "biomaterial_description": "This is a dummy donor specimen",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "genotype": "DRB1 0401 protective allele",
-            "biosd_biomaterial": "SAMN00000000",
-            "insdc_biomaterial": "SRS0000000"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "organ": {
-            "text": "brain",
-            "ontology": "UBERON:0000955",
-            "ontology_label": "brain"
-        },
-        "organ_part": {
-            "text": "amygdala",
-            "ontology": "UBERON:0001876",
-            "ontology_label": "amygdala"
-        },
-        "diseases": [
-            {
-                "text": "H syndrome",
-                "ontology": "MONDO:0011273",
-                "ontology_label": "H syndrome"
-            }
-        ],
-        "state_of_specimen": {
-            "autolysis_score": "none",
-            "gross_description": "normal color and size"
-        },
-        "provenance": {
-            "document_id": "f3531ee2-d408-4075-b63e-0d0e2b01116c",
-            "submission_date": "2019-03-17T22:00:57.694Z",
-            "update_date": "2019-03-17T22:01:03.535Z"
-        }
-    },
-    "donor_organism_0.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/14.0.3/donor_organism",
-        "schema_type": "biomaterial",
-        "biomaterial_core": {
-            "biomaterial_id": "donor_ID_1",
-            "biomaterial_name": "This is a dummy donor",
-            "biomaterial_description": "This is a dummy donor description",
-            "ncbi_taxon_id": [
-                9606
-            ],
-            "genotype": "DRB1 0401 protective allele",
-            "biosd_biomaterial": "SAMN00000000",
-            "insdc_biomaterial": "SRS0000000"
-        },
-        "human_specific": {
-            "body_mass_index": 36.4,
-            "ethnicity": [
-                {
-                    "text": "European",
-                    "ontology": "HANCESTRO:0005",
-                    "ontology_label": "European"
-                }
-            ]
-        },
-        "death": {
-            "cause_of_death": "motor vehicle accident",
-            "cold_perfused": false,
-            "days_on_ventilator": 4.0,
-            "hardy_scale": 0,
-            "time_of_death": "1999-01-21T00:00:00Z",
-            "organ_donation_death_type": "Donation after circulatory death (DCD)"
-        },
-        "medical_history": {
-            "alcohol_history": "1 units/day",
-            "medication": "Naproxen 500mg/day,",
-            "nutritional_state": "normal",
-            "smoking_history": "Smoker, 5/day for 10 years, stopped 1995"
-        },
-        "genus_species": [
-            {
-                "text": "Homo sapiens",
-                "ontology": "NCBITaxon:9606",
-                "ontology_label": "Homo sapiens"
-            }
-        ],
-        "organism_age": "20",
-        "organism_age_unit": {
-            "text": "year",
-            "ontology": "UO:0000036",
-            "ontology_label": "year"
-        },
-        "development_stage": {
-            "text": "human adult stage",
-            "ontology": "HsapDv:0000087"
-        },
-        "diseases": [
-            {
-                "text": "H syndrome",
-                "ontology": "MONDO:0011273",
-                "ontology_label": "H syndrome"
-            }
-        ],
-        "gestational_age": "5-7",
-        "height": "160",
-        "height_unit": {
-            "text": "cm",
-            "ontology": "UO:0000015",
-            "ontology_label": "centimeter"
-        },
-        "is_living": "no",
-        "weight": "60",
-        "weight_unit": {
-            "text": "kg",
-            "ontology": "UO:0000009",
-            "ontology_label": "kilogram"
-        },
-        "sex": "male",
-        "provenance": {
-            "document_id": "20db3238-9ce6-4820-8495-6753e4147d51",
-            "submission_date": "2019-03-17T22:00:57.690Z",
-            "update_date": "2019-03-17T22:01:03.211Z"
-        }
-    },
-    "sequence_file_0.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/7.0.2/sequence_file",
-        "schema_type": "file",
-        "file_core": {
-            "file_name": "pbmc4k_1000_S1_L001_R1_001.fastq.gz",
-            "file_format": "fastq.gz",
-            "checksum": "eeaf6532a43b731e1ed9068bf32add47"
-        },
-        "read_index": "read1",
-        "lane_index": 1,
-        "read_length": 26,
-        "insdc_run": [
-            "SRR0000000"
-        ],
-        "provenance": {
-            "document_id": "6380c3bc-8bc3-459b-aea3-05dd6c0842ef",
-            "submission_date": "2019-03-17T22:00:57.704Z",
-            "update_date": "2019-03-17T22:03:04.130Z"
-        }
-    },
-    "sequence_file_1.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/7.0.2/sequence_file",
-        "schema_type": "file",
-        "file_core": {
-            "file_name": "pbmc4k_1000_S1_L001_R2_001.fastq.gz",
-            "file_format": "fastq.gz",
-            "checksum": "891e3067ff772d599a5c424f5a93bfd5"
-        },
-        "read_index": "read2",
-        "lane_index": 1,
-        "read_length": 98,
-        "insdc_run": [
-            "SRR0000000"
-        ],
-        "provenance": {
-            "document_id": "ceb4dfaa-ecaf-4757-ae54-9d83707f66cc",
-            "submission_date": "2019-03-17T22:00:57.714Z",
-            "update_date": "2019-03-17T22:03:06.010Z"
-        }
-    },
-    "sequence_file_2.json": {
-        "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/7.0.2/sequence_file",
-        "schema_type": "file",
-        "file_core": {
-            "file_name": "pbmc4k_1000_S1_L001_I1_001.fastq.gz",
-            "file_format": "fastq.gz",
-            "checksum": "3d252f83492bf030ddfd05a5a1411cdc"
-        },
-        "read_index": "index1",
-        "lane_index": 1,
-        "read_length": 8,
-        "insdc_run": [
-            "SRR0000000"
-        ],
-        "provenance": {
-            "document_id": "5201d410-d789-4df6-b3fd-9edac998e5f3",
-            "submission_date": "2019-03-17T22:00:57.719Z",
-            "update_date": "2019-03-17T22:03:03.738Z"
-        }
-    },
-    "project_0.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/project/11.0.0/project",
-        "schema_type": "project",
-        "project_core": {
-            "project_short_name": "staging/10x/2019-03-17T22:00:54Z",
-            "project_title": "10x 1 Run Integration Test",
-            "project_description": "Contains a small file set from the dataset: 4k PBMCs from a Healthy Donor, a Single Cell Gene Expression Dataset by Cell Ranger 2.1.0. Peripheral blood mononuclear cells (PBMCs) were taken from a healthy donor (same donor as pbmc8k). PBMCs are primary cells with relatively small amounts of RNA (~1pg RNA/cell). Data/Analysis can be found here https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/pbmc4k and all data is licensed under the creative commons attribution license (https://creativecommons.org/licenses/by/4.0/). This test also contains extensive metadata for browser testing. Metadata is fabricated."
-        },
-        "publications": [
-            {
-                "authors": [
-                    "Doe JD, Doe JJ"
-                ],
-                "publication_title": "A title of a publication goes here.",
-                "doi": "10.1016/j.cell.2016.07.054",
-                "pmid": 27565351,
-                "publication_url": "https://europepmc.org"
-            }
-        ],
-        "insdc_project_accessions": [
-            "SRP000000",
-            "SRP000001"
-        ],
-        "geo_series_accessions": [
-            "GSE00000"
-        ],
-        "array_express_accessions": [
-            "E-AAAA-00"
-        ],
-        "insdc_study_accessions": [
-            "PRJNA000000"
-        ],
-        "funders": [
-            {
-                "grant_title": "A title of a grant proposal.",
-                "grant_id": "BB/P0000001/1",
-                "organization": "Biotechnology and Biological Sciences Research Council (BBSRC)"
-            }
-        ],
-        "contributors": [
-            {
-                "contact_name": "John,D,Doe.",
-                "email": "dummy@email.com",
-                "phone": "(+1) 234-555-6789",
-                "institution": "EMBL-EBI",
-                "laboratory": "Department of Biology",
-                "address": "0000 Main Street, Nowheretown, MA, 12091",
-                "country": "USA",
-                "corresponding_contributor": false,
-                "project_role": "principal investigator",
-                "orcid_id": "0000-1111-2222-3333"
-            }
-        ],
-        "provenance": {
-            "document_id": "5014cd10-bbed-4e85-bc45-6fe3a8a0079b",
-            "submission_date": "2019-03-17T22:00:57.685Z",
-            "update_date": "2019-03-17T22:01:03.175Z"
-        }
-    },
-    "library_preparation_protocol_0.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/sequencing/4.4.6/library_preparation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "lib_prep_1",
-            "protocol_name": "A dummy library prep protocol",
-            "protocol_description": "A dummy library prep description",
-            "publication_doi": "10.1101/193219",
-            "protocols_io_doi": "10.17504/protocols.io.mgjc3un",
-            "document": "my_cool_protocol.pdf"
-        },
-        "input_nucleic_acid_molecule": {
-            "text": "polyA RNA",
-            "ontology": "OBI:0000869",
-            "ontology_label": "polyA RNA"
-        },
-        "nucleic_acid_source": "single cell",
-        "library_construction_approach": {
-            "text": "10x v2",
-            "ontology": "EFO:0009310",
-            "ontology_label": "10X v2 sequencing"
-        },
-        "end_bias": "3 prime tag",
-        "primer": "poly-dT",
-        "strand": "unstranded",
-        "umi_barcode": {
-            "barcode_read": "Read 1",
-            "barcode_offset": 0,
-            "barcode_length": 16
-        },
-        "library_preamplification_method": {
-            "text": "Rapid Amplification of cDNA Ends",
-            "ontology": "EFO:0004182",
-            "ontology_label": "Rapid Amplification of cDNA Ends"
-        },
-        "provenance": {
-            "document_id": "aa7e9a08-2a0c-4575-a9a9-13cab4e96e73",
-            "submission_date": "2019-03-17T22:00:57.735Z",
-            "update_date": "2019-03-17T22:01:03.138Z"
-        }
-    },
-    "sequencing_protocol_0.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/sequencing/9.0.11/sequencing_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "sequencing_protocol_1",
-            "protocol_name": "A dummy sequencing protocol",
-            "protocol_description": "A dummy sequencing protocol description",
-            "publication_doi": "10.1101/193219",
-            "protocols_io_doi": "10.17504/protocols.io.mgjc3un",
-            "document": "my_cool_protocol.pdf"
-        },
-        "instrument_manufacturer_model": {
-            "text": "Illumina HiSeq 2500",
-            "ontology": "EFO:0008565"
-        },
-        "local_machine_name": "Machine1",
-        "paired_end": false,
-        "sequencing_approach": {
-            "text": "full length single cell RNA sequencing",
-            "ontology": "EFO:0008441",
-            "ontology_label": "full length single cell RNA sequencing"
-        },
-        "10x": {
-            "fastq_method": "Cellranger mkfastq",
-            "fastq_method_version": "Cellranger 2.1.1",
-            "pooled_channels": 4.0,
-            "drop_uniformity": false
-        },
-        "provenance": {
-            "document_id": "4bc436f7-e429-4355-8d6e-853d8e639b37",
-            "submission_date": "2019-03-17T22:00:57.739Z",
-            "update_date": "2019-03-17T22:01:02.999Z"
-        }
-    },
-    "dissociation_protocol_0.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.8/dissociation_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "dissociation_protocol_1",
-            "protocol_name": "A dummy dissociation protocol",
-            "protocol_description": "A dummmy description of a dissociation protocol",
-            "publication_doi": "10.1101/193219",
-            "protocols_io_doi": "10.17504/protocols.io.mgjc3un",
-            "document": "my_cool_protocol.pdf"
-        },
-        "dissociation_method": {
-            "text": "fluorescence-activated cell sorting",
-            "ontology": "EFO:0009108",
-            "ontology_label": "fluorescence-activated cell sorting"
-        },
-        "provenance": {
-            "document_id": "1e9abdf3-54da-4c73-9e57-1297ceb39399",
-            "submission_date": "2019-03-17T22:00:57.728Z",
-            "update_date": "2019-03-17T22:01:03.046Z"
-        }
-    },
-    "enrichment_protocol_0.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.9/enrichment_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "enrichment_protocol_1",
-            "protocol_name": "an example enrichment protocol",
-            "protocol_description": "an example enrichemnt protocol description",
-            "publication_doi": "10.1101/193219",
-            "protocols_io_doi": "10.17504/protocols.io.mgjc3un",
-            "document": "my_cool_protocol.pdf"
-        },
-        "enrichment_method": {
-            "text": "fluorescence-activated cell sorting",
-            "ontology": "EFO:0009108",
-            "ontology_label": "fluorescence-activated cell sorting"
-        },
-        "markers": "CD4+ CD8-",
-        "min_size_selected": 70.0,
-        "max_size_selected": 90.0,
-        "provenance": {
-            "document_id": "df679627-ccb6-426d-a709-c259db607d84",
-            "submission_date": "2019-03-17T22:00:57.731Z",
-            "update_date": "2019-03-17T22:01:03.051Z"
-        }
-    },
-    "collection_protocol_0.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/8.2.11/collection_protocol",
-        "schema_type": "protocol",
-        "protocol_core": {
-            "protocol_id": "collection_protocol_1",
-            "protocol_name": "A dummy collection protocol",
-            "protocol_description": "A dummy collection protocol description",
-            "publication_doi": "10.1101/193219",
-            "protocols_io_doi": "10.17504/protocols.io.mgjc3un",
-            "document": "my_cool_protocol.pdf"
-        },
-        "collection_method": {
-            "text": "organ extraction",
-            "ontology": "EFO:0009124",
-            "ontology_label": "organ extraction"
-        },
-        "protocol_reagents": [
-            {
-                "retail_name": "SureCell WTA 3' Library Prep Kit",
-                "catalog_number": "20014279",
-                "manufacturer": "Illumina",
-                "lot_number": "10001A",
-                "expiry_date": "2018-01-31",
-                "kit_titer": "Titer: Specification is 3.0x10^7"
-            }
-        ],
-        "provenance": {
-            "document_id": "c3dabd8c-6f32-4c0b-a13b-11bb71cc95de",
-            "submission_date": "2019-03-17T22:00:57.724Z",
-            "update_date": "2019-03-17T22:01:03.060Z"
-        }
-    },
-    "process_0.json": {
-        "process_core": {
-            "process_id": "bundle1"
-        },
-        "schema_type": "process",
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/6.0.7/process",
-        "provenance": {
-            "document_id": "8a0879df-13e0-4dce-9776-20fb259796e9",
-            "submission_date": "2019-03-17T22:00:57.752Z",
-            "update_date": "2019-03-17T22:01:03.421Z"
-        }
-    },
-    "process_1.json": {
-        "process_core": {
-            "process_id": "process_id_2"
-        },
-        "schema_type": "process",
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/6.0.7/process",
-        "provenance": {
-            "document_id": "b2e86d49-6874-4522-a68c-43166e858bdd",
-            "submission_date": "2019-03-17T22:00:57.748Z",
-            "update_date": "2019-03-17T22:01:03.392Z"
-        }
-    },
-    "process_2.json": {
-        "process_core": {
-            "process_id": "process_id_1"
-        },
-        "schema_type": "process",
-        "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/6.0.7/process",
-        "provenance": {
-            "document_id": "b147df84-443b-4dd2-8327-7ea42adcd151",
-            "submission_date": "2019-03-17T22:00:57.743Z",
-            "update_date": "2019-03-17T22:01:03.254Z"
-        }
-    },
-    "links.json": {
-        "describedBy": "https://schema.staging.data.humancellatlas.org/system/1.1.5/links",
-        "schema_type": "link_bundle",
-        "schema_version": "1.1.5",
-        "links": [
-            {
-                "process": "8a0879df-13e0-4dce-9776-20fb259796e9",
-                "inputs": [
-                    "74a06f8b-dff1-44d2-b1a6-99e3d14b69d1"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "6380c3bc-8bc3-459b-aea3-05dd6c0842ef",
-                    "ceb4dfaa-ecaf-4757-ae54-9d83707f66cc",
-                    "5201d410-d789-4df6-b3fd-9edac998e5f3"
-                ],
-                "output_type": "file",
-                "protocols": [
-                    {
-                        "protocol_type": "library_preparation_protocol",
-                        "protocol_id": "aa7e9a08-2a0c-4575-a9a9-13cab4e96e73"
-                    },
-                    {
-                        "protocol_type": "sequencing_protocol",
-                        "protocol_id": "4bc436f7-e429-4355-8d6e-853d8e639b37"
-                    }
-                ]
-            },
-            {
-                "process": "b2e86d49-6874-4522-a68c-43166e858bdd",
-                "inputs": [
-                    "f3531ee2-d408-4075-b63e-0d0e2b01116c"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "74a06f8b-dff1-44d2-b1a6-99e3d14b69d1"
-                ],
-                "output_type": "biomaterial",
-                "protocols": [
-                    {
-                        "protocol_type": "dissociation_protocol",
-                        "protocol_id": "1e9abdf3-54da-4c73-9e57-1297ceb39399"
-                    },
-                    {
-                        "protocol_type": "enrichment_protocol",
-                        "protocol_id": "df679627-ccb6-426d-a709-c259db607d84"
-                    }
-                ]
-            },
-            {
-                "process": "b147df84-443b-4dd2-8327-7ea42adcd151",
-                "inputs": [
-                    "20db3238-9ce6-4820-8495-6753e4147d51"
-                ],
-                "input_type": "biomaterial",
-                "outputs": [
-                    "f3531ee2-d408-4075-b63e-0d0e2b01116c"
-                ],
-                "output_type": "biomaterial",
-                "protocols": [
-                    {
-                        "protocol_type": "collection_protocol",
-                        "protocol_id": "c3dabd8c-6f32-4c0b-a13b-11bb71cc95de"
-                    }
-                ]
-            }
-        ]
-    }
-}
diff --git a/test/hca_metadata_api/test.py b/test/hca_metadata_api/test.py
index 6a2af0981..4e696a1af 100644
--- a/test/hca_metadata_api/test.py
+++ b/test/hca_metadata_api/test.py
@@ -153,32 +153,29 @@ def _test_example_bundle(self, directory, **kwargs):
                             **kwargs)
 
     def _canned_bundle_path(self, directory, uuid, version):
-        return os.path.join(os.path.dirname(__file__), 'cans', directory, uuid, version)
+        name = f'{uuid}.{version}.json'
+        return os.path.join(os.path.dirname(__file__), 'cans', directory, name)
 
     def _can_bundle(self, directory, uuid, version, manifest, metadata_files):  # pragma: no cover
         """
         Save a bundle's manifest & metadata files to a local directory
         """
-        dir_path = self._canned_bundle_path(directory, uuid, version)
-        os.makedirs(dir_path, exist_ok=True)
-        with atomic_write(os.path.join(dir_path, 'manifest.json'), overwrite=True) as f:
-            json.dump(manifest, f)
-        with atomic_write(os.path.join(dir_path, 'metadata.json'), overwrite=True) as f:
-            json.dump(metadata_files, f)
+        path = self._canned_bundle_path(directory, uuid, version)
+        os.makedirs(directory, exist_ok=True)
+        with atomic_write(path, overwrite=True) as f:
+            json.dump({
+                'manifest': manifest,
+                'metadata': metadata_files
+            }, f)
 
     def _canned_bundle(self, directory, uuid, version):
         """
         Load a previously canned bundle
         """
         dir_path = self._canned_bundle_path(directory, uuid, version)
-        if os.path.isdir(dir_path):
-            with open(os.path.join(dir_path, 'manifest.json')) as f:
-                manifest = json.load(f)
-            with open(os.path.join(dir_path, 'metadata.json')) as f:
-                metadata_files = json.load(f)
-            return manifest, metadata_files
-        else:
-            return None, None
+        with open(dir_path) as f:
+            bundle = json.load(f)
+        return bundle['manifest'], bundle['metadata']
 
     def test_v5_bundle(self):
         """

From 42827eca80076478d345626ee3d882d413cd0d96 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Wed, 21 Aug 2024 15:22:55 -0700
Subject: [PATCH 10/20] Remove manifest entries for links.json (#4565)

This makes #4565 obsolete/invalid
---
 .../plugins/repository/tdr_hca/__init__.py    | 20 +++----------------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...a3fb4204953.2018-08-03T082009.272868Z.json | 12 -----------
 ...318dbb86000.2019-01-03T163633.780215Z.json | 12 -----------
 ...61d6da02d44.2019-09-20T103932.395795Z.json | 12 -----------
 ...a3fb4204953.2018-03-29T142048.835519Z.json | 12 -----------
 ...d019d1c9439.2019-05-15T222432.561000Z.json | 12 -----------
 ...08092b2dabe.2019-04-17T175706.867000Z.json | 12 -----------
 ...68e20ec4a2e.2019-02-02T065454.662896Z.json | 12 -----------
 ...19c1c2d9018.2018-10-07T130111.835234Z.json | 12 -----------
 ...406a478d5ab.2018-09-05T182535.846470Z.json | 12 -----------
 ...95a3f8deb9c.2019-04-03T103426.471000Z.json | 12 -----------
 ...720f33a5dde.2019-03-17T220646.332108Z.json | 12 -----------
 ...3-5e9d-52cd-b32d-af88edccabfa.dss.hca.json | 11 ----------
 ...5-71e2-48ca-a87b-e256938c6a98.dss.hca.json | 11 ----------
 ...3-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json | 11 ----------
 ...c-6778-423d-8fe9-869e2a515d35.dss.hca.json | 11 ----------
 ...8-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json | 12 -----------
 ...8-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json | 11 ----------
 ...5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json | 11 ----------
 ...8-658e-4c51-9de4-a768322f84c5.dss.hca.json | 11 ----------
 ...a-940e-49b1-9bcc-25699a55b295.dss.hca.json | 12 -----------
 ...f-61a7-4504-a57c-fc70f38d5b13.dss.hca.json | 12 -----------
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json | 12 -----------
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json | 12 -----------
 ...5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json | 11 ----------
 ...e-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json | 11 ----------
 ...4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json | 12 -----------
 ...0.2020-12-10T10:30:00.000000Z.dss.hca.json | 11 ----------
 ...f-8346-5420-b7e4-b486f99451a8.dss.hca.json | 11 ----------
 ...e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json | 11 ----------
 ...1-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json | 11 ----------
 ...e-9a5d-4e3d-ada2-0414b666b880.dss.hca.json | 12 -----------
 ...2-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json | 12 -----------
 ...3-f0ac-417a-8a29-221c77debde8.dss.hca.json | 12 -----------
 ...d.2018-11-02T11:33:44.698028Z.dss.hca.json | 12 -----------
 ...d.2018-11-04T11:33:44.698028Z.dss.hca.json | 12 -----------
 ...e-9b7b-4800-8977-fe7c94e131df.dss.hca.json | 12 -----------
 ...4-dc9f-439e-af29-f8eb75b0729d.dss.hca.json | 12 -----------
 ...4-9a58-4763-9e66-59894efbdaa8.dss.hca.json | 12 -----------
 ...d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json | 12 -----------
 ...1-4766-4210-966c-f9ee25d19190.dss.hca.json | 12 -----------
 ...a-2b51-4419-9cde-34df44c6458a.dss.hca.json | 12 -----------
 ...e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json | 12 -----------
 ...4-6b80-4eed-97c9-4984de81a47c.dss.hca.json | 12 -----------
 ...7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json | 12 -----------
 ...b-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json | 12 -----------
 ...7-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json | 11 ----------
 ...f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json | 12 -----------
 test/integration_test.py                      |  9 +--------
 55 files changed, 4 insertions(+), 647 deletions(-)

diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py
index df9b25986..c1043a682 100644
--- a/src/azul/plugins/repository/tdr_hca/__init__.py
+++ b/src/azul/plugins/repository/tdr_hca/__init__.py
@@ -343,10 +343,7 @@ def _emulate_bundle(self, bundle_fqid: TDRBundleFQID) -> TDRHCABundle:
                               manifest=[],
                               metadata_files={})
         entities, root_entities, links_jsons = self._stitch_bundles(bundle)
-        bundle.add_entity(entity_key='links.json',
-                          entity_type='links',
-                          entity_row=self._merge_links(links_jsons),
-                          is_stitched=False)
+        bundle.metadata_files['links.json'] = self._merge_links(links_jsons)
 
         with ThreadPoolExecutor(max_workers=config.num_tdr_workers) as executor:
             futures = {
@@ -555,12 +552,6 @@ def _merge_links(self, links_jsons: JSONs) -> JSON:
         """
         root, *stitched = links_jsons
         if stitched:
-            merged = {
-                'links_id': root['links_id'],
-                'version': root['version']
-            }
-            for common_key in ('project_id', 'schema_type'):
-                merged[common_key] = one({row[common_key] for row in links_jsons})
             source_contents = [row['content'] for row in links_jsons]
             # FIXME: Explicitly verify compatible schema versions for stitched subgraphs
             #        https://github.com/DataBiosphere/azul/issues/3215
@@ -574,14 +565,9 @@ def _merge_links(self, links_jsons: JSONs) -> JSON:
                 'describedBy': str(schema_url),
                 'links': sum((sc['links'] for sc in source_contents), start=[])
             }
-            merged['content'] = merged_content  # Keep result of parsed JSON for reuse
-            merged['content_size'] = len(json.dumps(merged_content))
-            assert merged.keys() == one({
-                frozenset(row.keys()) for row in links_jsons
-            }), merged
             assert merged_content.keys() == one({
                 frozenset(sc.keys()) for sc in source_contents
             }), merged_content
-            return merged
+            return merged_content
         else:
-            return root
+            return root['content']
diff --git a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 01627b98e..1f5712e7e 100644
--- a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -48,18 +48,6 @@
             "uuid": "821601f1-64e8-4427-8680-34a743b35b69",
             "version": "1"
         },
-        {
-            "crc32c": "DDAABBB6",
-            "sha1": "82c4c5273e31923bf6e12139804c3a4cf10b338d",
-            "sha256": "3de258c171a757d80e53a617ce1834e14710c87db0289c9b2012d0a14a3ea705",
-            "s3_etag": "4dc6069c891063f28a0ee155c6cd7b65",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 1856,
-            "uuid": "04e79979-489e-4cd8-93c3-1d8e99d09ec8",
-            "version": "1"
-        },
         {
             "crc32c": "522D96A7",
             "sha1": "9876adb67827ea0328566811a1304bcf49a31b02",
diff --git a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 1a798a5a8..ce91f3795 100644
--- a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -84,18 +84,6 @@
             "uuid": "5910c207-1093-4ef1-9537-dc614d128d14",
             "version": "1"
         },
-        {
-            "crc32c": "1CAA5E57",
-            "sha1": "e3d6064f20fa85351d9446be179ebb15458324e6",
-            "sha256": "e4529c8501160b286824388a51f50b6e94110d3f9a55998a3b088f918e92ae53",
-            "s3_etag": "1e11ded031de78c2c7cec5e5fb3b48a7",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 2381,
-            "uuid": "2aea848d-fbe7-472a-953d-2cd77716b939",
-            "version": "1"
-        },
         {
             "crc32c": "17049723",
             "sha1": "df812b18c751efd55e21318be9411200f3066513",
diff --git a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index eb9525ed0..959b66bbf 100644
--- a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
+++ b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
@@ -156,18 +156,6 @@
             "uuid": "597f5fae-db6a-4ebc-b2f0-b9c527f5b3ed",
             "version": "1"
         },
-        {
-            "crc32c": "E8D34C5D",
-            "sha1": "e3336e075787d319a239533d8620a4a60a793bac",
-            "sha256": "062e56b2f314b8fd81b916985767abaedc4e22923e80607b023a3bf68554d4e0",
-            "s3_etag": "3ae64d0365c9c2d857c4194f41b471a6",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 7860,
-            "uuid": "19f9d2c2-2d30-4262-8d19-a5de9ca13dd7",
-            "version": "1"
-        },
         {
             "crc32c": "27917E6E",
             "sha1": "6be5be8c979bf95b9be25df1f16c9856bb55bff3",
diff --git a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 3f9f9b81a..c7b3b4a1f 100644
--- a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -48,18 +48,6 @@
             "uuid": "3b8ffd02-7a9e-44ff-bec5-1387b87b0e34",
             "version": "1"
         },
-        {
-            "crc32c": "5AE674D4",
-            "sha1": "a2c43b27d4cdcd769ea9aa5fb6dc38d144a19448",
-            "sha256": "5444d86b7f7dde2c7521dde5821b12d04cd544ecae07464b45ee75ad98c9becc",
-            "s3_etag": "f2fb4a3a21e54e7b6455fcd9fac1e1b1",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 1856,
-            "uuid": "d6284ed3-ff4c-4153-90b5-a3f5fb10c799",
-            "version": "1"
-        },
         {
             "crc32c": "22B1F2B5",
             "sha1": "24335fec0fbe49e182b9a25d9953a7ef34f797fa",
diff --git a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 5c0f7246f..57480d942 100644
--- a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -60,18 +60,6 @@
             "uuid": "6aa1f675-a3be-4def-8da9-259ae0fcad68",
             "version": "1"
         },
-        {
-            "crc32c": "837B6FBF",
-            "sha1": "4534daa77cd865f34273f6c8a8d0fd3a96361bfe",
-            "sha256": "26c92efa3719bda131663c452d7b385925d927eb5a49f6b2e5ebb1497e871c64",
-            "s3_etag": "dc518a7c1b8faea79320eb70e7c239e6",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 2027,
-            "uuid": "447bd719-baa7-4f32-b4d6-7f64fabfe0f1",
-            "version": "1"
-        },
         {
             "crc32c": "93A97712",
             "sha1": "4365e3dbeeff6b4c23c9057e5b30aab65807a405",
diff --git a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 2acf73c7f..95a14aad9 100644
--- a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -36,18 +36,6 @@
             "uuid": "6ce66ac8-1e0f-49b4-a278-468f7b677ffe",
             "version": "1"
         },
-        {
-            "crc32c": "C0EF71FC",
-            "sha1": "79e8137293c18fc1ef1a4b2a532e59f6223fbec3",
-            "sha256": "d333cfe228457aaa476b4ccf39bdd4c620bfcf0f2c11ccfff83c9aacb7a17c13",
-            "s3_etag": "cbacd6ba075487820bcd49e2667581b6",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 1727,
-            "uuid": "169acedb-1e56-4b6d-a3d7-0d3e56d74098",
-            "version": "1"
-        },
         {
             "crc32c": "8D88697D",
             "sha1": "cfbab7537d593e0b1765b65b755e88244bd88ebc",
diff --git a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 6eea5c58b..31d2472cb 100644
--- a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -60,18 +60,6 @@
             "uuid": "1d64e884-84c1-438e-8f1b-7d42698942ad",
             "version": "1"
         },
-        {
-            "crc32c": "C1574314",
-            "sha1": "086e0e40e88c2ed0b4a1c68a3f2fd88e66454e6e",
-            "sha256": "88fa107073946ff3a01455ebeca62cb7a8c8253a10f90c68f8c37078f00be627",
-            "s3_etag": "151fe404519e0934fa5e24772d8002d6",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "links.json",
-            "size": 1643,
-            "uuid": "62f4b747-7bf2-4af5-b710-723a060f0d35",
-            "version": "1"
-        },
         {
             "crc32c": "D044B620",
             "sha1": "15c4e8085308b8f297b9b682c8aa892514e476de",
diff --git a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
index bb2a50bf8..0ca2b6573 100644
--- a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
+++ b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
@@ -512,18 +512,6 @@
             "uuid": "baa3a061-534c-4b6e-8c51-a11a8307f537",
             "version": "2019-01-03T120758.911000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "8296c70e",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "dcda06d2eb79d368ac84a47a06689773",
-            "sha1": "3d4d918d7deae23cade8abb3269ca957c315ad0d",
-            "sha256": "a0c53628a804b864567b1c6a87879a040dba1d24b539418710dc3979599301e1",
-            "size": 7860,
-            "uuid": "5b71a545-1f04-477b-98b5-f15664311970",
-            "version": "2019-01-03T163557.511721Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "dec968a1",
diff --git a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
index 8b58a1e79..816ed60ed 100644
--- a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
+++ b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
@@ -228,18 +228,6 @@
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diff --git a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
index 9f0938781..92c9521d6 100644
--- a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
+++ b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
@@ -83,18 +83,6 @@
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-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "4e6ce5dd",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "14c01392fd55df2b2cdbd08994009e24",
-            "sha1": "6ab7fdb229d9f0971a05e781ef52cbcfbf680e00",
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-            "version": "2018-03-29T142047.912393Z"
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diff --git a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
index c8cc3a2b3..015f5565f 100644
--- a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
+++ b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
@@ -120,18 +120,6 @@
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-            "crc32c": "2c25a3c2",
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diff --git a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
index dfb5dc797..fa59f5ed9 100644
--- a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
+++ b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
@@ -192,18 +192,6 @@
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diff --git a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
index b1eeeff62..fbb9c6a02 100644
--- a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
+++ b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
@@ -612,18 +612,6 @@
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diff --git a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
index c301e8a49..00eb2a89c 100644
--- a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
+++ b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
@@ -168,18 +168,6 @@
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diff --git a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
index 15a52e8e6..67fe8541e 100644
--- a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
+++ b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
@@ -156,18 +156,6 @@
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diff --git a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
index 6072f329f..f0ef040f7 100644
--- a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
+++ b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
@@ -2844,18 +2844,6 @@
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diff --git a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
index 6b5bd4ff6..f1be1bff2 100644
--- a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
+++ b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
@@ -180,18 +180,6 @@
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diff --git a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
index 8c4d7a98e..6a577e48d 100644
--- a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
+++ b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
@@ -1,16 +1,5 @@
 {
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-            "uuid": "00f48893-5e9d-52cd-b32d-af88edccabfa",
-            "version": "2020-02-03T10:30:00.000000Z",
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diff --git a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
index 3aa26458d..52244e823 100644
--- a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
+++ b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
@@ -33,17 +33,6 @@
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diff --git a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
index 8ce7cebd5..d4bed59fe 100644
--- a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
+++ b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
@@ -178,17 +178,6 @@
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diff --git a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
index d2d1e73cc..21d4beb7f 100644
--- a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
+++ b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
@@ -11,17 +11,6 @@
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diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
index c3e399acd..769139153 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
@@ -312,18 +312,6 @@
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diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
index 5f92b228c..2e377a6ca 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
@@ -96,17 +96,6 @@
             "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_385feda5-d1e3-5a51-8e55-f4f491a4e7bf"
         },
-        {
-            "name": "links.json",
-            "uuid": "1b6d8348-d6e9-406a-aa6a-7ee886e52bf9",
-            "version": "2019-09-24T09:35:06.958773Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 3786,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
-        },
         {
             "name": "IDC9_L001_R2.fastq.gz",
             "uuid": "1b9d4386-97ac-402d-a93d-40740b2c3c28",
diff --git a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
index a09cbdaf4..5db6250e6 100644
--- a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
+++ b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
@@ -33,17 +33,6 @@
             "crc32c": "",
             "sha256": ""
         },
-        {
-            "name": "links.json",
-            "uuid": "1fd499c5-f397-4bff-9af0-eb42c37d5fbe",
-            "version": "2021-03-18T11:38:49.884000Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 1630,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "process_1.json",
             "uuid": "1fd499c5-f397-4bff-9af0-eb42c37d5fbe",
diff --git a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
index 3eb746590..4f7fc5d64 100644
--- a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
+++ b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
@@ -1,16 +1,5 @@
 {
     "manifest": [
-        {
-            "name": "links.json",
-            "uuid": "2c7d06b8-658e-4c51-9de4-a768322f84c5",
-            "version": "2021-09-21T17:27:23.898000Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 1638,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "process_0.json",
             "uuid": "2c7d06b8-658e-4c51-9de4-a768322f84c5",
diff --git a/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
index 0140db290..c2694b954 100644
--- a/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
+++ b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
@@ -360,18 +360,6 @@
             "uuid": "8fa0c554-2503-408b-9f3b-6145463db850",
             "version": "2018-11-02T17:38:45.850000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "567cca4c",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "4a7aeb9e5b2d42d416248c035df24104",
-            "sha1": "2f9e6ece95cd5a7484f9b1913c00a0e0e168712c",
-            "sha256": "47d51681a3515d86141c98265b328881c5130743c02f07fa087e4c21e8cb1ca4",
-            "size": 7987,
-            "uuid": "a45e08a3-a4c0-4710-8be0-0fc3ab52ceb8",
-            "version": "2018-11-02T18:40:10.540316Z"
-        },
         {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "ce4f092f",
diff --git a/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
index 3a1276a7d..a232a860d 100644
--- a/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
+++ b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
@@ -576,18 +576,6 @@
             "uuid": "4a1432a1-ae18-45f2-b574-9869b7242289",
             "version": "2018-10-16T08:06:34.625000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "2bc3ad5f",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "d96e6fda9532e606b44d0ff2fcb0cc6d",
-            "sha1": "f3c05d096a45d3a3dc494268b358816e35b77c61",
-            "sha256": "a1a252c7eb207417f13d0ddbfc71dee83ab973dada71be5d78205993a9182886",
-            "size": 6414,
-            "uuid": "302206c2-e1d8-49d9-a4b9-7ffe15a77581",
-            "version": "2018-10-24T23:43:45.969008Z"
-        },
         {
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "7fea1984",
diff --git a/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index c32bc21ec..6d7cb2625 100644
--- a/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
+++ b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
@@ -684,18 +684,6 @@
             "uuid": "bb2365b9-5a5b-436f-92e3-4fc6d86a9efd",
             "version": "2018-10-11T21:18:10.586000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "e90e51d2",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "850967c36ce39ca1c39cb50fbbce2e3a",
-            "sha1": "f8819c84b8a3243f8383e044824ed418c4b9c123",
-            "sha256": "ef3b8c62921e5b016ec1609d93f348c7e48ec5452a7c9e0a9968b649c69c84f4",
-            "size": 24588,
-            "uuid": "4e4a6937-c54a-4933-913a-0ab2cddaaa6f",
-            "version": "2018-10-18T20:46:11.972661Z"
-        },
         {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "e511d1cf",
diff --git a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index 678ee4be7..185506e10 100644
--- a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
+++ b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
@@ -684,18 +684,6 @@
             "uuid": "bb2365b9-5a5b-436f-92e3-4fc6d86a9efd",
             "version": "2018-10-11T21:18:10.586000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "e90e51d2",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "850967c36ce39ca1c39cb50fbbce2e3a",
-            "sha1": "f8819c84b8a3243f8383e044824ed418c4b9c123",
-            "sha256": "ef3b8c62921e5b016ec1609d93f348c7e48ec5452a7c9e0a9968b649c69c84f4",
-            "size": 24588,
-            "uuid": "4e4a6937-c54a-4933-913a-0ab2cddaaa6f",
-            "version": "2018-10-18T20:46:11.972661Z"
-        },
         {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "e511d1cf",
diff --git a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
index 8ff3547e7..93c70d14a 100644
--- a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
+++ b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
@@ -78,17 +78,6 @@
             "crc32c": "",
             "sha256": ""
         },
-        {
-            "name": "links.json",
-            "uuid": "4426adc5-b3c5-5aab-ab86-51d8ce44dfbe",
-            "version": "2020-08-10T21:24:26.174274Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 3322,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "library_preparation_protocol_0.json",
             "uuid": "5b503dcb-dca6-4e4f-988b-f7100c030dc5",
diff --git a/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json b/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
index c0f2574fe..1363f86b3 100644
--- a/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
+++ b/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
@@ -23,17 +23,6 @@
             "crc32c": "5bf9776f",
             "sha256": "053074e25a96a463c081e38bcd02662ba1536dd0cb71411bd111b8a2086a03e1"
         },
-        {
-            "name": "links.json",
-            "uuid": "4b03c1ce-9df1-5cd5-a8e4-48a2fe095081",
-            "version": "2021-02-10T16:56:40.419579Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 935,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "supplementary_file_1.json",
             "uuid": "5b465aad-0981-5152-b468-e615e20f5884",
diff --git a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
index e8f318774..920040235 100644
--- a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
+++ b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
@@ -528,18 +528,6 @@
             "uuid": "908d468a-eb62-4d19-8706-c5f708a14940",
             "version": "2018-10-10T02:23:43.104000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "7b8cabc3",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "56f651d69c90f007ae6457f2bc7b1480",
-            "sha1": "b98a0163f28458ed17a4f30c7592e58d93870eb8",
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-            "size": 6069,
-            "uuid": "07086553-f0ef-446a-af5c-cd96295214b7",
-            "version": "2018-10-10T03:10:31.063705Z"
-        },
         {
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "074766b5",
diff --git a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
index 7254cc7cf..850a472aa 100644
--- a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
+++ b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
@@ -2222,17 +2222,6 @@
             "crc32c": "5238ca18",
             "sha256": "04b3c4a0b85159145d49208536b7020807b022fd9b7a2b031fe7695a1ba317c8"
         },
-        {
-            "name": "links.json",
-            "uuid": "79fa91b4-f1fc-534b-a935-b57342804a70",
-            "version": "2020-12-10T10:30:00.000000Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 76574,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "sequence_file_29.json",
             "uuid": "7a058660-f594-4eb5-b02f-bace314f6d76",
diff --git a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
index bd480066d..14032393d 100644
--- a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
+++ b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
@@ -143,17 +143,6 @@
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             "s3_etag": "be870140031523af537bbb3861fff77e-44"
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-        {
-            "name": "links.json",
-            "uuid": "7eb74d9f-8346-5420-b7e4-b486f99451a8",
-            "version": "2020-02-03T10:30:00.000000Z",
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-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "project_0.json",
             "uuid": "8185730f-4113-40d3-9cc3-929271784c2b",
diff --git a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
index 89ff6add9..4f8d05032 100644
--- a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
+++ b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
@@ -138,17 +138,6 @@
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-        {
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-            "uuid": "80baee6e-00a5-4fdc-bfe3-d339ff8a7178",
-            "version": "2021-03-12T22:43:32.330000Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 1725,
-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
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         {
             "name": "process_1.json",
             "uuid": "80baee6e-00a5-4fdc-bfe3-d339ff8a7178",
diff --git a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
index 146a0f535..658d4936f 100644
--- a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
+++ b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
@@ -57,17 +57,6 @@
             "crc32c": "",
             "sha256": ""
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-        {
-            "name": "links.json",
-            "uuid": "8338b891-f3fa-5e7b-885f-e4ee5689ee15",
-            "version": "2020-12-03T10:39:17.144517Z",
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-            "is_stitched": false,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "supplementary_file_2.json",
             "uuid": "8d2ba1c1-bc9f-5c2a-a74d-fe5e09bdfb18",
diff --git a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
index 6df1142ce..b8c0e4669 100644
--- a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
+++ b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
@@ -348,18 +348,6 @@
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             "uuid": "f4146a80-2737-4299-8d9a-0ec685dbac8b",
diff --git a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
index 88cb2f9df..78a1a3649 100644
--- a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
+++ b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
@@ -2844,18 +2844,6 @@
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-            "name": "links.json",
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diff --git a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
index 8403358ef..28629f6db 100644
--- a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
+++ b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
@@ -168,18 +168,6 @@
             "sha256": "b528a08d3135eef4d5331a203e1d7797699817717423c83cdf3beba0c5f4be1c",
             "s3_etag": "e16b715d16d5703a2d68bd1ec1c6e879"
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-        {
-            "name": "links.json",
-            "uuid": "63b2b373-b6e3-4553-a153-a262102f5739",
-            "version": "2019-10-14T19:54:43.467042Z",
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "size": 2266,
-            "indexed": true,
-            "crc32c": "f2d7c7c3",
-            "sha1": "b65099884d6700966385b1242b84fd9374fee38f",
-            "sha256": "557dc252c866fea4a762cde5ca096b58917cd20316ce670eb3a6709fcc144507",
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             "name": "E8.75_anterior_Rep1_barcodes.fastq.gz",
             "uuid": "1fdcd06c-ea5b-4e5a-b382-ae42dcfc8aca",
diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
index 35179cfc3..bbd43843e 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
@@ -156,18 +156,6 @@
             "uuid": "4674255d-5ecd-4860-9b8d-beae98772cd9",
             "version": "2018-11-02T10:12:03.520000Z"
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-            "crc32c": "aace07f3",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "77a21047cf9b7c706e72663090e67d4d",
-            "sha1": "766cefe20615e3f8aa5e0fc2042e4192d0494041",
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diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
index 4eb03b66e..b624f9147 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
@@ -156,18 +156,6 @@
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             "version": "2018-11-04T10:12:03.520000Z"
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-            "content-type": "application/json; dcp-type='metadata/links'",
-            "crc32c": "aace07f3",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "77a21047cf9b7c706e72663090e67d4d",
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diff --git a/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
index 842fb2e3c..ae2cf7e90 100644
--- a/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
+++ b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
@@ -180,18 +180,6 @@
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-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "8dabafdc",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "9187a3a62eac5c71798be5606a5db5b0",
-            "sha1": "590f7e494654860bfe36d95d180b604ae7291f0f",
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-            "uuid": "372dfa6d-fc17-4a6b-be36-9ddeebb8544b",
-            "version": "2018-09-12T12:11:53.763631Z"
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diff --git a/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
index bb295fec4..d3d010a16 100644
--- a/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
+++ b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
@@ -180,18 +180,6 @@
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-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "6fa63916",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "3d2c1f5323d5645a4946394ae97156f3",
-            "sha1": "801cfabd504abfd3d72c23367c0e7f6686f8db65",
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-            "uuid": "67d2808f-f774-4f00-96a9-9ef6d1ebb817",
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diff --git a/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
index edfb64ef2..cfdb0d0b0 100644
--- a/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
+++ b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
@@ -9372,18 +9372,6 @@
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-            "name": "links.json",
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diff --git a/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
index e7ea43adb..833ab0476 100644
--- a/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
+++ b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
@@ -528,18 +528,6 @@
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-            "indexed": true,
-            "name": "links.json",
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-            "sha1": "bc9ee2d73c5228a3b56a4f40442b86e09ac8696a",
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diff --git a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
index bc0849cc5..8d7d20190 100644
--- a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
+++ b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
@@ -684,18 +684,6 @@
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-            "indexed": true,
-            "name": "links.json",
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-            "uuid": "4e4a6937-c54a-4933-913a-0ab2cddaaa6f",
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diff --git a/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
index 277d529c1..2e9d79780 100644
--- a/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
+++ b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
@@ -216,18 +216,6 @@
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diff --git a/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
index 3cea1a695..aaeaf6953 100644
--- a/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
+++ b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
@@ -576,18 +576,6 @@
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-            "indexed": true,
-            "name": "links.json",
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diff --git a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
index 828c98423..2990aa646 100644
--- a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
+++ b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
@@ -3600,18 +3600,6 @@
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-            "crc32c": "927d1da3",
-            "indexed": true,
-            "name": "links.json",
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-            "sha1": "477428b0566112cf9a50d4b7fdf6716ad0b7d630",
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-            "uuid": "a3c7cdcb-131d-467e-852d-b556d307c40e",
-            "version": "2019-07-23T06:45:53.877413Z"
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diff --git a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
index 69e0dacd8..1368f8265 100644
--- a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
+++ b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
@@ -204,18 +204,6 @@
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diff --git a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
index 3498a6ab3..b7df8b085 100644
--- a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
+++ b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
@@ -360,18 +360,6 @@
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-            "indexed": true,
-            "name": "links.json",
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diff --git a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
index 45262fb29..acabe1388 100644
--- a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
+++ b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
@@ -7104,17 +7104,6 @@
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-            "uuid": "fce68057-b0f0-5d11-b9a7-30e8fa3259a8",
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-            "is_stitched": false,
-            "indexed": true,
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         {
             "name": "sequence_file_118.json",
             "uuid": "fd0752c7-210b-4acd-a7ef-df7ffcdfbd3d",
diff --git a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
index cc54819b5..2cd51a806 100644
--- a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
+++ b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
@@ -168,18 +168,6 @@
             "uuid": "c7070951-ec8a-492f-a7be-354b5670c056",
             "version": "2019-10-09T15:36:21.507000Z"
         },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/links\"",
-            "crc32c": "78d21cea",
-            "indexed": true,
-            "name": "links.json",
-            "s3_etag": "ea8c58448e80259d02399dd65103f32f",
-            "sha1": "f1fca16d8ecabb2833b896b1994dcbe11a92db03",
-            "sha256": "e1046b17e04ae20586dccb8b771248f05085bbdc8f719d068554e1368968927f",
-            "size": 2266,
-            "uuid": "29b2a53c-299e-4062-a87a-c2aa393fc347",
-            "version": "2019-10-09T17:22:51.165978Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "49a9085f",
diff --git a/test/integration_test.py b/test/integration_test.py
index 537690956..6f421705b 100644
--- a/test/integration_test.py
+++ b/test/integration_test.py
@@ -1937,14 +1937,7 @@ def _test_catalog(self, catalog: config.Catalog):
                 self.assertIsInstance(metadata, dict)
                 manifest_files = sorted(e['name'] for e in manifest if e['indexed'])
                 metadata_files = sorted(metadata.keys())
-
-                if catalog.plugins['repository'].name == 'canned':
-                    # FIXME: Manifest entry not generated for links.json by
-                    #        StagingArea.get_bundle
-                    #        https://github.com/DataBiosphere/hca-metadata-api/issues/52
-                    assert 'links.json' not in manifest_files
-                    metadata_files.remove('links.json')
-
+                metadata_files.remove('links.json')
                 self.assertListEqual(manifest_files, metadata_files)
             elif metadata_plugin_name == 'anvil':
                 self.assertEqual({'entities', 'links'}, bundle_json.keys())

From cab6ef4a60081e555aa4f5ae3738d7b37595998e Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Tue, 20 Aug 2024 17:56:26 -0700
Subject: [PATCH 11/20] Extract links.json to a separate bundle attribute

---
 src/azul/plugins/metadata/hca/__init__.py     |     3 +-
 src/azul/plugins/metadata/hca/bundle.py       |     9 +-
 .../plugins/metadata/hca/indexer/transform.py |     2 +-
 .../plugins/repository/canned/__init__.py     |     5 +-
 src/azul/plugins/repository/dss/__init__.py   |     2 +-
 .../plugins/repository/tdr_hca/__init__.py    |     5 +-
 src/humancellatlas/data/metadata/api.py       |     8 +-
 .../data/metadata/helpers/staging_area.py     |    12 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   114 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   140 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   468 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   114 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   122 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   106 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |    98 +-
 ...318dbb86000.2019-01-03T163633.780215Z.json |   468 +-
 ...61d6da02d44.2019-09-20T103932.395795Z.json |   136 +-
 ...a3fb4204953.2018-03-29T142048.835519Z.json |   290 +-
 ...d019d1c9439.2019-05-15T222432.561000Z.json |   154 +-
 ...08092b2dabe.2019-04-17T175706.867000Z.json |   156 +-
 ...68e20ec4a2e.2019-02-02T065454.662896Z.json |   386 +-
 ...19c1c2d9018.2018-10-07T130111.835234Z.json |   140 +-
 ...406a478d5ab.2018-09-05T182535.846470Z.json |   124 +-
 ...95a3f8deb9c.2019-04-03T103426.471000Z.json |   568 +-
 ...720f33a5dde.2019-03-17T220646.332108Z.json |   138 +-
 test/hca_metadata_api/test.py                 |    62 +-
 ...3-5e9d-52cd-b32d-af88edccabfa.dss.hca.json |  1294 +-
 ...5-71e2-48ca-a87b-e256938c6a98.dss.hca.json |  2326 +-
 ...3-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json | 33888 ++++++++--------
 ...c-6778-423d-8fe9-869e2a515d35.dss.hca.json |   186 +-
 ...8-01a0-464a-9599-7375fda3353d.dss.hca.json |   398 +-
 ...8-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json |   192 +-
 ...8-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json |   390 +-
 ...0-eaba-531d-ba9e-db80164d65ef.dss.hca.json |   204 +-
 ...4-fa14-5c6f-a474-a742540108a3.dss.hca.json |   160 +-
 ...5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json |   178 +-
 ...c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json |  7334 ++--
 ...8-658e-4c51-9de4-a768322f84c5.dss.hca.json |   180 +-
 ...3-93e1-56b4-b857-59497f5d942d.dss.hca.json |   152 +-
 ...a-940e-49b1-9bcc-25699a55b295.dss.hca.json |   442 +-
 ...f-61a7-4504-a57c-fc70f38d5b13.dss.hca.json |   334 +-
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json |  1434 +-
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json |  1434 +-
 ...5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json |   348 +-
 ...a-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json |  7334 ++--
 ...e-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json |    98 +-
 ...8-adab-59a9-b6c4-3a61242cc972.dss.hca.json |   176 +-
 ...e-7554-4b5d-96a2-7df127a7640b.dss.hca.json |   230 +-
 ...4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json |   318 +-
 ...0.2020-12-10T10:30:00.000000Z.dss.hca.json |  7666 ++--
 ...1-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json |   196 +-
 ...f-8346-5420-b7e4-b486f99451a8.dss.hca.json |   256 +-
 ...e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json |   186 +-
 ...1-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json |    58 +-
 ...f-4c01-48d5-a79f-1c5439659da3.dss.hca.json |   350 +-
 ...3-1885-545f-9381-0dab1edf6074.dss.hca.json |   176 +-
 ...e-9a5d-4e3d-ada2-0414b666b880.dss.hca.json |   170 +-
 ...2-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json |   568 +-
 ...3-f0ac-417a-8a29-221c77debde8.dss.hca.json |   134 +-
 ...6-ced8-448a-8e45-1fc7846d8995.dss.hca.json |   230 +-
 ...d.2018-11-02T11:33:44.698028Z.dss.hca.json |   124 +-
 ...d.2018-11-04T11:33:44.698028Z.dss.hca.json |   124 +-
 ...9-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json |  7334 ++--
 ...8-7eaa-45f4-8077-5a3fb4204953.dss.hca.json |   290 +-
 ...e-9b7b-4800-8977-fe7c94e131df.dss.hca.json |   166 +-
 ...9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json |  7106 ++--
 ...4-dc9f-439e-af29-f8eb75b0729d.dss.hca.json |   148 +-
 ...4-9a58-4763-9e66-59894efbdaa8.dss.hca.json | 30008 +++++++-------
 ...d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json |   304 +-
 ...f-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json |   206 +-
 ...1-4766-4210-966c-f9ee25d19190.dss.hca.json |  1434 +-
 ...a-2b51-4419-9cde-34df44c6458a.dss.hca.json |   182 +-
 ...e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json |   334 +-
 ...4-6b80-4eed-97c9-4984de81a47c.dss.hca.json |   748 +-
 ...7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json |   132 +-
 ...b-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json |   442 +-
 ...7-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json | 32710 +++++++--------
 ...f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json |   134 +-
 test/indexer/test_indexer.py                  |    13 +-
 test/indexer/test_tdr.py                      |     1 +
 test/integration_test.py                      |     8 +-
 test/service/test_manifest.py                 |    34 +-
 82 files changed, 77428 insertions(+), 77404 deletions(-)

diff --git a/src/azul/plugins/metadata/hca/__init__.py b/src/azul/plugins/metadata/hca/__init__.py
index 44c91bbe9..49c6ee3d1 100644
--- a/src/azul/plugins/metadata/hca/__init__.py
+++ b/src/azul/plugins/metadata/hca/__init__.py
@@ -80,7 +80,8 @@ def transformers(self,
         api_bundle = api.Bundle(uuid=bundle.uuid,
                                 version=bundle.version,
                                 manifest=bundle.manifest,
-                                metadata_files=bundle.metadata_files)
+                                metadata_files=bundle.metadata_files,
+                                links_json=bundle.links)
 
         def transformers():
             for transformer_cls in self.transformer_types():
diff --git a/src/azul/plugins/metadata/hca/bundle.py b/src/azul/plugins/metadata/hca/bundle.py
index 3219d841c..44e648d50 100644
--- a/src/azul/plugins/metadata/hca/bundle.py
+++ b/src/azul/plugins/metadata/hca/bundle.py
@@ -40,21 +40,26 @@ class HCABundle(Bundle[BUNDLE_FQID], ABC):
     }
     """
     metadata_files: MutableJSON
+    links: MutableJSON
 
     def reject_joiner(self, catalog: CatalogName):
         self._reject_joiner(self.manifest)
         self._reject_joiner(self.metadata_files)
+        self._reject_joiner(self.links)
 
     def to_json(self) -> MutableJSON:
         return {
             'manifest': self.manifest,
-            'metadata': self.metadata_files
+            'metadata': self.metadata_files,
+            'links': self.links,
         }
 
     @classmethod
     def from_json(cls, fqid: BUNDLE_FQID, json_: JSON) -> 'Bundle':
         manifest = json_['manifest']
         metadata = json_['metadata']
+        links = json_['links']
         assert isinstance(manifest, list), manifest
         assert isinstance(metadata, dict), metadata
-        return cls(fqid=fqid, manifest=manifest, metadata_files=metadata)
+        assert isinstance(links, dict), links
+        return cls(fqid=fqid, manifest=manifest, metadata_files=metadata, links=links)
diff --git a/src/azul/plugins/metadata/hca/indexer/transform.py b/src/azul/plugins/metadata/hca/indexer/transform.py
index 8c6a3829f..0ca2ccd61 100644
--- a/src/azul/plugins/metadata/hca/indexer/transform.py
+++ b/src/azul/plugins/metadata/hca/indexer/transform.py
@@ -511,7 +511,7 @@ def _add_replica(self,
         if not config.enable_replicas:
             replica = None
         elif self.entity_type() == 'bundles':
-            links = self.bundle.metadata_files['links.json']
+            links = self.bundle.links
             replica = self._replica(links, entity_ref, hub_ids)
         else:
             assert isinstance(entity, api.Entity), entity
diff --git a/src/azul/plugins/repository/canned/__init__.py b/src/azul/plugins/repository/canned/__init__.py
index 566945205..965c9ac25 100644
--- a/src/azul/plugins/repository/canned/__init__.py
+++ b/src/azul/plugins/repository/canned/__init__.py
@@ -192,14 +192,15 @@ def fetch_bundle(self, bundle_fqid: CannedBundleFQID) -> CannedBundle:
         self._assert_source(bundle_fqid.source)
         now = time.time()
         staging_area = self.staging_area(bundle_fqid.source.spec.name)
-        version, manifest, metadata = staging_area.get_bundle_parts(bundle_fqid.uuid)
+        version, manifest, metadata, links = staging_area.get_bundle_parts(bundle_fqid.uuid)
         if bundle_fqid.version is None:
             bundle_fqid = CannedBundleFQID(source=bundle_fqid.source,
                                            uuid=bundle_fqid.uuid,
                                            version=version)
         bundle = CannedBundle(fqid=bundle_fqid,
                               manifest=manifest,
-                              metadata_files=metadata)
+                              metadata_files=metadata,
+                              links=links)
         assert version == bundle.version, (version, bundle)
         log.info('It took %.003fs to download bundle %s.%s',
                  time.time() - now, bundle.uuid, bundle.version)
diff --git a/src/azul/plugins/repository/dss/__init__.py b/src/azul/plugins/repository/dss/__init__.py
index 57e796c59..d0863a4b3 100644
--- a/src/azul/plugins/repository/dss/__init__.py
+++ b/src/azul/plugins/repository/dss/__init__.py
@@ -140,7 +140,7 @@ def list_bundles(self,
     def fetch_bundle(self, bundle_fqid: DSSBundleFQID) -> DSSBundle:
         assert False, 'DSS is EOL'
         # noinspection PyUnreachableCode
-        return DSSBundle(fqid=bundle_fqid, manifest=[], metadata_files={})
+        return DSSBundle(fqid=bundle_fqid, manifest=[], metadata_files={}, links={})
 
     def dss_subscription_query(self, prefix: str) -> JSON:
         return {
diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py
index c1043a682..203f85040 100644
--- a/src/azul/plugins/repository/tdr_hca/__init__.py
+++ b/src/azul/plugins/repository/tdr_hca/__init__.py
@@ -341,9 +341,10 @@ def _query_unique_sorted(self,
     def _emulate_bundle(self, bundle_fqid: TDRBundleFQID) -> TDRHCABundle:
         bundle = TDRHCABundle(fqid=bundle_fqid,
                               manifest=[],
-                              metadata_files={})
+                              metadata_files={},
+                              links={})
         entities, root_entities, links_jsons = self._stitch_bundles(bundle)
-        bundle.metadata_files['links.json'] = self._merge_links(links_jsons)
+        bundle.links = self._merge_links(links_jsons)
 
         with ThreadPoolExecutor(max_workers=config.num_tdr_workers) as executor:
             futures = {
diff --git a/src/humancellatlas/data/metadata/api.py b/src/humancellatlas/data/metadata/api.py
index b1591af21..63b7cec50 100644
--- a/src/humancellatlas/data/metadata/api.py
+++ b/src/humancellatlas/data/metadata/api.py
@@ -994,7 +994,12 @@ class Bundle:
     entities: MutableMapping[UUID4, Entity] = field(repr=False)
     links: list[Link]
 
-    def __init__(self, uuid: str, version: str, manifest: MutableJSONs, metadata_files: Mapping[str, JSON]):
+    def __init__(self,
+                 uuid: str,
+                 version: str,
+                 manifest: MutableJSONs,
+                 metadata_files: Mapping[str, JSON],
+                 links_json: JSON):
         self.uuid = UUID4(uuid)
         self.version = version
         self.manifest = {m.name: m for m in map(ManifestEntry, manifest)}
@@ -1026,7 +1031,6 @@ def from_json_vx(core_cls: type[E],
 
         self.entities = {**self.projects, **self.biomaterials, **self.processes, **self.protocols, **self.files}
 
-        links_json = metadata_files['links.json']
         schema_version = tuple(map(int, links_json['schema_version'].split('.')))
         self.links = list(chain.from_iterable(
             Link.from_json(link, schema_version)
diff --git a/src/humancellatlas/data/metadata/helpers/staging_area.py b/src/humancellatlas/data/metadata/helpers/staging_area.py
index 716f9d570..026d99398 100644
--- a/src/humancellatlas/data/metadata/helpers/staging_area.py
+++ b/src/humancellatlas/data/metadata/helpers/staging_area.py
@@ -141,18 +141,16 @@ def get_bundle(self, subgraph_id: str) -> Bundle:
         """
         Return a bundle from the staging area
         """
-        version, manifest, metadata = self.get_bundle_parts(subgraph_id)
-        return Bundle(subgraph_id, version, manifest, metadata)
+        version, manifest, metadata, links = self.get_bundle_parts(subgraph_id)
+        return Bundle(subgraph_id, version, manifest, metadata, links)
 
-    def get_bundle_parts(self, subgraph_id: str) -> tuple[str, MutableJSONs, MutableJSON]:
+    def get_bundle_parts(self, subgraph_id: str) -> tuple[str, MutableJSONs, MutableJSON, MutableJSON]:
         """
         Return the components to create a bundle from the staging area
         """
         links_file = self.links[subgraph_id]
         manifest = []
-        metadata = {
-            'links.json': links_file.content
-        }
+        metadata = {}
         entity_ids_by_type = self._entity_ids_by_type(subgraph_id)
         for entity_type, entity_ids in entity_ids_by_type.items():
             # Sort entity_ids to produce the same ordering on multiple runs
@@ -179,7 +177,7 @@ def get_bundle_parts(self, subgraph_id: str) -> tuple[str, MutableJSONs, Mutable
                     manifest.append(file_manifest)
                 else:
                     pass
-        return links_file.version, manifest, metadata
+        return links_file.version, manifest, metadata, links_file.content
 
     def _entity_ids_by_type(self,
                             subgraph_id: str
diff --git a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 1f5712e7e..b43a40d08 100644
--- a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -281,63 +281,6 @@
                 "update_date": "2018-09-04T12:27:50.909Z"
             }
         },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.1",
-            "links": [
-                {
-                    "process": "d691bda4-ed01-48b6-a4ea-65b70f6a3946",
-                    "inputs": [
-                        "7b53bae2-2424-44c0-9d80-ad72e8bca136"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "36d7f891-8a43-4ae4-8472-a34dcb2be643"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "e4024c4a-dbce-4bda-bed8-21414091e7ce"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "aaa08845-5150-4a4f-9c44-5ea22add1fc3"
-                        }
-                    ]
-                },
-                {
-                    "process": "98442f49-9afb-491e-8347-f891f39d8d70",
-                    "inputs": [
-                        "6228558b-436a-46c9-9cd3-ea9b5c123070"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "7b53bae2-2424-44c0-9d80-ad72e8bca136"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "eebf404f-4fbb-41b0-a9c6-81586f729599"
-                        }
-                    ]
-                },
-                {
-                    "process": "5aa4645b-2802-4140-9b15-d1008338b1c9",
-                    "inputs": [
-                        "628e8b1d-a1ce-4dee-b15a-3fd33290eafe"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "6228558b-436a-46c9-9cd3-ea9b5c123070"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
-        },
         "process_0.json": {
             "process_core": {
                 "process_id": "process_id_128"
@@ -591,5 +534,62 @@
                 "update_date": "2018-09-04T12:27:13.378Z"
             }
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.1",
+        "links": [
+            {
+                "process": "d691bda4-ed01-48b6-a4ea-65b70f6a3946",
+                "inputs": [
+                    "7b53bae2-2424-44c0-9d80-ad72e8bca136"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "36d7f891-8a43-4ae4-8472-a34dcb2be643"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "e4024c4a-dbce-4bda-bed8-21414091e7ce"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "aaa08845-5150-4a4f-9c44-5ea22add1fc3"
+                    }
+                ]
+            },
+            {
+                "process": "98442f49-9afb-491e-8347-f891f39d8d70",
+                "inputs": [
+                    "6228558b-436a-46c9-9cd3-ea9b5c123070"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "7b53bae2-2424-44c0-9d80-ad72e8bca136"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "eebf404f-4fbb-41b0-a9c6-81586f729599"
+                    }
+                ]
+            },
+            {
+                "process": "5aa4645b-2802-4140-9b15-d1008338b1c9",
+                "inputs": [
+                    "628e8b1d-a1ce-4dee-b15a-3fd33290eafe"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "6228558b-436a-46c9-9cd3-ea9b5c123070"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index ce91f3795..0f8006f7a 100644
--- a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -372,76 +372,6 @@
                 "update_date": "2018-09-05T09:52:00.867Z"
             }
         },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.1",
-            "links": [
-                {
-                    "process": "bcfcb3d7-674a-429f-8bf9-347a0f222db2",
-                    "inputs": [
-                        "cc0d9bf0-6ad5-4489-994b-db26ff761c5a"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "a5806f2e-3f85-486a-9015-e02e5c805285"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "0ea30fa0-7183-4ffc-a4b8-537c6de32e65"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "2d0f835b-ced1-4cf1-a053-0cf109fdefeb"
-                        }
-                    ]
-                },
-                {
-                    "process": "f8e3c0b7-ed2a-464d-bff4-b80fac2a3849",
-                    "inputs": [
-                        "ff63b5d7-e702-40da-bbe9-619e52131b63"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "cc0d9bf0-6ad5-4489-994b-db26ff761c5a"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "a934e15c-e1ce-423b-b554-9203d4e93f41"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "77c71448-fb32-472f-9d44-ea9a42867a41"
-                        }
-                    ]
-                },
-                {
-                    "process": "4e504efb-a65b-4fe5-97f5-8148f6a8ed4d",
-                    "inputs": [
-                        "25e083e3-d747-4295-86c8-c7ddc4b975be"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "ff63b5d7-e702-40da-bbe9-619e52131b63"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "f8d9778f-0f72-4432-a929-1096fd9ca2f4"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "80921b90-fe8d-45e1-a5e5-4fdb55f9a3fa"
-                        }
-                    ]
-                }
-            ]
-        },
         "process_0.json": {
             "insdc_experiment": {
                 "insdc_experiment": "SRX3364233"
@@ -643,5 +573,75 @@
                 "update_date": "2018-09-05T09:50:44.523Z"
             }
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.1",
+        "links": [
+            {
+                "process": "bcfcb3d7-674a-429f-8bf9-347a0f222db2",
+                "inputs": [
+                    "cc0d9bf0-6ad5-4489-994b-db26ff761c5a"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "a5806f2e-3f85-486a-9015-e02e5c805285"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "0ea30fa0-7183-4ffc-a4b8-537c6de32e65"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "2d0f835b-ced1-4cf1-a053-0cf109fdefeb"
+                    }
+                ]
+            },
+            {
+                "process": "f8e3c0b7-ed2a-464d-bff4-b80fac2a3849",
+                "inputs": [
+                    "ff63b5d7-e702-40da-bbe9-619e52131b63"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "cc0d9bf0-6ad5-4489-994b-db26ff761c5a"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "a934e15c-e1ce-423b-b554-9203d4e93f41"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "77c71448-fb32-472f-9d44-ea9a42867a41"
+                    }
+                ]
+            },
+            {
+                "process": "4e504efb-a65b-4fe5-97f5-8148f6a8ed4d",
+                "inputs": [
+                    "25e083e3-d747-4295-86c8-c7ddc4b975be"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "ff63b5d7-e702-40da-bbe9-619e52131b63"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "f8d9778f-0f72-4432-a929-1096fd9ca2f4"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "80921b90-fe8d-45e1-a5e5-4fdb55f9a3fa"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 959b66bbf..4591e9d13 100644
--- a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
+++ b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
@@ -1098,240 +1098,6 @@
                 "update_date": "2018-09-05T09:25:09.008Z"
             }
         },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.1",
-            "links": [
-                {
-                    "process": "88ef68b1-0c0b-4594-be46-4bb0bcf2025d",
-                    "inputs": [
-                        "8fc8b364-98bb-4082-98af-e3fdffcf82b7"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "740b2221-41c6-498d-87de-8b2937a5ebed",
-                        "a3f614b3-e6cf-4751-a15d-ff623efea62a",
-                        "56c2a158-e389-40a3-97a7-0f2966a393b8"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "853c2086-1ac4-488e-b3b3-fe7956e74283"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "0b1dfbd4-1fbe-42a4-9213-b66dac4d4ac0"
-                        }
-                    ]
-                },
-                {
-                    "process": "d3c8ba6e-e552-48cc-ab34-38a95712b3f7",
-                    "inputs": [
-                        "77a87953-5d2d-4e22-9c8b-c012fa8656b9",
-                        "e4307721-7d92-4f92-a6f1-6f1d4ecf1835",
-                        "08936dad-6f12-4f43-8bd2-b6863f166a21",
-                        "dfd95ce4-c5be-4175-9e9a-249b1b09f5d9"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "8fc8b364-98bb-4082-98af-e3fdffcf82b7"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "58334256-af4f-4754-9455-668fb31bbcff"
-                        }
-                    ]
-                },
-                {
-                    "process": "3ef770a1-1f72-47f2-952e-9fd584e74598",
-                    "inputs": [
-                        "cc5c8bd6-3bd6-49d6-87b3-b24ef3a577a4"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "77a87953-5d2d-4e22-9c8b-c012fa8656b9"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "537b3c44-998f-43c2-8146-7e3e2932c30b"
-                        }
-                    ]
-                },
-                {
-                    "process": "1c4b3da5-41c3-40bd-b128-4a4a94fb876e",
-                    "inputs": [
-                        "440a306a-54c6-4193-9b60-ad4423c8a62b"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "cc5c8bd6-3bd6-49d6-87b3-b24ef3a577a4"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "ipsc_induction_protocol",
-                            "protocol_id": "9e3b5ef9-cbb0-43ef-a194-1ce1969cfd62"
-                        }
-                    ]
-                },
-                {
-                    "process": "359f3d8c-e29c-41f1-b058-1854a7d7e79e",
-                    "inputs": [
-                        "eea3dd19-90e0-45c4-803d-4620d1fab90d"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "440a306a-54c6-4193-9b60-ad4423c8a62b"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "df40cef2-60ae-400c-bece-947329b40946",
-                    "inputs": [
-                        "304fadde-e22a-4ff9-9544-f8ec097b6135"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "e4307721-7d92-4f92-a6f1-6f1d4ecf1835"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "537b3c44-998f-43c2-8146-7e3e2932c30b"
-                        }
-                    ]
-                },
-                {
-                    "process": "0ec71414-3c56-4347-85a2-a2b66a4a147d",
-                    "inputs": [
-                        "4eb07fdb-dcd8-4805-89ad-6068071c80c9"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "304fadde-e22a-4ff9-9544-f8ec097b6135"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "ipsc_induction_protocol",
-                            "protocol_id": "9e3b5ef9-cbb0-43ef-a194-1ce1969cfd62"
-                        }
-                    ]
-                },
-                {
-                    "process": "9c2903a9-d93e-41a4-88bf-61647c6990a6",
-                    "inputs": [
-                        "fbd4c071-58bd-4818-8ddd-2c31ddb60363"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "4eb07fdb-dcd8-4805-89ad-6068071c80c9"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "1ff79cfa-57e9-4af1-a754-51bdf36c4414",
-                    "inputs": [
-                        "8bd345cb-4635-4bf5-9435-bf144013b938"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "08936dad-6f12-4f43-8bd2-b6863f166a21"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "537b3c44-998f-43c2-8146-7e3e2932c30b"
-                        }
-                    ]
-                },
-                {
-                    "process": "94b7d3a9-2a09-40d1-ba0e-80e8410b3d55",
-                    "inputs": [
-                        "54046c37-b50d-41ae-a95f-2db29b1b706b"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "8bd345cb-4635-4bf5-9435-bf144013b938"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "ipsc_induction_protocol",
-                            "protocol_id": "9e3b5ef9-cbb0-43ef-a194-1ce1969cfd62"
-                        }
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-                },
-                {
-                    "process": "85e8adfd-f23b-47fb-9617-e51593923405",
-                    "inputs": [
-                        "62ee5119-4fa1-4508-95f3-59c7b0fddd34"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "54046c37-b50d-41ae-a95f-2db29b1b706b"
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-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "f999e1a4-31fc-4298-b958-8f567511935e",
-                    "inputs": [
-                        "6953e086-13cc-4467-b059-4d5f91f6f268"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "dfd95ce4-c5be-4175-9e9a-249b1b09f5d9"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "537b3c44-998f-43c2-8146-7e3e2932c30b"
-                        }
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-                },
-                {
-                    "process": "4e60bff4-9ede-42e2-9152-7f8f445938f5",
-                    "inputs": [
-                        "2b541914-778d-4b24-9680-9d2643cfeff9"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "6953e086-13cc-4467-b059-4d5f91f6f268"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "ipsc_induction_protocol",
-                            "protocol_id": "9e3b5ef9-cbb0-43ef-a194-1ce1969cfd62"
-                        }
-                    ]
-                },
-                {
-                    "process": "6ecf593a-c3d6-42a8-bf4e-a47549e7bb1f",
-                    "inputs": [
-                        "5554b939-a268-4619-9cef-0f09151454fc"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "2b541914-778d-4b24-9680-9d2643cfeff9"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
-        },
         "organoid_0.json": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.3.6/organoid",
             "schema_type": "biomaterial",
@@ -1966,5 +1732,239 @@
                 "update_date": "2018-09-05T09:25:02.980Z"
             }
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.1",
+        "links": [
+            {
+                "process": "88ef68b1-0c0b-4594-be46-4bb0bcf2025d",
+                "inputs": [
+                    "8fc8b364-98bb-4082-98af-e3fdffcf82b7"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "740b2221-41c6-498d-87de-8b2937a5ebed",
+                    "a3f614b3-e6cf-4751-a15d-ff623efea62a",
+                    "56c2a158-e389-40a3-97a7-0f2966a393b8"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "853c2086-1ac4-488e-b3b3-fe7956e74283"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "0b1dfbd4-1fbe-42a4-9213-b66dac4d4ac0"
+                    }
+                ]
+            },
+            {
+                "process": "d3c8ba6e-e552-48cc-ab34-38a95712b3f7",
+                "inputs": [
+                    "77a87953-5d2d-4e22-9c8b-c012fa8656b9",
+                    "e4307721-7d92-4f92-a6f1-6f1d4ecf1835",
+                    "08936dad-6f12-4f43-8bd2-b6863f166a21",
+                    "dfd95ce4-c5be-4175-9e9a-249b1b09f5d9"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "8fc8b364-98bb-4082-98af-e3fdffcf82b7"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "58334256-af4f-4754-9455-668fb31bbcff"
+                    }
+                ]
+            },
+            {
+                "process": "3ef770a1-1f72-47f2-952e-9fd584e74598",
+                "inputs": [
+                    "cc5c8bd6-3bd6-49d6-87b3-b24ef3a577a4"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "77a87953-5d2d-4e22-9c8b-c012fa8656b9"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "differentiation_protocol",
+                        "protocol_id": "537b3c44-998f-43c2-8146-7e3e2932c30b"
+                    }
+                ]
+            },
+            {
+                "process": "1c4b3da5-41c3-40bd-b128-4a4a94fb876e",
+                "inputs": [
+                    "440a306a-54c6-4193-9b60-ad4423c8a62b"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "cc5c8bd6-3bd6-49d6-87b3-b24ef3a577a4"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "ipsc_induction_protocol",
+                        "protocol_id": "9e3b5ef9-cbb0-43ef-a194-1ce1969cfd62"
+                    }
+                ]
+            },
+            {
+                "process": "359f3d8c-e29c-41f1-b058-1854a7d7e79e",
+                "inputs": [
+                    "eea3dd19-90e0-45c4-803d-4620d1fab90d"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "440a306a-54c6-4193-9b60-ad4423c8a62b"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "df40cef2-60ae-400c-bece-947329b40946",
+                "inputs": [
+                    "304fadde-e22a-4ff9-9544-f8ec097b6135"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "e4307721-7d92-4f92-a6f1-6f1d4ecf1835"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "differentiation_protocol",
+                        "protocol_id": "537b3c44-998f-43c2-8146-7e3e2932c30b"
+                    }
+                ]
+            },
+            {
+                "process": "0ec71414-3c56-4347-85a2-a2b66a4a147d",
+                "inputs": [
+                    "4eb07fdb-dcd8-4805-89ad-6068071c80c9"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "304fadde-e22a-4ff9-9544-f8ec097b6135"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "ipsc_induction_protocol",
+                        "protocol_id": "9e3b5ef9-cbb0-43ef-a194-1ce1969cfd62"
+                    }
+                ]
+            },
+            {
+                "process": "9c2903a9-d93e-41a4-88bf-61647c6990a6",
+                "inputs": [
+                    "fbd4c071-58bd-4818-8ddd-2c31ddb60363"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "4eb07fdb-dcd8-4805-89ad-6068071c80c9"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "1ff79cfa-57e9-4af1-a754-51bdf36c4414",
+                "inputs": [
+                    "8bd345cb-4635-4bf5-9435-bf144013b938"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "08936dad-6f12-4f43-8bd2-b6863f166a21"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "differentiation_protocol",
+                        "protocol_id": "537b3c44-998f-43c2-8146-7e3e2932c30b"
+                    }
+                ]
+            },
+            {
+                "process": "94b7d3a9-2a09-40d1-ba0e-80e8410b3d55",
+                "inputs": [
+                    "54046c37-b50d-41ae-a95f-2db29b1b706b"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "8bd345cb-4635-4bf5-9435-bf144013b938"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "ipsc_induction_protocol",
+                        "protocol_id": "9e3b5ef9-cbb0-43ef-a194-1ce1969cfd62"
+                    }
+                ]
+            },
+            {
+                "process": "85e8adfd-f23b-47fb-9617-e51593923405",
+                "inputs": [
+                    "62ee5119-4fa1-4508-95f3-59c7b0fddd34"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "54046c37-b50d-41ae-a95f-2db29b1b706b"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "f999e1a4-31fc-4298-b958-8f567511935e",
+                "inputs": [
+                    "6953e086-13cc-4467-b059-4d5f91f6f268"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "dfd95ce4-c5be-4175-9e9a-249b1b09f5d9"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "differentiation_protocol",
+                        "protocol_id": "537b3c44-998f-43c2-8146-7e3e2932c30b"
+                    }
+                ]
+            },
+            {
+                "process": "4e60bff4-9ede-42e2-9152-7f8f445938f5",
+                "inputs": [
+                    "2b541914-778d-4b24-9680-9d2643cfeff9"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "6953e086-13cc-4467-b059-4d5f91f6f268"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "ipsc_induction_protocol",
+                        "protocol_id": "9e3b5ef9-cbb0-43ef-a194-1ce1969cfd62"
+                    }
+                ]
+            },
+            {
+                "process": "6ecf593a-c3d6-42a8-bf4e-a47549e7bb1f",
+                "inputs": [
+                    "5554b939-a268-4619-9cef-0f09151454fc"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "2b541914-778d-4b24-9680-9d2643cfeff9"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index c7b3b4a1f..b9138a275 100644
--- a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -274,63 +274,6 @@
                 "update_date": "2018-09-05T12:17:48.051Z"
             }
         },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.1",
-            "links": [
-                {
-                    "process": "aa67d2ed-e4ea-4cdf-92ed-7d5e6dc1f6fa",
-                    "inputs": [
-                        "1200f5bf-7d45-4f26-865e-b560797f1808"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "60471337-a47b-4b9c-95e7-4a19349a5e05"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "079bc155-71c9-45ab-bd12-cab025890d82"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "3aece946-4be6-4a0c-af23-ac884a87bcbb"
-                        }
-                    ]
-                },
-                {
-                    "process": "443b4672-3f14-4f1e-b7be-862ae02493dc",
-                    "inputs": [
-                        "38002d8f-eac5-4ee4-8290-03d323bf780e"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "1200f5bf-7d45-4f26-865e-b560797f1808"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "6029a289-861c-4349-9614-4c244103be21"
-                        }
-                    ]
-                },
-                {
-                    "process": "738243c5-e336-4c55-a8b6-b192b6f98fe7",
-                    "inputs": [
-                        "8bb4258a-90c7-4af6-8a1b-c4ab6c5483e2"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "38002d8f-eac5-4ee4-8290-03d323bf780e"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
-        },
         "process_0.json": {
             "insdc_experiment": {
                 "insdc_experiment": "ERX1700368"
@@ -547,5 +490,62 @@
                 "update_date": "2018-09-05T12:14:29.994Z"
             }
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.1",
+        "links": [
+            {
+                "process": "aa67d2ed-e4ea-4cdf-92ed-7d5e6dc1f6fa",
+                "inputs": [
+                    "1200f5bf-7d45-4f26-865e-b560797f1808"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "60471337-a47b-4b9c-95e7-4a19349a5e05"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "079bc155-71c9-45ab-bd12-cab025890d82"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "3aece946-4be6-4a0c-af23-ac884a87bcbb"
+                    }
+                ]
+            },
+            {
+                "process": "443b4672-3f14-4f1e-b7be-862ae02493dc",
+                "inputs": [
+                    "38002d8f-eac5-4ee4-8290-03d323bf780e"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "1200f5bf-7d45-4f26-865e-b560797f1808"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "6029a289-861c-4349-9614-4c244103be21"
+                    }
+                ]
+            },
+            {
+                "process": "738243c5-e336-4c55-a8b6-b192b6f98fe7",
+                "inputs": [
+                    "8bb4258a-90c7-4af6-8a1b-c4ab6c5483e2"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "38002d8f-eac5-4ee4-8290-03d323bf780e"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 57480d942..149c49ade 100644
--- a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -302,67 +302,6 @@
                 "update_date": "2018-09-04T12:55:56.069Z"
             }
         },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.1",
-            "links": [
-                {
-                    "process": "e9c888db-256a-4c78-af5d-2977fa6bc22c",
-                    "inputs": [
-                        "1446ca36-ba75-45ea-b6ab-a80641a88812"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "b93897c4-0681-407a-bc0c-fb791b919fa4"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "38e07040-6198-4a46-b195-88c0680ef283"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "2c530a47-d87a-4d50-bfb9-74d15fdb1fd9"
-                        }
-                    ]
-                },
-                {
-                    "process": "3c85210e-6554-450c-88fb-c5d5035cf134",
-                    "inputs": [
-                        "6dc01fb6-6aba-432e-828e-ae3045914f34"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "1446ca36-ba75-45ea-b6ab-a80641a88812"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "7142ed25-3237-4156-b10d-0aa74b2c37b3"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "4a19c599-e429-4eda-9644-3a46c1202c7f"
-                        }
-                    ]
-                },
-                {
-                    "process": "ab9f0b8f-3195-4ccd-8bdf-52d91a2c9029",
-                    "inputs": [
-                        "b56697f5-d350-4e1d-93b2-72eee68c972e"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "6dc01fb6-6aba-432e-828e-ae3045914f34"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
-        },
         "process_0.json": {
             "process_core": {
                 "process_id": "process_id_55"
@@ -576,5 +515,66 @@
                 "update_date": "2018-09-04T13:10:12.581Z"
             }
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.1",
+        "links": [
+            {
+                "process": "e9c888db-256a-4c78-af5d-2977fa6bc22c",
+                "inputs": [
+                    "1446ca36-ba75-45ea-b6ab-a80641a88812"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "b93897c4-0681-407a-bc0c-fb791b919fa4"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "38e07040-6198-4a46-b195-88c0680ef283"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "2c530a47-d87a-4d50-bfb9-74d15fdb1fd9"
+                    }
+                ]
+            },
+            {
+                "process": "3c85210e-6554-450c-88fb-c5d5035cf134",
+                "inputs": [
+                    "6dc01fb6-6aba-432e-828e-ae3045914f34"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "1446ca36-ba75-45ea-b6ab-a80641a88812"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "7142ed25-3237-4156-b10d-0aa74b2c37b3"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "4a19c599-e429-4eda-9644-3a46c1202c7f"
+                    }
+                ]
+            },
+            {
+                "process": "ab9f0b8f-3195-4ccd-8bdf-52d91a2c9029",
+                "inputs": [
+                    "b56697f5-d350-4e1d-93b2-72eee68c972e"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "6dc01fb6-6aba-432e-828e-ae3045914f34"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 95a14aad9..9bc6d2ee6 100644
--- a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -256,59 +256,6 @@
                 "update_date": "2018-09-06T14:18:35.854Z"
             }
         },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.1",
-            "links": [
-                {
-                    "process": "5f868fc6-dc13-4f06-a82e-ff83497d03ee",
-                    "inputs": [
-                        "c61125ab-d5e0-4d93-b0a7-2deac1729f65"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "0494ee09-b1e2-437a-986f-06d5df4a6858",
-                        "baf745cd-9052-4a6c-8c1a-919390062c09"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "34c6db60-ef27-4502-9191-102d1a235adc"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "319dd8c8-e9d6-40df-bf72-e0423f4f5418"
-                        }
-                    ]
-                },
-                {
-                    "process": "6c357ba8-bd9a-41cb-9d74-b9442efb7217",
-                    "inputs": [
-                        "07282a68-dca4-449e-81b6-7b0da34230df"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "c61125ab-d5e0-4d93-b0a7-2deac1729f65"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "0aede7bd-0a5d-4dc5-a8e8-2d4ad6d01bfb",
-                    "inputs": [
-                        "cd379b0c-7b23-4093-b0b0-65d592ab2839"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "07282a68-dca4-449e-81b6-7b0da34230df"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
-        },
         "process_0.json": {
             "process_core": {
                 "process_id": "process_id_9"
@@ -482,5 +429,58 @@
                 "update_date": "2018-09-06T14:24:20.677Z"
             }
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.1",
+        "links": [
+            {
+                "process": "5f868fc6-dc13-4f06-a82e-ff83497d03ee",
+                "inputs": [
+                    "c61125ab-d5e0-4d93-b0a7-2deac1729f65"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "0494ee09-b1e2-437a-986f-06d5df4a6858",
+                    "baf745cd-9052-4a6c-8c1a-919390062c09"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "34c6db60-ef27-4502-9191-102d1a235adc"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "319dd8c8-e9d6-40df-bf72-e0423f4f5418"
+                    }
+                ]
+            },
+            {
+                "process": "6c357ba8-bd9a-41cb-9d74-b9442efb7217",
+                "inputs": [
+                    "07282a68-dca4-449e-81b6-7b0da34230df"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "c61125ab-d5e0-4d93-b0a7-2deac1729f65"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "0aede7bd-0a5d-4dc5-a8e8-2d4ad6d01bfb",
+                "inputs": [
+                    "cd379b0c-7b23-4093-b0b0-65d592ab2839"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "07282a68-dca4-449e-81b6-7b0da34230df"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 31d2472cb..dc6d04dfa 100644
--- a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -484,55 +484,6 @@
                 "update_date": "2018-09-05T09:15:02.223Z"
             }
         },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.1",
-            "links": [
-                {
-                    "process": "8b006d76-80c0-4e2c-866a-01fa5e900ab5",
-                    "inputs": [
-                        "932dae75-ba79-42a6-915a-c6a67b39835c"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "4d3839bf-e39f-4136-92a4-6f7009e88567"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "cc50851b-4c12-463b-b527-60d1c8d5ef60"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "29150a65-718c-46bc-8a7f-11ac585bf959"
-                        }
-                    ]
-                },
-                {
-                    "process": "a85a679d-38f0-4eb2-bfce-ed0e621769c8",
-                    "inputs": [
-                        "8909e260-7472-4c95-a96e-05d53d3c9221"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "932dae75-ba79-42a6-915a-c6a67b39835c"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "f1f2f791-f5f0-4eaa-8a4d-d6de9cf6807b"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "e8c1f3fe-d694-467c-a823-01426f44ed71"
-                        }
-                    ]
-                }
-            ]
-        },
         "process_0.json": {
             "process_core": {
                 "process_id": "process_id_1"
@@ -862,5 +813,54 @@
                 "update_date": "2018-09-05T09:14:55.825Z"
             }
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.1/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.1",
+        "links": [
+            {
+                "process": "8b006d76-80c0-4e2c-866a-01fa5e900ab5",
+                "inputs": [
+                    "932dae75-ba79-42a6-915a-c6a67b39835c"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "4d3839bf-e39f-4136-92a4-6f7009e88567"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "cc50851b-4c12-463b-b527-60d1c8d5ef60"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "29150a65-718c-46bc-8a7f-11ac585bf959"
+                    }
+                ]
+            },
+            {
+                "process": "a85a679d-38f0-4eb2-bfce-ed0e621769c8",
+                "inputs": [
+                    "8909e260-7472-4c95-a96e-05d53d3c9221"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "932dae75-ba79-42a6-915a-c6a67b39835c"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "f1f2f791-f5f0-4eaa-8a4d-d6de9cf6807b"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "e8c1f3fe-d694-467c-a823-01426f44ed71"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
index 0ca2b6573..783556e2b 100644
--- a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
+++ b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
@@ -1798,240 +1798,240 @@
                 "submission_date": "2019-01-03T12:07:51.362Z",
                 "update_date": "2019-01-03T12:07:58.911Z"
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.4/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.4",
-            "links": [
-                {
-                    "process": "54438211-29fb-4e57-87f4-95412e5d8b15",
-                    "inputs": [
-                        "c2396f83-22e4-4a2d-8cce-a30feb533603"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "9c49bbf2-cf62-4f94-9b9d-a3da42e2d52a",
-                        "ac93d656-4aa5-4f6c-b273-dc1d8be1934c",
-                        "5989ca50-45b5-4834-bfde-d290a8dfa97e"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "65ce5281-b07e-4b21-be8d-66ac5dea4d69"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "1547584e-d9e4-4519-a72a-91db0d0fec3c"
-                        }
-                    ]
-                },
-                {
-                    "process": "7d683bc4-6e59-4c7e-bbc8-5dad46fe2684",
-                    "inputs": [
-                        "a690df06-cc52-4346-a926-fe5e5b3a7547",
-                        "f0b636ce-505c-4339-a69c-2305352b6796",
-                        "46e7ed04-5916-4c10-8a05-fe510eda819a",
-                        "d49998ff-c873-41fd-bb44-f221f89b8f15"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "c2396f83-22e4-4a2d-8cce-a30feb533603"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "c23de226-536c-403d-a757-f4200cb1777b"
-                        }
-                    ]
-                },
-                {
-                    "process": "d1a9aae1-99dc-4b49-bee3-af685b7f013a",
-                    "inputs": [
-                        "a689172e-cae2-4e2c-b1d2-5aeff0a90171"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "a690df06-cc52-4346-a926-fe5e5b3a7547"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "3ec905f4-5950-4cfa-bd0b-86cc0370fd47"
-                        }
-                    ]
-                },
-                {
-                    "process": "a02a2a59-cdb4-4261-b220-b0cfebaec5ac",
-                    "inputs": [
-                        "597b4050-0778-4a81-b882-e1704ab0b6ad"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "a689172e-cae2-4e2c-b1d2-5aeff0a90171"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "ipsc_induction_protocol",
-                            "protocol_id": "97a30135-246f-4c0d-aef8-4e33183d1ff7"
-                        }
-                    ]
-                },
-                {
-                    "process": "01e52705-77de-4715-b35f-442aff9312be",
-                    "inputs": [
-                        "4934d9c3-753b-47bc-b2d5-468ce255a139"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "597b4050-0778-4a81-b882-e1704ab0b6ad"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "58a58315-2f03-4a36-9cea-dd306b609ba9",
-                    "inputs": [
-                        "37833da3-505d-4bb2-916e-26aa8985d183"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "f0b636ce-505c-4339-a69c-2305352b6796"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "3ec905f4-5950-4cfa-bd0b-86cc0370fd47"
-                        }
-                    ]
-                },
-                {
-                    "process": "56c911d5-6b99-486c-9ce7-141ee41528eb",
-                    "inputs": [
-                        "1fc181fe-60c6-4b94-85c1-1f227be60658"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "37833da3-505d-4bb2-916e-26aa8985d183"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "ipsc_induction_protocol",
-                            "protocol_id": "97a30135-246f-4c0d-aef8-4e33183d1ff7"
-                        }
-                    ]
-                },
-                {
-                    "process": "23fe1739-6bbe-4a86-be96-bd75f19f8375",
-                    "inputs": [
-                        "7c3a6d87-9f43-4de5-b47d-6fa78a897624"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "1fc181fe-60c6-4b94-85c1-1f227be60658"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "831dc734-9813-4c34-a163-16dd5b75d9a0",
-                    "inputs": [
-                        "d954547d-94bc-401d-bdff-ccd727251c74"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "46e7ed04-5916-4c10-8a05-fe510eda819a"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "3ec905f4-5950-4cfa-bd0b-86cc0370fd47"
-                        }
-                    ]
-                },
-                {
-                    "process": "d8f1d436-6bc3-4638-9801-8a9241996d28",
-                    "inputs": [
-                        "ad702cb9-3b40-4f8f-b9a5-331eeb153d9b"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "d954547d-94bc-401d-bdff-ccd727251c74"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "ipsc_induction_protocol",
-                            "protocol_id": "97a30135-246f-4c0d-aef8-4e33183d1ff7"
-                        }
-                    ]
-                },
-                {
-                    "process": "a9a39b30-8243-4d08-8f36-8f2e1275e8d0",
-                    "inputs": [
-                        "3322ea3a-30ea-4e6e-b187-18525de4ee3e"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "ad702cb9-3b40-4f8f-b9a5-331eeb153d9b"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "024c9f05-1743-4d66-83b7-134a31cd1c27",
-                    "inputs": [
-                        "95deef55-86e9-42be-9f82-3102b0d89dbe"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "d49998ff-c873-41fd-bb44-f221f89b8f15"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "3ec905f4-5950-4cfa-bd0b-86cc0370fd47"
-                        }
-                    ]
-                },
-                {
-                    "process": "50d53f80-5e54-4cda-97f0-5acb4d686d3e",
-                    "inputs": [
-                        "2e32e319-53d4-4e69-af0f-c43e2b15a94f"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "95deef55-86e9-42be-9f82-3102b0d89dbe"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "ipsc_induction_protocol",
-                            "protocol_id": "97a30135-246f-4c0d-aef8-4e33183d1ff7"
-                        }
-                    ]
-                },
-                {
-                    "process": "baa3a061-534c-4b6e-8c51-a11a8307f537",
-                    "inputs": [
-                        "872169f4-8479-4476-9646-20b3997e1f01"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "2e32e319-53d4-4e69-af0f-c43e2b15a94f"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.4/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.4",
+        "links": [
+            {
+                "process": "54438211-29fb-4e57-87f4-95412e5d8b15",
+                "inputs": [
+                    "c2396f83-22e4-4a2d-8cce-a30feb533603"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "9c49bbf2-cf62-4f94-9b9d-a3da42e2d52a",
+                    "ac93d656-4aa5-4f6c-b273-dc1d8be1934c",
+                    "5989ca50-45b5-4834-bfde-d290a8dfa97e"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "65ce5281-b07e-4b21-be8d-66ac5dea4d69"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "1547584e-d9e4-4519-a72a-91db0d0fec3c"
+                    }
+                ]
+            },
+            {
+                "process": "7d683bc4-6e59-4c7e-bbc8-5dad46fe2684",
+                "inputs": [
+                    "a690df06-cc52-4346-a926-fe5e5b3a7547",
+                    "f0b636ce-505c-4339-a69c-2305352b6796",
+                    "46e7ed04-5916-4c10-8a05-fe510eda819a",
+                    "d49998ff-c873-41fd-bb44-f221f89b8f15"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "c2396f83-22e4-4a2d-8cce-a30feb533603"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "c23de226-536c-403d-a757-f4200cb1777b"
+                    }
+                ]
+            },
+            {
+                "process": "d1a9aae1-99dc-4b49-bee3-af685b7f013a",
+                "inputs": [
+                    "a689172e-cae2-4e2c-b1d2-5aeff0a90171"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "a690df06-cc52-4346-a926-fe5e5b3a7547"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "differentiation_protocol",
+                        "protocol_id": "3ec905f4-5950-4cfa-bd0b-86cc0370fd47"
+                    }
+                ]
+            },
+            {
+                "process": "a02a2a59-cdb4-4261-b220-b0cfebaec5ac",
+                "inputs": [
+                    "597b4050-0778-4a81-b882-e1704ab0b6ad"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "a689172e-cae2-4e2c-b1d2-5aeff0a90171"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "ipsc_induction_protocol",
+                        "protocol_id": "97a30135-246f-4c0d-aef8-4e33183d1ff7"
+                    }
+                ]
+            },
+            {
+                "process": "01e52705-77de-4715-b35f-442aff9312be",
+                "inputs": [
+                    "4934d9c3-753b-47bc-b2d5-468ce255a139"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "597b4050-0778-4a81-b882-e1704ab0b6ad"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "58a58315-2f03-4a36-9cea-dd306b609ba9",
+                "inputs": [
+                    "37833da3-505d-4bb2-916e-26aa8985d183"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "f0b636ce-505c-4339-a69c-2305352b6796"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "differentiation_protocol",
+                        "protocol_id": "3ec905f4-5950-4cfa-bd0b-86cc0370fd47"
+                    }
+                ]
+            },
+            {
+                "process": "56c911d5-6b99-486c-9ce7-141ee41528eb",
+                "inputs": [
+                    "1fc181fe-60c6-4b94-85c1-1f227be60658"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "37833da3-505d-4bb2-916e-26aa8985d183"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "ipsc_induction_protocol",
+                        "protocol_id": "97a30135-246f-4c0d-aef8-4e33183d1ff7"
+                    }
+                ]
+            },
+            {
+                "process": "23fe1739-6bbe-4a86-be96-bd75f19f8375",
+                "inputs": [
+                    "7c3a6d87-9f43-4de5-b47d-6fa78a897624"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "1fc181fe-60c6-4b94-85c1-1f227be60658"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "831dc734-9813-4c34-a163-16dd5b75d9a0",
+                "inputs": [
+                    "d954547d-94bc-401d-bdff-ccd727251c74"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "46e7ed04-5916-4c10-8a05-fe510eda819a"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "differentiation_protocol",
+                        "protocol_id": "3ec905f4-5950-4cfa-bd0b-86cc0370fd47"
+                    }
+                ]
+            },
+            {
+                "process": "d8f1d436-6bc3-4638-9801-8a9241996d28",
+                "inputs": [
+                    "ad702cb9-3b40-4f8f-b9a5-331eeb153d9b"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "d954547d-94bc-401d-bdff-ccd727251c74"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "ipsc_induction_protocol",
+                        "protocol_id": "97a30135-246f-4c0d-aef8-4e33183d1ff7"
+                    }
+                ]
+            },
+            {
+                "process": "a9a39b30-8243-4d08-8f36-8f2e1275e8d0",
+                "inputs": [
+                    "3322ea3a-30ea-4e6e-b187-18525de4ee3e"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "ad702cb9-3b40-4f8f-b9a5-331eeb153d9b"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "024c9f05-1743-4d66-83b7-134a31cd1c27",
+                "inputs": [
+                    "95deef55-86e9-42be-9f82-3102b0d89dbe"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "d49998ff-c873-41fd-bb44-f221f89b8f15"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "differentiation_protocol",
+                        "protocol_id": "3ec905f4-5950-4cfa-bd0b-86cc0370fd47"
+                    }
+                ]
+            },
+            {
+                "process": "50d53f80-5e54-4cda-97f0-5acb4d686d3e",
+                "inputs": [
+                    "2e32e319-53d4-4e69-af0f-c43e2b15a94f"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "95deef55-86e9-42be-9f82-3102b0d89dbe"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "ipsc_induction_protocol",
+                        "protocol_id": "97a30135-246f-4c0d-aef8-4e33183d1ff7"
+                    }
+                ]
+            },
+            {
+                "process": "baa3a061-534c-4b6e-8c51-a11a8307f537",
+                "inputs": [
+                    "872169f4-8479-4476-9646-20b3997e1f01"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "2e32e319-53d4-4e69-af0f-c43e2b15a94f"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
index 816ed60ed..fa187ba7e 100644
--- a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
+++ b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
@@ -987,74 +987,74 @@
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.5",
-            "links": [
-                {
-                    "process": "a29d4d8a-e8bf-4e1a-aacc-eeea8f3b65d2",
-                    "inputs": [
-                        "eb27c398-f017-4ef1-acc8-3f51af87fe17"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "12484c33-24ec-4293-8f96-4cb1a43a6479",
-                        "f85b458b-b189-4ee7-939a-c905b70ae431",
-                        "18feeb7d-66ca-4ea4-a019-a10e5b762465"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "6ce5a9c7-b4f7-41e5-a182-21e85627feee"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "e01aa420-488b-4189-a8c8-98ada395ee91"
-                        }
-                    ]
-                },
-                {
-                    "process": "b6e09f03-0ddc-44ff-8cc9-7caf9eb70f57",
-                    "inputs": [
-                        "0a63e007-09d0-4330-989b-ca248f8b3c3c"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "eb27c398-f017-4ef1-acc8-3f51af87fe17"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "a3623f22-83e7-4207-b204-34041abb54e2"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "76f64d5b-fa01-4efe-ad4a-097d70311581"
-                        }
-                    ]
-                },
-                {
-                    "process": "b3cddf6f-65ee-4aa8-8682-60f00c55be73",
-                    "inputs": [
-                        "fa1bd656-7f7b-4288-84c6-d511232cfe95"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "0a63e007-09d0-4330-989b-ca248f8b3c3c"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "9a46c161-fb6e-4a4f-8c8d-a91a3c7b99c2"
-                        }
-                    ]
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.5",
+        "links": [
+            {
+                "process": "a29d4d8a-e8bf-4e1a-aacc-eeea8f3b65d2",
+                "inputs": [
+                    "eb27c398-f017-4ef1-acc8-3f51af87fe17"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "12484c33-24ec-4293-8f96-4cb1a43a6479",
+                    "f85b458b-b189-4ee7-939a-c905b70ae431",
+                    "18feeb7d-66ca-4ea4-a019-a10e5b762465"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "6ce5a9c7-b4f7-41e5-a182-21e85627feee"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "e01aa420-488b-4189-a8c8-98ada395ee91"
+                    }
+                ]
+            },
+            {
+                "process": "b6e09f03-0ddc-44ff-8cc9-7caf9eb70f57",
+                "inputs": [
+                    "0a63e007-09d0-4330-989b-ca248f8b3c3c"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "eb27c398-f017-4ef1-acc8-3f51af87fe17"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "a3623f22-83e7-4207-b204-34041abb54e2"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "76f64d5b-fa01-4efe-ad4a-097d70311581"
+                    }
+                ]
+            },
+            {
+                "process": "b3cddf6f-65ee-4aa8-8682-60f00c55be73",
+                "inputs": [
+                    "fa1bd656-7f7b-4288-84c6-d511232cfe95"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "0a63e007-09d0-4330-989b-ca248f8b3c3c"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "9a46c161-fb6e-4a4f-8c8d-a91a3c7b99c2"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
index 92c9521d6..66bf6d7b8 100644
--- a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
+++ b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
@@ -516,151 +516,151 @@
                 "updateDate": "2018-03-28T14:30:39.321Z",
                 "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
             }
-        },
-        "links.json": {
-            "links": [
-                {
-                    "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
-                    "source_type": "biomaterial",
-                    "destination_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "source_type": "dissociation_process",
-                    "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "source_type": "dissociation_process",
-                    "destination_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
-                    "source_type": "process",
-                    "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
-                    "source_type": "biomaterial",
-                    "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
-                    "source_type": "biomaterial",
-                    "destination_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
-                    "destination_type": "enrichment_process"
-                },
-                {
-                    "source_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
-                    "source_type": "enrichment_process",
-                    "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
-                    "source_type": "enrichment_process",
-                    "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
-                    "source_type": "process",
-                    "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
-                    "source_type": "biomaterial",
-                    "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
-                    "source_type": "biomaterial",
-                    "destination_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
-                    "destination_type": "enrichment_process"
-                },
-                {
-                    "source_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
-                    "source_type": "enrichment_process",
-                    "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
-                    "source_type": "enrichment_process",
-                    "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
-                    "source_type": "process",
-                    "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
-                    "source_type": "biomaterial",
-                    "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "603a818f-dbe7-466a-8241-58b9c1618846",
-                    "source_type": "biomaterial",
-                    "destination_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "destination_type": "library_preparation_process"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "aa662c76-d220-49f4-8316-f4af5820d60b",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "603a818f-dbe7-466a-8241-58b9c1618846",
-                    "source_type": "biomaterial",
-                    "destination_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
-                    "destination_type": "sequencing_process"
-                },
-                {
-                    "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
-                    "source_type": "sequencing_process",
-                    "destination_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
-                    "source_type": "sequencing_process",
-                    "destination_id": "aa662c76-d220-49f4-8316-f4af5820d60b",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
-                    "source_type": "sequencing_process",
-                    "destination_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9",
-                    "destination_type": "protocol"
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
-            "schema_version": "1.0.0",
-            "schema_type": "link_bundle"
         }
+    },
+    "links": {
+        "links": [
+            {
+                "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                "source_type": "biomaterial",
+                "destination_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "destination_type": "dissociation_process"
+            },
+            {
+                "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "source_type": "dissociation_process",
+                "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "source_type": "dissociation_process",
+                "destination_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                "source_type": "process",
+                "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
+                "source_type": "biomaterial",
+                "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                "source_type": "biomaterial",
+                "destination_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
+                "destination_type": "enrichment_process"
+            },
+            {
+                "source_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
+                "source_type": "enrichment_process",
+                "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
+                "source_type": "enrichment_process",
+                "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                "source_type": "process",
+                "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
+                "source_type": "biomaterial",
+                "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                "source_type": "biomaterial",
+                "destination_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
+                "destination_type": "enrichment_process"
+            },
+            {
+                "source_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
+                "source_type": "enrichment_process",
+                "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
+                "source_type": "enrichment_process",
+                "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                "source_type": "process",
+                "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
+                "source_type": "biomaterial",
+                "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                "source_type": "biomaterial",
+                "destination_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "destination_type": "library_preparation_process"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "aa662c76-d220-49f4-8316-f4af5820d60b",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                "source_type": "biomaterial",
+                "destination_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
+                "destination_type": "sequencing_process"
+            },
+            {
+                "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
+                "source_type": "sequencing_process",
+                "destination_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
+                "source_type": "sequencing_process",
+                "destination_id": "aa662c76-d220-49f4-8316-f4af5820d60b",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
+                "source_type": "sequencing_process",
+                "destination_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9",
+                "destination_type": "protocol"
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
+        "schema_version": "1.0.0",
+        "schema_type": "link_bundle"
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
index 015f5565f..9db2e962c 100644
--- a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
+++ b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
@@ -306,84 +306,84 @@
                 "submission_date": "2019-05-14T11:12:15.946Z",
                 "update_date": "2019-05-14T12:26:52.545Z"
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/2.0.0/links",
-            "schema_type": "link_bundle",
-            "schema_version": "2.0.0",
-            "links": [
-                {
-                    "link_type": "process_link",
-                    "process_id": "91f475ec-be51-4f1e-a904-74b10b7259f1",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "cell_suspension",
-                            "input_id": "01ba6be9-ed4b-4c6b-ae05-2e06aadc2019"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "61fd5348-92c5-446b-a57a-746330cebf76"
-                        }
-                    ],
-                    "protocols": []
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "e521d67d-c134-4dbd-9555-29e23f0463c5",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "74eb3cb5-918a-49fc-9e15-3ac49fd54caf"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "cell_suspension",
-                            "output_id": "01ba6be9-ed4b-4c6b-ae05-2e06aadc2019"
-                        }
-                    ],
-                    "protocols": []
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "453a352c-94fb-4d3b-b609-df1e7abf8c09",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "63818269-c4d9-429b-85a3-db39c0dd7fa0"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "74eb3cb5-918a-49fc-9e15-3ac49fd54caf"
-                        }
-                    ],
-                    "protocols": []
+        }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/2.0.0/links",
+        "schema_type": "link_bundle",
+        "schema_version": "2.0.0",
+        "links": [
+            {
+                "link_type": "process_link",
+                "process_id": "91f475ec-be51-4f1e-a904-74b10b7259f1",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "01ba6be9-ed4b-4c6b-ae05-2e06aadc2019"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "61fd5348-92c5-446b-a57a-746330cebf76"
+                    }
+                ],
+                "protocols": []
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "e521d67d-c134-4dbd-9555-29e23f0463c5",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "74eb3cb5-918a-49fc-9e15-3ac49fd54caf"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "01ba6be9-ed4b-4c6b-ae05-2e06aadc2019"
+                    }
+                ],
+                "protocols": []
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "453a352c-94fb-4d3b-b609-df1e7abf8c09",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "63818269-c4d9-429b-85a3-db39c0dd7fa0"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "74eb3cb5-918a-49fc-9e15-3ac49fd54caf"
+                    }
+                ],
+                "protocols": []
+            },
+            {
+                "link_type": "supplementary_file_link",
+                "entity": {
+                    "entity_type": "project",
+                    "entity_id": "8c3c290d-dfff-4553-8868-54ce45f4ba7f"
                 },
-                {
-                    "link_type": "supplementary_file_link",
-                    "entity": {
-                        "entity_type": "project",
-                        "entity_id": "8c3c290d-dfff-4553-8868-54ce45f4ba7f"
+                "files": [
+                    {
+                        "file_id": "e738a267-87fc-4070-abc7-b3be6442c6d0",
+                        "file_type": "supplementary_file"
                     },
-                    "files": [
-                        {
-                            "file_id": "e738a267-87fc-4070-abc7-b3be6442c6d0",
-                            "file_type": "supplementary_file"
-                        },
-                        {
-                            "file_id": "01a1d04b-05d0-4904-b627-68b0dc02bc17",
-                            "file_type": "supplementary_file"
-                        }
-                    ]
-                }
-            ]
-        }
+                    {
+                        "file_id": "01a1d04b-05d0-4904-b627-68b0dc02bc17",
+                        "file_type": "supplementary_file"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
index fa59f5ed9..48c7229c8 100644
--- a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
+++ b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
@@ -838,84 +838,84 @@
                 "submission_date": "2019-04-17T16:53:30.570Z",
                 "update_date": "2019-04-17T16:59:59.680Z"
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.5",
-            "links": [
-                {
-                    "process": "3d88118e-44df-4c1a-a364-bf92ff2ca0e6",
-                    "inputs": [
-                        "e4c205cd-746f-4665-8c29-149c6e109e9d"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "a31d51c9-7354-4c8c-91e6-a9d2a2e10616",
-                        "a2db643f-decd-426d-94db-13c3279ea80a"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "60085aee-e5a6-40ac-bda1-855c052550b5"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "9ccabcf3-7203-4f07-837f-6dde903d4cec"
-                        }
-                    ]
-                },
-                {
-                    "process": "2fbc1012-55ae-4fde-9069-fbf5376ca535",
-                    "inputs": [
-                        "961092cd-dcff-4b59-a0d2-ceeef0aece74"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "e4c205cd-746f-4665-8c29-149c6e109e9d"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "348b04e9-d131-4d45-b198-0c75300ee4a3"
-                        },
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "31b89ceb-0625-4f88-9623-85a18bbb84ee"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "958d38c4-fd0a-4352-9b1d-d95e28e2085e"
-                        }
-                    ]
-                },
-                {
-                    "process": "466050f5-213c-4554-939e-4bb8298130dd",
-                    "inputs": [
-                        "a72a2ac2-c91b-406a-968c-28c8e15a2eaf"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "961092cd-dcff-4b59-a0d2-ceeef0aece74"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "4276c1dd-50aa-4ffa-a618-dee757bff479",
-                    "inputs": [
-                        "6c6973d5-9b4a-426d-9d88-825b464500f8"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "a72a2ac2-c91b-406a-968c-28c8e15a2eaf"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.5",
+        "links": [
+            {
+                "process": "3d88118e-44df-4c1a-a364-bf92ff2ca0e6",
+                "inputs": [
+                    "e4c205cd-746f-4665-8c29-149c6e109e9d"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "a31d51c9-7354-4c8c-91e6-a9d2a2e10616",
+                    "a2db643f-decd-426d-94db-13c3279ea80a"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "60085aee-e5a6-40ac-bda1-855c052550b5"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "9ccabcf3-7203-4f07-837f-6dde903d4cec"
+                    }
+                ]
+            },
+            {
+                "process": "2fbc1012-55ae-4fde-9069-fbf5376ca535",
+                "inputs": [
+                    "961092cd-dcff-4b59-a0d2-ceeef0aece74"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "e4c205cd-746f-4665-8c29-149c6e109e9d"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "differentiation_protocol",
+                        "protocol_id": "348b04e9-d131-4d45-b198-0c75300ee4a3"
+                    },
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "31b89ceb-0625-4f88-9623-85a18bbb84ee"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "958d38c4-fd0a-4352-9b1d-d95e28e2085e"
+                    }
+                ]
+            },
+            {
+                "process": "466050f5-213c-4554-939e-4bb8298130dd",
+                "inputs": [
+                    "a72a2ac2-c91b-406a-968c-28c8e15a2eaf"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "961092cd-dcff-4b59-a0d2-ceeef0aece74"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "4276c1dd-50aa-4ffa-a618-dee757bff479",
+                "inputs": [
+                    "6c6973d5-9b4a-426d-9d88-825b464500f8"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "a72a2ac2-c91b-406a-968c-28c8e15a2eaf"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
index fbb9c6a02..c1b4fb447 100644
--- a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
+++ b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
@@ -2494,199 +2494,199 @@
                 "submission_date": "2019-01-23T10:34:00.619Z",
                 "update_date": "2019-01-23T11:05:44.002Z"
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.4/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.4",
-            "links": [
-                {
-                    "process": "d6c56c65-bed0-4d6e-bf89-7e0d71bd3026",
-                    "inputs": [
-                        "c15ee840-4702-45f7-bb19-693de19a742a",
-                        "5f5d9c84-3565-4398-886c-2e50ad4c3964"
-                    ],
-                    "input_type": "file",
-                    "outputs": [
-                        "b91aca7b-e71b-4014-ab09-5d87e52bc305",
-                        "34e92010-0e2d-49af-b4b7-bed7a2c9e490",
-                        "3db4d80f-cbd5-45da-9048-6fe8e2e4d0d2",
-                        "ed37a61e-4449-4bce-a774-7cbd732781c8",
-                        "b70e4907-383c-4466-a244-3e7ce9890dae",
-                        "7ee496ab-286c-4962-919a-70244090e315",
-                        "c15427d1-e5b7-4bee-91fe-d98b04dc6a01",
-                        "b11e96c4-2472-4317-b45b-5bc1c9b55704",
-                        "828d7e40-4f6b-42e1-8cd2-6ddccb5b0e6c",
-                        "6804b943-fda7-4e8f-bfba-23e368843e63",
-                        "aeb5aebe-9e45-4c9d-931a-883f8fa71225",
-                        "7c5a87c1-e3b6-42aa-8d68-0f534ded7d2d",
-                        "87bd704c-3d36-4620-bdf2-5ad28c5a3d56",
-                        "0aa4b2f3-b969-40d7-97f9-f33af0088915",
-                        "697a869d-079b-48d4-9a7d-c04cf05dd0a9",
-                        "6d928f58-2e83-46a0-84a2-d08744a42abd",
-                        "cc958050-fd69-4919-8529-6f91552ce0ea",
-                        "0a5730dc-eeeb-4f25-bcc7-24cb7d15ac01",
-                        "42fffad8-d47d-4da5-8318-45b0f5577c08",
-                        "2842a995-c205-4d80-959f-fcb9ff8719ee",
-                        "90d148ed-a6eb-44c3-a398-df29459943ff",
-                        "269a143b-a2c2-40cd-9394-41a13321581d",
-                        "1dda8255-de1c-4bfa-aa79-dbc501d3a112",
-                        "d76f404c-d294-49f2-bfd5-d475e08fa783",
-                        "3f672b26-ea2f-4e94-ba77-f463c3cb7c38",
-                        "4bc5b41c-9fea-4baa-9bf9-75fa4f4a9818",
-                        "3e44e8f9-e76d-4158-a7af-eeb9602cf8cc",
-                        "3fe1e9e8-1b0f-4683-a402-ae970b33f144",
-                        "e53c14f5-1a4f-44d6-9773-53faac32233b",
-                        "7a26e63d-fcf2-419a-a945-bca9e539480f",
-                        "644b261b-450e-453c-bb5e-0498a1cf5804",
-                        "b367129a-e83f-4a2b-9278-b5f7930ad457",
-                        "6d4785d0-bd42-4f98-8f7a-ab9ca8fcab39"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "analysis_protocol",
-                            "protocol_id": "bb17ee61-193e-4ae1-a014-4f1b1c19b8b7"
-                        }
-                    ]
-                },
-                {
-                    "process": "55faef19-0c09-41ef-b21c-ad25a89ea2e3",
-                    "inputs": [
-                        "9ea49dd1-7511-48f8-be12-237e3d0690c0"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "c15ee840-4702-45f7-bb19-693de19a742a",
-                        "5f5d9c84-3565-4398-886c-2e50ad4c3964"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "edda2708-1172-47f0-9c8b-b6771f463db1"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "46f58d61-c784-47fb-9c75-7af37871810e"
-                        }
-                    ]
-                },
-                {
-                    "process": "e84cac5b-1467-4055-a029-48d67a5505d6",
-                    "inputs": [
-                        "e7049663-aa57-4001-8bb4-870e341b4f0b"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "9ea49dd1-7511-48f8-be12-237e3d0690c0"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "dcfe8429-af02-491e-96e9-4ac0569cd5d1"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "55dd1cfc-cc9c-4a03-aa43-2cb92b843253"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "3d2707fa-83ad-472b-8282-7b6191f96bc2"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "88bd21a4-8d6c-48ce-ab57-8b5e0b582cca"
-                        }
-                    ]
-                },
-                {
-                    "process": "832b39e3-ebba-4686-a724-52babb96056f",
-                    "inputs": [
-                        "a879fffa-3b98-4204-ae5a-603180007ca0"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "e7049663-aa57-4001-8bb4-870e341b4f0b"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "477b201f-67f0-4f97-86d5-de32a7afc267"
-                        }
-                    ]
-                },
-                {
-                    "process": "55faef19-0c09-41ef-b21c-ad25a89ea2e3",
-                    "inputs": [
-                        "9ea49dd1-7511-48f8-be12-237e3d0690c0"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "c15ee840-4702-45f7-bb19-693de19a742a",
-                        "5f5d9c84-3565-4398-886c-2e50ad4c3964"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "edda2708-1172-47f0-9c8b-b6771f463db1"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "46f58d61-c784-47fb-9c75-7af37871810e"
-                        }
-                    ]
-                },
-                {
-                    "process": "e84cac5b-1467-4055-a029-48d67a5505d6",
-                    "inputs": [
-                        "e7049663-aa57-4001-8bb4-870e341b4f0b"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "9ea49dd1-7511-48f8-be12-237e3d0690c0"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "dcfe8429-af02-491e-96e9-4ac0569cd5d1"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "55dd1cfc-cc9c-4a03-aa43-2cb92b843253"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "3d2707fa-83ad-472b-8282-7b6191f96bc2"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "88bd21a4-8d6c-48ce-ab57-8b5e0b582cca"
-                        }
-                    ]
-                },
-                {
-                    "process": "832b39e3-ebba-4686-a724-52babb96056f",
-                    "inputs": [
-                        "a879fffa-3b98-4204-ae5a-603180007ca0"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "e7049663-aa57-4001-8bb4-870e341b4f0b"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "477b201f-67f0-4f97-86d5-de32a7afc267"
-                        }
-                    ]
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.4/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.4",
+        "links": [
+            {
+                "process": "d6c56c65-bed0-4d6e-bf89-7e0d71bd3026",
+                "inputs": [
+                    "c15ee840-4702-45f7-bb19-693de19a742a",
+                    "5f5d9c84-3565-4398-886c-2e50ad4c3964"
+                ],
+                "input_type": "file",
+                "outputs": [
+                    "b91aca7b-e71b-4014-ab09-5d87e52bc305",
+                    "34e92010-0e2d-49af-b4b7-bed7a2c9e490",
+                    "3db4d80f-cbd5-45da-9048-6fe8e2e4d0d2",
+                    "ed37a61e-4449-4bce-a774-7cbd732781c8",
+                    "b70e4907-383c-4466-a244-3e7ce9890dae",
+                    "7ee496ab-286c-4962-919a-70244090e315",
+                    "c15427d1-e5b7-4bee-91fe-d98b04dc6a01",
+                    "b11e96c4-2472-4317-b45b-5bc1c9b55704",
+                    "828d7e40-4f6b-42e1-8cd2-6ddccb5b0e6c",
+                    "6804b943-fda7-4e8f-bfba-23e368843e63",
+                    "aeb5aebe-9e45-4c9d-931a-883f8fa71225",
+                    "7c5a87c1-e3b6-42aa-8d68-0f534ded7d2d",
+                    "87bd704c-3d36-4620-bdf2-5ad28c5a3d56",
+                    "0aa4b2f3-b969-40d7-97f9-f33af0088915",
+                    "697a869d-079b-48d4-9a7d-c04cf05dd0a9",
+                    "6d928f58-2e83-46a0-84a2-d08744a42abd",
+                    "cc958050-fd69-4919-8529-6f91552ce0ea",
+                    "0a5730dc-eeeb-4f25-bcc7-24cb7d15ac01",
+                    "42fffad8-d47d-4da5-8318-45b0f5577c08",
+                    "2842a995-c205-4d80-959f-fcb9ff8719ee",
+                    "90d148ed-a6eb-44c3-a398-df29459943ff",
+                    "269a143b-a2c2-40cd-9394-41a13321581d",
+                    "1dda8255-de1c-4bfa-aa79-dbc501d3a112",
+                    "d76f404c-d294-49f2-bfd5-d475e08fa783",
+                    "3f672b26-ea2f-4e94-ba77-f463c3cb7c38",
+                    "4bc5b41c-9fea-4baa-9bf9-75fa4f4a9818",
+                    "3e44e8f9-e76d-4158-a7af-eeb9602cf8cc",
+                    "3fe1e9e8-1b0f-4683-a402-ae970b33f144",
+                    "e53c14f5-1a4f-44d6-9773-53faac32233b",
+                    "7a26e63d-fcf2-419a-a945-bca9e539480f",
+                    "644b261b-450e-453c-bb5e-0498a1cf5804",
+                    "b367129a-e83f-4a2b-9278-b5f7930ad457",
+                    "6d4785d0-bd42-4f98-8f7a-ab9ca8fcab39"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "analysis_protocol",
+                        "protocol_id": "bb17ee61-193e-4ae1-a014-4f1b1c19b8b7"
+                    }
+                ]
+            },
+            {
+                "process": "55faef19-0c09-41ef-b21c-ad25a89ea2e3",
+                "inputs": [
+                    "9ea49dd1-7511-48f8-be12-237e3d0690c0"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "c15ee840-4702-45f7-bb19-693de19a742a",
+                    "5f5d9c84-3565-4398-886c-2e50ad4c3964"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "edda2708-1172-47f0-9c8b-b6771f463db1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "46f58d61-c784-47fb-9c75-7af37871810e"
+                    }
+                ]
+            },
+            {
+                "process": "e84cac5b-1467-4055-a029-48d67a5505d6",
+                "inputs": [
+                    "e7049663-aa57-4001-8bb4-870e341b4f0b"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "9ea49dd1-7511-48f8-be12-237e3d0690c0"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "dcfe8429-af02-491e-96e9-4ac0569cd5d1"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "55dd1cfc-cc9c-4a03-aa43-2cb92b843253"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "3d2707fa-83ad-472b-8282-7b6191f96bc2"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "88bd21a4-8d6c-48ce-ab57-8b5e0b582cca"
+                    }
+                ]
+            },
+            {
+                "process": "832b39e3-ebba-4686-a724-52babb96056f",
+                "inputs": [
+                    "a879fffa-3b98-4204-ae5a-603180007ca0"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "e7049663-aa57-4001-8bb4-870e341b4f0b"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "477b201f-67f0-4f97-86d5-de32a7afc267"
+                    }
+                ]
+            },
+            {
+                "process": "55faef19-0c09-41ef-b21c-ad25a89ea2e3",
+                "inputs": [
+                    "9ea49dd1-7511-48f8-be12-237e3d0690c0"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "c15ee840-4702-45f7-bb19-693de19a742a",
+                    "5f5d9c84-3565-4398-886c-2e50ad4c3964"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "edda2708-1172-47f0-9c8b-b6771f463db1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "46f58d61-c784-47fb-9c75-7af37871810e"
+                    }
+                ]
+            },
+            {
+                "process": "e84cac5b-1467-4055-a029-48d67a5505d6",
+                "inputs": [
+                    "e7049663-aa57-4001-8bb4-870e341b4f0b"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "9ea49dd1-7511-48f8-be12-237e3d0690c0"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "dcfe8429-af02-491e-96e9-4ac0569cd5d1"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "55dd1cfc-cc9c-4a03-aa43-2cb92b843253"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "3d2707fa-83ad-472b-8282-7b6191f96bc2"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "88bd21a4-8d6c-48ce-ab57-8b5e0b582cca"
+                    }
+                ]
+            },
+            {
+                "process": "832b39e3-ebba-4686-a724-52babb96056f",
+                "inputs": [
+                    "a879fffa-3b98-4204-ae5a-603180007ca0"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "e7049663-aa57-4001-8bb4-870e341b4f0b"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "477b201f-67f0-4f97-86d5-de32a7afc267"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
index 00eb2a89c..89a5d0c41 100644
--- a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
+++ b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
@@ -585,76 +585,76 @@
                 "submission_date": "2018-10-07T11:58:47.999Z",
                 "update_date": "2018-10-07T12:05:17.018Z"
             }
-        },
-        "links.json": {
-            "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.3/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.3",
-            "links": [
-                {
-                    "process": "18d49b08-d095-4371-bb34-151037f9f461",
-                    "inputs": [
-                        "ef97eef1-a436-4462-a152-1a2b86ee8831"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "f3d5c7cb-7ab4-4903-8e0e-dc942121fe27"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "5f82b9c4-f3d7-410c-b843-0e5cdec9efa5"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "d678165b-2753-4393-bf3b-5e2a09ba892c"
-                        }
-                    ]
-                },
-                {
-                    "process": "d13a5a85-b8c7-4a07-9c0c-9180bd0a78eb",
-                    "inputs": [
-                        "80cb479b-dcb4-4dbb-a75d-0249a964bb70"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "ef97eef1-a436-4462-a152-1a2b86ee8831"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "920078d0-b17e-4f23-8cf6-0674b19e7bec"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "644c5f2d-33c8-4bf4-b411-b2dbec8b8227"
-                        }
-                    ]
-                },
-                {
-                    "process": "5a15ed38-5e37-44ff-ba35-0d17bb8564bd",
-                    "inputs": [
-                        "6c992ba4-c132-4dd3-840e-13cf3f38243e"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "80cb479b-dcb4-4dbb-a75d-0249a964bb70"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "403b586f-fd8d-45f2-a431-4bb6cc33d7d4"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "9ab53e6a-464e-44b1-aa24-12daca989969"
-                        }
-                    ]
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.3/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.3",
+        "links": [
+            {
+                "process": "18d49b08-d095-4371-bb34-151037f9f461",
+                "inputs": [
+                    "ef97eef1-a436-4462-a152-1a2b86ee8831"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "f3d5c7cb-7ab4-4903-8e0e-dc942121fe27"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "5f82b9c4-f3d7-410c-b843-0e5cdec9efa5"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "d678165b-2753-4393-bf3b-5e2a09ba892c"
+                    }
+                ]
+            },
+            {
+                "process": "d13a5a85-b8c7-4a07-9c0c-9180bd0a78eb",
+                "inputs": [
+                    "80cb479b-dcb4-4dbb-a75d-0249a964bb70"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "ef97eef1-a436-4462-a152-1a2b86ee8831"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "920078d0-b17e-4f23-8cf6-0674b19e7bec"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "644c5f2d-33c8-4bf4-b411-b2dbec8b8227"
+                    }
+                ]
+            },
+            {
+                "process": "5a15ed38-5e37-44ff-ba35-0d17bb8564bd",
+                "inputs": [
+                    "6c992ba4-c132-4dd3-840e-13cf3f38243e"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "80cb479b-dcb4-4dbb-a75d-0249a964bb70"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "403b586f-fd8d-45f2-a431-4bb6cc33d7d4"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "9ab53e6a-464e-44b1-aa24-12daca989969"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
index 67fe8541e..b127a2a0d 100644
--- a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
+++ b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
@@ -422,68 +422,68 @@
                 "submission_date": "2018-09-05T18:24:06.058Z",
                 "update_date": "2018-09-05T18:24:09.861Z"
             }
-        },
-        "links.json": {
-            "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.1/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.1",
-            "links": [
-                {
-                    "process": "bf7360ae-511e-4803-821e-c03167107588",
-                    "inputs": [
-                        "a31a0e93-5be4-44b8-b152-9e25b066e1e5"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "20474552-c0a3-471e-8fa0-d3c5aa05c017",
-                        "177a9d2c-99d4-4fb6-aab7-5869923e9d6a"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "f77e65be-ca7a-4711-a7a9-701ad372901a"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "9d3c0c92-2716-410b-85c6-963a29c24fe0"
-                        }
-                    ]
-                },
-                {
-                    "process": "b78f4279-9c6f-49da-890f-98499d8fb84a",
-                    "inputs": [
-                        "e964f81f-54d9-4600-a9e9-981b1f1a6ca2"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "a31a0e93-5be4-44b8-b152-9e25b066e1e5"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "d08422cf-7d04-46cd-9452-394bb2864ba7"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "f3304cfe-c133-444c-a2db-92294d3f6a4d"
-                        }
-                    ]
-                },
-                {
-                    "process": "6284381f-de72-4015-ae51-fa17e13677f8",
-                    "inputs": [
-                        "c6001597-990c-4753-80bb-c5a01c9dda0d"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "e964f81f-54d9-4600-a9e9-981b1f1a6ca2"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.1/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.1",
+        "links": [
+            {
+                "process": "bf7360ae-511e-4803-821e-c03167107588",
+                "inputs": [
+                    "a31a0e93-5be4-44b8-b152-9e25b066e1e5"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "20474552-c0a3-471e-8fa0-d3c5aa05c017",
+                    "177a9d2c-99d4-4fb6-aab7-5869923e9d6a"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "f77e65be-ca7a-4711-a7a9-701ad372901a"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "9d3c0c92-2716-410b-85c6-963a29c24fe0"
+                    }
+                ]
+            },
+            {
+                "process": "b78f4279-9c6f-49da-890f-98499d8fb84a",
+                "inputs": [
+                    "e964f81f-54d9-4600-a9e9-981b1f1a6ca2"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "a31a0e93-5be4-44b8-b152-9e25b066e1e5"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "d08422cf-7d04-46cd-9452-394bb2864ba7"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "f3304cfe-c133-444c-a2db-92294d3f6a4d"
+                    }
+                ]
+            },
+            {
+                "process": "6284381f-de72-4015-ae51-fa17e13677f8",
+                "inputs": [
+                    "c6001597-990c-4753-80bb-c5a01c9dda0d"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "e964f81f-54d9-4600-a9e9-981b1f1a6ca2"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
index f0ef040f7..c8824d066 100644
--- a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
+++ b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
@@ -11681,290 +11681,290 @@
                 "submission_date": "2019-04-03T10:13:42.326Z",
                 "update_date": "2019-04-03T10:13:53.834Z"
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.staging.data.humancellatlas.org/system/1.1.5/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.5",
-            "links": [
-                {
-                    "process": "da265acd-5601-49c5-855e-d792d51b4042",
-                    "inputs": [
-                        "87f58f88-ef8b-4323-bd19-cde1a2497b59"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "6baa3aff-b2a5-4e49-82f7-25c108a6107a",
-                        "06dcfc33-21da-485f-8e50-49d294713a9e",
-                        "404dd50b-4bc9-4c82-8c18-f53c68eed2fc",
-                        "5ceb5dc3-9194-494a-b1df-42bb75ab1a04",
-                        "76e52f76-ede7-4088-b7f6-d6e5f6152292",
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+                    "44cf15ec-3d4e-4698-bb14-107c34891191",
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+                    "bc60bbd4-8b09-425c-b507-9da24a84f412",
+                    "1f054ccf-f8dd-4127-a6f8-c577d7dd93dc",
+                    "9954cb4b-b0a4-4479-b31d-0bee1e75d9c7",
+                    "5f67c32c-a154-4620-8603-0b64979b04a4",
+                    "7d5bffb2-8bf9-4366-a8b2-762ebb4d6c5d",
+                    "dcee6df0-9e87-4935-8873-f8d30d449d76",
+                    "7d6bdde6-523f-46cb-bed5-d6cfa8fea80c",
+                    "e6d00b0c-3641-4ec4-a553-8fd742193dba",
+                    "e5034863-0528-4f55-be95-c8501c29f9fe",
+                    "cc61b14a-59d9-477b-8cb1-43c4ee4cf434",
+                    "33d332c9-aefe-4db5-8830-b8daddaed0d2",
+                    "bb3b6fc7-0902-432d-bad1-6b3f61951314",
+                    "2b734e88-3a33-4c73-92bb-82e0b8f8c13b"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "imaging_protocol",
+                        "protocol_id": "96ecb94d-e848-4d7b-8df9-f19af6ab17b8"
+                    }
+                ]
+            },
+            {
+                "process": "07acb7d0-3f1c-47f7-9ef9-851c4f1caaec",
+                "inputs": [
+                    "edd1d525-a6ae-4658-a6bf-6c31d7ab6948"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "87f58f88-ef8b-4323-bd19-cde1a2497b59"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "imaging_preparation_protocol",
+                        "protocol_id": "a6d431b0-4373-4eaf-a3af-8c3fe461ab38"
+                    }
+                ]
+            },
+            {
+                "process": "fee8a188-5783-44cd-a1c1-ed9d5d7c32a9",
+                "inputs": [
+                    "6cb9fc09-7755-4a35-b6b1-0d6fe696b2d4"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "edd1d525-a6ae-4658-a6bf-6c31d7ab6948"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "caf94c25-8327-4379-b88e-2a6642cd7513"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
index f1be1bff2..ee4eba07a 100644
--- a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
+++ b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
@@ -705,74 +705,74 @@
                 "submission_date": "2019-03-17T22:00:57.743Z",
                 "update_date": "2019-03-17T22:01:03.254Z"
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.staging.data.humancellatlas.org/system/1.1.5/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.5",
-            "links": [
-                {
-                    "process": "8a0879df-13e0-4dce-9776-20fb259796e9",
-                    "inputs": [
-                        "74a06f8b-dff1-44d2-b1a6-99e3d14b69d1"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "6380c3bc-8bc3-459b-aea3-05dd6c0842ef",
-                        "ceb4dfaa-ecaf-4757-ae54-9d83707f66cc",
-                        "5201d410-d789-4df6-b3fd-9edac998e5f3"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "aa7e9a08-2a0c-4575-a9a9-13cab4e96e73"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "4bc436f7-e429-4355-8d6e-853d8e639b37"
-                        }
-                    ]
-                },
-                {
-                    "process": "b2e86d49-6874-4522-a68c-43166e858bdd",
-                    "inputs": [
-                        "f3531ee2-d408-4075-b63e-0d0e2b01116c"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "74a06f8b-dff1-44d2-b1a6-99e3d14b69d1"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "1e9abdf3-54da-4c73-9e57-1297ceb39399"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "df679627-ccb6-426d-a709-c259db607d84"
-                        }
-                    ]
-                },
-                {
-                    "process": "b147df84-443b-4dd2-8327-7ea42adcd151",
-                    "inputs": [
-                        "20db3238-9ce6-4820-8495-6753e4147d51"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "f3531ee2-d408-4075-b63e-0d0e2b01116c"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "c3dabd8c-6f32-4c0b-a13b-11bb71cc95de"
-                        }
-                    ]
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "https://schema.staging.data.humancellatlas.org/system/1.1.5/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.5",
+        "links": [
+            {
+                "process": "8a0879df-13e0-4dce-9776-20fb259796e9",
+                "inputs": [
+                    "74a06f8b-dff1-44d2-b1a6-99e3d14b69d1"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "6380c3bc-8bc3-459b-aea3-05dd6c0842ef",
+                    "ceb4dfaa-ecaf-4757-ae54-9d83707f66cc",
+                    "5201d410-d789-4df6-b3fd-9edac998e5f3"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "aa7e9a08-2a0c-4575-a9a9-13cab4e96e73"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4bc436f7-e429-4355-8d6e-853d8e639b37"
+                    }
+                ]
+            },
+            {
+                "process": "b2e86d49-6874-4522-a68c-43166e858bdd",
+                "inputs": [
+                    "f3531ee2-d408-4075-b63e-0d0e2b01116c"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "74a06f8b-dff1-44d2-b1a6-99e3d14b69d1"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "1e9abdf3-54da-4c73-9e57-1297ceb39399"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "df679627-ccb6-426d-a709-c259db607d84"
+                    }
+                ]
+            },
+            {
+                "process": "b147df84-443b-4dd2-8327-7ea42adcd151",
+                "inputs": [
+                    "20db3238-9ce6-4820-8495-6753e4147d51"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "f3531ee2-d408-4075-b63e-0d0e2b01116c"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "c3dabd8c-6f32-4c0b-a13b-11bb71cc95de"
+                    }
+                ]
+            }
+        ]
     }
-}
+}
\ No newline at end of file
diff --git a/test/hca_metadata_api/test.py b/test/hca_metadata_api/test.py
index 4e696a1af..2dd4cfbf5 100644
--- a/test/hca_metadata_api/test.py
+++ b/test/hca_metadata_api/test.py
@@ -144,19 +144,20 @@ def _test_example_bundle(self, directory, **kwargs):
         uuid = 'b2216048-7eaa-45f4-8077-5a3fb4204953'
         version = '2018-08-03T082009.272868Z'
         canning_directory = os.path.join('examples', directory)
-        manifest, metadata_files = self._canned_bundle(canning_directory, uuid, version)
+        manifest, metadata_files, links = self._canned_bundle(canning_directory, uuid, version)
         self.assertIsNotNone(manifest)
         self._assert_bundle(uuid=uuid,
                             version=version,
                             manifest=manifest,
                             metadata_files=metadata_files,
+                            links=links,
                             **kwargs)
 
     def _canned_bundle_path(self, directory, uuid, version):
         name = f'{uuid}.{version}.json'
         return os.path.join(os.path.dirname(__file__), 'cans', directory, name)
 
-    def _can_bundle(self, directory, uuid, version, manifest, metadata_files):  # pragma: no cover
+    def _can_bundle(self, directory, uuid, version, manifest, metadata_files, links):  # pragma: no cover
         """
         Save a bundle's manifest & metadata files to a local directory
         """
@@ -165,7 +166,8 @@ def _can_bundle(self, directory, uuid, version, manifest, metadata_files):  # pr
         with atomic_write(path, overwrite=True) as f:
             json.dump({
                 'manifest': manifest,
-                'metadata': metadata_files
+                'metadata': metadata_files,
+                'links': links
             }, f)
 
     def _canned_bundle(self, directory, uuid, version):
@@ -175,7 +177,7 @@ def _canned_bundle(self, directory, uuid, version):
         dir_path = self._canned_bundle_path(directory, uuid, version)
         with open(dir_path) as f:
             bundle = json.load(f)
-        return bundle['manifest'], bundle['metadata']
+        return bundle['manifest'], bundle['metadata'], bundle['links']
 
     def test_v5_bundle(self):
         """
@@ -340,8 +342,8 @@ def test_file_core_bundle(self):
     def test_sequencing_process_paired_end(self):
         uuid = '6b498499-c5b4-452f-9ff9-2318dbb86000'
         version = '2019-01-03T163633.780215Z'
-        manifest, metadata_files = self._canned_bundle('prod', uuid, version)
-        bundle = Bundle(uuid, version, manifest, metadata_files)
+        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
+        bundle = Bundle(uuid, version, manifest, metadata_files, links)
         sequencing_protocols = [p for p in bundle.protocols.values() if isinstance(p, SequencingProtocol)]
         self.assertEqual(len(sequencing_protocols), 1)
         self.assertEqual(sequencing_protocols[0].paired_end, True)
@@ -353,15 +355,16 @@ def _test_bundle(self,
                      **assertion_kwargs
                      ) -> Bundle:
 
-        manifest, metadata_files = self._canned_bundle(deployment, uuid, version)
+        manifest, metadata_files, links = self._canned_bundle(deployment, uuid, version)
 
         return self._assert_bundle(uuid=uuid,
                                    version=version,
                                    manifest=manifest,
                                    metadata_files=metadata_files,
+                                   links=links,
                                    **assertion_kwargs)
 
-    def _assert_bundle(self, uuid, version, manifest, metadata_files,
+    def _assert_bundle(self, uuid, version, manifest, metadata_files, links,
                        age_range=None,
                        diseases=frozenset({None}),
                        project_roles=frozenset({None}),
@@ -378,7 +381,7 @@ def _assert_bundle(self, uuid, version, manifest, metadata_files,
                        slice_thickness=None,
                        ncbi_taxon_ids=None,
                        content_description=None) -> Bundle:
-        bundle = Bundle(uuid, version, manifest, metadata_files)
+        bundle = Bundle(uuid, version, manifest, metadata_files, links)
 
         # Every data file's manifest entry should be referenced by a metadata
         # entity that describes the data file. id() is used to work around the
@@ -514,8 +517,8 @@ def test_canned_staging_area(self):
     def test_analysis_protocol(self):
         uuid = 'ffee7f29-5c38-461a-8771-a68e20ec4a2e'
         version = '2019-02-02T065454.662896Z'
-        manifest, metadata_files = self._canned_bundle('prod', uuid, version)
-        bundle = Bundle(uuid, version, manifest, metadata_files)
+        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
+        bundle = Bundle(uuid, version, manifest, metadata_files, links)
         analysis_protocols = [p for p in bundle.protocols.values() if isinstance(p, AnalysisProtocol)]
         self.assertEqual(len(analysis_protocols), 1)
         self.assertEqual(str(analysis_protocols[0].document_id), 'bb17ee61-193e-4ae1-a014-4f1b1c19b8b7')
@@ -525,8 +528,8 @@ def test_analysis_protocol(self):
     def test_imaging_protocol(self):
         uuid = '94f2ba52-30c8-4de0-a78e-f95a3f8deb9c'
         version = '2019-04-03T103426.471000Z'
-        manifest, metadata_files = self._canned_bundle('staging', uuid, version)
-        bundle = Bundle(uuid, version, manifest, metadata_files)
+        manifest, metadata_files, links = self._canned_bundle('staging', uuid, version)
+        bundle = Bundle(uuid, version, manifest, metadata_files, links)
         imaging_protocol = one(p for p in bundle.protocols.values() if isinstance(p, ImagingProtocol))
         self.assertEqual(len(imaging_protocol.probe), 240)
         assay_types = {probe.assay_type for probe in imaging_protocol.probe}
@@ -535,8 +538,8 @@ def test_imaging_protocol(self):
     def test_cell_line(self):
         uuid = 'ffee3a9b-14de-4dda-980f-c08092b2dabe'
         version = '2019-04-17T175706.867000Z'
-        manifest, metadata_files = self._canned_bundle('prod', uuid, version)
-        bundle = Bundle(uuid, version, manifest, metadata_files)
+        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
+        bundle = Bundle(uuid, version, manifest, metadata_files, links)
         cell_lines = [cl for cl in bundle.biomaterials.values() if isinstance(cl, CellLine)]
         self.assertEqual(len(cell_lines), 1)
         self.assertEqual(str(cell_lines[0].document_id), '961092cd-dcff-4b59-a0d2-ceeef0aece74')
@@ -553,8 +556,8 @@ def test_links_json_v2_0_0(self):
         """
         uuid = 'cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439'
         version = '2019-05-15T222432.561000Z'
-        manifest, metadata_files = self._canned_bundle('prod', uuid, version)
-        bundle = Bundle(uuid, version, manifest, metadata_files)
+        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
+        bundle = Bundle(uuid, version, manifest, metadata_files, links)
         for expected_count, link_type in [(6, 'process_link'), (2, 'supplementary_file_link')]:
             actual_count = sum(1 for link in bundle.links if link.link_type == link_type)
             self.assertEqual(expected_count, actual_count)
@@ -569,10 +572,10 @@ def test_links_json_v2_0_0(self):
     def test_project_fields(self):
         uuid = '68bdc676-c442-4581-923e-319c1c2d9018'
         version = '2018-10-07T130111.835234Z'
-        manifest, metadata_files = self._canned_bundle('staging', uuid, version)
+        manifest, metadata_files, links = self._canned_bundle('staging', uuid, version)
 
         def assert_bundle():
-            bundle = Bundle(uuid, version, manifest, metadata_files)
+            bundle = Bundle(uuid, version, manifest, metadata_files, links)
             project = bundle.projects[UUID('519b58ef-6462-4ed3-8c0d-375b54f53c31')]
             self.assertEqual(len(project.publications), 1)
             publication = project.publications.pop()
@@ -603,10 +606,10 @@ def assert_bundle():
     def test_project_contact(self):
         uuid = '6b498499-c5b4-452f-9ff9-2318dbb86000'
         version = '2019-01-03T163633.780215Z'
-        manifest, metadata_files = self._canned_bundle('prod', uuid, version)
+        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
 
         def assert_bundle():
-            bundle = Bundle(uuid, version, manifest, metadata_files)
+            bundle = Bundle(uuid, version, manifest, metadata_files, links)
             project = bundle.projects[UUID('d96c2451-6e22-441f-a3e6-70fd0878bb1b')]
             self.assertEqual(len(project.contributors), 5)
             expected_names = {
@@ -630,10 +633,10 @@ def assert_bundle():
     def test_file_format(self):
         uuid = '6b498499-c5b4-452f-9ff9-2318dbb86000'
         version = '2019-01-03T163633.780215Z'
-        manifest, metadata_files = self._canned_bundle('prod', uuid, version)
+        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
 
         def assert_bundle():
-            bundle = Bundle(uuid, version, manifest, metadata_files)
+            bundle = Bundle(uuid, version, manifest, metadata_files, links)
             self.assertEqual(len(bundle.files), 6)
             for file in bundle.files.values():
                 if isinstance(file, SequenceFile):
@@ -654,10 +657,10 @@ def assert_bundle():
     def test_link_destination_type(self):
         uuid = '6b498499-c5b4-452f-9ff9-2318dbb86000'
         version = '2019-01-03T163633.780215Z'
-        manifest, metadata_files = self._canned_bundle('prod', uuid, version)
+        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
 
         def assert_bundle():
-            bundle = Bundle(uuid, version, manifest, metadata_files)
+            bundle = Bundle(uuid, version, manifest, metadata_files, links)
             destination_types = {link.destination_type for link in bundle.links}
             expected_types = {
                 'library_preparation_protocol',
@@ -673,7 +676,7 @@ def assert_bundle():
 
         assert_bundle()
 
-        for link in metadata_files['links.json']['links']:
+        for link in links['links']:
             for protocol in link['protocols']:
                 self._rename_keys(protocol, type='protocol_type')
 
@@ -698,7 +701,8 @@ def test_missing_mandatory_checksums(self):
                                **case
                            }
                        ],
-                       metadata_files={})
+                       metadata_files={},
+                       links_json={})
             self.assertEqual(cm.exception.args[0], 'Property cannot be absent or None')
             checksums.append(cm.exception.args[1])
         self.assertEqual(['crc32c', 'crc32c', 'sha256', 'sha256'], checksums)
@@ -706,7 +710,7 @@ def test_missing_mandatory_checksums(self):
     def test_name_substitution(self):
         uuid = 'ffee7f29-5c38-461a-8771-a68e20ec4a2e'
         version = '2019-02-02T065454.662896Z'
-        manifest, metadata_files = self._canned_bundle('prod', uuid, version)
+        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
 
         files_before = [f['name'] for f in manifest]
         with_bang_before = set(f for f in files_before if '!' in f)
@@ -732,7 +736,7 @@ def test_name_substitution(self):
         with_slash_before = set(f for f in files_before if '/' in f)
         self.assertEqual(set(), with_slash_before)
 
-        bundle = Bundle(uuid, version, manifest, metadata_files)
+        bundle = Bundle(uuid, version, manifest, metadata_files, links)
 
         expected_slash_after = set(f1.replace('!', '/') for f1 in with_bang_before)
         entity_json_file_names = set(e.json['file_core']['file_name']
diff --git a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
index 6a577e48d..747dabfc9 100644
--- a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
+++ b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
@@ -1048,652 +1048,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "schema_type": "links",
-            "schema_version": "3.0.0",
-            "describedBy": "https://schema.humancellatlas.org/system/3.0.0/links",
-            "links": [
-                {
-                    "inputs": [
-                        {
-                            "input_id": "d90280cc-a294-57de-b350-5234a5278c19",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "a7915c55-1d80-5724-9c81-6dd0a9130361",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "f51568e8-b84c-504b-82f0-3ad5975d4bcb",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "759bad57-b725-5346-b3ff-9fb80b27cfe7",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "bc111cd3-bf54-57ce-8af1-88f5997a0a9d",
-                            "input_type": "analysis_file"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "fec17064-9014-50b0-9e1a-dfaef2fbb4fc",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "c8430132-0f12-43ec-8b8d-bbcfcd401dab",
-                    "process_type": "analysis_process",
-                    "protocols": [
-                        {
-                            "protocol_id": "432a7422-59b5-5c46-8983-a7953f196781",
-                            "protocol_type": "analysis_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "a7b21a25-e76e-420d-8892-538062bfefbf",
-                            "input_type": "sequence_file"
-                        },
-                        {
-                            "input_id": "15f64718-69cf-462c-9704-e8a1f54c27c8",
-                            "input_type": "sequence_file"
-                        },
-                        {
-                            "input_id": "799f314f-7c6c-4981-be36-8e1310bf38e6",
-                            "input_type": "sequence_file"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "759bad57-b725-5346-b3ff-9fb80b27cfe7",
-                            "output_type": "analysis_file"
-                        },
-                        {
-                            "output_id": "70ff6783-333f-5c1b-8208-3b495df95620",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "76502973-5eb8-40b1-a0dc-17c4f772edaa",
-                    "process_type": "analysis_process",
-                    "protocols": [
-                        {
-                            "protocol_id": "289ec28b-ce11-5be8-89ab-92fbceb874a0",
-                            "protocol_type": "analysis_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "33682180-6cdf-4d0c-9fe0-e1c029ac13b2",
-                            "input_type": "sequence_file"
-                        },
-                        {
-                            "input_id": "e92c42c7-f238-44ea-b147-e199b768d450",
-                            "input_type": "sequence_file"
-                        },
-                        {
-                            "input_id": "b01b2e61-3ebd-48cc-b071-f2e8cb42ff7c",
-                            "input_type": "sequence_file"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "a7915c55-1d80-5724-9c81-6dd0a9130361",
-                            "output_type": "analysis_file"
-                        },
-                        {
-                            "output_id": "7a96a0c2-e22a-57ad-ac46-4c2433a63d94",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "3f615b1d-d507-4912-82c5-9cb575cd19c1",
-                    "process_type": "analysis_process",
-                    "protocols": [
-                        {
-                            "protocol_id": "289ec28b-ce11-5be8-89ab-92fbceb874a0",
-                            "protocol_type": "analysis_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "6d52232d-dc77-4070-bdb1-9bb0ee59d309",
-                            "input_type": "sequence_file"
-                        },
-                        {
-                            "input_id": "52149e21-dcd2-4288-a5eb-e526c3dcf745",
-                            "input_type": "sequence_file"
-                        },
-                        {
-                            "input_id": "e0efcd8d-8433-4b40-9eee-11dafb699a5a",
-                            "input_type": "sequence_file"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "f51568e8-b84c-504b-82f0-3ad5975d4bcb",
-                            "output_type": "analysis_file"
-                        },
-                        {
-                            "output_id": "4c866eb3-7470-5ee8-91b9-942246f19fde",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "9b4ae2d9-d681-4f08-b111-6f1878145b35",
-                    "process_type": "analysis_process",
-                    "protocols": [
-                        {
-                            "protocol_id": "289ec28b-ce11-5be8-89ab-92fbceb874a0",
-                            "protocol_type": "analysis_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "6bd884d2-fccf-4227-8efc-184751527dfb",
-                            "input_type": "sequence_file"
-                        },
-                        {
-                            "input_id": "1016adeb-cdc3-47d6-a89e-771c763dd2e7",
-                            "input_type": "sequence_file"
-                        },
-                        {
-                            "input_id": "f6407a7a-eecc-4735-a96a-b8bb634118e4",
-                            "input_type": "sequence_file"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "bc111cd3-bf54-57ce-8af1-88f5997a0a9d",
-                            "output_type": "analysis_file"
-                        },
-                        {
-                            "output_id": "43598186-06cd-5f4b-95d9-fecb0a35d3ab",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "366c7a41-3b80-4c7d-af4b-20248e69425f",
-                    "process_type": "analysis_process",
-                    "protocols": [
-                        {
-                            "protocol_id": "289ec28b-ce11-5be8-89ab-92fbceb874a0",
-                            "protocol_type": "analysis_protocol"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_type": "process",
-                    "process_id": "ad220152-0eb4-4f85-a03e-c7e81ea3f167",
-                    "inputs": [
-                        {
-                            "input_type": "cell_suspension",
-                            "input_id": "1d3e48d7-d80f-4b99-85bd-04ff393288e7"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "f6407a7a-eecc-4735-a96a-b8bb634118e4"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "6bd884d2-fccf-4227-8efc-184751527dfb"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "1016adeb-cdc3-47d6-a89e-771c763dd2e7"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "fa99959f-faa2-4d69-a092-48333e59f5f3"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "a166be3d-6e84-4058-a1bd-edf90cf3ee88"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_type": "process",
-                    "process_id": "3ad5d964-6c2c-4adc-badb-9100ceada68c",
-                    "inputs": [
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "1dda6a28-cbaa-4506-be47-fa117e8f463c"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "cell_suspension",
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@@ -4892,5 +4246,651 @@
                 "update_date": "2019-09-13T08:37:53.821Z"
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+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "ad220152-0eb4-4f85-a03e-c7e81ea3f167",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "1d3e48d7-d80f-4b99-85bd-04ff393288e7"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "f6407a7a-eecc-4735-a96a-b8bb634118e4"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "6bd884d2-fccf-4227-8efc-184751527dfb"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "1016adeb-cdc3-47d6-a89e-771c763dd2e7"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "fa99959f-faa2-4d69-a092-48333e59f5f3"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "a166be3d-6e84-4058-a1bd-edf90cf3ee88"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "3ad5d964-6c2c-4adc-badb-9100ceada68c",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "1dda6a28-cbaa-4506-be47-fa117e8f463c"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "1d3e48d7-d80f-4b99-85bd-04ff393288e7"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "2509f42a-0328-4e33-8d21-79d37560d846"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ba595d79-aa43-4e3a-ad10-89f92ef4f22f"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "e511e7ff-e67c-4eb3-b0db-13aecefb5486",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "427c0a62-9baf-42ab-a3a3-f48d10544280"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "1dda6a28-cbaa-4506-be47-fa117e8f463c"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "3030903f-4a4b-4b30-ab93-3b10183181e0"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "8b81f0c2-3b57-4072-8a10-c169fece543e",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "eb32bfc6-e7be-4093-8959-b8bf27f2404f"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "799f314f-7c6c-4981-be36-8e1310bf38e6"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "a7b21a25-e76e-420d-8892-538062bfefbf"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "15f64718-69cf-462c-9704-e8a1f54c27c8"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "fa99959f-faa2-4d69-a092-48333e59f5f3"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "a166be3d-6e84-4058-a1bd-edf90cf3ee88"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "4054b722-a585-4e90-8d74-a02fb4d98202",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "edc72947-b776-4150-8bfe-b7331acfa66f"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "eb32bfc6-e7be-4093-8959-b8bf27f2404f"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "2509f42a-0328-4e33-8d21-79d37560d846"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ba595d79-aa43-4e3a-ad10-89f92ef4f22f"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "a5e37780-0b71-4610-8a7c-26142dedfcec",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "b8049daa-7458-47bf-8ec2-3f5c56d2cb34"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "edc72947-b776-4150-8bfe-b7331acfa66f"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "3030903f-4a4b-4b30-ab93-3b10183181e0"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "39255288-6791-45b0-ac7e-b3ef4c981a3b",
+                        "input_type": "sequence_file"
+                    },
+                    {
+                        "input_id": "9f8f5212-0749-460b-9a46-2949dea45d52",
+                        "input_type": "sequence_file"
+                    },
+                    {
+                        "input_id": "30040306-be5c-48f9-b221-e666e279ab5b",
+                        "input_type": "sequence_file"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "d90280cc-a294-57de-b350-5234a5278c19",
+                        "output_type": "analysis_file"
+                    },
+                    {
+                        "output_id": "b949e4b6-c3fb-58b4-865b-40cb3ef2b6c6",
+                        "output_type": "analysis_file"
+                    }
+                ],
+                "process_id": "3d7a4690-8760-491c-98f9-9a1aea3f79b5",
+                "process_type": "analysis_process",
+                "protocols": [
+                    {
+                        "protocol_id": "289ec28b-ce11-5be8-89ab-92fbceb874a0",
+                        "protocol_type": "analysis_protocol"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "262f55a3-d03d-49ae-8080-1a6208fddb4f",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "b1b6ea44-e0b7-425a-9faa-51ecff56783e"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "b01b2e61-3ebd-48cc-b071-f2e8cb42ff7c"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "33682180-6cdf-4d0c-9fe0-e1c029ac13b2"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "e92c42c7-f238-44ea-b147-e199b768d450"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "fa99959f-faa2-4d69-a092-48333e59f5f3"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "a166be3d-6e84-4058-a1bd-edf90cf3ee88"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "25999eea-6f12-40a8-aecf-d1524c7cf564",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "1dda6a28-cbaa-4506-be47-fa117e8f463c"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "b1b6ea44-e0b7-425a-9faa-51ecff56783e"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "2509f42a-0328-4e33-8d21-79d37560d846"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ba595d79-aa43-4e3a-ad10-89f92ef4f22f"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "e511e7ff-e67c-4eb3-b0db-13aecefb5486",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "427c0a62-9baf-42ab-a3a3-f48d10544280"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "1dda6a28-cbaa-4506-be47-fa117e8f463c"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "3030903f-4a4b-4b30-ab93-3b10183181e0"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "2f8a07c2-4a6b-47ac-a304-0dead66eee9e",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "0aabed05-6a89-4141-9384-828a33581419"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "e0efcd8d-8433-4b40-9eee-11dafb699a5a"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "6d52232d-dc77-4070-bdb1-9bb0ee59d309"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "52149e21-dcd2-4288-a5eb-e526c3dcf745"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "fa99959f-faa2-4d69-a092-48333e59f5f3"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "a166be3d-6e84-4058-a1bd-edf90cf3ee88"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "98c88684-6469-4bb3-90aa-57a4ea101244",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "252b008d-8b5a-450c-a17c-4e779a17ff26"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "0aabed05-6a89-4141-9384-828a33581419"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "2509f42a-0328-4e33-8d21-79d37560d846"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ba595d79-aa43-4e3a-ad10-89f92ef4f22f"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "48a0c58c-ea67-4014-8752-6339de02b70e",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "66b7152c-8e94-412b-b0e4-f8fbf554df5a"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "252b008d-8b5a-450c-a17c-4e779a17ff26"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "3030903f-4a4b-4b30-ab93-3b10183181e0"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "1116b396-448e-4dd1-b9c9-78357c511e15",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "932000d6-c63b-40f0-bdd5-469fa4db8be2"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "30040306-be5c-48f9-b221-e666e279ab5b"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "39255288-6791-45b0-ac7e-b3ef4c981a3b"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "9f8f5212-0749-460b-9a46-2949dea45d52"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "fa99959f-faa2-4d69-a092-48333e59f5f3"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "a166be3d-6e84-4058-a1bd-edf90cf3ee88"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "b360251f-7550-4c08-b576-781858554ea1",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "edc72947-b776-4150-8bfe-b7331acfa66f"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "932000d6-c63b-40f0-bdd5-469fa4db8be2"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "2509f42a-0328-4e33-8d21-79d37560d846"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ba595d79-aa43-4e3a-ad10-89f92ef4f22f"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "a5e37780-0b71-4610-8a7c-26142dedfcec",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "b8049daa-7458-47bf-8ec2-3f5c56d2cb34"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "edc72947-b776-4150-8bfe-b7331acfa66f"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "3030903f-4a4b-4b30-ab93-3b10183181e0"
+                    }
+                ]
+            }
+        ]
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
index 52244e823..c431a7e9a 100644
--- a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
+++ b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
@@ -868,1168 +868,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "schema_type": "links",
-            "schema_version": "3.0.0",
-            "describedBy": "https://schema.humancellatlas.org/system/3.0.0/links",
-            "links": [
-                {
-                    "link_type": "process_link",
-                    "process_id": "02e69c25-71e2-48ca-a87b-e256938c6a98",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "cell_suspension",
-                            "input_id": "db4b5711-0abd-44cd-ac94-cdaca0cb1de3"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "1697aa82-0910-44e6-ac07-2020248e1977"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "989f8f5d-710f-4529-b89b-0bfbf592951c"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "49eefca3-6441-4a63-a0f0-178d6fc2573d"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "c375019a-ef94-452b-b111-32244bdc054a"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "6b2c7ae7-1d15-4914-a9e9-14233afd5c3f"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "4b963d42-aad1-4f26-94d2-c13c8321c09d",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "63170a26-263d-4207-8eab-871b687e234d"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "5e9f5040-c83a-4442-8944-db144717107a"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "6254fedf-0978-45ee-af82-e7f30ffebf0c"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "b9a0edf6-77bc-4e4a-a200-5cda4f902c04"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "b5a382bd-34e5-429d-9013-3ff025ab322a"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "9b1c871e-20db-487f-9acc-36740b75877b"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "5608f2b1-d42f-4198-8d52-96e40e5239e4"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "e6b8f32e-7c8e-4308-b596-91006cde4b51"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "cell_suspension",
-                            "output_id": "db4b5711-0abd-44cd-ac94-cdaca0cb1de3"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "ab3e3079-2eea-49cd-836f-5b9f4cf27b86"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "d3372c5a-20ea-4239-bfef-c11894862897"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "771e716e-9906-4f5d-b41a-2fa7cc9bd77b",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "c10356c8-e081-4f97-8e85-0ea87b8eb84b"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "63170a26-263d-4207-8eab-871b687e234d"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "7e90d996-b643-4732-af87-ac090325a6e8",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "c10356c8-e081-4f97-8e85-0ea87b8eb84b"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "5e9f5040-c83a-4442-8944-db144717107a"
-                        }
-                    ],
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-                            "input_id": "49eefca3-6441-4a63-a0f0-178d6fc2573d"
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-                    "outputs": [
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-                            "output_type": "analysis_file",
-                            "output_id": "4d64269d-bd3f-46c1-a179-1c27e1caeb30"
-                        },
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-                            "output_type": "analysis_file",
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-                    "process_type": "process",
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-                        {
-                            "input_type": "cell_suspension",
-                            "input_id": "db4b5711-0abd-44cd-ac94-cdaca0cb1de3"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "1697aa82-0910-44e6-ac07-2020248e1977"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "989f8f5d-710f-4529-b89b-0bfbf592951c"
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-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "49eefca3-6441-4a63-a0f0-178d6fc2573d"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "c375019a-ef94-452b-b111-32244bdc054a"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "6b2c7ae7-1d15-4914-a9e9-14233afd5c3f"
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-                    "process_type": "process",
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-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "63170a26-263d-4207-8eab-871b687e234d"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "5e9f5040-c83a-4442-8944-db144717107a"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "6254fedf-0978-45ee-af82-e7f30ffebf0c"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "b9a0edf6-77bc-4e4a-a200-5cda4f902c04"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "b5a382bd-34e5-429d-9013-3ff025ab322a"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "9b1c871e-20db-487f-9acc-36740b75877b"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "5608f2b1-d42f-4198-8d52-96e40e5239e4"
-                        },
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "e6b8f32e-7c8e-4308-b596-91006cde4b51"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "cell_suspension",
-                            "output_id": "db4b5711-0abd-44cd-ac94-cdaca0cb1de3"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "ab3e3079-2eea-49cd-836f-5b9f4cf27b86"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "d3372c5a-20ea-4239-bfef-c11894862897"
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-                },
-                {
-                    "link_type": "process_link",
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-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "c10356c8-e081-4f97-8e85-0ea87b8eb84b"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "63170a26-263d-4207-8eab-871b687e234d"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
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-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "c10356c8-e081-4f97-8e85-0ea87b8eb84b"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "5e9f5040-c83a-4442-8944-db144717107a"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
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-                    "link_type": "process_link",
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-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "c10356c8-e081-4f97-8e85-0ea87b8eb84b"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "6254fedf-0978-45ee-af82-e7f30ffebf0c"
-                        }
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-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
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-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "c10356c8-e081-4f97-8e85-0ea87b8eb84b"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "b9a0edf6-77bc-4e4a-a200-5cda4f902c04"
-                        }
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-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
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-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "014494a0-adde-4ac6-90c1-2b5824a8717c"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "b5a382bd-34e5-429d-9013-3ff025ab322a"
-                        }
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-                            "input_id": "014494a0-adde-4ac6-90c1-2b5824a8717c"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "9b1c871e-20db-487f-9acc-36740b75877b"
-                        }
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-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
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-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "014494a0-adde-4ac6-90c1-2b5824a8717c"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "5608f2b1-d42f-4198-8d52-96e40e5239e4"
-                        }
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-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
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-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "014494a0-adde-4ac6-90c1-2b5824a8717c"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "e6b8f32e-7c8e-4308-b596-91006cde4b51"
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-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
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-                    "link_type": "process_link",
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-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "6b94ce38-27b9-460e-ab1b-bceb18275c71"
-                        },
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "9610cb70-57c1-466d-b9c9-faa22aa7b917"
-                        },
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "bca273dd-1758-4439-b7e0-745755dcffa0"
-                        },
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "7c1802b3-0be5-4202-b14e-141974ca7fb3"
-                        },
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "c87f6dbf-1062-4e72-a19d-db779f1d3e66"
-                        },
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "06d54587-f54b-490c-8d29-3d84025e3b14"
-                        },
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "000d1e4b-4c1f-40de-8fd6-8a3d1a26e1d2"
-                        },
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "ee52ecd1-68c0-48dd-82c2-6d3e45869b38"
-                        },
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "a97f4858-0f13-405a-8b28-98ee5f997999"
-                        },
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "dc5b2d96-ba74-4bd0-bcf0-747548e1c6d7"
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-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "d86c34c4-0aeb-4f50-a53e-5a0983c906b7"
-                        },
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "eacaacbb-f514-49bb-bfbf-ccb123c5bf2e"
-                        },
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "1697aa82-0910-44e6-ac07-2020248e1977"
-                        },
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "989f8f5d-710f-4529-b89b-0bfbf592951c"
-                        },
-                        {
-                            "input_type": "sequence_file",
-                            "input_id": "49eefca3-6441-4a63-a0f0-178d6fc2573d"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "analysis_file",
-                            "output_id": "4d64269d-bd3f-46c1-a179-1c27e1caeb30"
-                        },
-                        {
-                            "output_type": "analysis_file",
-                            "output_id": "6ccd1b16-d3a9-4ba4-9dda-99aa882dfc2c"
-                        },
-                        {
-                            "output_type": "analysis_file",
-                            "output_id": "004d18f2-f23c-4fd1-af2e-f0a6a9e13cc9"
-                        },
-                        {
-                            "output_type": "analysis_file",
-                            "output_id": "ad3f7b5e-77ed-4df1-a9af-5355f7951af4"
-                        },
-                        {
-                            "output_type": "analysis_file",
-                            "output_id": "cde6359a-a2b0-421d-a898-c53278c21399"
-                        },
-                        {
-                            "output_type": "analysis_file",
-                            "output_id": "c61a76f4-aebe-4a18-b272-e2e78307bb4a"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "analysis_protocol",
-                            "protocol_id": "89808d14-a99e-47d2-82cd-ff9621a32206"
-                        }
-                    ]
-                }
-            ]
-        },
         "process_0.json": {
             "insdc_experiment": {
                 "insdc_experiment_accession": "SRX5499352"
@@ -3691,5 +2529,1167 @@
                 "schema_minor_version": 1
             }
         }
+    },
+    "links": {
+        "schema_type": "links",
+        "schema_version": "3.0.0",
+        "describedBy": "https://schema.humancellatlas.org/system/3.0.0/links",
+        "links": [
+            {
+                "link_type": "process_link",
+                "process_id": "02e69c25-71e2-48ca-a87b-e256938c6a98",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "db4b5711-0abd-44cd-ac94-cdaca0cb1de3"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "1697aa82-0910-44e6-ac07-2020248e1977"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "989f8f5d-710f-4529-b89b-0bfbf592951c"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "49eefca3-6441-4a63-a0f0-178d6fc2573d"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "c375019a-ef94-452b-b111-32244bdc054a"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "6b2c7ae7-1d15-4914-a9e9-14233afd5c3f"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "4b963d42-aad1-4f26-94d2-c13c8321c09d",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "63170a26-263d-4207-8eab-871b687e234d"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "5e9f5040-c83a-4442-8944-db144717107a"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "6254fedf-0978-45ee-af82-e7f30ffebf0c"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "b9a0edf6-77bc-4e4a-a200-5cda4f902c04"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "b5a382bd-34e5-429d-9013-3ff025ab322a"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "9b1c871e-20db-487f-9acc-36740b75877b"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "5608f2b1-d42f-4198-8d52-96e40e5239e4"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "e6b8f32e-7c8e-4308-b596-91006cde4b51"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "db4b5711-0abd-44cd-ac94-cdaca0cb1de3"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "ab3e3079-2eea-49cd-836f-5b9f4cf27b86"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "d3372c5a-20ea-4239-bfef-c11894862897"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "771e716e-9906-4f5d-b41a-2fa7cc9bd77b",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "c10356c8-e081-4f97-8e85-0ea87b8eb84b"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "63170a26-263d-4207-8eab-871b687e234d"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "7e90d996-b643-4732-af87-ac090325a6e8",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "c10356c8-e081-4f97-8e85-0ea87b8eb84b"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "5e9f5040-c83a-4442-8944-db144717107a"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
+                    }
+                ]
+            },
+            {
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+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "1697aa82-0910-44e6-ac07-2020248e1977"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "989f8f5d-710f-4529-b89b-0bfbf592951c"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "49eefca3-6441-4a63-a0f0-178d6fc2573d"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "4d64269d-bd3f-46c1-a179-1c27e1caeb30"
+                    },
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "6ccd1b16-d3a9-4ba4-9dda-99aa882dfc2c"
+                    },
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "004d18f2-f23c-4fd1-af2e-f0a6a9e13cc9"
+                    },
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "ad3f7b5e-77ed-4df1-a9af-5355f7951af4"
+                    },
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "cde6359a-a2b0-421d-a898-c53278c21399"
+                    },
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "c61a76f4-aebe-4a18-b272-e2e78307bb4a"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "analysis_protocol",
+                        "protocol_id": "89808d14-a99e-47d2-82cd-ff9621a32206"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "02e69c25-71e2-48ca-a87b-e256938c6a98",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "db4b5711-0abd-44cd-ac94-cdaca0cb1de3"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "1697aa82-0910-44e6-ac07-2020248e1977"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "989f8f5d-710f-4529-b89b-0bfbf592951c"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "49eefca3-6441-4a63-a0f0-178d6fc2573d"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "c375019a-ef94-452b-b111-32244bdc054a"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "6b2c7ae7-1d15-4914-a9e9-14233afd5c3f"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "4b963d42-aad1-4f26-94d2-c13c8321c09d",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "63170a26-263d-4207-8eab-871b687e234d"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "5e9f5040-c83a-4442-8944-db144717107a"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "6254fedf-0978-45ee-af82-e7f30ffebf0c"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "b9a0edf6-77bc-4e4a-a200-5cda4f902c04"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "b5a382bd-34e5-429d-9013-3ff025ab322a"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "9b1c871e-20db-487f-9acc-36740b75877b"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "5608f2b1-d42f-4198-8d52-96e40e5239e4"
+                    },
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "e6b8f32e-7c8e-4308-b596-91006cde4b51"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "db4b5711-0abd-44cd-ac94-cdaca0cb1de3"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "ab3e3079-2eea-49cd-836f-5b9f4cf27b86"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "d3372c5a-20ea-4239-bfef-c11894862897"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "771e716e-9906-4f5d-b41a-2fa7cc9bd77b",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "c10356c8-e081-4f97-8e85-0ea87b8eb84b"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "63170a26-263d-4207-8eab-871b687e234d"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "7e90d996-b643-4732-af87-ac090325a6e8",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "c10356c8-e081-4f97-8e85-0ea87b8eb84b"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "5e9f5040-c83a-4442-8944-db144717107a"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "3798c749-7f72-4847-a9d1-d99112f98162",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "c10356c8-e081-4f97-8e85-0ea87b8eb84b"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "6254fedf-0978-45ee-af82-e7f30ffebf0c"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "721fcf01-ab0d-4220-9dfc-396ca6991d1d",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "c10356c8-e081-4f97-8e85-0ea87b8eb84b"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "b9a0edf6-77bc-4e4a-a200-5cda4f902c04"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "a85ceb28-cdb0-4021-98c8-752b9d07170a",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "014494a0-adde-4ac6-90c1-2b5824a8717c"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "b5a382bd-34e5-429d-9013-3ff025ab322a"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "bd774f12-82e6-4036-8779-d8674bce9205",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "014494a0-adde-4ac6-90c1-2b5824a8717c"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "9b1c871e-20db-487f-9acc-36740b75877b"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "341460a3-edf2-4f77-9625-7c6b92ac863e",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "014494a0-adde-4ac6-90c1-2b5824a8717c"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "5608f2b1-d42f-4198-8d52-96e40e5239e4"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "9a8d9df1-c511-4b6b-b6d3-cacc0eaf76c1",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "014494a0-adde-4ac6-90c1-2b5824a8717c"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "e6b8f32e-7c8e-4308-b596-91006cde4b51"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "133e78ac-aa06-4a0b-b43f-0e9e2148d528"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "da317018-1b0b-4e4f-b508-2c1c7d049507",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "6b94ce38-27b9-460e-ab1b-bceb18275c71"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "9610cb70-57c1-466d-b9c9-faa22aa7b917"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "bca273dd-1758-4439-b7e0-745755dcffa0"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "7c1802b3-0be5-4202-b14e-141974ca7fb3"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "c87f6dbf-1062-4e72-a19d-db779f1d3e66"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "06d54587-f54b-490c-8d29-3d84025e3b14"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "000d1e4b-4c1f-40de-8fd6-8a3d1a26e1d2"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "ee52ecd1-68c0-48dd-82c2-6d3e45869b38"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "a97f4858-0f13-405a-8b28-98ee5f997999"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "dc5b2d96-ba74-4bd0-bcf0-747548e1c6d7"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "d86c34c4-0aeb-4f50-a53e-5a0983c906b7"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "eacaacbb-f514-49bb-bfbf-ccb123c5bf2e"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "1697aa82-0910-44e6-ac07-2020248e1977"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "989f8f5d-710f-4529-b89b-0bfbf592951c"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "49eefca3-6441-4a63-a0f0-178d6fc2573d"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "4d64269d-bd3f-46c1-a179-1c27e1caeb30"
+                    },
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "6ccd1b16-d3a9-4ba4-9dda-99aa882dfc2c"
+                    },
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "004d18f2-f23c-4fd1-af2e-f0a6a9e13cc9"
+                    },
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "ad3f7b5e-77ed-4df1-a9af-5355f7951af4"
+                    },
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "cde6359a-a2b0-421d-a898-c53278c21399"
+                    },
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "c61a76f4-aebe-4a18-b272-e2e78307bb4a"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "analysis_protocol",
+                        "protocol_id": "89808d14-a99e-47d2-82cd-ff9621a32206"
+                    }
+                ]
+            }
+        ]
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
index d4bed59fe..3fead213a 100644
--- a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
+++ b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
@@ -9781,16949 +9781,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "schema_type": "links",
-            "schema_version": "3.0.0",
-            "describedBy": "https://schema.humancellatlas.org/system/3.0.0/links",
-            "links": [
-                {
-                    "link_type": "process_link",
-                    "process_id": "04836733-0449-4e57-be2e-6f3b8fbdfb12",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "cell_suspension",
-                            "input_id": "f21781e9-e5c7-48ff-9d7d-0e3637968279"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "d3661383-3d73-41a0-8676-295926c07eeb"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "9766ad67-37fa-402a-9649-181a1752e5b2"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "559b84d3-e7ff-48fb-9b1e-395a7ee5b6d0"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "f8c2ac32-ceee-4043-8c37-9e8b9f5b55ad"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "e0dd6ad5-0582-47de-9cbf-7351ebd5e005"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "a60154cf-58b6-461f-8908-b789cdd78ee8"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "11d171f7-7775-40a4-90a4-df995775b1c4"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "9fa70333-418c-476c-b93b-382096a9cdcb"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "6593f54e-682c-4eb4-b2ed-e3c3278d4880"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "c3182931-cc4c-4cb7-aab5-4b50093eebea"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "3001b82f-bbea-4072-9760-a14a4f00b7d3"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "2b62614e-dc4d-46ea-bf29-727d5c33effa"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "726a68e9-4fa9-425a-90e7-d0fef30c9d4c"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "09610000-dc5c-4665-a72e-b0dad51edf6d"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "92951c73-28a3-4820-89d6-15a73fa192cf"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "6d9709e5-ce90-46d3-bc95-d5105cafc67a"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "523c6c55-66da-4edc-b66a-a33fe20d4102"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "75e38979-23f0-4749-bfcc-d8e92db7f2b0"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "3fcc4232-b40f-4cca-bd1d-d12a03e4fed0"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "80347bc1-ffca-4f66-9ebd-812d22ab3d3f"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "28e8f3eb-fedc-4942-8d6b-836fbb7e3441"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "40f24220-4c6d-43c4-ab82-1db21d683b07"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "b8ca1ceb-f27a-4fc4-b816-5abf6e1f1477"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "b7826640-f0cc-4891-860e-7815a8848006"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "72975432-3c46-449a-a4d9-809712d10577"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "63db242f-a88b-4deb-b1e4-3677ade32d18"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "d7875d0d-da64-49d0-8540-e601d445107c",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "5bd31092-57c0-4d69-aa2b-72d902872cca"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "cell_suspension",
-                            "output_id": "f21781e9-e5c7-48ff-9d7d-0e3637968279"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "0e1884e4-310f-4afb-9721-e0721a290498"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "48f7f503-d213-4447-9ee4-3602da1066d7"
-                        }
-                    ]
-                },
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-                            "output_type": "analysis_file",
-                            "output_id": "581ee2ac-fd9a-4563-b8eb-d9cfb96f65ca"
-                        },
-                        {
-                            "output_type": "analysis_file",
-                            "output_id": "31e6cb06-0062-4096-84f5-c2d1c2621a82"
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-                            "output_id": "d3b3abc2-0da6-4163-acb8-251fe079284c"
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-                    "protocols": [
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-        },
         "sequence_file_0.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
@@ -39331,5 +22388,16948 @@
                 "schema_minor_version": 1
             }
         }
+    },
+    "links": {
+        "schema_type": "links",
+        "schema_version": "3.0.0",
+        "describedBy": "https://schema.humancellatlas.org/system/3.0.0/links",
+        "links": [
+            {
+                "link_type": "process_link",
+                "process_id": "04836733-0449-4e57-be2e-6f3b8fbdfb12",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "f21781e9-e5c7-48ff-9d7d-0e3637968279"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "d3661383-3d73-41a0-8676-295926c07eeb"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "9766ad67-37fa-402a-9649-181a1752e5b2"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "559b84d3-e7ff-48fb-9b1e-395a7ee5b6d0"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "f8c2ac32-ceee-4043-8c37-9e8b9f5b55ad"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "e0dd6ad5-0582-47de-9cbf-7351ebd5e005"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "a60154cf-58b6-461f-8908-b789cdd78ee8"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "11d171f7-7775-40a4-90a4-df995775b1c4"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "9fa70333-418c-476c-b93b-382096a9cdcb"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "6593f54e-682c-4eb4-b2ed-e3c3278d4880"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "c3182931-cc4c-4cb7-aab5-4b50093eebea"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "3001b82f-bbea-4072-9760-a14a4f00b7d3"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "2b62614e-dc4d-46ea-bf29-727d5c33effa"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "726a68e9-4fa9-425a-90e7-d0fef30c9d4c"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "09610000-dc5c-4665-a72e-b0dad51edf6d"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "92951c73-28a3-4820-89d6-15a73fa192cf"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "6d9709e5-ce90-46d3-bc95-d5105cafc67a"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "523c6c55-66da-4edc-b66a-a33fe20d4102"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "75e38979-23f0-4749-bfcc-d8e92db7f2b0"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "3fcc4232-b40f-4cca-bd1d-d12a03e4fed0"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "80347bc1-ffca-4f66-9ebd-812d22ab3d3f"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "28e8f3eb-fedc-4942-8d6b-836fbb7e3441"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "40f24220-4c6d-43c4-ab82-1db21d683b07"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "b8ca1ceb-f27a-4fc4-b816-5abf6e1f1477"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "b7826640-f0cc-4891-860e-7815a8848006"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "72975432-3c46-449a-a4d9-809712d10577"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "63db242f-a88b-4deb-b1e4-3677ade32d18"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "d7875d0d-da64-49d0-8540-e601d445107c",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "5bd31092-57c0-4d69-aa2b-72d902872cca"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "f21781e9-e5c7-48ff-9d7d-0e3637968279"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "0e1884e4-310f-4afb-9721-e0721a290498"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "48f7f503-d213-4447-9ee4-3602da1066d7"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "9e346701-eb3c-40b3-b3dd-75ce047bcb78",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "cf1aab9f-caf1-4fe3-9724-61f6475f332b"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "5bd31092-57c0-4d69-aa2b-72d902872cca"
+                    }
+                ],
+                "protocols": [
+                    {
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+                        "protocol_id": "dbeb62b8-e3e8-40f4-a06d-477ed495dfd9"
+                    }
+                ]
+            },
+            {
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+                "process_type": "process",
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+                    },
+                    {
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+                    {
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+                    {
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+                        "input_id": "2aba7a6a-6d70-4310-9e64-071c6adbe16b"
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+                    {
+                        "input_type": "sequence_file",
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+                    {
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+                    {
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+                        "input_id": "e9def19b-3967-47e7-a2dd-1bc5f9297959"
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+                    {
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+                    {
+                        "input_type": "sequence_file",
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+                    {
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+                        "input_id": "0fa69e92-febb-4bab-857c-4b67a2b17ff6"
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+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "09a53782-90ea-4911-a793-706e74127adb"
+                    },
+                    {
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+                    {
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+                        "input_id": "5b80431f-c95a-41ef-8aa7-98816f00e4d6"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "70291c50-770c-4e51-8f1b-60be28ea419f"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "38e1a4f4-f9ec-44cf-b6bb-1a9566456d38"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "154dffeb-efd7-4081-a73c-bf1b73ca9a90"
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+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "c9517b55-fb72-463a-aab6-e4f64b95c2fc"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "c3d3c4a3-527b-490f-8107-bc1b44566df0"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "83865a27-24a8-4a70-a8bd-650affa7df5c"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "6e650029-386f-4d8e-868e-8780782baa4b"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "f859d1ff-df51-4548-b8a4-9eca26bf7454"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "79426c6b-bd79-4343-b9fa-ee1e9cfc2aef"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "0697146c-0105-4d6f-baff-d9147593eadb"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "65fae226-b417-43cd-a5c8-cf2336b8cff5"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "7240ec36-6433-4e5c-ba0f-d2770817f963"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "d20547e4-3f00-42af-9a7f-9477ff43de0d"
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+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "0256729b-47ee-4ed3-adc7-2c0813bb99b9"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "7eb2244c-6b4d-4d91-bfc6-44ec12d9319b"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "b2a6b8c1-f0bc-4509-b255-8618d7cff205"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "bf6cb18e-07de-404d-bebe-4a943dfb44f7"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "6ca6b611-2a38-41e7-a0ab-c9fd6cbb32c0"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "5a172f54-33a5-4e0d-bc0d-1760bad3beb6"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "ee36a1ac-7426-4253-81b8-715f37a2ba69"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "d7b3de6f-1ed9-461a-bb0a-d1517e9b68fc"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "5f5e80b2-0779-4df0-9a18-35bc0db72fdf"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "e6b33ccb-99f6-4c02-aa69-e7b581832d04"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "9d98496f-f6d8-4106-8b6a-c118ed6ff229"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "22343575-1465-455f-8360-4e716aab17fb"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "7cb5e572-fb2b-4416-8ff9-05af3bd1bcf4"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "9f709f2c-701a-43bc-8417-77fac81c3633"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "a4152d0c-ca88-4cad-af08-40a2e799bec7"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "2c4d6e65-8271-4542-97ee-7ba8a6b628d9"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "668a508d-34fa-4468-86e8-523380a34da8"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "b5c2e557-c303-42cc-8779-bf3b2256c422"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "f9eef16f-b9cc-43bb-b9f3-bf0948766e7e"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "061936ce-8fbb-4576-8c0c-ed871767917f"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "762c2720-f65c-4804-844f-2302bc33ebbc"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "fedc286a-9bbc-4db0-8bf5-b3f0b69fb559"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "43f476f9-cbfc-431a-a774-5885904b434c"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "65b78fda-7874-455f-9c9a-bf7aca375a0b"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "82fc0df9-9828-433e-ac6d-73f4bbceefcf"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "fb771836-467f-4897-a755-a17ab281a385"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "5f6e0f4b-3541-4197-a67f-01dddc0cf105"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "c7970499-e36d-49f3-b1f2-6886746333c9"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "6bd02c9a-1d0a-4093-bc0b-26d1f6ebdb47"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "e4d6ced4-50a3-402a-bbbc-ae329cd3689d"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "792fd4bd-9b01-42bf-a883-c651789a198a"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "10b3b42b-3612-48fb-849b-bfc036c248a6"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "6fc7505d-33db-4d19-99a1-5756cd9a0a1c"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "64309a91-ba2b-4b0e-baa9-7cfce3c5d445"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "64eedb4a-2f73-4b60-a4b1-99b5ffd0486b"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "79d181d1-5b70-4306-a229-74a2a3d5278e"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "102b8410-1c0e-46f5-90fe-609ab117221c"
+                    },
+                    {
+                        "input_type": "sequence_file",
+                        "input_id": "449ec63a-dca8-4a61-98b5-e6789d4946a1"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "581ee2ac-fd9a-4563-b8eb-d9cfb96f65ca"
+                    },
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "31e6cb06-0062-4096-84f5-c2d1c2621a82"
+                    },
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "d3b3abc2-0da6-4163-acb8-251fe079284c"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "analysis_protocol",
+                        "protocol_id": "07f1f962-dd38-4a0b-b0b5-f4efe30d21e2"
+                    }
+                ]
+            }
+        ]
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
index 21d4beb7f..19613f43d 100644
--- a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
+++ b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
@@ -195,98 +195,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "links": [
-                {
-                    "link_type": "process_link",
-                    "process_id": "0722b70c-6778-423d-8fe9-869e2a515d35",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "cell_suspension",
-                            "input_id": "b2feeafc-bd19-4c54-b669-648ce3ee5b52"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "95595c66-2121-4ebc-9f2e-b5b61d193f25"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "54647cbb-7814-4d9a-b7f8-a6605c2f7aa6"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "ca16fcf2-48df-4b2a-bd48-a5fce6b0cd75"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "328e83cc-1e31-4d49-bf69-3504a7d1d4ba"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "70b02064-3cf5-4e97-88f8-731c6e246965",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "organoid",
-                            "input_id": "df23c109-59f0-46d3-bd09-660175b51bda"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "cell_suspension",
-                            "output_id": "b2feeafc-bd19-4c54-b669-648ce3ee5b52"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "59eeb73e-64d6-4959-9c69-b85570a20900"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "f4234276-bdac-4ad1-b4a0-4b5d595ae04c"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "0d48b9ba-5fea-4260-abbc-2949ac357f75",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "cell_line",
-                            "input_id": "d91bbbd5-c2c1-4bb7-906f-494ee686658e"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "organoid",
-                            "output_id": "df23c109-59f0-46d3-bd09-660175b51bda"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "0a8112d1-d401-4c0d-8334-8cda8f8532c8"
-                        },
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "0078130e-8a91-47d0-9ff7-854ae772b8ea"
-                        }
-                    ]
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links",
-            "schema_version": "2.1.1",
-            "schema_type": "links"
-        },
         "dissociation_protocol_0.json": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "method": {
@@ -779,5 +687,97 @@
                 "schema_minor_version": 2
             }
         }
+    },
+    "links": {
+        "links": [
+            {
+                "link_type": "process_link",
+                "process_id": "0722b70c-6778-423d-8fe9-869e2a515d35",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "b2feeafc-bd19-4c54-b669-648ce3ee5b52"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "95595c66-2121-4ebc-9f2e-b5b61d193f25"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "54647cbb-7814-4d9a-b7f8-a6605c2f7aa6"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "ca16fcf2-48df-4b2a-bd48-a5fce6b0cd75"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "328e83cc-1e31-4d49-bf69-3504a7d1d4ba"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "70b02064-3cf5-4e97-88f8-731c6e246965",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "organoid",
+                        "input_id": "df23c109-59f0-46d3-bd09-660175b51bda"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "b2feeafc-bd19-4c54-b669-648ce3ee5b52"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "59eeb73e-64d6-4959-9c69-b85570a20900"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "f4234276-bdac-4ad1-b4a0-4b5d595ae04c"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "0d48b9ba-5fea-4260-abbc-2949ac357f75",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_line",
+                        "input_id": "d91bbbd5-c2c1-4bb7-906f-494ee686658e"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "organoid",
+                        "output_id": "df23c109-59f0-46d3-bd09-660175b51bda"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "0a8112d1-d401-4c0d-8334-8cda8f8532c8"
+                    },
+                    {
+                        "protocol_type": "differentiation_protocol",
+                        "protocol_id": "0078130e-8a91-47d0-9ff7-854ae772b8ea"
+                    }
+                ]
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links",
+        "schema_version": "2.1.1",
+        "schema_type": "links"
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json b/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
index e387a8926..fd0370015 100644
--- a/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
+++ b/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
@@ -678,205 +678,205 @@
                 "updateDate": "2018-03-27T13:10:45.995Z",
                 "document_id": "73b0c9ae-a5bb-446e-9c7b-d0954e6af425"
             }
-        },
-        "links.json": {
-            "links": [
-                {
-                    "source_id": "d231b8f3-8fa3-4f3b-a8e5-66eca6228ae7",
-                    "source_type": "biomaterial",
-                    "destination_id": "7d3747dc-9e3a-4740-8504-82086ad1d63a",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "7d3747dc-9e3a-4740-8504-82086ad1d63a",
-                    "source_type": "process",
-                    "destination_id": "a86b1fda-bb1d-4ef8-87d9-392517d4a937",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "8797a64c-b498-4de6-aea7-86401199bee4",
-                    "source_type": "process",
-                    "destination_id": "d231b8f3-8fa3-4f3b-a8e5-66eca6228ae7",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "9a7acc6d-8352-497e-b162-5e63b380366f",
-                    "source_type": "biomaterial",
-                    "destination_id": "8797a64c-b498-4de6-aea7-86401199bee4",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "a86b1fda-bb1d-4ef8-87d9-392517d4a937",
-                    "source_type": "biomaterial",
-                    "destination_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "destination_type": "library_preparation_process"
-                },
-                {
-                    "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "49fddace-4c59-41c1-8930-0707460132d7",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "771d9bcb-a5ff-43b5-b3e8-e738cc4c05bf",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "8ebfd02e-2a74-4367-80db-48082f331625",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "fea5cc65-6d94-4d1e-a807-ec248f79b83d",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "cee5b925-919c-4c77-8ea2-be51a1728e2b",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "c548066c-9994-415a-98cb-3df2933937ff",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "b7d8d43c-bee6-48eb-bb36-0c07701c47b5",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "6bc5b7ef-68f8-445d-8460-f04180c4fae1",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "17add91c-4063-4684-859d-d739baa4b9bb",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "b7554cb7-dc5a-4b07-9c7a-c04466d30576",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "5239e70b-7d8d-4285-971f-9a156441c2f2",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "024c5cb6-f473-40c9-9eb3-da08caf3180e",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "73b0c9ae-a5bb-446e-9c7b-d0954e6af425",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "a86b1fda-bb1d-4ef8-87d9-392517d4a937",
-                    "source_type": "biomaterial",
-                    "destination_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "destination_type": "sequencing_process"
-                },
-                {
-                    "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "source_type": "sequencing_process",
-                    "destination_id": "49fddace-4c59-41c1-8930-0707460132d7",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "source_type": "sequencing_process",
-                    "destination_id": "771d9bcb-a5ff-43b5-b3e8-e738cc4c05bf",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "source_type": "sequencing_process",
-                    "destination_id": "8ebfd02e-2a74-4367-80db-48082f331625",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "source_type": "sequencing_process",
-                    "destination_id": "fea5cc65-6d94-4d1e-a807-ec248f79b83d",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "source_type": "sequencing_process",
-                    "destination_id": "cee5b925-919c-4c77-8ea2-be51a1728e2b",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "source_type": "sequencing_process",
-                    "destination_id": "c548066c-9994-415a-98cb-3df2933937ff",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "source_type": "sequencing_process",
-                    "destination_id": "b7d8d43c-bee6-48eb-bb36-0c07701c47b5",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "source_type": "sequencing_process",
-                    "destination_id": "6bc5b7ef-68f8-445d-8460-f04180c4fae1",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "source_type": "sequencing_process",
-                    "destination_id": "17add91c-4063-4684-859d-d739baa4b9bb",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "source_type": "sequencing_process",
-                    "destination_id": "b7554cb7-dc5a-4b07-9c7a-c04466d30576",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "source_type": "sequencing_process",
-                    "destination_id": "5239e70b-7d8d-4285-971f-9a156441c2f2",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "source_type": "sequencing_process",
-                    "destination_id": "024c5cb6-f473-40c9-9eb3-da08caf3180e",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
-                    "source_type": "sequencing_process",
-                    "destination_id": "73b0c9ae-a5bb-446e-9c7b-d0954e6af425",
-                    "destination_type": "protocol"
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
-            "schema_version": "1.0.0",
-            "schema_type": "link_bundle"
         }
+    },
+    "links": {
+        "links": [
+            {
+                "source_id": "d231b8f3-8fa3-4f3b-a8e5-66eca6228ae7",
+                "source_type": "biomaterial",
+                "destination_id": "7d3747dc-9e3a-4740-8504-82086ad1d63a",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "7d3747dc-9e3a-4740-8504-82086ad1d63a",
+                "source_type": "process",
+                "destination_id": "a86b1fda-bb1d-4ef8-87d9-392517d4a937",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "8797a64c-b498-4de6-aea7-86401199bee4",
+                "source_type": "process",
+                "destination_id": "d231b8f3-8fa3-4f3b-a8e5-66eca6228ae7",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "9a7acc6d-8352-497e-b162-5e63b380366f",
+                "source_type": "biomaterial",
+                "destination_id": "8797a64c-b498-4de6-aea7-86401199bee4",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "a86b1fda-bb1d-4ef8-87d9-392517d4a937",
+                "source_type": "biomaterial",
+                "destination_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "destination_type": "library_preparation_process"
+            },
+            {
+                "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "source_type": "library_preparation_process",
+                "destination_id": "49fddace-4c59-41c1-8930-0707460132d7",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "source_type": "library_preparation_process",
+                "destination_id": "771d9bcb-a5ff-43b5-b3e8-e738cc4c05bf",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "source_type": "library_preparation_process",
+                "destination_id": "8ebfd02e-2a74-4367-80db-48082f331625",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "source_type": "library_preparation_process",
+                "destination_id": "fea5cc65-6d94-4d1e-a807-ec248f79b83d",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "source_type": "library_preparation_process",
+                "destination_id": "cee5b925-919c-4c77-8ea2-be51a1728e2b",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "source_type": "library_preparation_process",
+                "destination_id": "c548066c-9994-415a-98cb-3df2933937ff",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "source_type": "library_preparation_process",
+                "destination_id": "b7d8d43c-bee6-48eb-bb36-0c07701c47b5",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "source_type": "library_preparation_process",
+                "destination_id": "6bc5b7ef-68f8-445d-8460-f04180c4fae1",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "source_type": "library_preparation_process",
+                "destination_id": "17add91c-4063-4684-859d-d739baa4b9bb",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "source_type": "library_preparation_process",
+                "destination_id": "b7554cb7-dc5a-4b07-9c7a-c04466d30576",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "source_type": "library_preparation_process",
+                "destination_id": "5239e70b-7d8d-4285-971f-9a156441c2f2",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "source_type": "library_preparation_process",
+                "destination_id": "024c5cb6-f473-40c9-9eb3-da08caf3180e",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "fa9febdf-425e-41bc-925f-b17f27b96e61",
+                "source_type": "library_preparation_process",
+                "destination_id": "73b0c9ae-a5bb-446e-9c7b-d0954e6af425",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "a86b1fda-bb1d-4ef8-87d9-392517d4a937",
+                "source_type": "biomaterial",
+                "destination_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "destination_type": "sequencing_process"
+            },
+            {
+                "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "source_type": "sequencing_process",
+                "destination_id": "49fddace-4c59-41c1-8930-0707460132d7",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "source_type": "sequencing_process",
+                "destination_id": "771d9bcb-a5ff-43b5-b3e8-e738cc4c05bf",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "source_type": "sequencing_process",
+                "destination_id": "8ebfd02e-2a74-4367-80db-48082f331625",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "source_type": "sequencing_process",
+                "destination_id": "fea5cc65-6d94-4d1e-a807-ec248f79b83d",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "source_type": "sequencing_process",
+                "destination_id": "cee5b925-919c-4c77-8ea2-be51a1728e2b",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "source_type": "sequencing_process",
+                "destination_id": "c548066c-9994-415a-98cb-3df2933937ff",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "source_type": "sequencing_process",
+                "destination_id": "b7d8d43c-bee6-48eb-bb36-0c07701c47b5",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "source_type": "sequencing_process",
+                "destination_id": "6bc5b7ef-68f8-445d-8460-f04180c4fae1",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "source_type": "sequencing_process",
+                "destination_id": "17add91c-4063-4684-859d-d739baa4b9bb",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "source_type": "sequencing_process",
+                "destination_id": "b7554cb7-dc5a-4b07-9c7a-c04466d30576",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "source_type": "sequencing_process",
+                "destination_id": "5239e70b-7d8d-4285-971f-9a156441c2f2",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "source_type": "sequencing_process",
+                "destination_id": "024c5cb6-f473-40c9-9eb3-da08caf3180e",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8",
+                "source_type": "sequencing_process",
+                "destination_id": "73b0c9ae-a5bb-446e-9c7b-d0954e6af425",
+                "destination_type": "protocol"
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
+        "schema_version": "1.0.0",
+        "schema_type": "link_bundle"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
index 769139153..395685928 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
@@ -1262,101 +1262,101 @@
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.5",
-            "links": [
-                {
-                    "process": "15de6ce1-c185-4852-ade4-43614c5d048b",
-                    "inputs": [
-                        "906f8f09-deaa-40bb-bf50-27d2336b2dc4"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "5f68ea73-350b-4d37-a341-3004139fb699",
-                        "23f8e139-f4fa-4476-ba59-ff5d37003c34",
-                        "3c3d882a-cc38-4eea-ac53-0885f906852e",
-                        "35e07477-76cb-4a92-99b6-7b3bbb02ec06",
-                        "63051b9f-87d4-4853-a4a0-5cc742ef6e72",
-                        "6ca8e43f-5f40-4eb9-bfa9-294c54dbeade",
-                        "3dffc456-caaf-4823-9f65-fc0db7abacbc",
-                        "a2f4b05d-0dae-4655-acfd-ef3b91ae0ad0",
-                        "98ee0901-d34c-48a5-915a-0511bac325ec",
-                        "27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6",
-                        "133f2a25-f3aa-49a7-b9b6-d185d302fb26",
-                        "e46af70a-0396-41db-9b74-330cb8244124"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "2945bb1f-90de-42a3-afa1-f57a62c853f0"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "08b09d15-ef99-4278-9b88-65127adb51b9"
-                        }
-                    ]
-                },
-                {
-                    "process": "47ca0565-ab7d-42bd-8731-ce5d30cfd6c7",
-                    "inputs": [
-                        "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda",
-                        "70054038-cb12-429d-bb37-69185ff1deee"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "906f8f09-deaa-40bb-bf50-27d2336b2dc4"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "eaf15851-97e3-4e4b-b81b-0e625098f4d5"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "345bcbd2-f3a7-4f57-a806-fbb0ce4a25da"
-                        }
-                    ]
-                },
-                {
-                    "process": "df5114c9-9f52-451b-afde-3673392fc864",
-                    "inputs": [
-                        "2b7adb0a-82a4-4319-80d1-4a73d879dec1"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "8612862e-beb1-416b-a807-0a83fae8d168"
-                        }
-                    ]
-                },
-                {
-                    "process": "c5cf9180-535a-4d1c-bdee-4f6ce7845b1e",
-                    "inputs": [
-                        "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "70054038-cb12-429d-bb37-69185ff1deee"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "eaf15851-97e3-4e4b-b81b-0e625098f4d5"
-                        }
-                    ]
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.5",
+        "links": [
+            {
+                "process": "15de6ce1-c185-4852-ade4-43614c5d048b",
+                "inputs": [
+                    "906f8f09-deaa-40bb-bf50-27d2336b2dc4"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "5f68ea73-350b-4d37-a341-3004139fb699",
+                    "23f8e139-f4fa-4476-ba59-ff5d37003c34",
+                    "3c3d882a-cc38-4eea-ac53-0885f906852e",
+                    "35e07477-76cb-4a92-99b6-7b3bbb02ec06",
+                    "63051b9f-87d4-4853-a4a0-5cc742ef6e72",
+                    "6ca8e43f-5f40-4eb9-bfa9-294c54dbeade",
+                    "3dffc456-caaf-4823-9f65-fc0db7abacbc",
+                    "a2f4b05d-0dae-4655-acfd-ef3b91ae0ad0",
+                    "98ee0901-d34c-48a5-915a-0511bac325ec",
+                    "27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6",
+                    "133f2a25-f3aa-49a7-b9b6-d185d302fb26",
+                    "e46af70a-0396-41db-9b74-330cb8244124"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "2945bb1f-90de-42a3-afa1-f57a62c853f0"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "08b09d15-ef99-4278-9b88-65127adb51b9"
+                    }
+                ]
+            },
+            {
+                "process": "47ca0565-ab7d-42bd-8731-ce5d30cfd6c7",
+                "inputs": [
+                    "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda",
+                    "70054038-cb12-429d-bb37-69185ff1deee"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "906f8f09-deaa-40bb-bf50-27d2336b2dc4"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "eaf15851-97e3-4e4b-b81b-0e625098f4d5"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "345bcbd2-f3a7-4f57-a806-fbb0ce4a25da"
+                    }
+                ]
+            },
+            {
+                "process": "df5114c9-9f52-451b-afde-3673392fc864",
+                "inputs": [
+                    "2b7adb0a-82a4-4319-80d1-4a73d879dec1"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "8612862e-beb1-416b-a807-0a83fae8d168"
+                    }
+                ]
+            },
+            {
+                "process": "c5cf9180-535a-4d1c-bdee-4f6ce7845b1e",
+                "inputs": [
+                    "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "70054038-cb12-429d-bb37-69185ff1deee"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "eaf15851-97e3-4e4b-b81b-0e625098f4d5"
+                    }
+                ]
+            }
+        ]
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
index 2e377a6ca..feca4bb2a 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
@@ -1330,200 +1330,6 @@
                 "schema_minor_version": 2
             }
         },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
-            "schema_type": "links",
-            "schema_version": "2.0.0",
-            "links": [
-                {
-                    "inputs": [
-                        {
-                            "input_id": "906f8f09-deaa-40bb-bf50-27d2336b2dc4",
-                            "input_type": "cell_suspension"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_id": "5f68ea73-350b-4d37-a341-3004139fb699",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "23f8e139-f4fa-4476-ba59-ff5d37003c34",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "3c3d882a-cc38-4eea-ac53-0885f906852e",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "35e07477-76cb-4a92-99b6-7b3bbb02ec06",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "63051b9f-87d4-4853-a4a0-5cc742ef6e72",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "6ca8e43f-5f40-4eb9-bfa9-294c54dbeade",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "3dffc456-caaf-4823-9f65-fc0db7abacbc",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "a2f4b05d-0dae-4655-acfd-ef3b91ae0ad0",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "98ee0901-d34c-48a5-915a-0511bac325ec",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "133f2a25-f3aa-49a7-b9b6-d185d302fb26",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "e46af70a-0396-41db-9b74-330cb8244124",
-                            "output_type": "sequence_file"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "2945bb1f-90de-42a3-afa1-f57a62c853f0"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "08b09d15-ef99-4278-9b88-65127adb51b9"
-                        }
-                    ],
-                    "process_id": "15de6ce1-c185-4852-ade4-43614c5d048b",
-                    "process_type": "process",
-                    "link_type": "process_link"
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda",
-                            "input_type": "specimen_from_organism"
-                        },
-                        {
-                            "input_id": "70054038-cb12-429d-bb37-69185ff1deee",
-                            "input_type": "cell_line"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_id": "906f8f09-deaa-40bb-bf50-27d2336b2dc4",
-                            "output_type": "cell_suspension"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "eaf15851-97e3-4e4b-b81b-0e625098f4d5"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "345bcbd2-f3a7-4f57-a806-fbb0ce4a25da"
-                        }
-                    ],
-                    "process_id": "47ca0565-ab7d-42bd-8731-ce5d30cfd6c7",
-                    "process_type": "process",
-                    "link_type": "process_link"
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "2b7adb0a-82a4-4319-80d1-4a73d879dec1",
-                            "input_type": "donor_organism"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_id": "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda",
-                            "output_type": "specimen_from_organism"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "8612862e-beb1-416b-a807-0a83fae8d168"
-                        }
-                    ],
-                    "process_id": "df5114c9-9f52-451b-afde-3673392fc864",
-                    "process_type": "process",
-                    "link_type": "process_link"
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda",
-                            "input_type": "specimen_from_organism"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_id": "70054038-cb12-429d-bb37-69185ff1deee",
-                            "output_type": "cell_line"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "eaf15851-97e3-4e4b-b81b-0e625098f4d5"
-                        }
-                    ],
-                    "process_id": "c5cf9180-535a-4d1c-bdee-4f6ce7845b1e",
-                    "process_type": "process",
-                    "link_type": "process_link"
-                },
-                {
-                    "link_type": "supplementary_file_link",
-                    "entity": {
-                        "entity_type": "project",
-                        "entity_id": "116965f3-f094-4769-9d28-ae675c1b569c"
-                    },
-                    "files": [
-                        {
-                            "file_type": "supplementary_file",
-                            "file_id": "22561f93-d5e0-57eb-a54e-2d9d565cc234"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "supplementary_file_link",
-                    "entity": {
-                        "entity_type": "project",
-                        "entity_id": "116965f3-f094-4769-9d28-ae675c1b569c"
-                    },
-                    "files": [
-                        {
-                            "file_type": "supplementary_file",
-                            "file_id": "507d2814-1688-54e7-b73e-2f831aa34368"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "supplementary_file_link",
-                    "entity": {
-                        "entity_type": "project",
-                        "entity_id": "116965f3-f094-4769-9d28-ae675c1b569c"
-                    },
-                    "files": [
-                        {
-                            "file_type": "supplementary_file",
-                            "file_id": "c343a47d-683f-571d-99c4-1331841b4e63"
-                        }
-                    ]
-                }
-            ]
-        },
         "supplementary_file_0.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/2.2.0/supplementary_file/supplementary_file",
             "schema_type": "file",
@@ -1560,5 +1366,199 @@
                 "format": "unknown"
             }
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
+        "schema_type": "links",
+        "schema_version": "2.0.0",
+        "links": [
+            {
+                "inputs": [
+                    {
+                        "input_id": "906f8f09-deaa-40bb-bf50-27d2336b2dc4",
+                        "input_type": "cell_suspension"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_id": "5f68ea73-350b-4d37-a341-3004139fb699",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "23f8e139-f4fa-4476-ba59-ff5d37003c34",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "3c3d882a-cc38-4eea-ac53-0885f906852e",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "35e07477-76cb-4a92-99b6-7b3bbb02ec06",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "63051b9f-87d4-4853-a4a0-5cc742ef6e72",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "6ca8e43f-5f40-4eb9-bfa9-294c54dbeade",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "3dffc456-caaf-4823-9f65-fc0db7abacbc",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "a2f4b05d-0dae-4655-acfd-ef3b91ae0ad0",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "98ee0901-d34c-48a5-915a-0511bac325ec",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "133f2a25-f3aa-49a7-b9b6-d185d302fb26",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "e46af70a-0396-41db-9b74-330cb8244124",
+                        "output_type": "sequence_file"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "2945bb1f-90de-42a3-afa1-f57a62c853f0"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "08b09d15-ef99-4278-9b88-65127adb51b9"
+                    }
+                ],
+                "process_id": "15de6ce1-c185-4852-ade4-43614c5d048b",
+                "process_type": "process",
+                "link_type": "process_link"
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda",
+                        "input_type": "specimen_from_organism"
+                    },
+                    {
+                        "input_id": "70054038-cb12-429d-bb37-69185ff1deee",
+                        "input_type": "cell_line"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_id": "906f8f09-deaa-40bb-bf50-27d2336b2dc4",
+                        "output_type": "cell_suspension"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "eaf15851-97e3-4e4b-b81b-0e625098f4d5"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "345bcbd2-f3a7-4f57-a806-fbb0ce4a25da"
+                    }
+                ],
+                "process_id": "47ca0565-ab7d-42bd-8731-ce5d30cfd6c7",
+                "process_type": "process",
+                "link_type": "process_link"
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "2b7adb0a-82a4-4319-80d1-4a73d879dec1",
+                        "input_type": "donor_organism"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_id": "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda",
+                        "output_type": "specimen_from_organism"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "8612862e-beb1-416b-a807-0a83fae8d168"
+                    }
+                ],
+                "process_id": "df5114c9-9f52-451b-afde-3673392fc864",
+                "process_type": "process",
+                "link_type": "process_link"
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda",
+                        "input_type": "specimen_from_organism"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_id": "70054038-cb12-429d-bb37-69185ff1deee",
+                        "output_type": "cell_line"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "eaf15851-97e3-4e4b-b81b-0e625098f4d5"
+                    }
+                ],
+                "process_id": "c5cf9180-535a-4d1c-bdee-4f6ce7845b1e",
+                "process_type": "process",
+                "link_type": "process_link"
+            },
+            {
+                "link_type": "supplementary_file_link",
+                "entity": {
+                    "entity_type": "project",
+                    "entity_id": "116965f3-f094-4769-9d28-ae675c1b569c"
+                },
+                "files": [
+                    {
+                        "file_type": "supplementary_file",
+                        "file_id": "22561f93-d5e0-57eb-a54e-2d9d565cc234"
+                    }
+                ]
+            },
+            {
+                "link_type": "supplementary_file_link",
+                "entity": {
+                    "entity_type": "project",
+                    "entity_id": "116965f3-f094-4769-9d28-ae675c1b569c"
+                },
+                "files": [
+                    {
+                        "file_type": "supplementary_file",
+                        "file_id": "507d2814-1688-54e7-b73e-2f831aa34368"
+                    }
+                ]
+            },
+            {
+                "link_type": "supplementary_file_link",
+                "entity": {
+                    "entity_type": "project",
+                    "entity_id": "116965f3-f094-4769-9d28-ae675c1b569c"
+                },
+                "files": [
+                    {
+                        "file_type": "supplementary_file",
+                        "file_id": "c343a47d-683f-571d-99c4-1331841b4e63"
+                    }
+                ]
+            }
+        ]
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json b/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
index f68635d48..42b024d94 100644
--- a/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
+++ b/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
@@ -206,108 +206,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
-            "links": [
-                {
-                    "inputs": [
-                        {
-                            "input_id": "6ff38054-9296-5d4c-b238-6a3b01a15175",
-                            "input_type": "cell_suspension"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "de17aa7d-be28-53c1-b7a3-1f4b3989e3e6",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "8da4bdb9-ab64-5a90-8bce-f0ed5106ea41",
-                            "output_type": "sequence_file"
-                        }
-                    ],
-                    "process_id": "1ed68210-eaba-531d-ba9e-db80164d65ef",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "767282b2-2fc1-5559-b020-29686b810206",
-                            "protocol_type": "library_preparation_protocol"
-                        },
-                        {
-                            "protocol_id": "1b8dfafd-178f-5826-a661-8a022334aaeb",
-                            "protocol_type": "sequencing_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "119c4135-7b77-5003-a150-f052e22c6834",
-                            "input_type": "cell_suspension"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "6ff38054-9296-5d4c-b238-6a3b01a15175",
-                            "output_type": "cell_suspension"
-                        }
-                    ],
-                    "process_id": "b0092a47-b19d-5b34-b004-cb8edd8c625b",
-                    "process_type": "process",
-                    "protocols": []
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "3bee0c9a-aced-52f2-b97f-89518f826b36",
-                            "input_type": "specimen_from_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "119c4135-7b77-5003-a150-f052e22c6834",
-                            "output_type": "cell_suspension"
-                        }
-                    ],
-                    "process_id": "bd6a4a38-c44b-5d17-b2b1-d0d4c4531bf0",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "46435803-7ee8-5157-8569-8a61ad50c315",
-                            "protocol_type": "enrichment_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "5bc2bf2f-eb98-5510-a386-172cef38f2f2",
-                            "input_type": "donor_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "3bee0c9a-aced-52f2-b97f-89518f826b36",
-                            "output_type": "specimen_from_organism"
-                        }
-                    ],
-                    "process_id": "37e91a9f-b04e-5313-bbc0-4c394406247e",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "e7f864e3-6ba7-53c8-842f-2a05cb90e1b7",
-                            "protocol_type": "collection_protocol"
-                        }
-                    ]
-                }
-            ],
-            "schema_type": "links",
-            "schema_version": "3.1.0"
-        },
         "project_0.json": {
             "array_express_accessions": [
                 "E-MTAB-10026"
@@ -767,5 +665,107 @@
             },
             "schema_type": "protocol"
         }
+    },
+    "links": {
+        "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
+        "links": [
+            {
+                "inputs": [
+                    {
+                        "input_id": "6ff38054-9296-5d4c-b238-6a3b01a15175",
+                        "input_type": "cell_suspension"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "de17aa7d-be28-53c1-b7a3-1f4b3989e3e6",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "8da4bdb9-ab64-5a90-8bce-f0ed5106ea41",
+                        "output_type": "sequence_file"
+                    }
+                ],
+                "process_id": "1ed68210-eaba-531d-ba9e-db80164d65ef",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "767282b2-2fc1-5559-b020-29686b810206",
+                        "protocol_type": "library_preparation_protocol"
+                    },
+                    {
+                        "protocol_id": "1b8dfafd-178f-5826-a661-8a022334aaeb",
+                        "protocol_type": "sequencing_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "119c4135-7b77-5003-a150-f052e22c6834",
+                        "input_type": "cell_suspension"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "6ff38054-9296-5d4c-b238-6a3b01a15175",
+                        "output_type": "cell_suspension"
+                    }
+                ],
+                "process_id": "b0092a47-b19d-5b34-b004-cb8edd8c625b",
+                "process_type": "process",
+                "protocols": []
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "3bee0c9a-aced-52f2-b97f-89518f826b36",
+                        "input_type": "specimen_from_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "119c4135-7b77-5003-a150-f052e22c6834",
+                        "output_type": "cell_suspension"
+                    }
+                ],
+                "process_id": "bd6a4a38-c44b-5d17-b2b1-d0d4c4531bf0",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "46435803-7ee8-5157-8569-8a61ad50c315",
+                        "protocol_type": "enrichment_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "5bc2bf2f-eb98-5510-a386-172cef38f2f2",
+                        "input_type": "donor_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "3bee0c9a-aced-52f2-b97f-89518f826b36",
+                        "output_type": "specimen_from_organism"
+                    }
+                ],
+                "process_id": "37e91a9f-b04e-5313-bbc0-4c394406247e",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "e7f864e3-6ba7-53c8-842f-2a05cb90e1b7",
+                        "protocol_type": "collection_protocol"
+                    }
+                ]
+            }
+        ],
+        "schema_type": "links",
+        "schema_version": "3.1.0"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json b/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
index 84844102f..308cd36dd 100644
--- a/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
+++ b/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
@@ -158,86 +158,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
-            "links": [
-                {
-                    "inputs": [
-                        {
-                            "input_id": "0bf91a05-85df-5d7d-bcc0-a625c5921de2",
-                            "input_type": "imaged_specimen"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "2645ed0a-a291-5fe2-a262-7b796b05d647",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "1f6afb64-fa14-5c6f-a474-a742540108a3",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "5e1fa49c-f0e9-5c2c-be16-386ccd60dfd7",
-                            "protocol_type": "analysis_protocol"
-                        },
-                        {
-                            "protocol_id": "83f14748-af1c-57aa-9088-6cb1cdd4bba4",
-                            "protocol_type": "library_preparation_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "9a0bb729-552a-5f6e-9ed6-1f988c259531",
-                            "input_type": "specimen_from_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "0bf91a05-85df-5d7d-bcc0-a625c5921de2",
-                            "output_type": "imaged_specimen"
-                        }
-                    ],
-                    "process_id": "ae8529dc-3bc9-5061-828a-3c5dfacded64",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "7cd840db-f395-5a61-bd17-72c2b2319c23",
-                            "protocol_type": "imaging_preparation_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "2d7b50d8-cd06-5408-9fde-1faed01c9ab2",
-                            "input_type": "donor_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "9a0bb729-552a-5f6e-9ed6-1f988c259531",
-                            "output_type": "specimen_from_organism"
-                        }
-                    ],
-                    "process_id": "c6b932ff-69f1-58b1-a6e6-30319f04541b",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "c5752f73-3511-55e1-95af-040ab3924bce",
-                            "protocol_type": "collection_protocol"
-                        }
-                    ]
-                }
-            ],
-            "schema_type": "links",
-            "schema_version": "3.1.0"
-        },
         "project_0.json": {
             "array_express_accessions": [
                 "E-MTAB-10026"
@@ -614,5 +534,85 @@
             },
             "schema_type": "protocol"
         }
+    },
+    "links": {
+        "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
+        "links": [
+            {
+                "inputs": [
+                    {
+                        "input_id": "0bf91a05-85df-5d7d-bcc0-a625c5921de2",
+                        "input_type": "imaged_specimen"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "2645ed0a-a291-5fe2-a262-7b796b05d647",
+                        "output_type": "analysis_file"
+                    }
+                ],
+                "process_id": "1f6afb64-fa14-5c6f-a474-a742540108a3",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "5e1fa49c-f0e9-5c2c-be16-386ccd60dfd7",
+                        "protocol_type": "analysis_protocol"
+                    },
+                    {
+                        "protocol_id": "83f14748-af1c-57aa-9088-6cb1cdd4bba4",
+                        "protocol_type": "library_preparation_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "9a0bb729-552a-5f6e-9ed6-1f988c259531",
+                        "input_type": "specimen_from_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "0bf91a05-85df-5d7d-bcc0-a625c5921de2",
+                        "output_type": "imaged_specimen"
+                    }
+                ],
+                "process_id": "ae8529dc-3bc9-5061-828a-3c5dfacded64",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "7cd840db-f395-5a61-bd17-72c2b2319c23",
+                        "protocol_type": "imaging_preparation_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "2d7b50d8-cd06-5408-9fde-1faed01c9ab2",
+                        "input_type": "donor_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "9a0bb729-552a-5f6e-9ed6-1f988c259531",
+                        "output_type": "specimen_from_organism"
+                    }
+                ],
+                "process_id": "c6b932ff-69f1-58b1-a6e6-30319f04541b",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "c5752f73-3511-55e1-95af-040ab3924bce",
+                        "protocol_type": "collection_protocol"
+                    }
+                ]
+            }
+        ],
+        "schema_type": "links",
+        "schema_version": "3.1.0"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
index 5db6250e6..1bc9e5dda 100644
--- a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
+++ b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
@@ -184,94 +184,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "links": [
-                {
-                    "link_type": "process_link",
-                    "process_id": "1fd499c5-f397-4bff-9af0-eb42c37d5fbe",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "cell_suspension",
-                            "input_id": "d1bc1192-b584-41c2-8591-6cea79fb7729"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "0d352174-7bf3-44b3-9b7b-7ef3056ed085"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "853dbcbd-8aaf-479d-8e57-134e11c61b72"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "bf7e7b5d-2ffa-4fb7-977f-c42c5c334bbe"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "328e83cc-1e31-4d49-bf69-3504a7d1d4ba"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "04446f99-f9ed-4a4a-82ec-203ed468cbc0",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "70d2b85a-8055-4027-a0d9-29452a49d668"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "cell_suspension",
-                            "output_id": "d1bc1192-b584-41c2-8591-6cea79fb7729"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "ef41ddaf-a324-40da-a149-dd27c6bb5f04"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "fb9f9cf3-28f9-4903-b191-10217bc18da6"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "5f1f265f-edd3-4172-b5ae-5b9d39a389d2",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "b111e5bf-e907-47f9-8eed-75b2ec5536c5"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "70d2b85a-8055-4027-a0d9-29452a49d668"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "acf142b9-0657-4ffb-b039-cd0dd5317e25"
-                        }
-                    ]
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links",
-            "schema_version": "2.1.1",
-            "schema_type": "links"
-        },
         "process_0.json": {
             "process_core": {
                 "process_id": "process_id_50"
@@ -756,5 +668,93 @@
                 "schema_minor_version": 1
             }
         }
+    },
+    "links": {
+        "links": [
+            {
+                "link_type": "process_link",
+                "process_id": "1fd499c5-f397-4bff-9af0-eb42c37d5fbe",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "d1bc1192-b584-41c2-8591-6cea79fb7729"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "0d352174-7bf3-44b3-9b7b-7ef3056ed085"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "853dbcbd-8aaf-479d-8e57-134e11c61b72"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "bf7e7b5d-2ffa-4fb7-977f-c42c5c334bbe"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "328e83cc-1e31-4d49-bf69-3504a7d1d4ba"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "04446f99-f9ed-4a4a-82ec-203ed468cbc0",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "70d2b85a-8055-4027-a0d9-29452a49d668"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "d1bc1192-b584-41c2-8591-6cea79fb7729"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "ef41ddaf-a324-40da-a149-dd27c6bb5f04"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "fb9f9cf3-28f9-4903-b191-10217bc18da6"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "5f1f265f-edd3-4172-b5ae-5b9d39a389d2",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "b111e5bf-e907-47f9-8eed-75b2ec5536c5"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "70d2b85a-8055-4027-a0d9-29452a49d668"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "acf142b9-0657-4ffb-b039-cd0dd5317e25"
+                    }
+                ]
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links",
+        "schema_version": "2.1.1",
+        "schema_type": "links"
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json b/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
index 6955a5cb9..ad30a46e3 100644
--- a/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
+++ b/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
@@ -9128,3673 +9128,3673 @@
                 "updateDate": "2018-03-26T16:59:27.537Z",
                 "document_id": "e99eed63-5794-4d8d-baf9-9c6888e91e6d"
             }
-        },
-        "links.json": {
-            "links": [
-                {
-                    "source_id": "78e48232-86ed-4b68-ae64-df114f02fa80",
-                    "source_type": "biomaterial",
-                    "destination_id": "b34ed0ee-2f70-4ae8-8e15-3493e5c92d70",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "b34ed0ee-2f70-4ae8-8e15-3493e5c92d70",
-                    "source_type": "dissociation_process",
-                    "destination_id": "6d98e8a4-dc7e-4ee8-aad6-9861b744e9fe",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "b34ed0ee-2f70-4ae8-8e15-3493e5c92d70",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "6ab99524-b114-42c5-9881-0bc2724f9889",
-                    "source_type": "process",
-                    "destination_id": "78e48232-86ed-4b68-ae64-df114f02fa80",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "7d2dcb65-b759-40b8-9eb0-7b9951b7c036",
-                    "source_type": "biomaterial",
-                    "destination_id": "6ab99524-b114-42c5-9881-0bc2724f9889",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "2fe26d80-85fb-4926-bad1-a92a6e8c20c1",
-                    "source_type": "biomaterial",
-                    "destination_id": "fc53f40f-3005-4393-8589-17850fb564de",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "fc53f40f-3005-4393-8589-17850fb564de",
-                    "source_type": "dissociation_process",
-                    "destination_id": "01f2d4b7-7746-4dc0-88d7-4cb0b3dbb370",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "fc53f40f-3005-4393-8589-17850fb564de",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "27d241a3-05fb-44f7-a3e3-1e84adc14c09",
-                    "source_type": "process",
-                    "destination_id": "2fe26d80-85fb-4926-bad1-a92a6e8c20c1",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "0a69e7c4-56a3-498e-a867-aaf84c1344c8",
-                    "source_type": "biomaterial",
-                    "destination_id": "27d241a3-05fb-44f7-a3e3-1e84adc14c09",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "24796176-5825-47a3-966a-38a865d541ab",
-                    "source_type": "biomaterial",
-                    "destination_id": "cc620d3d-f823-47b0-957c-3c7170dd9ede",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "cc620d3d-f823-47b0-957c-3c7170dd9ede",
-                    "source_type": "dissociation_process",
-                    "destination_id": "ed887207-2034-4c85-bbec-4e69a745d009",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "cc620d3d-f823-47b0-957c-3c7170dd9ede",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "896e543d-e666-4380-aafe-ed0ff214de9d",
-                    "source_type": "process",
-                    "destination_id": "24796176-5825-47a3-966a-38a865d541ab",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "06d98ad8-bbac-40df-9eb6-d5b1a424568a",
-                    "source_type": "biomaterial",
-                    "destination_id": "896e543d-e666-4380-aafe-ed0ff214de9d",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "1ff0b001-3753-491f-8424-dc30a1e47953",
-                    "source_type": "biomaterial",
-                    "destination_id": "4ac1c779-d396-402f-b6ff-15479c60ec13",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "4ac1c779-d396-402f-b6ff-15479c60ec13",
-                    "source_type": "dissociation_process",
-                    "destination_id": "e1db28a3-83c8-43ce-8e41-40b0429c2c4e",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "4ac1c779-d396-402f-b6ff-15479c60ec13",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "402807c3-8b87-4f76-9609-b6526d88d6ad",
-                    "source_type": "process",
-                    "destination_id": "1ff0b001-3753-491f-8424-dc30a1e47953",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "5caa7ca2-308a-424d-8bae-9204a2be2502",
-                    "source_type": "biomaterial",
-                    "destination_id": "402807c3-8b87-4f76-9609-b6526d88d6ad",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "73022d99-f258-427b-a574-f9a046c20c81",
-                    "source_type": "biomaterial",
-                    "destination_id": "be06fd42-358a-43d4-9be9-02ee37ab8bb7",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "be06fd42-358a-43d4-9be9-02ee37ab8bb7",
-                    "source_type": "dissociation_process",
-                    "destination_id": "10ddecf6-ad4c-4d20-889f-93c83e3d5562",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "be06fd42-358a-43d4-9be9-02ee37ab8bb7",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "1a81ba59-5458-4983-b600-2d9b3fc716ee",
-                    "source_type": "process",
-                    "destination_id": "73022d99-f258-427b-a574-f9a046c20c81",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "5caa7ca2-308a-424d-8bae-9204a2be2502",
-                    "source_type": "biomaterial",
-                    "destination_id": "1a81ba59-5458-4983-b600-2d9b3fc716ee",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "a003d338-753f-433e-bb6c-f36650e76b6a",
-                    "source_type": "biomaterial",
-                    "destination_id": "4a75ceaf-c488-492d-9cc0-869a887c97a3",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "4a75ceaf-c488-492d-9cc0-869a887c97a3",
-                    "source_type": "dissociation_process",
-                    "destination_id": "f564e3b1-d887-4667-9383-1d9b8cbbbd0f",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "4a75ceaf-c488-492d-9cc0-869a887c97a3",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "1b8fe79e-48da-43a4-aa56-b71100ebf553",
-                    "source_type": "process",
-                    "destination_id": "a003d338-753f-433e-bb6c-f36650e76b6a",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "5caa7ca2-308a-424d-8bae-9204a2be2502",
-                    "source_type": "biomaterial",
-                    "destination_id": "1b8fe79e-48da-43a4-aa56-b71100ebf553",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "d56760e7-0605-4e8e-9ee0-09b37b3bdf14",
-                    "source_type": "biomaterial",
-                    "destination_id": "a3447292-5309-4412-af13-d2b81e4684a2",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "a3447292-5309-4412-af13-d2b81e4684a2",
-                    "source_type": "dissociation_process",
-                    "destination_id": "bd59eb0f-46e3-497a-9dd1-a5d0e5ca3ac4",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "a3447292-5309-4412-af13-d2b81e4684a2",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "609711e7-b252-4303-b711-e203f0513d74",
-                    "source_type": "process",
-                    "destination_id": "d56760e7-0605-4e8e-9ee0-09b37b3bdf14",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "0a69e7c4-56a3-498e-a867-aaf84c1344c8",
-                    "source_type": "biomaterial",
-                    "destination_id": "609711e7-b252-4303-b711-e203f0513d74",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "4d5d375f-dd74-476e-8f62-071aa6853bea",
-                    "source_type": "biomaterial",
-                    "destination_id": "c7eae156-78ca-4c59-9d43-ef360fe8c5fc",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "c7eae156-78ca-4c59-9d43-ef360fe8c5fc",
-                    "source_type": "dissociation_process",
-                    "destination_id": "4064ed72-cf76-4418-8ca1-f916aca95680",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "c7eae156-78ca-4c59-9d43-ef360fe8c5fc",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "8b43cec2-3941-46d1-98fa-5a20b662ca95",
-                    "source_type": "process",
-                    "destination_id": "4d5d375f-dd74-476e-8f62-071aa6853bea",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "7d2dcb65-b759-40b8-9eb0-7b9951b7c036",
-                    "source_type": "biomaterial",
-                    "destination_id": "8b43cec2-3941-46d1-98fa-5a20b662ca95",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "89426736-1779-4ceb-ae11-7935299ee579",
-                    "source_type": "biomaterial",
-                    "destination_id": "581ae735-fcdb-4642-bfe8-4f89e58e3b5f",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "581ae735-fcdb-4642-bfe8-4f89e58e3b5f",
-                    "source_type": "dissociation_process",
-                    "destination_id": "b08c7d38-caa6-4573-ba7e-37da8aa66605",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "581ae735-fcdb-4642-bfe8-4f89e58e3b5f",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "ee6b760e-be5e-4cd4-975f-fd5c355ee499",
-                    "source_type": "process",
-                    "destination_id": "89426736-1779-4ceb-ae11-7935299ee579",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "7d2dcb65-b759-40b8-9eb0-7b9951b7c036",
-                    "source_type": "biomaterial",
-                    "destination_id": "ee6b760e-be5e-4cd4-975f-fd5c355ee499",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "e31c73aa-39bb-4a9c-a3fb-7912046742a8",
-                    "source_type": "biomaterial",
-                    "destination_id": "66cd42fa-9fde-4be7-a21b-f225142786d5",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "66cd42fa-9fde-4be7-a21b-f225142786d5",
-                    "source_type": "dissociation_process",
-                    "destination_id": "4027035b-3251-44b9-a281-fc9182de7579",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "66cd42fa-9fde-4be7-a21b-f225142786d5",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "73f01b56-5c1e-496f-b6a3-c2e19a53bea4",
-                    "source_type": "process",
-                    "destination_id": "e31c73aa-39bb-4a9c-a3fb-7912046742a8",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "06d98ad8-bbac-40df-9eb6-d5b1a424568a",
-                    "source_type": "biomaterial",
-                    "destination_id": "73f01b56-5c1e-496f-b6a3-c2e19a53bea4",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "cb55025a-b76a-41f3-9d6d-68723fea2e0e",
-                    "source_type": "biomaterial",
-                    "destination_id": "88c9f910-860b-418f-8668-afba756c282b",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "88c9f910-860b-418f-8668-afba756c282b",
-                    "source_type": "dissociation_process",
-                    "destination_id": "33fbab10-cbbe-4b44-9e5b-df07df548949",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "88c9f910-860b-418f-8668-afba756c282b",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "eea88216-55c5-4700-9e22-577bb20fcbe8",
-                    "source_type": "process",
-                    "destination_id": "cb55025a-b76a-41f3-9d6d-68723fea2e0e",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "5caa7ca2-308a-424d-8bae-9204a2be2502",
-                    "source_type": "biomaterial",
-                    "destination_id": "eea88216-55c5-4700-9e22-577bb20fcbe8",
-                    "destination_type": "process"
-                },
-                {
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+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "5da8e6f2-a26e-448b-b017-33ac69ca80f7",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "c59d880d-7847-4525-990b-ab283257a166",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "614a69c9-4212-46bf-948e-d7affd2310e5",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "40c497af-80ea-4c54-a628-a57486c0f8ec",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "b23a12bd-3372-4542-a5e6-0f9bcdcb51dd",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "7844a2e7-6307-4e70-af10-fdcff29496e2",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "66e5a918-007f-4ef6-a514-b8043bcc6128",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "452b88e0-94cf-4243-b44e-94b16c936896",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "32aeb59b-d1f7-4660-9b98-f72ebe671864",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "751ad2cb-994b-40d2-b6ba-9d4f59112f12",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "1705dea1-fff5-4f39-985d-b2a70f5d2ea1",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "05dcbcdd-7288-4e17-94dc-bb9e099a2a20",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "f97c6247-15c6-403e-9a15-62113f9dc24a",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "3c4864ae-619e-479d-8138-c1489e7f10bb",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "5703221a-e4bf-4f4a-a5a0-747aa74d46b2",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "463a120d-ee95-476c-8329-c633b43ab1aa",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "98f19741-b0fe-4aff-ab8c-9a77af8e36ce",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "9820fbb5-07b7-41ce-b135-16e21b371c94",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "cab74e16-3229-4808-922a-743447d7da23",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "fac833de-2bb8-4f4a-a1dd-6136fbc288b1",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "5506a837-6ff5-4004-8c2c-673a8d93c510",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "6d7e8891-156b-4b23-848c-8ef75230cbbd",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "8eca3a7d-67f1-412d-9d3a-704c8218cee2",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "57d69572-96ae-4a29-97f5-0c1a491ed2a5",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "b55fd000-cd16-4976-b264-8df9e012df4e",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "d7e6574e-dae6-4e6f-8db0-370693adea27",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "ac66a331-f88f-4ec0-b08a-79612fde6b37",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "551caaec-e076-4794-9096-7b8f5176e9c3",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "415a6ab3-aa59-4e68-8993-64fd1a0715be",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "13bcdac2-f7f5-405d-b860-9ce88b423d80",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "2bdc88a5-faf4-4f07-8818-a95428defe3a",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "2c659838-791d-498e-a3fa-f0c8eb1b2559",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "ffa21ee7-98c7-4275-a28f-ab87350b6317",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "30a446dd-cb56-4055-bf82-6b3b06d47ee7",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "5fbc6d6e-8905-4ef4-92c7-b13c7fc1b33c",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "5c1ccd4f-d639-43d0-94b6-3baca6f8210d",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "0cf26327-ce69-4e4e-b1ad-efdc3ffd9195",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "7f2b78dc-2b1c-4912-b456-170ba3891464",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "722bf139-3585-4349-bd60-2108cdea9783",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "85f9f0a9-6b8e-4fba-a360-8d14931a7929",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "ffa34fcb-1a7d-45cd-95be-c29cd95e73da",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "70e83656-b4c8-4453-9d99-08989b2baf6e",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "712084da-4b68-47e0-acff-aafb48cc21db",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "ab9fcfa0-6a1c-4fcd-a0f8-73737ddfb027",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "fe25d73e-ecb7-4228-bfa5-b87ea5f1eb91",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "0bf66ea5-3dee-422b-b8f0-837033556d99",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "94f47ceb-f4b3-4e6c-9fb4-55c428507e75",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "05c46800-9101-4151-9b4b-3a0fe981e76e",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "af80a9d5-0e61-4a4a-a32c-6a22ca542ea5",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "a64e2f58-8fbc-4382-9ca9-845f32a7133f",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "f379d8e5-1741-4992-a46f-692f352d81e2",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464",
+                "source_type": "sequencing_process",
+                "destination_id": "e99eed63-5794-4d8d-baf9-9c6888e91e6d",
+                "destination_type": "protocol"
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
+        "schema_version": "1.0.0",
+        "schema_type": "link_bundle"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
index 4f7fc5d64..ef0488229 100644
--- a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
+++ b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
@@ -170,94 +170,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "links": [
-                {
-                    "link_type": "process_link",
-                    "process_id": "2c7d06b8-658e-4c51-9de4-a768322f84c5",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "cell_suspension",
-                            "input_id": "809b90b1-e216-46e9-b4e3-0c06ded1c344"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "analysis_file",
-                            "output_id": "30038dc4-4de3-4fdb-abd3-a50ea36cb225"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "analysis_protocol",
-                            "protocol_id": "d42d3386-e7b7-4a26-8477-8ba867d10e2e"
-                        },
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "56e28cda-b5a6-40e5-801e-221a7c49e47f"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "c2f2fee0-c8dc-4511-9e4a-3db4ab6b2dce"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "bb7cdb75-8a5a-414b-a40b-d20dcbfa9b15",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "3c219f11-db59-48b9-987a-a827400b9c7a"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "cell_suspension",
-                            "output_id": "809b90b1-e216-46e9-b4e3-0c06ded1c344"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "c44dab69-861e-45f2-abbf-f785a552b10a"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "948945f9-1a3e-4be0-9119-960cc008bfa9"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "6f500f25-8ea3-46e6-a30b-c11bb991e3a2",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "7ec2d69f-714f-450e-a687-73c1c0c98b6f"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "3c219f11-db59-48b9-987a-a827400b9c7a"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "5a1041e3-ef49-45c3-a14b-636d22aae731"
-                        }
-                    ]
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/system/3.0.0/links",
-            "schema_version": "3.0.0",
-            "schema_type": "links"
-        },
         "sequencing_protocol_0.json": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
@@ -675,7 +587,7 @@
                     "organization": "NIDCR Combined Technical Research Core"
                 }
             ],
-             "hca_bionetworks": [
+            "hca_bionetworks": [
                 {
                     "name": "Kidney"
                 },
@@ -804,5 +716,93 @@
                 "schema_minor_version": 3
             }
         }
+    },
+    "links": {
+        "links": [
+            {
+                "link_type": "process_link",
+                "process_id": "2c7d06b8-658e-4c51-9de4-a768322f84c5",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "809b90b1-e216-46e9-b4e3-0c06ded1c344"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "analysis_file",
+                        "output_id": "30038dc4-4de3-4fdb-abd3-a50ea36cb225"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "analysis_protocol",
+                        "protocol_id": "d42d3386-e7b7-4a26-8477-8ba867d10e2e"
+                    },
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "56e28cda-b5a6-40e5-801e-221a7c49e47f"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "c2f2fee0-c8dc-4511-9e4a-3db4ab6b2dce"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "bb7cdb75-8a5a-414b-a40b-d20dcbfa9b15",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "3c219f11-db59-48b9-987a-a827400b9c7a"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "809b90b1-e216-46e9-b4e3-0c06ded1c344"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "c44dab69-861e-45f2-abbf-f785a552b10a"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "948945f9-1a3e-4be0-9119-960cc008bfa9"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "6f500f25-8ea3-46e6-a30b-c11bb991e3a2",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "7ec2d69f-714f-450e-a687-73c1c0c98b6f"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "3c219f11-db59-48b9-987a-a827400b9c7a"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "5a1041e3-ef49-45c3-a14b-636d22aae731"
+                    }
+                ]
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/system/3.0.0/links",
+        "schema_version": "3.0.0",
+        "schema_type": "links"
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json b/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
index 68f2b8687..9cf666e5a 100644
--- a/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
+++ b/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
@@ -146,82 +146,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
-            "links": [
-                {
-                    "inputs": [
-                        {
-                            "input_id": "0bf91a05-85df-5d7d-bcc0-a625c5921de2",
-                            "input_type": "imaged_specimen"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "b29a331e-2d7b-507f-8e47-d6151bfeeb21",
-                            "output_type": "image_file"
-                        }
-                    ],
-                    "process_id": "3ac62c33-93e1-56b4-b857-59497f5d942d",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "50150415-898c-5dff-826e-55f9cb937b93",
-                            "protocol_type": "imaging_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "9a0bb729-552a-5f6e-9ed6-1f988c259531",
-                            "input_type": "specimen_from_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "0bf91a05-85df-5d7d-bcc0-a625c5921de2",
-                            "output_type": "imaged_specimen"
-                        }
-                    ],
-                    "process_id": "ae8529dc-3bc9-5061-828a-3c5dfacded64",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "7cd840db-f395-5a61-bd17-72c2b2319c23",
-                            "protocol_type": "imaging_preparation_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "2d7b50d8-cd06-5408-9fde-1faed01c9ab2",
-                            "input_type": "donor_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "9a0bb729-552a-5f6e-9ed6-1f988c259531",
-                            "output_type": "specimen_from_organism"
-                        }
-                    ],
-                    "process_id": "c6b932ff-69f1-58b1-a6e6-30319f04541b",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "c5752f73-3511-55e1-95af-040ab3924bce",
-                            "protocol_type": "collection_protocol"
-                        }
-                    ]
-                }
-            ],
-            "schema_type": "links",
-            "schema_version": "3.1.0"
-        },
         "project_0.json": {
             "array_express_accessions": [
                 "E-MTAB-10026"
@@ -563,5 +487,81 @@
             },
             "schema_type": "protocol"
         }
+    },
+    "links": {
+        "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
+        "links": [
+            {
+                "inputs": [
+                    {
+                        "input_id": "0bf91a05-85df-5d7d-bcc0-a625c5921de2",
+                        "input_type": "imaged_specimen"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "b29a331e-2d7b-507f-8e47-d6151bfeeb21",
+                        "output_type": "image_file"
+                    }
+                ],
+                "process_id": "3ac62c33-93e1-56b4-b857-59497f5d942d",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "50150415-898c-5dff-826e-55f9cb937b93",
+                        "protocol_type": "imaging_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "9a0bb729-552a-5f6e-9ed6-1f988c259531",
+                        "input_type": "specimen_from_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "0bf91a05-85df-5d7d-bcc0-a625c5921de2",
+                        "output_type": "imaged_specimen"
+                    }
+                ],
+                "process_id": "ae8529dc-3bc9-5061-828a-3c5dfacded64",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "7cd840db-f395-5a61-bd17-72c2b2319c23",
+                        "protocol_type": "imaging_preparation_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "2d7b50d8-cd06-5408-9fde-1faed01c9ab2",
+                        "input_type": "donor_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "9a0bb729-552a-5f6e-9ed6-1f988c259531",
+                        "output_type": "specimen_from_organism"
+                    }
+                ],
+                "process_id": "c6b932ff-69f1-58b1-a6e6-30319f04541b",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "c5752f73-3511-55e1-95af-040ab3924bce",
+                        "protocol_type": "collection_protocol"
+                    }
+                ]
+            }
+        ],
+        "schema_type": "links",
+        "schema_version": "3.1.0"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
index c2694b954..12762e864 100644
--- a/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
+++ b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
@@ -1361,227 +1361,227 @@
                 "submission_date": "2018-11-02T17:38:40.299Z",
                 "update_date": "2018-11-02T17:38:45.850Z"
             }
-        },
-        "links.json": {
-            "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.3/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.3",
-            "links": [
-                {
-                    "process": "b7a172d6-dbb1-41f3-8ae4-7807e1eca803",
-                    "inputs": [
-                        "6f725a94-5c81-45e5-8d16-96520aa99703",
-                        "2db43e94-5208-405e-bc2a-ffade59b94c0",
-                        "62d33b9a-d413-45d0-b8c7-c3135922b4b1"
-                    ],
-                    "input_type": "file",
-                    "outputs": [
-                        "2e072336-b906-4c9b-a475-ca03f51c8452",
-                        "2f7c43a5-30e5-443b-951b-b2b5d32bea06",
-                        "052ee573-ff99-41b8-ad19-eea77a9cce7f",
-                        "d2cc22c0-6281-4f31-9ca1-b6ab6f27d2b1",
-                        "69559434-0da7-4bdd-a8f4-8be55cdcf45e",
-                        "a1007d9b-6636-4909-9918-4aa85f99e9e7",
-                        "265c105c-803e-4468-a67d-8ba10011fcf1",
-                        "eb4073be-f278-47f3-9f41-8a6e7284b49d",
-                        "487ccf21-6270-4880-b93d-6c80a7e03ca3",
-                        "2046e0bc-be29-4933-8f1a-094aa2bf3172",
-                        "f3049150-14c7-4dae-a76c-3a1af9e951a1",
-                        "79dc63a1-8114-495f-80cb-b0c0003d1f5b",
-                        "2097f789-3a94-44f0-adc0-b3e76233b5dc"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "analysis_protocol",
-                            "protocol_id": "4d6f7580-ce81-4a81-9c2c-872fcb23b7cd"
-                        }
-                    ]
-                },
-                {
-                    "process": "8818b2e9-1c7d-4dd3-9acc-64de03c6f304",
-                    "inputs": [
-                        "74bc8f6d-ce89-4128-bb4e-f0d527e84e83"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "6f725a94-5c81-45e5-8d16-96520aa99703",
-                        "2db43e94-5208-405e-bc2a-ffade59b94c0",
-                        "62d33b9a-d413-45d0-b8c7-c3135922b4b1"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "7d50cf99-37b1-413d-ab4f-37428f9ce723"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "94ca10f5-6937-4b13-b7ce-2935cad90f94"
-                        }
-                    ]
-                },
-                {
-                    "process": "3809cc86-0ccb-4d2e-8520-24dcd9eda874",
-                    "inputs": [
-                        "20356094-b09a-4ed9-bc29-7629ab2c716c"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "74bc8f6d-ce89-4128-bb4e-f0d527e84e83"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "b0dac4c3-a81c-4241-ba52-3e468746618b"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "5077e4f3-3be8-463a-8cc9-024d7905c65e"
-                        }
-                    ]
-                },
-                {
-                    "process": "8fa0c554-2503-408b-9f3b-6145463db850",
-                    "inputs": [
-                        "560dcb19-ddbb-4c8b-b2d9-fece4d167d7b"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "20356094-b09a-4ed9-bc29-7629ab2c716c"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "139304c2-732a-4603-97e5-2db92ab6ec9f"
-                        }
-                    ]
-                },
-                {
-                    "process": "8818b2e9-1c7d-4dd3-9acc-64de03c6f304",
-                    "inputs": [
-                        "74bc8f6d-ce89-4128-bb4e-f0d527e84e83"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "6f725a94-5c81-45e5-8d16-96520aa99703",
-                        "2db43e94-5208-405e-bc2a-ffade59b94c0",
-                        "62d33b9a-d413-45d0-b8c7-c3135922b4b1"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "7d50cf99-37b1-413d-ab4f-37428f9ce723"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "94ca10f5-6937-4b13-b7ce-2935cad90f94"
-                        }
-                    ]
-                },
-                {
-                    "process": "3809cc86-0ccb-4d2e-8520-24dcd9eda874",
-                    "inputs": [
-                        "20356094-b09a-4ed9-bc29-7629ab2c716c"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "74bc8f6d-ce89-4128-bb4e-f0d527e84e83"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "b0dac4c3-a81c-4241-ba52-3e468746618b"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "5077e4f3-3be8-463a-8cc9-024d7905c65e"
-                        }
-                    ]
-                },
-                {
-                    "process": "8fa0c554-2503-408b-9f3b-6145463db850",
-                    "inputs": [
-                        "560dcb19-ddbb-4c8b-b2d9-fece4d167d7b"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "20356094-b09a-4ed9-bc29-7629ab2c716c"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "139304c2-732a-4603-97e5-2db92ab6ec9f"
-                        }
-                    ]
-                },
-                {
-                    "process": "8818b2e9-1c7d-4dd3-9acc-64de03c6f304",
-                    "inputs": [
-                        "74bc8f6d-ce89-4128-bb4e-f0d527e84e83"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "6f725a94-5c81-45e5-8d16-96520aa99703",
-                        "2db43e94-5208-405e-bc2a-ffade59b94c0",
-                        "62d33b9a-d413-45d0-b8c7-c3135922b4b1"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "7d50cf99-37b1-413d-ab4f-37428f9ce723"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "94ca10f5-6937-4b13-b7ce-2935cad90f94"
-                        }
-                    ]
-                },
-                {
-                    "process": "3809cc86-0ccb-4d2e-8520-24dcd9eda874",
-                    "inputs": [
-                        "20356094-b09a-4ed9-bc29-7629ab2c716c"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "74bc8f6d-ce89-4128-bb4e-f0d527e84e83"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "b0dac4c3-a81c-4241-ba52-3e468746618b"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "5077e4f3-3be8-463a-8cc9-024d7905c65e"
-                        }
-                    ]
-                },
-                {
-                    "process": "8fa0c554-2503-408b-9f3b-6145463db850",
-                    "inputs": [
-                        "560dcb19-ddbb-4c8b-b2d9-fece4d167d7b"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "20356094-b09a-4ed9-bc29-7629ab2c716c"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "139304c2-732a-4603-97e5-2db92ab6ec9f"
-                        }
-                    ]
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.3/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.3",
+        "links": [
+            {
+                "process": "b7a172d6-dbb1-41f3-8ae4-7807e1eca803",
+                "inputs": [
+                    "6f725a94-5c81-45e5-8d16-96520aa99703",
+                    "2db43e94-5208-405e-bc2a-ffade59b94c0",
+                    "62d33b9a-d413-45d0-b8c7-c3135922b4b1"
+                ],
+                "input_type": "file",
+                "outputs": [
+                    "2e072336-b906-4c9b-a475-ca03f51c8452",
+                    "2f7c43a5-30e5-443b-951b-b2b5d32bea06",
+                    "052ee573-ff99-41b8-ad19-eea77a9cce7f",
+                    "d2cc22c0-6281-4f31-9ca1-b6ab6f27d2b1",
+                    "69559434-0da7-4bdd-a8f4-8be55cdcf45e",
+                    "a1007d9b-6636-4909-9918-4aa85f99e9e7",
+                    "265c105c-803e-4468-a67d-8ba10011fcf1",
+                    "eb4073be-f278-47f3-9f41-8a6e7284b49d",
+                    "487ccf21-6270-4880-b93d-6c80a7e03ca3",
+                    "2046e0bc-be29-4933-8f1a-094aa2bf3172",
+                    "f3049150-14c7-4dae-a76c-3a1af9e951a1",
+                    "79dc63a1-8114-495f-80cb-b0c0003d1f5b",
+                    "2097f789-3a94-44f0-adc0-b3e76233b5dc"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "analysis_protocol",
+                        "protocol_id": "4d6f7580-ce81-4a81-9c2c-872fcb23b7cd"
+                    }
+                ]
+            },
+            {
+                "process": "8818b2e9-1c7d-4dd3-9acc-64de03c6f304",
+                "inputs": [
+                    "74bc8f6d-ce89-4128-bb4e-f0d527e84e83"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "6f725a94-5c81-45e5-8d16-96520aa99703",
+                    "2db43e94-5208-405e-bc2a-ffade59b94c0",
+                    "62d33b9a-d413-45d0-b8c7-c3135922b4b1"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "7d50cf99-37b1-413d-ab4f-37428f9ce723"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "94ca10f5-6937-4b13-b7ce-2935cad90f94"
+                    }
+                ]
+            },
+            {
+                "process": "3809cc86-0ccb-4d2e-8520-24dcd9eda874",
+                "inputs": [
+                    "20356094-b09a-4ed9-bc29-7629ab2c716c"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "74bc8f6d-ce89-4128-bb4e-f0d527e84e83"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "b0dac4c3-a81c-4241-ba52-3e468746618b"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "5077e4f3-3be8-463a-8cc9-024d7905c65e"
+                    }
+                ]
+            },
+            {
+                "process": "8fa0c554-2503-408b-9f3b-6145463db850",
+                "inputs": [
+                    "560dcb19-ddbb-4c8b-b2d9-fece4d167d7b"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "20356094-b09a-4ed9-bc29-7629ab2c716c"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "139304c2-732a-4603-97e5-2db92ab6ec9f"
+                    }
+                ]
+            },
+            {
+                "process": "8818b2e9-1c7d-4dd3-9acc-64de03c6f304",
+                "inputs": [
+                    "74bc8f6d-ce89-4128-bb4e-f0d527e84e83"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "6f725a94-5c81-45e5-8d16-96520aa99703",
+                    "2db43e94-5208-405e-bc2a-ffade59b94c0",
+                    "62d33b9a-d413-45d0-b8c7-c3135922b4b1"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "7d50cf99-37b1-413d-ab4f-37428f9ce723"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "94ca10f5-6937-4b13-b7ce-2935cad90f94"
+                    }
+                ]
+            },
+            {
+                "process": "3809cc86-0ccb-4d2e-8520-24dcd9eda874",
+                "inputs": [
+                    "20356094-b09a-4ed9-bc29-7629ab2c716c"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "74bc8f6d-ce89-4128-bb4e-f0d527e84e83"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "b0dac4c3-a81c-4241-ba52-3e468746618b"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "5077e4f3-3be8-463a-8cc9-024d7905c65e"
+                    }
+                ]
+            },
+            {
+                "process": "8fa0c554-2503-408b-9f3b-6145463db850",
+                "inputs": [
+                    "560dcb19-ddbb-4c8b-b2d9-fece4d167d7b"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "20356094-b09a-4ed9-bc29-7629ab2c716c"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "139304c2-732a-4603-97e5-2db92ab6ec9f"
+                    }
+                ]
+            },
+            {
+                "process": "8818b2e9-1c7d-4dd3-9acc-64de03c6f304",
+                "inputs": [
+                    "74bc8f6d-ce89-4128-bb4e-f0d527e84e83"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "6f725a94-5c81-45e5-8d16-96520aa99703",
+                    "2db43e94-5208-405e-bc2a-ffade59b94c0",
+                    "62d33b9a-d413-45d0-b8c7-c3135922b4b1"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "7d50cf99-37b1-413d-ab4f-37428f9ce723"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "94ca10f5-6937-4b13-b7ce-2935cad90f94"
+                    }
+                ]
+            },
+            {
+                "process": "3809cc86-0ccb-4d2e-8520-24dcd9eda874",
+                "inputs": [
+                    "20356094-b09a-4ed9-bc29-7629ab2c716c"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "74bc8f6d-ce89-4128-bb4e-f0d527e84e83"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "b0dac4c3-a81c-4241-ba52-3e468746618b"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "5077e4f3-3be8-463a-8cc9-024d7905c65e"
+                    }
+                ]
+            },
+            {
+                "process": "8fa0c554-2503-408b-9f3b-6145463db850",
+                "inputs": [
+                    "560dcb19-ddbb-4c8b-b2d9-fece4d167d7b"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "20356094-b09a-4ed9-bc29-7629ab2c716c"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "139304c2-732a-4603-97e5-2db92ab6ec9f"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
index a232a860d..9aa314dea 100644
--- a/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
+++ b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
@@ -2218,173 +2218,173 @@
                 "submission_date": "2018-10-16T07:53:53.709Z",
                 "update_date": "2018-10-16T08:06:34.625Z"
             }
-        },
-        "links.json": {
-            "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.3/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.3",
-            "links": [
-                {
-                    "process": "4460eba6-6517-4283-992f-0e0d3ce0ef45",
-                    "inputs": [
-                        "b66c9d19-322c-42d4-8b65-3478fd0afa6a",
-                        "02c8352d-b2ba-4de4-a574-335eb9a61e0e"
-                    ],
-                    "input_type": "file",
-                    "outputs": [
-                        "3404deaa-6274-4b78-99ae-442dd401714c",
-                        "884d5482-3432-4259-b551-955ba35becc2",
-                        "77d3b337-d169-44a5-9b6a-be1c6d1b31b7",
-                        "b115459d-d690-418c-a608-48ede1cc5a43",
-                        "05ea34ca-995b-4c30-9f87-81ad07e61305",
-                        "03e676dd-1718-40e0-a246-f3c6a594e334",
-                        "19fee968-3d70-43a1-a64a-a778d656bd2e",
-                        "edd03152-3219-41cd-9129-62f2e8944e91",
-                        "e8972873-6e54-40d8-85ca-790a8d5688d0",
-                        "babd98f7-c1ae-4a5d-bf85-7cb347a3ce96",
-                        "3314dd32-6acf-4841-83a4-03d4807d1365",
-                        "f6e76583-bc31-41e1-8695-7198e7842ea0",
-                        "f2473460-2b19-4b16-97c7-6eaa9060df6f",
-                        "0fa2c00a-02e4-444d-998d-b812d647565f",
-                        "09989709-cca8-4f82-a07f-6fa6a9fa3e03",
-                        "020634de-da4b-47bb-b084-8c2d7e70ae17",
-                        "f6a47716-c494-4229-85e9-bd1f20afa5d1",
-                        "c82423e7-a621-4fee-bed2-5efa916124e3",
-                        "401a3d93-c4c9-4f59-960e-41de71839619",
-                        "f06c17a5-8197-4b6f-928a-55ffa8d796d2",
-                        "95bdd09a-cc14-4a7b-b0f8-96cd4d6dcb1c",
-                        "a3d20426-80af-4c2b-90a6-6e6644539aad",
-                        "f6cdb1dd-df7c-4dab-bdd1-4bb59a2044f7",
-                        "4de506d4-78d1-4de2-9780-e91f8a9d7b6d",
-                        "c8aa1527-f40c-4e50-b7ca-51646562422b",
-                        "6cc5378a-295b-4e72-80a2-370434fd2b94",
-                        "75178504-d0ef-4d32-a3e6-6faa1026be84",
-                        "215add4a-6239-4443-9b0c-c5e2b6e7052f",
-                        "f894b6e3-98b3-4161-97e4-a8d4ac9ad677",
-                        "f909af01-995b-499a-9086-fd2a90123102",
-                        "75d692f4-e796-453d-b260-44a42f126c93",
-                        "08be64a7-9ef4-4d17-b7d8-41f79c24c987",
-                        "770c9eb2-f63f-4bd2-94c1-e2b6da1feeac"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "analysis_protocol",
-                            "protocol_id": "7a56f120-c055-4b63-acdf-8cc80c3555c1"
-                        }
-                    ]
-                },
-                {
-                    "process": "33d33846-5287-425b-a94f-2c3ec14a323c",
-                    "inputs": [
-                        "02201088-f3be-46ce-bb04-e7c464189900"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "b66c9d19-322c-42d4-8b65-3478fd0afa6a",
-                        "02c8352d-b2ba-4de4-a574-335eb9a61e0e"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "7faadd95-bcee-4627-8990-04b79cf617f9"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "dcf48263-da0f-4fb8-9af7-2cb0e3af5b09"
-                        }
-                    ]
-                },
-                {
-                    "process": "34cb3bc6-661b-4bbd-b51c-0b5e6f5e248d",
-                    "inputs": [
-                        "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "02201088-f3be-46ce-bb04-e7c464189900"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "2f0c9a0e-bf38-4df9-ba9c-d3502b843e2b"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "d9fdfade-52d2-40df-b299-e9aa292ea120"
-                        }
-                    ]
-                },
-                {
-                    "process": "4a1432a1-ae18-45f2-b574-9869b7242289",
-                    "inputs": [
-                        "d919428e-d58b-4815-b36a-c9f186df6582"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "33d33846-5287-425b-a94f-2c3ec14a323c",
-                    "inputs": [
-                        "02201088-f3be-46ce-bb04-e7c464189900"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "b66c9d19-322c-42d4-8b65-3478fd0afa6a",
-                        "02c8352d-b2ba-4de4-a574-335eb9a61e0e"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "7faadd95-bcee-4627-8990-04b79cf617f9"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "dcf48263-da0f-4fb8-9af7-2cb0e3af5b09"
-                        }
-                    ]
-                },
-                {
-                    "process": "34cb3bc6-661b-4bbd-b51c-0b5e6f5e248d",
-                    "inputs": [
-                        "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "02201088-f3be-46ce-bb04-e7c464189900"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "2f0c9a0e-bf38-4df9-ba9c-d3502b843e2b"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "d9fdfade-52d2-40df-b299-e9aa292ea120"
-                        }
-                    ]
-                },
-                {
-                    "process": "4a1432a1-ae18-45f2-b574-9869b7242289",
-                    "inputs": [
-                        "d919428e-d58b-4815-b36a-c9f186df6582"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.3/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.3",
+        "links": [
+            {
+                "process": "4460eba6-6517-4283-992f-0e0d3ce0ef45",
+                "inputs": [
+                    "b66c9d19-322c-42d4-8b65-3478fd0afa6a",
+                    "02c8352d-b2ba-4de4-a574-335eb9a61e0e"
+                ],
+                "input_type": "file",
+                "outputs": [
+                    "3404deaa-6274-4b78-99ae-442dd401714c",
+                    "884d5482-3432-4259-b551-955ba35becc2",
+                    "77d3b337-d169-44a5-9b6a-be1c6d1b31b7",
+                    "b115459d-d690-418c-a608-48ede1cc5a43",
+                    "05ea34ca-995b-4c30-9f87-81ad07e61305",
+                    "03e676dd-1718-40e0-a246-f3c6a594e334",
+                    "19fee968-3d70-43a1-a64a-a778d656bd2e",
+                    "edd03152-3219-41cd-9129-62f2e8944e91",
+                    "e8972873-6e54-40d8-85ca-790a8d5688d0",
+                    "babd98f7-c1ae-4a5d-bf85-7cb347a3ce96",
+                    "3314dd32-6acf-4841-83a4-03d4807d1365",
+                    "f6e76583-bc31-41e1-8695-7198e7842ea0",
+                    "f2473460-2b19-4b16-97c7-6eaa9060df6f",
+                    "0fa2c00a-02e4-444d-998d-b812d647565f",
+                    "09989709-cca8-4f82-a07f-6fa6a9fa3e03",
+                    "020634de-da4b-47bb-b084-8c2d7e70ae17",
+                    "f6a47716-c494-4229-85e9-bd1f20afa5d1",
+                    "c82423e7-a621-4fee-bed2-5efa916124e3",
+                    "401a3d93-c4c9-4f59-960e-41de71839619",
+                    "f06c17a5-8197-4b6f-928a-55ffa8d796d2",
+                    "95bdd09a-cc14-4a7b-b0f8-96cd4d6dcb1c",
+                    "a3d20426-80af-4c2b-90a6-6e6644539aad",
+                    "f6cdb1dd-df7c-4dab-bdd1-4bb59a2044f7",
+                    "4de506d4-78d1-4de2-9780-e91f8a9d7b6d",
+                    "c8aa1527-f40c-4e50-b7ca-51646562422b",
+                    "6cc5378a-295b-4e72-80a2-370434fd2b94",
+                    "75178504-d0ef-4d32-a3e6-6faa1026be84",
+                    "215add4a-6239-4443-9b0c-c5e2b6e7052f",
+                    "f894b6e3-98b3-4161-97e4-a8d4ac9ad677",
+                    "f909af01-995b-499a-9086-fd2a90123102",
+                    "75d692f4-e796-453d-b260-44a42f126c93",
+                    "08be64a7-9ef4-4d17-b7d8-41f79c24c987",
+                    "770c9eb2-f63f-4bd2-94c1-e2b6da1feeac"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "analysis_protocol",
+                        "protocol_id": "7a56f120-c055-4b63-acdf-8cc80c3555c1"
+                    }
+                ]
+            },
+            {
+                "process": "33d33846-5287-425b-a94f-2c3ec14a323c",
+                "inputs": [
+                    "02201088-f3be-46ce-bb04-e7c464189900"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "b66c9d19-322c-42d4-8b65-3478fd0afa6a",
+                    "02c8352d-b2ba-4de4-a574-335eb9a61e0e"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "7faadd95-bcee-4627-8990-04b79cf617f9"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "dcf48263-da0f-4fb8-9af7-2cb0e3af5b09"
+                    }
+                ]
+            },
+            {
+                "process": "34cb3bc6-661b-4bbd-b51c-0b5e6f5e248d",
+                "inputs": [
+                    "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "02201088-f3be-46ce-bb04-e7c464189900"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "2f0c9a0e-bf38-4df9-ba9c-d3502b843e2b"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "d9fdfade-52d2-40df-b299-e9aa292ea120"
+                    }
+                ]
+            },
+            {
+                "process": "4a1432a1-ae18-45f2-b574-9869b7242289",
+                "inputs": [
+                    "d919428e-d58b-4815-b36a-c9f186df6582"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "33d33846-5287-425b-a94f-2c3ec14a323c",
+                "inputs": [
+                    "02201088-f3be-46ce-bb04-e7c464189900"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "b66c9d19-322c-42d4-8b65-3478fd0afa6a",
+                    "02c8352d-b2ba-4de4-a574-335eb9a61e0e"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "7faadd95-bcee-4627-8990-04b79cf617f9"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "dcf48263-da0f-4fb8-9af7-2cb0e3af5b09"
+                    }
+                ]
+            },
+            {
+                "process": "34cb3bc6-661b-4bbd-b51c-0b5e6f5e248d",
+                "inputs": [
+                    "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "02201088-f3be-46ce-bb04-e7c464189900"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "2f0c9a0e-bf38-4df9-ba9c-d3502b843e2b"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "d9fdfade-52d2-40df-b299-e9aa292ea120"
+                    }
+                ]
+            },
+            {
+                "process": "4a1432a1-ae18-45f2-b574-9869b7242289",
+                "inputs": [
+                    "d919428e-d58b-4815-b36a-c9f186df6582"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index 6d7cb2625..4e5006c45 100644
--- a/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
+++ b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
@@ -2392,723 +2392,723 @@
                 "submission_date": "2018-10-11T21:18:03.026Z",
                 "update_date": "2018-10-11T21:18:10.586Z"
             }
-        },
-        "links.json": {
-            "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.3/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.3",
-            "links": [
-                {
-                    "process": "228fd33a-3627-4dea-bda9-e9cdc3b924b6",
-                    "inputs": [
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+                    {
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+                        "protocol_id": "8f4a8e7c-e7ee-44dc-8e09-f4012355060f"
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+                "output_type": "biomaterial",
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+                    {
+                        "protocol_type": "ipsc_induction_protocol",
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+                    {
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+                        "protocol_id": "8f4a8e7c-e7ee-44dc-8e09-f4012355060f"
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+                "output_type": "biomaterial",
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+                    {
+                        "protocol_type": "ipsc_induction_protocol",
+                        "protocol_id": "cdfe38f2-1d90-4700-a199-d8105ce299df"
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+                "input_type": "biomaterial",
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+                "output_type": "biomaterial",
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+            },
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+                "input_type": "biomaterial",
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+                    "73f10dad-afc5-4d1d-a71c-4a8b6fff9172"
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+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "differentiation_protocol",
+                        "protocol_id": "8f4a8e7c-e7ee-44dc-8e09-f4012355060f"
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+                "inputs": [
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+                "input_type": "biomaterial",
+                "outputs": [
+                    "6a16de30-176d-4488-81de-9337a1a6d8c5"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "ipsc_induction_protocol",
+                        "protocol_id": "cdfe38f2-1d90-4700-a199-d8105ce299df"
+                    }
+                ]
+            },
+            {
+                "process": "bb2365b9-5a5b-436f-92e3-4fc6d86a9efd",
+                "inputs": [
+                    "96757312-0221-447a-84f1-7a737b5afd01"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "82368936-7b99-4864-9f49-b8fee3906d47"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index 185506e10..8586061d3 100644
--- a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
+++ b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
@@ -2392,723 +2392,723 @@
                 "submission_date": "2018-10-11T21:18:03.026Z",
                 "update_date": "2018-10-11T21:18:10.586Z"
             }
-        },
-        "links.json": {
-            "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.3/links",
-            "schema_type": "link_bundle",
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-            "links": [
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-                    "process": "228fd33a-3627-4dea-bda9-e9cdc3b924b6",
-                    "inputs": [
-                        "281c2d08-9e43-47f9-b937-e733e3ba3322",
-                        "ae1d6fa7-964f-465a-8c78-565206827434",
-                        "f518a8cc-e1d9-4fc9-bc32-491dd8543902",
-                        "213381ea-6161-4159-853e-cfcae4968001",
-                        "9ee3da9e-83ca-4c02-84d6-ac09702b12ba",
-                        "330a08ca-ae8e-4f1f-aa03-970abcd27f39"
-                    ],
-                    "input_type": "file",
-                    "outputs": [
-                        "cf93f747-1392-4670-8eb3-3ac60a96855e",
-                        "477c0b3e-4a06-4214-8f27-58199ba63528",
-                        "ad6d5170-d74b-408c-af6b-25a14315c9da",
-                        "50be9b67-fae5-4472-9719-478dd1303d6e",
-                        "fd16b62e-e540-4f03-8ba0-07d0c204e3c8",
-                        "3c41b5b6-f480-4d47-8c5e-155e7c1adf54",
-                        "022a217c-384d-4d9d-8631-6397b6838e3a",
-                        "9b778e46-0c51-4260-8e3f-000ecc145f0a",
-                        "af025a74-53f1-4972-b50d-53095b5ffac2",
-                        "e8395271-7c8e-4ec4-9598-495df43fe5fd",
-                        "211a8fbf-b190-4576-ac2f-2b1a91743abb",
-                        "17222e3a-5757-45e9-9dfe-c4b6aa10f28a",
-                        "2fb8a975-b50c-4528-b850-838a19e19a1e"
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-                    "inputs": [
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-                    "input_type": "biomaterial",
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-                        "9ee3da9e-83ca-4c02-84d6-ac09702b12ba",
-                        "330a08ca-ae8e-4f1f-aa03-970abcd27f39"
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-                    "output_type": "file",
-                    "protocols": [
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-                            "protocol_type": "library_preparation_protocol",
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-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "102cdbf3-b0e5-4dd5-9168-51150a9ebb6b"
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-                    "inputs": [
-                        "2d8282f0-6cbb-4d5a-822c-4b01718b4d0d",
-                        "b7214641-1ac5-4f60-b795-cb33a7c25434",
-                        "308eea51-d14b-4036-8cd1-cfd81d7532c3",
-                        "73f10dad-afc5-4d1d-a71c-4a8b6fff9172"
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+                "inputs": [
+                    "8f328973-9bc0-46b9-8a1f-38893e77b3b5"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "a3651f83-dee6-49b2-ba4e-0ce20f02467d"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "ipsc_induction_protocol",
+                        "protocol_id": "cdfe38f2-1d90-4700-a199-d8105ce299df"
+                    }
+                ]
+            },
+            {
+                "process": "76e685c9-fcf2-4582-bbfa-5e0369eb5bdb",
+                "inputs": [
+                    "931528fa-820b-49ca-af1e-ae9a2c0ef551"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "8f328973-9bc0-46b9-8a1f-38893e77b3b5"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "bce97917-252e-40f2-af8e-df591099acd8",
+                "inputs": [
+                    "6a16de30-176d-4488-81de-9337a1a6d8c5"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "73f10dad-afc5-4d1d-a71c-4a8b6fff9172"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "differentiation_protocol",
+                        "protocol_id": "8f4a8e7c-e7ee-44dc-8e09-f4012355060f"
+                    }
+                ]
+            },
+            {
+                "process": "6458ae59-0aed-471e-95a0-4de534d449ca",
+                "inputs": [
+                    "82368936-7b99-4864-9f49-b8fee3906d47"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "6a16de30-176d-4488-81de-9337a1a6d8c5"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "ipsc_induction_protocol",
+                        "protocol_id": "cdfe38f2-1d90-4700-a199-d8105ce299df"
+                    }
+                ]
+            },
+            {
+                "process": "bb2365b9-5a5b-436f-92e3-4fc6d86a9efd",
+                "inputs": [
+                    "96757312-0221-447a-84f1-7a737b5afd01"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "82368936-7b99-4864-9f49-b8fee3906d47"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
index 93c70d14a..2c9aa4a67 100644
--- a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
+++ b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
@@ -316,179 +316,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/3.0.0/links",
-            "schema_type": "links",
-            "schema_version": "3.0.0",
-            "links": [
-                {
-                    "inputs": [
-                        {
-                            "input_id": "8f8b9587-237f-4995-9461-c96eac53d615",
-                            "input_type": "sequence_file"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "b8b76328-854c-5862-a688-9b761a9cea86",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "848c816e-4ae8-4c9a-9e3d-ebe447519ff4",
-                    "process_type": "analysis_process",
-                    "protocols": [
-                        {
-                            "protocol_id": "099457a1-a453-54c6-aae5-b70dafa33bbd",
-                            "protocol_type": "analysis_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "ee7404a4-c183-4a75-8bd1-34b5fc140e81",
-                            "input_type": "sequence_file"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "7a015307-6db9-541f-aaae-db9fdb41000f",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "848c816e-4ae8-4c9a-9e3d-ebe447519ff4",
-                    "process_type": "analysis_process",
-                    "protocols": [
-                        {
-                            "protocol_id": "099457a1-a453-54c6-aae5-b70dafa33bbd",
-                            "protocol_type": "analysis_protocol"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_type": "process",
-                    "process_id": "6f5ddf2c-382d-4c0a-a506-3a5286067c83",
-                    "inputs": [
-                        {
-                            "input_type": "cell_suspension",
-                            "input_id": "201ae4d0-c7c6-4777-947f-18f5268884b6"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "8f8b9587-237f-4995-9461-c96eac53d615"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "5b503dcb-dca6-4e4f-988b-f7100c030dc5"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "eca2ab79-ad61-411f-815a-4f6d936d992b"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_type": "process",
-                    "process_id": "33e31f6f-fe78-45bd-ae57-10d2d14253cf",
-                    "inputs": [
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "5d82b884-7db4-47fa-9ccd-03054065c509"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "cell_suspension",
-                            "output_id": "201ae4d0-c7c6-4777-947f-18f5268884b6"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "fcba26aa-658c-4120-ab31-cc5a5a00f759"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "dd7f3d64-4b79-48f0-9d8c-4324594fe820"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_type": "process",
-                    "process_id": "6f5ddf2c-382d-4c0a-a506-3a5286067c83",
-                    "inputs": [
-                        {
-                            "input_type": "cell_suspension",
-                            "input_id": "201ae4d0-c7c6-4777-947f-18f5268884b6"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "ee7404a4-c183-4a75-8bd1-34b5fc140e81"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "5b503dcb-dca6-4e4f-988b-f7100c030dc5"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "eca2ab79-ad61-411f-815a-4f6d936d992b"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_type": "process",
-                    "process_id": "c0d18b81-0b54-4a11-864b-cd3f43b7e7bf",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "3211ef8f-a60c-4892-ae55-91d6752dcd75"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "5d82b884-7db4-47fa-9ccd-03054065c509"
-                        }
-                    ],
-                    "protocols": []
-                },
-                {
-                    "link_type": "supplementary_file_link",
-                    "entity": {
-                        "entity_type": "project",
-                        "entity_id": "116965f3-f094-4769-9d28-ae675c1b569c"
-                    },
-                    "files": [
-                        {
-                            "file_id": "e738a267-87fc-4070-abc7-b3be6442c6d0",
-                            "file_type": "supplementary_file"
-                        },
-                        {
-                            "file_id": "01a1d04b-05d0-4904-b627-68b0dc02bc17",
-                            "file_type": "supplementary_file"
-                        },
-                        {
-                            "file_id": "a06cb5d5-2675-4d64-aeb8-79e0103715f3",
-                            "file_type": "supplementary_file"
-                        }
-                    ]
-                }
-            ]
-        },
         "sequence_file_0.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.0.0/sequence_file",
             "schema_type": "file",
@@ -1044,5 +871,178 @@
                 "update_date": "2019-05-14T11:06:42.781Z"
             }
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/3.0.0/links",
+        "schema_type": "links",
+        "schema_version": "3.0.0",
+        "links": [
+            {
+                "inputs": [
+                    {
+                        "input_id": "8f8b9587-237f-4995-9461-c96eac53d615",
+                        "input_type": "sequence_file"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "b8b76328-854c-5862-a688-9b761a9cea86",
+                        "output_type": "analysis_file"
+                    }
+                ],
+                "process_id": "848c816e-4ae8-4c9a-9e3d-ebe447519ff4",
+                "process_type": "analysis_process",
+                "protocols": [
+                    {
+                        "protocol_id": "099457a1-a453-54c6-aae5-b70dafa33bbd",
+                        "protocol_type": "analysis_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "ee7404a4-c183-4a75-8bd1-34b5fc140e81",
+                        "input_type": "sequence_file"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "7a015307-6db9-541f-aaae-db9fdb41000f",
+                        "output_type": "analysis_file"
+                    }
+                ],
+                "process_id": "848c816e-4ae8-4c9a-9e3d-ebe447519ff4",
+                "process_type": "analysis_process",
+                "protocols": [
+                    {
+                        "protocol_id": "099457a1-a453-54c6-aae5-b70dafa33bbd",
+                        "protocol_type": "analysis_protocol"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "6f5ddf2c-382d-4c0a-a506-3a5286067c83",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "201ae4d0-c7c6-4777-947f-18f5268884b6"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "8f8b9587-237f-4995-9461-c96eac53d615"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "5b503dcb-dca6-4e4f-988b-f7100c030dc5"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "eca2ab79-ad61-411f-815a-4f6d936d992b"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "33e31f6f-fe78-45bd-ae57-10d2d14253cf",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "5d82b884-7db4-47fa-9ccd-03054065c509"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "201ae4d0-c7c6-4777-947f-18f5268884b6"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "fcba26aa-658c-4120-ab31-cc5a5a00f759"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "dd7f3d64-4b79-48f0-9d8c-4324594fe820"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "6f5ddf2c-382d-4c0a-a506-3a5286067c83",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "201ae4d0-c7c6-4777-947f-18f5268884b6"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "ee7404a4-c183-4a75-8bd1-34b5fc140e81"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "5b503dcb-dca6-4e4f-988b-f7100c030dc5"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "eca2ab79-ad61-411f-815a-4f6d936d992b"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "c0d18b81-0b54-4a11-864b-cd3f43b7e7bf",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "3211ef8f-a60c-4892-ae55-91d6752dcd75"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "5d82b884-7db4-47fa-9ccd-03054065c509"
+                    }
+                ],
+                "protocols": []
+            },
+            {
+                "link_type": "supplementary_file_link",
+                "entity": {
+                    "entity_type": "project",
+                    "entity_id": "116965f3-f094-4769-9d28-ae675c1b569c"
+                },
+                "files": [
+                    {
+                        "file_id": "e738a267-87fc-4070-abc7-b3be6442c6d0",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "01a1d04b-05d0-4904-b627-68b0dc02bc17",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "a06cb5d5-2675-4d64-aeb8-79e0103715f3",
+                        "file_type": "supplementary_file"
+                    }
+                ]
+            }
+        ]
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json b/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json
index 860e0de64..6c391784d 100644
--- a/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json
+++ b/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json
@@ -9128,3673 +9128,3673 @@
                 "updateDate": "2018-03-26T16:59:27.537Z",
                 "document_id": "e99eed63-5794-4d8d-baf9-9c6888e91e6d"
             }
-        },
-        "links.json": {
-            "links": [
-                {
-                    "source_id": "642c8a0a-ffa1-4e06-aab6-f777cafda07b",
-                    "source_type": "biomaterial",
-                    "destination_id": "09c4b005-1357-4cca-a21a-2e63a71e00eb",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "09c4b005-1357-4cca-a21a-2e63a71e00eb",
-                    "source_type": "dissociation_process",
-                    "destination_id": "f2cfbb32-066f-44cb-9f74-a4b4acec7692",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "09c4b005-1357-4cca-a21a-2e63a71e00eb",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "534bf336-7af6-44e5-9f01-11d4ca6d03db",
-                    "source_type": "process",
-                    "destination_id": "642c8a0a-ffa1-4e06-aab6-f777cafda07b",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "769cad8e-8c03-4318-b6e8-4c832365a884",
-                    "source_type": "biomaterial",
-                    "destination_id": "534bf336-7af6-44e5-9f01-11d4ca6d03db",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "d890548c-3c98-4e30-8c9c-05d2dc6e28c2",
-                    "source_type": "biomaterial",
-                    "destination_id": "f51f836c-ae21-4576-a107-a42ae6c2bb58",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "f51f836c-ae21-4576-a107-a42ae6c2bb58",
-                    "source_type": "dissociation_process",
-                    "destination_id": "bcbb8300-0d6f-42c2-b393-4e167a6529d4",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "f51f836c-ae21-4576-a107-a42ae6c2bb58",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "d7800343-3c9e-484a-8abb-9bfcb92d0734",
-                    "source_type": "process",
-                    "destination_id": "d890548c-3c98-4e30-8c9c-05d2dc6e28c2",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "f7e3dec8-e286-4784-a8b0-e5fabc0de841",
-                    "source_type": "biomaterial",
-                    "destination_id": "d7800343-3c9e-484a-8abb-9bfcb92d0734",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "1ffa73eb-a01a-45d2-9b99-fd55d76f4f74",
-                    "source_type": "biomaterial",
-                    "destination_id": "25f66e31-2091-426f-957b-e66e888b1f00",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "25f66e31-2091-426f-957b-e66e888b1f00",
-                    "source_type": "dissociation_process",
-                    "destination_id": "fb51b6f2-5a7b-4a07-97d9-f1833a48d559",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "25f66e31-2091-426f-957b-e66e888b1f00",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "ea7ccba0-8939-4336-8b52-4ffceacb539c",
-                    "source_type": "process",
-                    "destination_id": "1ffa73eb-a01a-45d2-9b99-fd55d76f4f74",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "d4895ad7-10b5-4d70-af74-02a8df78532c",
-                    "source_type": "biomaterial",
-                    "destination_id": "ea7ccba0-8939-4336-8b52-4ffceacb539c",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "cf6e873c-48a4-4422-93d6-5403a4f63f72",
-                    "source_type": "biomaterial",
-                    "destination_id": "31dc39b4-3ea3-4731-a558-d5e831ae363a",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "31dc39b4-3ea3-4731-a558-d5e831ae363a",
-                    "source_type": "dissociation_process",
-                    "destination_id": "6bf48eba-1309-43dc-af97-ea4a37f8d2a8",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "31dc39b4-3ea3-4731-a558-d5e831ae363a",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
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+                "destination_type": "file"
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+                "destination_id": "11726713-72bb-43d6-9fd0-e09d4940f7fd",
+                "destination_type": "file"
+            },
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+                "source_type": "sequencing_process",
+                "destination_id": "f256f4d1-bb92-4b1e-a320-0a8c65b02f47",
+                "destination_type": "file"
+            },
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+                "source_type": "sequencing_process",
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+                "destination_type": "file"
+            },
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+                "source_type": "sequencing_process",
+                "destination_id": "74409b42-8580-4e4d-8c08-1e70d9c693ea",
+                "destination_type": "file"
+            },
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+                "source_type": "sequencing_process",
+                "destination_id": "0671d6de-6840-4fc8-b67d-f7d662beea88",
+                "destination_type": "file"
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+                "destination_id": "43a5906d-d880-49ef-b743-261a69c7024f",
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+                "source_type": "sequencing_process",
+                "destination_id": "f087e6a6-b9cd-4f26-8932-167d246a6e02",
+                "destination_type": "file"
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+                "source_type": "sequencing_process",
+                "destination_id": "2198238f-d7a8-4e94-9e03-b63f8a7e6bd3",
+                "destination_type": "file"
+            },
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+                "source_type": "sequencing_process",
+                "destination_id": "edff548f-d6ac-469e-a136-d59a501e3f90",
+                "destination_type": "file"
+            },
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+                "source_type": "sequencing_process",
+                "destination_id": "8ba887c3-e44d-4644-8cd6-a58b7cfcf2c0",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "49aa3970-895a-44bb-9433-3b49373794f3",
+                "source_type": "sequencing_process",
+                "destination_id": "ddd7bb64-91d4-4114-b2cc-a93d86aa98e1",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "49aa3970-895a-44bb-9433-3b49373794f3",
+                "source_type": "sequencing_process",
+                "destination_id": "e823513d-c147-4219-b1c3-33e1cd7b0862",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "49aa3970-895a-44bb-9433-3b49373794f3",
+                "source_type": "sequencing_process",
+                "destination_id": "d4f454d6-3ffc-4b0c-9449-212ecdbd9d25",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "49aa3970-895a-44bb-9433-3b49373794f3",
+                "source_type": "sequencing_process",
+                "destination_id": "e918cb31-af72-4d87-a414-4c499305bdd5",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "49aa3970-895a-44bb-9433-3b49373794f3",
+                "source_type": "sequencing_process",
+                "destination_id": "6b6c9e11-8918-45c7-b80a-cecb591a79cb",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "49aa3970-895a-44bb-9433-3b49373794f3",
+                "source_type": "sequencing_process",
+                "destination_id": "72cfdf1c-8509-4d36-9751-35537c2a7a9d",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "49aa3970-895a-44bb-9433-3b49373794f3",
+                "source_type": "sequencing_process",
+                "destination_id": "946889b2-c18d-45ff-b5dc-df818f2c98b7",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "49aa3970-895a-44bb-9433-3b49373794f3",
+                "source_type": "sequencing_process",
+                "destination_id": "e99eed63-5794-4d8d-baf9-9c6888e91e6d",
+                "destination_type": "protocol"
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
+        "schema_version": "1.0.0",
+        "schema_type": "link_bundle"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json b/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
index 1363f86b3..10a3d0b1a 100644
--- a/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
+++ b/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
@@ -197,54 +197,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links",
-            "schema_type": "links",
-            "schema_version": "2.1.1",
-            "links": [
-                {
-                    "link_type": "supplementary_file_link",
-                    "entity": {
-                        "entity_type": "project",
-                        "entity_id": "8185730f-4113-40d3-9cc3-929271784c2b"
-                    },
-                    "files": [
-                        {
-                            "file_id": "b905c8be-2e2d-592c-8481-3eb7a87c6484",
-                            "file_type": "supplementary_file"
-                        },
-                        {
-                            "file_id": "87f31102-ebbc-5875-abdf-4fa5cea48e8d",
-                            "file_type": "supplementary_file"
-                        },
-                        {
-                            "file_id": "733318e0-19c2-51e8-9ad6-d94ad562dd46",
-                            "file_type": "supplementary_file"
-                        },
-                        {
-                            "file_id": "c59e2de5-01fe-56eb-be56-679ed14161bf",
-                            "file_type": "supplementary_file"
-                        },
-                        {
-                            "file_id": "68bda896-3b3e-5f2a-9212-f4030a0f37e2",
-                            "file_type": "supplementary_file"
-                        },
-                        {
-                            "file_id": "0c5ab869-da2d-5c11-b4ae-f978a052899f",
-                            "file_type": "supplementary_file"
-                        },
-                        {
-                            "file_id": "cade4593-bfba-56ed-80ab-080d0de7d5a4",
-                            "file_type": "supplementary_file"
-                        },
-                        {
-                            "file_id": "5b465aad-0981-5152-b468-e615e20f5884",
-                            "file_type": "supplementary_file"
-                        }
-                    ]
-                }
-            ]
-        },
         "supplementary_file_0.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/2.2.0/supplementary_file",
             "schema_type": "file",
@@ -849,5 +801,53 @@
                 "update_date": "2019-09-13T08:37:53.825Z"
             }
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links",
+        "schema_type": "links",
+        "schema_version": "2.1.1",
+        "links": [
+            {
+                "link_type": "supplementary_file_link",
+                "entity": {
+                    "entity_type": "project",
+                    "entity_id": "8185730f-4113-40d3-9cc3-929271784c2b"
+                },
+                "files": [
+                    {
+                        "file_id": "b905c8be-2e2d-592c-8481-3eb7a87c6484",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "87f31102-ebbc-5875-abdf-4fa5cea48e8d",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "733318e0-19c2-51e8-9ad6-d94ad562dd46",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "c59e2de5-01fe-56eb-be56-679ed14161bf",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "68bda896-3b3e-5f2a-9212-f4030a0f37e2",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "0c5ab869-da2d-5c11-b4ae-f978a052899f",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "cade4593-bfba-56ed-80ab-080d0de7d5a4",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "5b465aad-0981-5152-b468-e615e20f5884",
+                        "file_type": "supplementary_file"
+                    }
+                ]
+            }
+        ]
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json b/test/indexer/data/4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json
index 5318717ee..805546939 100644
--- a/test/indexer/data/4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json
+++ b/test/indexer/data/4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json
@@ -182,94 +182,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
-            "links": [
-                {
-                    "inputs": [
-                        {
-                            "input_id": "d9eaaffe-4c93-5503-984f-762e8dfddce4",
-                            "input_type": "cell_suspension"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "cf5d9300-3b81-52eb-a02f-25fb1364419e",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "4da04038-adab-59a9-b6c4-3a61242cc972",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "811adf54-7f27-5aec-9ed7-c6084c4c3a1b",
-                            "protocol_type": "analysis_protocol"
-                        },
-                        {
-                            "protocol_id": "f08df8f8-4966-5265-b127-36625c77deae",
-                            "protocol_type": "library_preparation_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "224d3750-f1f7-5b04-bbce-e23f09eea7d7",
-                            "input_type": "specimen_from_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "d9eaaffe-4c93-5503-984f-762e8dfddce4",
-                            "output_type": "cell_suspension"
-                        }
-                    ],
-                    "process_id": "296b47c2-7c35-5fdb-bb11-95323011507c",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "9462efe9-1b1a-5a18-81bb-e510137ae743",
-                            "protocol_type": "enrichment_protocol"
-                        },
-                        {
-                            "protocol_id": "6d009d64-1ae9-50b2-a706-6a30e47bdc52",
-                            "protocol_type": "enrichment_protocol"
-                        },
-                        {
-                            "protocol_id": "0f959f0b-5efa-5cc8-9c46-097b0cb574d5",
-                            "protocol_type": "treatment_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "9173ee6a-f1b2-5762-9272-3433b5ef7530",
-                            "input_type": "donor_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "224d3750-f1f7-5b04-bbce-e23f09eea7d7",
-                            "output_type": "specimen_from_organism"
-                        }
-                    ],
-                    "process_id": "223d54fb-46c9-5c30-9cae-6b8d5ea71b7e",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "ff0c24dd-afd3-5d7a-b982-6191e19314e3",
-                            "protocol_type": "collection_protocol"
-                        }
-                    ]
-                }
-            ],
-            "schema_type": "links",
-            "schema_version": "3.1.0"
-        },
         "project_0.json": {
             "array_express_accessions": [
                 "E-MTAB-10026"
@@ -727,5 +639,93 @@
             },
             "schema_type": "protocol"
         }
+    },
+    "links": {
+        "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
+        "links": [
+            {
+                "inputs": [
+                    {
+                        "input_id": "d9eaaffe-4c93-5503-984f-762e8dfddce4",
+                        "input_type": "cell_suspension"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "cf5d9300-3b81-52eb-a02f-25fb1364419e",
+                        "output_type": "analysis_file"
+                    }
+                ],
+                "process_id": "4da04038-adab-59a9-b6c4-3a61242cc972",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "811adf54-7f27-5aec-9ed7-c6084c4c3a1b",
+                        "protocol_type": "analysis_protocol"
+                    },
+                    {
+                        "protocol_id": "f08df8f8-4966-5265-b127-36625c77deae",
+                        "protocol_type": "library_preparation_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "224d3750-f1f7-5b04-bbce-e23f09eea7d7",
+                        "input_type": "specimen_from_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "d9eaaffe-4c93-5503-984f-762e8dfddce4",
+                        "output_type": "cell_suspension"
+                    }
+                ],
+                "process_id": "296b47c2-7c35-5fdb-bb11-95323011507c",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "9462efe9-1b1a-5a18-81bb-e510137ae743",
+                        "protocol_type": "enrichment_protocol"
+                    },
+                    {
+                        "protocol_id": "6d009d64-1ae9-50b2-a706-6a30e47bdc52",
+                        "protocol_type": "enrichment_protocol"
+                    },
+                    {
+                        "protocol_id": "0f959f0b-5efa-5cc8-9c46-097b0cb574d5",
+                        "protocol_type": "treatment_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "9173ee6a-f1b2-5762-9272-3433b5ef7530",
+                        "input_type": "donor_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "224d3750-f1f7-5b04-bbce-e23f09eea7d7",
+                        "output_type": "specimen_from_organism"
+                    }
+                ],
+                "process_id": "223d54fb-46c9-5c30-9cae-6b8d5ea71b7e",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "ff0c24dd-afd3-5d7a-b982-6191e19314e3",
+                        "protocol_type": "collection_protocol"
+                    }
+                ]
+            }
+        ],
+        "schema_type": "links",
+        "schema_version": "3.1.0"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json b/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json
index 9ac543d2c..b5359ad6e 100644
--- a/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json
+++ b/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json
@@ -97,121 +97,6 @@
                 "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
             }
         },
-        "links.json": {
-            "links": [
-                {
-                    "source_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
-                    "source_type": "biomaterial",
-                    "destination_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "source_type": "dissociation_process",
-                    "destination_id": "04e58fb0-384e-4997-a9e9-575d9887e737",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "source_type": "dissociation_process",
-                    "destination_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
-                    "source_type": "process",
-                    "destination_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "689311a2-bfaf-4196-a753-554e69ab59b2",
-                    "source_type": "biomaterial",
-                    "destination_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
-                    "source_type": "biomaterial",
-                    "destination_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4",
-                    "destination_type": "enrichment_process"
-                },
-                {
-                    "source_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4",
-                    "source_type": "enrichment_process",
-                    "destination_id": "04e58fb0-384e-4997-a9e9-575d9887e737",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4",
-                    "source_type": "enrichment_process",
-                    "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
-                    "source_type": "process",
-                    "destination_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "689311a2-bfaf-4196-a753-554e69ab59b2",
-                    "source_type": "biomaterial",
-                    "destination_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "04e58fb0-384e-4997-a9e9-575d9887e737",
-                    "source_type": "biomaterial",
-                    "destination_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "destination_type": "library_preparation_process"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "2d8cdf91-8162-4321-9923-e00e90fd9133",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "d9087c74-a41e-4702-8481-cea3ef68379c",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "04e58fb0-384e-4997-a9e9-575d9887e737",
-                    "source_type": "biomaterial",
-                    "destination_id": "4624400f-00c5-476a-9bd6-589e87ddb0fe",
-                    "destination_type": "sequencing_process"
-                },
-                {
-                    "source_id": "4624400f-00c5-476a-9bd6-589e87ddb0fe",
-                    "source_type": "sequencing_process",
-                    "destination_id": "2d8cdf91-8162-4321-9923-e00e90fd9133",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "4624400f-00c5-476a-9bd6-589e87ddb0fe",
-                    "source_type": "sequencing_process",
-                    "destination_id": "d9087c74-a41e-4702-8481-cea3ef68379c",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "4624400f-00c5-476a-9bd6-589e87ddb0fe",
-                    "source_type": "sequencing_process",
-                    "destination_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9",
-                    "destination_type": "protocol"
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
-            "schema_version": "1.0.0",
-            "schema_type": "link_bundle"
-        },
         "project_0.json": {
             "content": {
                 "describedBy": "https://schema.humancellatlas.org/type/project/9.0.2/project",
@@ -580,5 +465,120 @@
                 "document_id": "d9087c74-a41e-4702-8481-cea3ef68379c"
             }
         }
+    },
+    "links": {
+        "links": [
+            {
+                "source_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
+                "source_type": "biomaterial",
+                "destination_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "destination_type": "dissociation_process"
+            },
+            {
+                "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "source_type": "dissociation_process",
+                "destination_id": "04e58fb0-384e-4997-a9e9-575d9887e737",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "source_type": "dissociation_process",
+                "destination_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
+                "source_type": "process",
+                "destination_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "689311a2-bfaf-4196-a753-554e69ab59b2",
+                "source_type": "biomaterial",
+                "destination_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
+                "source_type": "biomaterial",
+                "destination_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4",
+                "destination_type": "enrichment_process"
+            },
+            {
+                "source_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4",
+                "source_type": "enrichment_process",
+                "destination_id": "04e58fb0-384e-4997-a9e9-575d9887e737",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4",
+                "source_type": "enrichment_process",
+                "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
+                "source_type": "process",
+                "destination_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "689311a2-bfaf-4196-a753-554e69ab59b2",
+                "source_type": "biomaterial",
+                "destination_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "04e58fb0-384e-4997-a9e9-575d9887e737",
+                "source_type": "biomaterial",
+                "destination_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "destination_type": "library_preparation_process"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "2d8cdf91-8162-4321-9923-e00e90fd9133",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "d9087c74-a41e-4702-8481-cea3ef68379c",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "04e58fb0-384e-4997-a9e9-575d9887e737",
+                "source_type": "biomaterial",
+                "destination_id": "4624400f-00c5-476a-9bd6-589e87ddb0fe",
+                "destination_type": "sequencing_process"
+            },
+            {
+                "source_id": "4624400f-00c5-476a-9bd6-589e87ddb0fe",
+                "source_type": "sequencing_process",
+                "destination_id": "2d8cdf91-8162-4321-9923-e00e90fd9133",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "4624400f-00c5-476a-9bd6-589e87ddb0fe",
+                "source_type": "sequencing_process",
+                "destination_id": "d9087c74-a41e-4702-8481-cea3ef68379c",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "4624400f-00c5-476a-9bd6-589e87ddb0fe",
+                "source_type": "sequencing_process",
+                "destination_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9",
+                "destination_type": "protocol"
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
+        "schema_version": "1.0.0",
+        "schema_type": "link_bundle"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
index 920040235..bb0cb58b2 100644
--- a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
+++ b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
@@ -1978,165 +1978,165 @@
                 "submission_date": "2018-10-10T02:23:39.658Z",
                 "update_date": "2018-10-10T02:23:43.104Z"
             }
-        },
-        "links.json": {
-            "describedBy": "http://schema.integration.data.humancellatlas.org/system/1.1.3/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.3",
-            "links": [
-                {
-                    "process": "d2323ee7-3623-4713-8b27-01cc003e2061",
-                    "inputs": [
-                        "5f0cdf49-aabe-40f4-8af3-033115805bb0",
-                        "74c8c730-139e-40a5-b77e-f46088fa4d95"
-                    ],
-                    "input_type": "file",
-                    "outputs": [
-                        "48e42fe3-41cd-49bd-b7f4-1e3c49682131",
-                        "8b4ed86d-99a8-4665-8f56-5a54fac6cb12",
-                        "416e31c0-b0ec-4674-ab37-ab8506a9f219",
-                        "0b34a80b-c818-4010-b193-e44a77036e27",
-                        "9a827f0b-d74a-436f-a39f-f8c8c9eadfa3",
-                        "1d77c6c5-24b6-4d43-ad5d-b02fba050025",
-                        "18791e67-0c74-43e0-be28-f0c3cd78c7a4",
-                        "9d88ec61-e189-4618-ac15-992a134749a8",
-                        "c059ee58-fbea-40d9-b552-acc1285138a3",
-                        "28220905-f58d-48a1-9258-53f97dd9d388",
-                        "21319798-fe9e-40a4-bcdb-a4c0780ee7bf",
-                        "fd67cd38-2483-49ff-8a9b-0fe1f2607901",
-                        "a5acdc07-18bf-4c06-b212-2b36e52173ef",
-                        "da510e7a-5495-40c5-964d-b5291372102c",
-                        "14d63962-7cd3-43fc-a4d6-dc8f761c9ebd",
-                        "b7f69b47-cbdf-4ec9-be6e-d316827aad8e",
-                        "a3b39c62-3dd8-48f9-bcba-08a16f43a40b",
-                        "b4767274-c12b-401f-8bc1-9c9213149442",
-                        "dfa9da1b-3f48-4c76-86a2-833ded3e2745",
-                        "11d84aef-c087-4fd1-bdc9-0c3402a0db01",
-                        "345c5bd6-ac02-4b5d-9d53-e2ec7d7928aa",
-                        "5aa074b9-f6e6-4790-9608-b5eb37425341",
-                        "b9672a5e-03be-41a6-9155-b29626815e11",
-                        "c0da3d0b-128b-4b37-a3d6-9538ab29e9b6",
-                        "46465f1a-a0cc-413f-aebc-505e4714c6b2",
-                        "7ba06d4d-c134-4324-84e6-3a37e57af2ce",
-                        "7cd4f7cc-8712-4ffd-b91d-9cb7c6182f52",
-                        "54604922-909e-4094-83d7-9d8ac7e7cdbd",
-                        "e0fc82a4-9bc2-4219-b763-99c865e4f9c0",
-                        "5c3246df-9ee8-42fe-ab19-ddd0ddea3e15"
-                    ],
-                    "output_type": "file",
-                    "protocols": []
-                },
-                {
-                    "process": "5afa951e-1591-4bad-a4f8-2e13cbdb760c",
-                    "inputs": [
-                        "377f2f5a-4a45-4c62-8fb0-db9ef33f5cf0"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "5f0cdf49-aabe-40f4-8af3-033115805bb0",
-                        "74c8c730-139e-40a5-b77e-f46088fa4d95"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "92bc8cf5-b595-4536-b0e8-46eb702b4f4f"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "da614ddd-0384-49ca-a6e1-2141ace13a01"
-                        }
-                    ]
-                },
-                {
-                    "process": "27b9dad1-b670-4fc3-aad3-24e51e70dfba",
-                    "inputs": [
-                        "b5894cf5-ecdc-4ea6-a0b9-5335ab678c7a"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "377f2f5a-4a45-4c62-8fb0-db9ef33f5cf0"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "63d78c21-061c-4e94-bb68-a5914f811447"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "d7820ce6-f0f4-4778-9353-423626dbd7c0"
-                        }
-                    ]
-                },
-                {
-                    "process": "908d468a-eb62-4d19-8706-c5f708a14940",
-                    "inputs": [
-                        "242e38d2-c975-47ee-800a-6645b47e92d2"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "b5894cf5-ecdc-4ea6-a0b9-5335ab678c7a"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "5afa951e-1591-4bad-a4f8-2e13cbdb760c",
-                    "inputs": [
-                        "377f2f5a-4a45-4c62-8fb0-db9ef33f5cf0"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "5f0cdf49-aabe-40f4-8af3-033115805bb0",
-                        "74c8c730-139e-40a5-b77e-f46088fa4d95"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "92bc8cf5-b595-4536-b0e8-46eb702b4f4f"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "da614ddd-0384-49ca-a6e1-2141ace13a01"
-                        }
-                    ]
-                },
-                {
-                    "process": "27b9dad1-b670-4fc3-aad3-24e51e70dfba",
-                    "inputs": [
-                        "b5894cf5-ecdc-4ea6-a0b9-5335ab678c7a"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "377f2f5a-4a45-4c62-8fb0-db9ef33f5cf0"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "63d78c21-061c-4e94-bb68-a5914f811447"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "d7820ce6-f0f4-4778-9353-423626dbd7c0"
-                        }
-                    ]
-                },
-                {
-                    "process": "908d468a-eb62-4d19-8706-c5f708a14940",
-                    "inputs": [
-                        "242e38d2-c975-47ee-800a-6645b47e92d2"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "b5894cf5-ecdc-4ea6-a0b9-5335ab678c7a"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "http://schema.integration.data.humancellatlas.org/system/1.1.3/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.3",
+        "links": [
+            {
+                "process": "d2323ee7-3623-4713-8b27-01cc003e2061",
+                "inputs": [
+                    "5f0cdf49-aabe-40f4-8af3-033115805bb0",
+                    "74c8c730-139e-40a5-b77e-f46088fa4d95"
+                ],
+                "input_type": "file",
+                "outputs": [
+                    "48e42fe3-41cd-49bd-b7f4-1e3c49682131",
+                    "8b4ed86d-99a8-4665-8f56-5a54fac6cb12",
+                    "416e31c0-b0ec-4674-ab37-ab8506a9f219",
+                    "0b34a80b-c818-4010-b193-e44a77036e27",
+                    "9a827f0b-d74a-436f-a39f-f8c8c9eadfa3",
+                    "1d77c6c5-24b6-4d43-ad5d-b02fba050025",
+                    "18791e67-0c74-43e0-be28-f0c3cd78c7a4",
+                    "9d88ec61-e189-4618-ac15-992a134749a8",
+                    "c059ee58-fbea-40d9-b552-acc1285138a3",
+                    "28220905-f58d-48a1-9258-53f97dd9d388",
+                    "21319798-fe9e-40a4-bcdb-a4c0780ee7bf",
+                    "fd67cd38-2483-49ff-8a9b-0fe1f2607901",
+                    "a5acdc07-18bf-4c06-b212-2b36e52173ef",
+                    "da510e7a-5495-40c5-964d-b5291372102c",
+                    "14d63962-7cd3-43fc-a4d6-dc8f761c9ebd",
+                    "b7f69b47-cbdf-4ec9-be6e-d316827aad8e",
+                    "a3b39c62-3dd8-48f9-bcba-08a16f43a40b",
+                    "b4767274-c12b-401f-8bc1-9c9213149442",
+                    "dfa9da1b-3f48-4c76-86a2-833ded3e2745",
+                    "11d84aef-c087-4fd1-bdc9-0c3402a0db01",
+                    "345c5bd6-ac02-4b5d-9d53-e2ec7d7928aa",
+                    "5aa074b9-f6e6-4790-9608-b5eb37425341",
+                    "b9672a5e-03be-41a6-9155-b29626815e11",
+                    "c0da3d0b-128b-4b37-a3d6-9538ab29e9b6",
+                    "46465f1a-a0cc-413f-aebc-505e4714c6b2",
+                    "7ba06d4d-c134-4324-84e6-3a37e57af2ce",
+                    "7cd4f7cc-8712-4ffd-b91d-9cb7c6182f52",
+                    "54604922-909e-4094-83d7-9d8ac7e7cdbd",
+                    "e0fc82a4-9bc2-4219-b763-99c865e4f9c0",
+                    "5c3246df-9ee8-42fe-ab19-ddd0ddea3e15"
+                ],
+                "output_type": "file",
+                "protocols": []
+            },
+            {
+                "process": "5afa951e-1591-4bad-a4f8-2e13cbdb760c",
+                "inputs": [
+                    "377f2f5a-4a45-4c62-8fb0-db9ef33f5cf0"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "5f0cdf49-aabe-40f4-8af3-033115805bb0",
+                    "74c8c730-139e-40a5-b77e-f46088fa4d95"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "92bc8cf5-b595-4536-b0e8-46eb702b4f4f"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "da614ddd-0384-49ca-a6e1-2141ace13a01"
+                    }
+                ]
+            },
+            {
+                "process": "27b9dad1-b670-4fc3-aad3-24e51e70dfba",
+                "inputs": [
+                    "b5894cf5-ecdc-4ea6-a0b9-5335ab678c7a"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "377f2f5a-4a45-4c62-8fb0-db9ef33f5cf0"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "63d78c21-061c-4e94-bb68-a5914f811447"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "d7820ce6-f0f4-4778-9353-423626dbd7c0"
+                    }
+                ]
+            },
+            {
+                "process": "908d468a-eb62-4d19-8706-c5f708a14940",
+                "inputs": [
+                    "242e38d2-c975-47ee-800a-6645b47e92d2"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "b5894cf5-ecdc-4ea6-a0b9-5335ab678c7a"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "5afa951e-1591-4bad-a4f8-2e13cbdb760c",
+                "inputs": [
+                    "377f2f5a-4a45-4c62-8fb0-db9ef33f5cf0"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "5f0cdf49-aabe-40f4-8af3-033115805bb0",
+                    "74c8c730-139e-40a5-b77e-f46088fa4d95"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "92bc8cf5-b595-4536-b0e8-46eb702b4f4f"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "da614ddd-0384-49ca-a6e1-2141ace13a01"
+                    }
+                ]
+            },
+            {
+                "process": "27b9dad1-b670-4fc3-aad3-24e51e70dfba",
+                "inputs": [
+                    "b5894cf5-ecdc-4ea6-a0b9-5335ab678c7a"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "377f2f5a-4a45-4c62-8fb0-db9ef33f5cf0"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "63d78c21-061c-4e94-bb68-a5914f811447"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "d7820ce6-f0f4-4778-9353-423626dbd7c0"
+                    }
+                ]
+            },
+            {
+                "process": "908d468a-eb62-4d19-8706-c5f708a14940",
+                "inputs": [
+                    "242e38d2-c975-47ee-800a-6645b47e92d2"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "b5894cf5-ecdc-4ea6-a0b9-5335ab678c7a"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
index 850a472aa..26154b0f7 100644
--- a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
+++ b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
@@ -4477,3838 +4477,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "schema_type": "links",
-            "schema_version": "3.0.0",
-            "describedBy": "https://schema.humancellatlas.org/system/3.0.0/links",
-            "links": [
-                {
-                    "inputs": [
-                        {
-                            "input_id": "689bcda6-eb41-588a-b4a9-8827e22b1856",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "df5af5d4-56e1-517b-8f47-7bf4888c853a",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "febe54b0-6388-5024-a971-fa88862a4e62",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "2b9f7c89-d1c2-53ef-a769-80fec2f7d9e6",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "caee5d2b-466f-5762-a565-8fa4a520faba",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "448173cc-00c9-56e1-9bde-a8136521dc6f",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "5ef41564-04c4-5260-b974-9b37fcc73e35",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "32c69d68-1792-53af-9f42-0e97c9afc94b",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "9a41c791-004c-5d89-a10c-d58d2ef7eca3",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "57c38b28-848d-5716-8c68-a3b3222aac6e",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "509608f1-e1d5-561c-b0d6-54348f0adb29",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "f9b8be35-2641-5f85-af13-c0390b7bfe23",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "4db3cc2d-f0ac-5cdf-8656-4c9b096a0092",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "50547806-882a-5915-b217-5bbc692239b9",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "b149162c-3450-5301-b057-c3930459584d",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "9702f6ba-fd5b-5972-80d4-629e8a8fa8e9",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "3cd78fb7-b7bc-5ab1-b122-47585f0023d4",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "44175006-91f3-5d95-9a08-b33e08ed1ae3",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "b666cb1a-1a4f-511f-859e-2779aad16fa0",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "4d411b9c-06de-5805-bb7f-eca54e1c42cc",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "fbcc2483-8a75-50ec-8cb6-8148a5087dce",
-                            "input_type": "analysis_file"
-                        },
-                        {
-                            "input_id": "38a0ef48-9df1-5fef-8eb6-b32fbb67aabd",
-                            "input_type": "analysis_file"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "c60bf214-0340-53c0-b75b-af84a82808d6",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "9531ad31-8210-463c-a6c4-171fb50e4cd1",
-                    "process_type": "analysis_process",
-                    "protocols": [
-                        {
-                            "protocol_id": "432a7422-59b5-5c46-8983-a7953f196781",
-                            "protocol_type": "analysis_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "59e40d0b-dfbc-4668-bb8a-d0b39d25ca88",
-                            "input_type": "sequence_file"
-                        },
-                        {
-                            "input_id": "154ff85c-da53-4b85-b02b-002211631867",
-                            "input_type": "sequence_file"
-                        },
-                        {
-                            "input_id": "e3777b07-1706-4434-a523-1335f0b96b30",
-                            "input_type": "sequence_file"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "50547806-882a-5915-b217-5bbc692239b9",
-                            "output_type": "analysis_file"
-                        },
-                        {
-                            "output_id": "5f89237b-83d8-5b2b-880c-2fc4f0c1db1c",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "70341236-6291-4b53-b161-17bca3b50cb9",
-                    "process_type": "analysis_process",
-                    "protocols": [
-                        {
-                            "protocol_id": "289ec28b-ce11-5be8-89ab-92fbceb874a0",
-                            "protocol_type": "analysis_protocol"
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-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "2dd22fa3-fe29-4d60-b890-a8ee8b9731ce",
-                            "input_type": "sequence_file"
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+                        "output_type": "sequence_file",
+                        "output_id": "1f50a6ba-90e5-4162-b6ac-6f8d5bfe72cc"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "6500ad38-5b46-4186-9208-6a9494679191"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "db9fbac5-641e-4dad-af15-a7afa407654b"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "71efd7ce-0ec0-4423-9eb2-9bd42f40a33f"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "fe71fe4a-0903-42e0-9a65-d985abd943ca"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "a228f157-78ea-4e3c-85bc-dc90ccd3ec44",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "442f68c7-502a-4fc7-a3b8-94e9574cd22d"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "5355142f-f257-49bb-9589-2fd932361519"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "60d4e19b-aa28-4ed1-9ac5-1db33d287b0a"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ca78a1a9-375c-4aa8-bfdc-822279d0eca3"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "4cc61094-94b9-4d21-a8f8-edbd73129049",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "91f51e13-dc56-4526-9e39-92a6c6778e16"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "442f68c7-502a-4fc7-a3b8-94e9574cd22d"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "f44d6b65-0866-47d5-bfb2-8173b1b6a2b3"
+                    }
+                ]
+            },
+            {
+                "link_type": "supplementary_file_link",
+                "entity": {
+                    "entity_type": "project",
+                    "entity_id": "abe1a013-af7a-45ed-8c26-f3793c24a1f4"
+                },
+                "files": [
+                    {
+                        "file_id": "f1aecf03-b60d-483c-a09f-69223cc1ad0e",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "1c531e83-02f4-4c00-b161-f186a1b5e1fb",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "63a1acfd-ca01-451d-a41d-d3a7ffd1655b",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "c72eb744-4971-4525-802c-d898349b392a",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "53089129-f71b-412c-ae2d-f7e8e50044c3",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "5b84bbca-dfde-462c-9c79-c914f32e03c4",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "06e90b33-4403-41e8-b783-e65bf7de982a",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "944589e7-48a4-4333-b773-8e632ccb8865",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "182c7357-0ac0-483d-8189-b321cb3e8d74",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "77700dee-f8b3-40d1-b527-e0e53562eb49",
+                        "file_type": "supplementary_file"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "548a75b4-ba45-4700-b7bb-656c3995c316",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "15ec2b2a-c3fe-4946-8cf6-9386bb87eec1"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "8f6318ea-e692-4085-a693-02f4ff3204b5"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "be64dbc9-183f-44c9-8b15-d8298ee6c4e9"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "c8758f13-7e9b-464a-bada-b41b8b9e925f"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "71efd7ce-0ec0-4423-9eb2-9bd42f40a33f"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "fe71fe4a-0903-42e0-9a65-d985abd943ca"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "12995713-3c1b-4e13-a7b9-26d242e9ad71",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "f47bb6a8-a753-4d40-8254-28fee9d03c1b"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "15ec2b2a-c3fe-4946-8cf6-9386bb87eec1"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "9d5c8595-a80c-4a12-b869-0b6c45ad6e16"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "741ffe1e-7bb1-4307-9d55-9ab77258314c"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "5878b562-defb-486f-8fa2-f4573bcd7322",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "a6116756-3aeb-48f2-8952-caccbfd3f57b"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "f47bb6a8-a753-4d40-8254-28fee9d03c1b"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "f870bf7e-2cb7-44b2-a299-f4e06da4453c"
+                    }
+                ]
+            },
+            {
+                "link_type": "supplementary_file_link",
+                "entity": {
+                    "entity_type": "project",
+                    "entity_id": "abe1a013-af7a-45ed-8c26-f3793c24a1f4"
+                },
+                "files": [
+                    {
+                        "file_id": "f1aecf03-b60d-483c-a09f-69223cc1ad0e",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "1c531e83-02f4-4c00-b161-f186a1b5e1fb",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "63a1acfd-ca01-451d-a41d-d3a7ffd1655b",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "c72eb744-4971-4525-802c-d898349b392a",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "53089129-f71b-412c-ae2d-f7e8e50044c3",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "5b84bbca-dfde-462c-9c79-c914f32e03c4",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "06e90b33-4403-41e8-b783-e65bf7de982a",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "944589e7-48a4-4333-b773-8e632ccb8865",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "182c7357-0ac0-483d-8189-b321cb3e8d74",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "77700dee-f8b3-40d1-b527-e0e53562eb49",
+                        "file_type": "supplementary_file"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "b6dec4a6-2d9b-40ac-80c4-41dce01aea46",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "9fa78638-59a3-45d6-b065-ed1fbf84fa96"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "a6a5f2ec-2b8c-4419-82a9-f6bdb80e849c"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "be252ee9-c27b-4937-8e96-e971c25ed794"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "d8577b2c-16a2-484f-9269-9196d7cca451"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "71efd7ce-0ec0-4423-9eb2-9bd42f40a33f"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "fe71fe4a-0903-42e0-9a65-d985abd943ca"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "7a625379-2c08-4bde-aa32-1081132bdeb7",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "5fbd4bb4-e761-4345-99b8-bd5e141a8b94"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "9fa78638-59a3-45d6-b065-ed1fbf84fa96"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "60d4e19b-aa28-4ed1-9ac5-1db33d287b0a"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "5238fd9b-f4c2-46d9-bb44-6cebc9371a52"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "36bbd76b-b6ab-4c84-a5ec-965af8c40a28",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "9fde0deb-9630-4007-aea6-e7a7b1e68c2a"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "5fbd4bb4-e761-4345-99b8-bd5e141a8b94"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "b9a9d40e-7b4f-48f1-a893-f678e917a96d"
+                    }
+                ]
+            },
+            {
+                "link_type": "supplementary_file_link",
+                "entity": {
+                    "entity_type": "project",
+                    "entity_id": "abe1a013-af7a-45ed-8c26-f3793c24a1f4"
+                },
+                "files": [
+                    {
+                        "file_id": "f1aecf03-b60d-483c-a09f-69223cc1ad0e",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "1c531e83-02f4-4c00-b161-f186a1b5e1fb",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "63a1acfd-ca01-451d-a41d-d3a7ffd1655b",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "c72eb744-4971-4525-802c-d898349b392a",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "53089129-f71b-412c-ae2d-f7e8e50044c3",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "5b84bbca-dfde-462c-9c79-c914f32e03c4",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "06e90b33-4403-41e8-b783-e65bf7de982a",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "944589e7-48a4-4333-b773-8e632ccb8865",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "182c7357-0ac0-483d-8189-b321cb3e8d74",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "77700dee-f8b3-40d1-b527-e0e53562eb49",
+                        "file_type": "supplementary_file"
+                    }
+                ]
+            }
+        ]
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json b/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
index e1b087c71..b4aee82a8 100644
--- a/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
+++ b/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
@@ -182,104 +182,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
-            "links": [
-                {
-                    "inputs": [
-                        {
-                            "input_id": "6ff38054-9296-5d4c-b238-6a3b01a15175",
-                            "input_type": "cell_suspension"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "caf6d2a8-2272-5689-b3d8-9c97370d6c29",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "7a330531-ec7f-5aee-84d4-2ba24d66e93b",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "811adf54-7f27-5aec-9ed7-c6084c4c3a1b",
-                            "protocol_type": "analysis_protocol"
-                        },
-                        {
-                            "protocol_id": "767282b2-2fc1-5559-b020-29686b810206",
-                            "protocol_type": "library_preparation_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "119c4135-7b77-5003-a150-f052e22c6834",
-                            "input_type": "cell_suspension"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "6ff38054-9296-5d4c-b238-6a3b01a15175",
-                            "output_type": "cell_suspension"
-                        }
-                    ],
-                    "process_id": "b0092a47-b19d-5b34-b004-cb8edd8c625b",
-                    "process_type": "process",
-                    "protocols": []
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "3bee0c9a-aced-52f2-b97f-89518f826b36",
-                            "input_type": "specimen_from_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "119c4135-7b77-5003-a150-f052e22c6834",
-                            "output_type": "cell_suspension"
-                        }
-                    ],
-                    "process_id": "bd6a4a38-c44b-5d17-b2b1-d0d4c4531bf0",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "46435803-7ee8-5157-8569-8a61ad50c315",
-                            "protocol_type": "enrichment_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "5bc2bf2f-eb98-5510-a386-172cef38f2f2",
-                            "input_type": "donor_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "3bee0c9a-aced-52f2-b97f-89518f826b36",
-                            "output_type": "specimen_from_organism"
-                        }
-                    ],
-                    "process_id": "37e91a9f-b04e-5313-bbc0-4c394406247e",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "e7f864e3-6ba7-53c8-842f-2a05cb90e1b7",
-                            "protocol_type": "collection_protocol"
-                        }
-                    ]
-                }
-            ],
-            "schema_type": "links",
-            "schema_version": "3.1.0"
-        },
         "project_0.json": {
             "array_express_accessions": [
                 "E-MTAB-10026"
@@ -731,5 +633,103 @@
             },
             "schema_type": "protocol"
         }
+    },
+    "links": {
+        "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
+        "links": [
+            {
+                "inputs": [
+                    {
+                        "input_id": "6ff38054-9296-5d4c-b238-6a3b01a15175",
+                        "input_type": "cell_suspension"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "caf6d2a8-2272-5689-b3d8-9c97370d6c29",
+                        "output_type": "analysis_file"
+                    }
+                ],
+                "process_id": "7a330531-ec7f-5aee-84d4-2ba24d66e93b",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "811adf54-7f27-5aec-9ed7-c6084c4c3a1b",
+                        "protocol_type": "analysis_protocol"
+                    },
+                    {
+                        "protocol_id": "767282b2-2fc1-5559-b020-29686b810206",
+                        "protocol_type": "library_preparation_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "119c4135-7b77-5003-a150-f052e22c6834",
+                        "input_type": "cell_suspension"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "6ff38054-9296-5d4c-b238-6a3b01a15175",
+                        "output_type": "cell_suspension"
+                    }
+                ],
+                "process_id": "b0092a47-b19d-5b34-b004-cb8edd8c625b",
+                "process_type": "process",
+                "protocols": []
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "3bee0c9a-aced-52f2-b97f-89518f826b36",
+                        "input_type": "specimen_from_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "119c4135-7b77-5003-a150-f052e22c6834",
+                        "output_type": "cell_suspension"
+                    }
+                ],
+                "process_id": "bd6a4a38-c44b-5d17-b2b1-d0d4c4531bf0",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "46435803-7ee8-5157-8569-8a61ad50c315",
+                        "protocol_type": "enrichment_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "5bc2bf2f-eb98-5510-a386-172cef38f2f2",
+                        "input_type": "donor_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "3bee0c9a-aced-52f2-b97f-89518f826b36",
+                        "output_type": "specimen_from_organism"
+                    }
+                ],
+                "process_id": "37e91a9f-b04e-5313-bbc0-4c394406247e",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "e7f864e3-6ba7-53c8-842f-2a05cb90e1b7",
+                        "protocol_type": "collection_protocol"
+                    }
+                ]
+            }
+        ],
+        "schema_type": "links",
+        "schema_version": "3.1.0"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
index 14032393d..f93a841a6 100644
--- a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
+++ b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
@@ -277,133 +277,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "schema_type": "links",
-            "schema_version": "3.0.0",
-            "describedBy": "https://schema.humancellatlas.org/system/3.0.0/links",
-            "links": [
-                {
-                    "inputs": [
-                        {
-                            "input_id": "39255288-6791-45b0-ac7e-b3ef4c981a3b",
-                            "input_type": "sequence_file"
-                        },
-                        {
-                            "input_id": "9f8f5212-0749-460b-9a46-2949dea45d52",
-                            "input_type": "sequence_file"
-                        },
-                        {
-                            "input_id": "30040306-be5c-48f9-b221-e666e279ab5b",
-                            "input_type": "sequence_file"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "d90280cc-a294-57de-b350-5234a5278c19",
-                            "output_type": "analysis_file"
-                        },
-                        {
-                            "output_id": "b949e4b6-c3fb-58b4-865b-40cb3ef2b6c6",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "3d7a4690-8760-491c-98f9-9a1aea3f79b5",
-                    "process_type": "analysis_process",
-                    "protocols": [
-                        {
-                            "protocol_id": "289ec28b-ce11-5be8-89ab-92fbceb874a0",
-                            "protocol_type": "analysis_protocol"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_type": "process",
-                    "process_id": "1116b396-448e-4dd1-b9c9-78357c511e15",
-                    "inputs": [
-                        {
-                            "input_type": "cell_suspension",
-                            "input_id": "932000d6-c63b-40f0-bdd5-469fa4db8be2"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "30040306-be5c-48f9-b221-e666e279ab5b"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "39255288-6791-45b0-ac7e-b3ef4c981a3b"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "9f8f5212-0749-460b-9a46-2949dea45d52"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "fa99959f-faa2-4d69-a092-48333e59f5f3"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "a166be3d-6e84-4058-a1bd-edf90cf3ee88"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_type": "process",
-                    "process_id": "b360251f-7550-4c08-b576-781858554ea1",
-                    "inputs": [
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "edc72947-b776-4150-8bfe-b7331acfa66f"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "cell_suspension",
-                            "output_id": "932000d6-c63b-40f0-bdd5-469fa4db8be2"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "2509f42a-0328-4e33-8d21-79d37560d846"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "ba595d79-aa43-4e3a-ad10-89f92ef4f22f"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_type": "process",
-                    "process_id": "a5e37780-0b71-4610-8a7c-26142dedfcec",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "b8049daa-7458-47bf-8ec2-3f5c56d2cb34"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "edc72947-b776-4150-8bfe-b7331acfa66f"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "3030903f-4a4b-4b30-ab93-3b10183181e0"
-                        }
-                    ]
-                }
-            ]
-        },
         "analysis_protocol_0.json": {
             "computational_method": "Optimus",
             "describedBy": "https://schema.humancellatlas.org/type/protocol/analysis/9.1.0/analysis_protocol",
@@ -1522,5 +1395,132 @@
                 "update_date": "2019-09-13T08:37:53.821Z"
             }
         }
+    },
+    "links": {
+        "schema_type": "links",
+        "schema_version": "3.0.0",
+        "describedBy": "https://schema.humancellatlas.org/system/3.0.0/links",
+        "links": [
+            {
+                "inputs": [
+                    {
+                        "input_id": "39255288-6791-45b0-ac7e-b3ef4c981a3b",
+                        "input_type": "sequence_file"
+                    },
+                    {
+                        "input_id": "9f8f5212-0749-460b-9a46-2949dea45d52",
+                        "input_type": "sequence_file"
+                    },
+                    {
+                        "input_id": "30040306-be5c-48f9-b221-e666e279ab5b",
+                        "input_type": "sequence_file"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "d90280cc-a294-57de-b350-5234a5278c19",
+                        "output_type": "analysis_file"
+                    },
+                    {
+                        "output_id": "b949e4b6-c3fb-58b4-865b-40cb3ef2b6c6",
+                        "output_type": "analysis_file"
+                    }
+                ],
+                "process_id": "3d7a4690-8760-491c-98f9-9a1aea3f79b5",
+                "process_type": "analysis_process",
+                "protocols": [
+                    {
+                        "protocol_id": "289ec28b-ce11-5be8-89ab-92fbceb874a0",
+                        "protocol_type": "analysis_protocol"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "1116b396-448e-4dd1-b9c9-78357c511e15",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "932000d6-c63b-40f0-bdd5-469fa4db8be2"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "30040306-be5c-48f9-b221-e666e279ab5b"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "39255288-6791-45b0-ac7e-b3ef4c981a3b"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "9f8f5212-0749-460b-9a46-2949dea45d52"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "fa99959f-faa2-4d69-a092-48333e59f5f3"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "a166be3d-6e84-4058-a1bd-edf90cf3ee88"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "b360251f-7550-4c08-b576-781858554ea1",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "edc72947-b776-4150-8bfe-b7331acfa66f"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "932000d6-c63b-40f0-bdd5-469fa4db8be2"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "2509f42a-0328-4e33-8d21-79d37560d846"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ba595d79-aa43-4e3a-ad10-89f92ef4f22f"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_type": "process",
+                "process_id": "a5e37780-0b71-4610-8a7c-26142dedfcec",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "b8049daa-7458-47bf-8ec2-3f5c56d2cb34"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "edc72947-b776-4150-8bfe-b7331acfa66f"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "3030903f-4a4b-4b30-ab93-3b10183181e0"
+                    }
+                ]
+            }
+        ]
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
index 4f8d05032..22ea45006 100644
--- a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
+++ b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
@@ -195,98 +195,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "links": [
-                {
-                    "link_type": "process_link",
-                    "process_id": "80baee6e-00a5-4fdc-bfe3-d339ff8a7178",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "cell_suspension",
-                            "input_id": "38f53d63-e470-491a-a98a-83bf0c47b630"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "64f1a275-671c-46a2-ba7f-6647e672c8d7"
-                        },
-                        {
-                            "output_type": "sequence_file",
-                            "output_id": "e27de859-4b05-43d6-8437-7f7dfc0507d1"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "9b9f5554-0f48-4af5-a765-c45226e0531c"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "58612e7a-c83a-4c7d-ab53-974b207291eb"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "4ce6bcb3-6402-4265-b18e-fa3ebea6e786",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "specimen_from_organism",
-                            "input_id": "5b2453cf-dffd-42e4-8868-73aec60b1418"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "cell_suspension",
-                            "output_id": "38f53d63-e470-491a-a98a-83bf0c47b630"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "97c799c5-5db6-4d57-8a03-0fb877039255"
-                        },
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "37aee665-8ee9-451c-b1ef-e998cc268481"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "46299069-e6aa-4b95-b134-5dcbd4685cb3"
-                        }
-                    ]
-                },
-                {
-                    "link_type": "process_link",
-                    "process_id": "f188ad1d-17dc-4f21-a35d-c24a1d53e728",
-                    "process_type": "process",
-                    "inputs": [
-                        {
-                            "input_type": "donor_organism",
-                            "input_id": "270341ef-ab2d-4e88-9ae1-b49684fc60e0"
-                        }
-                    ],
-                    "outputs": [
-                        {
-                            "output_type": "specimen_from_organism",
-                            "output_id": "5b2453cf-dffd-42e4-8868-73aec60b1418"
-                        }
-                    ],
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "5f886847-ef33-4a9b-b971-f2fe9f429cc4"
-                        }
-                    ]
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links",
-            "schema_version": "2.1.1",
-            "schema_type": "links"
-        },
         "sequencing_protocol_0.json": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
@@ -835,5 +743,97 @@
                 "schema_minor_version": 2
             }
         }
+    },
+    "links": {
+        "links": [
+            {
+                "link_type": "process_link",
+                "process_id": "80baee6e-00a5-4fdc-bfe3-d339ff8a7178",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "38f53d63-e470-491a-a98a-83bf0c47b630"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "64f1a275-671c-46a2-ba7f-6647e672c8d7"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "e27de859-4b05-43d6-8437-7f7dfc0507d1"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "9b9f5554-0f48-4af5-a765-c45226e0531c"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "58612e7a-c83a-4c7d-ab53-974b207291eb"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "4ce6bcb3-6402-4265-b18e-fa3ebea6e786",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "5b2453cf-dffd-42e4-8868-73aec60b1418"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "38f53d63-e470-491a-a98a-83bf0c47b630"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "97c799c5-5db6-4d57-8a03-0fb877039255"
+                    },
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "37aee665-8ee9-451c-b1ef-e998cc268481"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "46299069-e6aa-4b95-b134-5dcbd4685cb3"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "f188ad1d-17dc-4f21-a35d-c24a1d53e728",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "270341ef-ab2d-4e88-9ae1-b49684fc60e0"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "5b2453cf-dffd-42e4-8868-73aec60b1418"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "5f886847-ef33-4a9b-b971-f2fe9f429cc4"
+                    }
+                ]
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links",
+        "schema_version": "2.1.1",
+        "schema_type": "links"
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
index 658d4936f..558da1965 100644
--- a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
+++ b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
@@ -82,34 +82,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links",
-            "schema_type": "links",
-            "schema_version": "2.1.1",
-            "links": [
-                {
-                    "link_type": "supplementary_file_link",
-                    "entity": {
-                        "entity_type": "project",
-                        "entity_id": "8185730f-4113-40d3-9cc3-929271784c2b"
-                    },
-                    "files": [
-                        {
-                            "file_id": "538faa28-3235-5e4b-a998-5672e2d964e8",
-                            "file_type": "supplementary_file"
-                        },
-                        {
-                            "file_id": "8d2ba1c1-bc9f-5c2a-a74d-fe5e09bdfb18",
-                            "file_type": "supplementary_file"
-                        },
-                        {
-                            "file_id": "6c142250-567c-5b63-bd4f-0d78499863f8",
-                            "file_type": "supplementary_file"
-                        }
-                    ]
-                }
-            ]
-        },
         "supplementary_file_0.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/2.2.0/supplementary_file",
             "schema_type": "file",
@@ -599,5 +571,33 @@
                 "update_date": "2019-09-13T08:37:53.825Z"
             }
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links",
+        "schema_type": "links",
+        "schema_version": "2.1.1",
+        "links": [
+            {
+                "link_type": "supplementary_file_link",
+                "entity": {
+                    "entity_type": "project",
+                    "entity_id": "8185730f-4113-40d3-9cc3-929271784c2b"
+                },
+                "files": [
+                    {
+                        "file_id": "538faa28-3235-5e4b-a998-5672e2d964e8",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "8d2ba1c1-bc9f-5c2a-a74d-fe5e09bdfb18",
+                        "file_type": "supplementary_file"
+                    },
+                    {
+                        "file_id": "6c142250-567c-5b63-bd4f-0d78499863f8",
+                        "file_type": "supplementary_file"
+                    }
+                ]
+            }
+        ]
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json b/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
index 0f18ef57e..ed5b8ff49 100644
--- a/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
+++ b/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
@@ -502,181 +502,181 @@
                 "updateDate": "2018-03-28T14:30:39.321Z",
                 "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
             }
-        },
-        "links.json": {
-            "links": [
-                {
-                    "source_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
-                    "source_type": "biomaterial",
-                    "destination_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "source_type": "dissociation_process",
-                    "destination_id": "54a80c57-0409-4f57-9699-8a2f8cbace43",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "source_type": "dissociation_process",
-                    "destination_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
-                    "source_type": "process",
-                    "destination_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "665b75b4-8638-4a15-83e5-f3928dd29314",
-                    "source_type": "biomaterial",
-                    "destination_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
-                    "source_type": "biomaterial",
-                    "destination_id": "87beb50f-521d-4102-9cb0-ca7b6f151afc",
-                    "destination_type": "enrichment_process"
-                },
-                {
-                    "source_id": "87beb50f-521d-4102-9cb0-ca7b6f151afc",
-                    "source_type": "enrichment_process",
-                    "destination_id": "54a80c57-0409-4f57-9699-8a2f8cbace43",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "87beb50f-521d-4102-9cb0-ca7b6f151afc",
-                    "source_type": "enrichment_process",
-                    "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
-                    "source_type": "process",
-                    "destination_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "665b75b4-8638-4a15-83e5-f3928dd29314",
-                    "source_type": "biomaterial",
-                    "destination_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
-                    "source_type": "biomaterial",
-                    "destination_id": "8caf3d2b-7dba-40ca-a2d7-c69b433ba70b",
-                    "destination_type": "enrichment_process"
-                },
-                {
-                    "source_id": "8caf3d2b-7dba-40ca-a2d7-c69b433ba70b",
-                    "source_type": "enrichment_process",
-                    "destination_id": "54a80c57-0409-4f57-9699-8a2f8cbace43",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "8caf3d2b-7dba-40ca-a2d7-c69b433ba70b",
-                    "source_type": "enrichment_process",
-                    "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
-                    "source_type": "process",
-                    "destination_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "665b75b4-8638-4a15-83e5-f3928dd29314",
-                    "source_type": "biomaterial",
-                    "destination_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
-                    "source_type": "biomaterial",
-                    "destination_id": "5a801f3d-12b0-4374-aed9-deee905b55ef",
-                    "destination_type": "enrichment_process"
-                },
-                {
-                    "source_id": "5a801f3d-12b0-4374-aed9-deee905b55ef",
-                    "source_type": "enrichment_process",
-                    "destination_id": "54a80c57-0409-4f57-9699-8a2f8cbace43",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "5a801f3d-12b0-4374-aed9-deee905b55ef",
-                    "source_type": "enrichment_process",
-                    "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
-                    "source_type": "process",
-                    "destination_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "665b75b4-8638-4a15-83e5-f3928dd29314",
-                    "source_type": "biomaterial",
-                    "destination_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "54a80c57-0409-4f57-9699-8a2f8cbace43",
-                    "source_type": "biomaterial",
-                    "destination_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "destination_type": "library_preparation_process"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "b2cd6fb7-6612-4ab9-a1c5-e475663437e3",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "f599ea3f-14bb-4504-82ce-d9c1f26e55fa",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "54a80c57-0409-4f57-9699-8a2f8cbace43",
-                    "source_type": "biomaterial",
-                    "destination_id": "66551017-88b4-431d-ab33-c3a805f37bdf",
-                    "destination_type": "sequencing_process"
-                },
-                {
-                    "source_id": "66551017-88b4-431d-ab33-c3a805f37bdf",
-                    "source_type": "sequencing_process",
-                    "destination_id": "b2cd6fb7-6612-4ab9-a1c5-e475663437e3",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "66551017-88b4-431d-ab33-c3a805f37bdf",
-                    "source_type": "sequencing_process",
-                    "destination_id": "f599ea3f-14bb-4504-82ce-d9c1f26e55fa",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "66551017-88b4-431d-ab33-c3a805f37bdf",
-                    "source_type": "sequencing_process",
-                    "destination_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9",
-                    "destination_type": "protocol"
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
-            "schema_version": "1.0.0",
-            "schema_type": "link_bundle"
         }
+    },
+    "links": {
+        "links": [
+            {
+                "source_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
+                "source_type": "biomaterial",
+                "destination_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "destination_type": "dissociation_process"
+            },
+            {
+                "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "source_type": "dissociation_process",
+                "destination_id": "54a80c57-0409-4f57-9699-8a2f8cbace43",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "source_type": "dissociation_process",
+                "destination_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
+                "source_type": "process",
+                "destination_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "665b75b4-8638-4a15-83e5-f3928dd29314",
+                "source_type": "biomaterial",
+                "destination_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
+                "source_type": "biomaterial",
+                "destination_id": "87beb50f-521d-4102-9cb0-ca7b6f151afc",
+                "destination_type": "enrichment_process"
+            },
+            {
+                "source_id": "87beb50f-521d-4102-9cb0-ca7b6f151afc",
+                "source_type": "enrichment_process",
+                "destination_id": "54a80c57-0409-4f57-9699-8a2f8cbace43",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "87beb50f-521d-4102-9cb0-ca7b6f151afc",
+                "source_type": "enrichment_process",
+                "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
+                "source_type": "process",
+                "destination_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "665b75b4-8638-4a15-83e5-f3928dd29314",
+                "source_type": "biomaterial",
+                "destination_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
+                "source_type": "biomaterial",
+                "destination_id": "8caf3d2b-7dba-40ca-a2d7-c69b433ba70b",
+                "destination_type": "enrichment_process"
+            },
+            {
+                "source_id": "8caf3d2b-7dba-40ca-a2d7-c69b433ba70b",
+                "source_type": "enrichment_process",
+                "destination_id": "54a80c57-0409-4f57-9699-8a2f8cbace43",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "8caf3d2b-7dba-40ca-a2d7-c69b433ba70b",
+                "source_type": "enrichment_process",
+                "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
+                "source_type": "process",
+                "destination_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "665b75b4-8638-4a15-83e5-f3928dd29314",
+                "source_type": "biomaterial",
+                "destination_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
+                "source_type": "biomaterial",
+                "destination_id": "5a801f3d-12b0-4374-aed9-deee905b55ef",
+                "destination_type": "enrichment_process"
+            },
+            {
+                "source_id": "5a801f3d-12b0-4374-aed9-deee905b55ef",
+                "source_type": "enrichment_process",
+                "destination_id": "54a80c57-0409-4f57-9699-8a2f8cbace43",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "5a801f3d-12b0-4374-aed9-deee905b55ef",
+                "source_type": "enrichment_process",
+                "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
+                "source_type": "process",
+                "destination_id": "b3623b88-c369-46c9-a2e9-a16042d2c589",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "665b75b4-8638-4a15-83e5-f3928dd29314",
+                "source_type": "biomaterial",
+                "destination_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "54a80c57-0409-4f57-9699-8a2f8cbace43",
+                "source_type": "biomaterial",
+                "destination_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "destination_type": "library_preparation_process"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "b2cd6fb7-6612-4ab9-a1c5-e475663437e3",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "f599ea3f-14bb-4504-82ce-d9c1f26e55fa",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "54a80c57-0409-4f57-9699-8a2f8cbace43",
+                "source_type": "biomaterial",
+                "destination_id": "66551017-88b4-431d-ab33-c3a805f37bdf",
+                "destination_type": "sequencing_process"
+            },
+            {
+                "source_id": "66551017-88b4-431d-ab33-c3a805f37bdf",
+                "source_type": "sequencing_process",
+                "destination_id": "b2cd6fb7-6612-4ab9-a1c5-e475663437e3",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "66551017-88b4-431d-ab33-c3a805f37bdf",
+                "source_type": "sequencing_process",
+                "destination_id": "f599ea3f-14bb-4504-82ce-d9c1f26e55fa",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "66551017-88b4-431d-ab33-c3a805f37bdf",
+                "source_type": "sequencing_process",
+                "destination_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9",
+                "destination_type": "protocol"
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
+        "schema_version": "1.0.0",
+        "schema_type": "link_bundle"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json b/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
index f919a2c22..df8102870 100644
--- a/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
+++ b/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
@@ -206,94 +206,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
-            "links": [
-                {
-                    "inputs": [
-                        {
-                            "input_id": "0bf91a05-85df-5d7d-bcc0-a625c5921de2",
-                            "input_type": "imaged_specimen"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "31786d8d-d046-58d1-b7b4-49bc1114a0f8",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "6a0e071d-9bfc-5e12-b1b9-e887885e12f6",
-                            "output_type": "sequence_file"
-                        },
-                        {
-                            "output_id": "f6abda5c-65f3-5015-8167-ae78b96f5693",
-                            "output_type": "sequence_file"
-                        }
-                    ],
-                    "process_id": "8c1773c3-1885-545f-9381-0dab1edf6074",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "83f14748-af1c-57aa-9088-6cb1cdd4bba4",
-                            "protocol_type": "library_preparation_protocol"
-                        },
-                        {
-                            "protocol_id": "1b8dfafd-178f-5826-a661-8a022334aaeb",
-                            "protocol_type": "sequencing_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "9a0bb729-552a-5f6e-9ed6-1f988c259531",
-                            "input_type": "specimen_from_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "0bf91a05-85df-5d7d-bcc0-a625c5921de2",
-                            "output_type": "imaged_specimen"
-                        }
-                    ],
-                    "process_id": "ae8529dc-3bc9-5061-828a-3c5dfacded64",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "7cd840db-f395-5a61-bd17-72c2b2319c23",
-                            "protocol_type": "imaging_preparation_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "2d7b50d8-cd06-5408-9fde-1faed01c9ab2",
-                            "input_type": "donor_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "9a0bb729-552a-5f6e-9ed6-1f988c259531",
-                            "output_type": "specimen_from_organism"
-                        }
-                    ],
-                    "process_id": "c6b932ff-69f1-58b1-a6e6-30319f04541b",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "c5752f73-3511-55e1-95af-040ab3924bce",
-                            "protocol_type": "collection_protocol"
-                        }
-                    ]
-                }
-            ],
-            "schema_type": "links",
-            "schema_version": "3.1.0"
-        },
         "project_0.json": {
             "array_express_accessions": [
                 "E-MTAB-10026"
@@ -706,5 +618,93 @@
             },
             "schema_type": "protocol"
         }
+    },
+    "links": {
+        "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
+        "links": [
+            {
+                "inputs": [
+                    {
+                        "input_id": "0bf91a05-85df-5d7d-bcc0-a625c5921de2",
+                        "input_type": "imaged_specimen"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "31786d8d-d046-58d1-b7b4-49bc1114a0f8",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "6a0e071d-9bfc-5e12-b1b9-e887885e12f6",
+                        "output_type": "sequence_file"
+                    },
+                    {
+                        "output_id": "f6abda5c-65f3-5015-8167-ae78b96f5693",
+                        "output_type": "sequence_file"
+                    }
+                ],
+                "process_id": "8c1773c3-1885-545f-9381-0dab1edf6074",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "83f14748-af1c-57aa-9088-6cb1cdd4bba4",
+                        "protocol_type": "library_preparation_protocol"
+                    },
+                    {
+                        "protocol_id": "1b8dfafd-178f-5826-a661-8a022334aaeb",
+                        "protocol_type": "sequencing_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "9a0bb729-552a-5f6e-9ed6-1f988c259531",
+                        "input_type": "specimen_from_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "0bf91a05-85df-5d7d-bcc0-a625c5921de2",
+                        "output_type": "imaged_specimen"
+                    }
+                ],
+                "process_id": "ae8529dc-3bc9-5061-828a-3c5dfacded64",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "7cd840db-f395-5a61-bd17-72c2b2319c23",
+                        "protocol_type": "imaging_preparation_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "2d7b50d8-cd06-5408-9fde-1faed01c9ab2",
+                        "input_type": "donor_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "9a0bb729-552a-5f6e-9ed6-1f988c259531",
+                        "output_type": "specimen_from_organism"
+                    }
+                ],
+                "process_id": "c6b932ff-69f1-58b1-a6e6-30319f04541b",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "c5752f73-3511-55e1-95af-040ab3924bce",
+                        "protocol_type": "collection_protocol"
+                    }
+                ]
+            }
+        ],
+        "schema_type": "links",
+        "schema_version": "3.1.0"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
index b8c0e4669..13f42e0e2 100644
--- a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
+++ b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
@@ -1611,91 +1611,91 @@
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.5",
-            "links": [
-                {
-                    "process": "c56e2990-d6a0-40f5-add2-793bc1f12d69",
-                    "inputs": [
-                        "26dd8b99-f4ad-4802-8d6d-cf372c819dcc"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "c0a69095-57ba-4eca-8cc7-fed514f35f43",
-                        "4a9b689f-5aad-4c30-b347-7b0d52ab3ecb",
-                        "6fc876bc-5a8a-445c-8b41-77526203973b",
-                        "d47c381f-cef0-432a-b2bb-49fb7a546ac1",
-                        "b2a466dd-9de4-428c-9eda-f779d9ad672f",
-                        "86102761-0ba7-43b6-a442-666db1296154",
-                        "0c4b6682-12ab-46e7-9756-07ec104b14b1",
-                        "f31358bc-064c-4185-ae23-af044804d591",
-                        "a652744c-2d55-4181-b903-db411fa589b4",
-                        "da3b3aa5-3bea-441b-b1d0-022f842ddda6",
-                        "96ae6850-32c6-4d89-87cb-2f5005ac65aa",
-                        "bb4b0758-444b-48c3-89a6-9ddcf61fe912",
-                        "b4308ad2-8a51-4b1e-95a3-da961a13dd70",
-                        "2fa236c1-deb5-48a8-9961-3e2ee5cae2db",
-                        "ff664ba7-b1f9-4fd2-b6ae-a12eb0111721",
-                        "899e967e-06c8-49d9-bd3f-4bef8d04e22b"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "58df9607-ab66-48e0-a47b-1f897baae139"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "6282594c-1b9d-4f26-a4f3-a26066878740"
-                        }
-                    ]
-                },
-                {
-                    "process": "6a14efb0-0c28-421f-968b-5fc022df2395",
-                    "inputs": [
-                        "efa34a7f-6a0b-4728-9038-b947d47a63c6"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "26dd8b99-f4ad-4802-8d6d-cf372c819dcc"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "acaf2d60-e6fb-4381-a81e-2fec565fc8fa"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "1c9774bf-979a-4023-9756-b297cba4e371"
-                        }
-                    ]
-                },
-                {
-                    "process": "055b2189-7f89-4392-be1d-28a7274fe563",
-                    "inputs": [
-                        "a53d95b5-d1c7-4548-b2c0-479788085ab8"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "efa34a7f-6a0b-4728-9038-b947d47a63c6"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "e95ebc23-53b9-48a0-acd4-185969122f2d"
-                        },
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "6ec6ce63-3c6f-41d1-a616-5ebb20fe9a8b"
-                        }
-                    ]
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.5",
+        "links": [
+            {
+                "process": "c56e2990-d6a0-40f5-add2-793bc1f12d69",
+                "inputs": [
+                    "26dd8b99-f4ad-4802-8d6d-cf372c819dcc"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "c0a69095-57ba-4eca-8cc7-fed514f35f43",
+                    "4a9b689f-5aad-4c30-b347-7b0d52ab3ecb",
+                    "6fc876bc-5a8a-445c-8b41-77526203973b",
+                    "d47c381f-cef0-432a-b2bb-49fb7a546ac1",
+                    "b2a466dd-9de4-428c-9eda-f779d9ad672f",
+                    "86102761-0ba7-43b6-a442-666db1296154",
+                    "0c4b6682-12ab-46e7-9756-07ec104b14b1",
+                    "f31358bc-064c-4185-ae23-af044804d591",
+                    "a652744c-2d55-4181-b903-db411fa589b4",
+                    "da3b3aa5-3bea-441b-b1d0-022f842ddda6",
+                    "96ae6850-32c6-4d89-87cb-2f5005ac65aa",
+                    "bb4b0758-444b-48c3-89a6-9ddcf61fe912",
+                    "b4308ad2-8a51-4b1e-95a3-da961a13dd70",
+                    "2fa236c1-deb5-48a8-9961-3e2ee5cae2db",
+                    "ff664ba7-b1f9-4fd2-b6ae-a12eb0111721",
+                    "899e967e-06c8-49d9-bd3f-4bef8d04e22b"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "58df9607-ab66-48e0-a47b-1f897baae139"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "6282594c-1b9d-4f26-a4f3-a26066878740"
+                    }
+                ]
+            },
+            {
+                "process": "6a14efb0-0c28-421f-968b-5fc022df2395",
+                "inputs": [
+                    "efa34a7f-6a0b-4728-9038-b947d47a63c6"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "26dd8b99-f4ad-4802-8d6d-cf372c819dcc"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "acaf2d60-e6fb-4381-a81e-2fec565fc8fa"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "1c9774bf-979a-4023-9756-b297cba4e371"
+                    }
+                ]
+            },
+            {
+                "process": "055b2189-7f89-4392-be1d-28a7274fe563",
+                "inputs": [
+                    "a53d95b5-d1c7-4548-b2c0-479788085ab8"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "efa34a7f-6a0b-4728-9038-b947d47a63c6"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "e95ebc23-53b9-48a0-acd4-185969122f2d"
+                    },
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "6ec6ce63-3c6f-41d1-a616-5ebb20fe9a8b"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
index 78a1a3649..610482401 100644
--- a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
+++ b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
@@ -11681,290 +11681,290 @@
                 "submission_date": "2019-04-03T10:13:42.326Z",
                 "update_date": "2019-04-03T10:13:53.834Z"
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.staging.data.humancellatlas.org/system/1.1.5/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.5",
-            "links": [
-                {
-                    "process": "da265acd-5601-49c5-855e-d792d51b4042",
-                    "inputs": [
-                        "87f58f88-ef8b-4323-bd19-cde1a2497b59"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "6baa3aff-b2a5-4e49-82f7-25c108a6107a",
-                        "06dcfc33-21da-485f-8e50-49d294713a9e",
-                        "404dd50b-4bc9-4c82-8c18-f53c68eed2fc",
-                        "5ceb5dc3-9194-494a-b1df-42bb75ab1a04",
-                        "76e52f76-ede7-4088-b7f6-d6e5f6152292",
-                        "2e496fe6-f500-4e27-b7f5-3c87fe43bbe5",
-                        "be66141d-84a3-457d-a8d2-2f0da8c91dff",
-                        "680cf532-ef0c-4155-b44d-a6ec3920743a",
-                        "08609f14-cf43-4188-b743-4a0b55b17347",
-                        "d10827a1-38f7-457d-9c9f-695f2fc7689c",
-                        "6f8eb2e5-7a0c-4c98-8da0-276457357071",
-                        "ca480df3-71bb-4634-8f71-b6a75aeb9f05",
-                        "03ae5f5e-65ac-4491-b0ce-eefc940e0224",
-                        "ff117ecb-767e-4e72-baa9-2bda4fcd3e62",
-                        "887f3d73-94d2-44ac-9047-67aca5225882",
-                        "896dfacd-206b-4e4f-a846-ba5b070060d9",
-                        "23303c88-01b1-47d0-b770-dca6802caa13",
-                        "3c1a388d-0577-4417-9cd2-ff33bfed9140",
-                        "67e71b34-7157-4a37-b495-0d740772b480",
-                        "cd3e5e62-6145-42d9-9a5b-046e1b49cf26",
-                        "5fbcb75e-3ee3-4429-8ede-b243afa0789f",
-                        "09226b24-6b11-4e4f-8052-2b544be461aa",
-                        "f67473fd-fbf8-4d69-9db1-556938ab5b87",
-                        "16acc1f2-9f1c-43c8-8ffe-4a9ea674e6ff",
-                        "017a2c88-4f6e-418e-bb96-f42f3a220f87",
-                        "30305240-004d-4632-84d4-37d7e7378782",
-                        "20c5a14a-aaf3-40e1-9ab7-f95c06ea4200",
-                        "3fd2781b-6855-4eaa-b2fb-81db386adb18",
-                        "40474d53-44a4-4ab2-9f20-61b71291f8aa",
-                        "aaa97d47-7124-4763-a3fc-f6d66eb6d990",
-                        "4adbed13-1cb6-4405-b892-fe8165050691",
-                        "2bbf0125-b9cc-4413-8dd7-78ea72beaa17",
-                        "5402916f-6de1-4842-8585-fc25c153992b",
-                        "75b78bfc-8d15-4a07-a07a-c62ae6d656b5",
-                        "8a78224e-4106-41d4-96cb-4d9a8b9ecad2",
-                        "cb92dd92-570c-4075-8893-eb19dbd837b8",
-                        "b36948c4-0646-42be-9db2-16626a757343",
-                        "c974f4eb-27b8-4ec3-913e-a6eb19572a51",
-                        "febb760d-1e9e-4432-9b88-ce2869a43c44",
-                        "054f40a4-68d0-41db-81e9-00239042d9fa",
-                        "ec7f06aa-e4f9-4f4f-afd1-0ecd39b2e3f5",
-                        "819e3227-cc54-4919-95af-c1f8194bf729",
-                        "b1e2b9d1-6973-41dc-acdf-95474303561f",
-                        "41ffc783-5ad4-4197-8fd1-c029903c43c0",
-                        "ec9c70f0-3ed8-461c-ad0b-2475bd48ac8f",
-                        "9014bbaf-a047-4b69-8e28-8356cc99f84e",
-                        "f7acf90c-2b32-463b-b832-8daa8529f727",
-                        "fae4f8b8-e6ad-4c1f-8126-e03ba8aca46e",
-                        "db22deab-498a-409c-8386-5bf4e60a080c",
-                        "07d600bc-0d55-4a8d-9a48-390fc4169845",
-                        "d0a032bb-cd0e-4873-b346-5cb19e45c202",
-                        "a161f60f-af92-4b09-9df0-dd7ff2bf571a",
-                        "25c6b755-7f62-49a3-a1b5-aafbc772b5dd",
-                        "f10fd9e2-5747-4d7a-8c0c-beba81749011",
-                        "553b6aab-4745-45f8-98ab-de6aadbf48e4",
-                        "3572abe9-6e42-4266-8671-ff24b592065c",
-                        "6882abf6-c247-4167-a18d-e3fec24bcba2",
-                        "15f8b73e-937c-444d-8362-fdf458abb651",
-                        "33b4e374-20ad-4fee-b682-aaa4fc12bec2",
-                        "0e83c507-2211-4561-b75a-92326fb2d4fd",
-                        "912c55cf-0774-4838-8874-352766984715",
-                        "b2f32e7c-fea2-44c2-a6ae-832c1c7b9e37",
-                        "5b8e3d96-e625-46b6-9689-110fa84fd721",
-                        "de43f9bc-ddec-4326-9cb1-7b9c5f76a84f",
-                        "6f3272d7-4a62-4a3c-8c44-11dda8756956",
-                        "168422c5-e89d-466c-9085-f29c02160143",
-                        "7331367a-cc43-4af0-8750-a2921d513f97",
-                        "edf83a09-2e60-4571-b650-abf4c7ff757b",
-                        "24bdb70c-4bd1-41e0-b5c2-a3a2e0e4ce5b",
-                        "be9d12b6-f8dd-407c-b1d7-844deb6a5023",
-                        "e3e59792-61e3-4bf0-a985-2acec75acafd",
-                        "095ee09c-1605-4c07-9324-b5382f20b78e",
-                        "77b96424-accb-4c6b-884c-756f2bb40929",
-                        "a0c2a5b4-7cc2-47f5-97a7-6b59019155da",
-                        "78518dc1-d38e-4230-88b8-887bdd83f965",
-                        "652dd3c5-6467-41ee-89b3-e4b3361fb533",
-                        "cae3d214-d485-4350-8cd2-f4142aca4aef",
-                        "2ab7ea06-08e0-4669-88e0-23c1e74a3b49",
-                        "de282263-0944-48d4-9819-6182636c76bd",
-                        "bfdbe9b5-42ac-419a-b297-843095de2cc2",
-                        "0ef6ffa4-e40f-476c-8ac9-10732ef6e42d",
-                        "e2763cda-3236-487e-9944-5169c0cb8856",
-                        "37018bd8-8537-47c3-a5a9-efb43552f30c",
-                        "a6c9b1ce-2054-4a48-b262-bb0723b8a567",
-                        "8319ee38-f199-49d7-989a-25b451656b38",
-                        "022841b6-8b7c-4d0c-b65f-06ba14253540",
-                        "299dfbe5-05f5-48a7-816b-61036f0e435a",
-                        "6b8b11aa-3600-4a63-a980-93465e681c9c",
-                        "35716168-df43-4273-b52f-72e3d18a47bc",
-                        "6be783ec-c132-4e09-90e0-0958efaf6619",
-                        "a11956c9-c24e-4efb-8af8-1167b3081e70",
-                        "b69a349b-0e07-4fbe-9e3b-9f2cea828b96",
-                        "753c2a57-b5f1-4984-b874-b2b10d582847",
-                        "e0b93b3d-075b-482b-838a-e36d8849607b",
-                        "96c8ed8d-8bd6-49f3-b97b-025b0d6bc9ec",
-                        "c647964a-7796-4dd2-9fa8-b23f012ac14e",
-                        "87a63649-9834-49b8-89a0-310211c1b5b3",
-                        "b2eb5b20-fd1a-403c-8b55-9eec5972d482",
-                        "4b3b36cb-cd90-4526-978d-2e7e8f7add39",
-                        "cdc774f8-3310-4f1f-8c67-03579c253640",
-                        "607370e0-7e7e-4d25-ba5c-957c00a73ac1",
-                        "3240d7ab-568b-4be5-adba-3178b3e8f85e",
-                        "c0b6ee98-677a-41d9-9d80-9ac63d251b08",
-                        "f34c01ec-06df-49e6-bc2f-c50c7f398851",
-                        "2047311b-f3ee-4137-8338-a45166e01d53",
-                        "44ea335a-1991-4504-be12-04f1a332ddfb",
-                        "59f3d0ab-1fe1-4cc8-b343-c12b520d769d",
-                        "58f9fb1a-b6be-42c4-98ed-a5c091a3c716",
-                        "6af3cb41-9e64-4b11-b272-be87adf0fa94",
-                        "7541d176-dfba-4e05-ba45-0c6964271dff",
-                        "8ee1e829-a507-40a5-87ac-7fd8379b87ce",
-                        "8e57554a-abb2-4664-87b6-a397f4da6555",
-                        "88fa5ec5-db7d-49bf-8c7e-86f348fbc84c",
-                        "a2b4ab97-84bd-4808-884d-bd8cc5e7b922",
-                        "56c83f8e-3ef2-4a3a-b808-52cc1e96ac8e",
-                        "8af22b64-2c3f-4aad-a2d5-5d9b122a7b1c",
-                        "f0cb4244-e19a-46a0-89f1-04143548872d",
-                        "73074f55-d009-41a2-929e-6fd9949bb1dd",
-                        "0c2a3965-fbd7-4dc2-bcf0-9c51650a7331",
-                        "3774ecbd-d397-4b46-ba08-a7cbc6da0c07",
-                        "146231bb-1b13-4db5-8157-9d9962cc3a3a",
-                        "1d1b3f27-4f67-4338-bb36-173fd6ecf14b",
-                        "7fe17380-3090-4fc3-9504-02b3f8ed95b6",
-                        "fc405b01-60ca-436f-a06c-2f38f7156a87",
-                        "bae92b53-c6c7-4712-865e-6cff3cba506e",
-                        "83662ec5-a202-42ab-9a47-a701d4f19de3",
-                        "a04957c6-8ce8-4fa6-950d-71812ff3d698",
-                        "9284d3a4-73bd-4aa0-847c-ab273d14185a",
-                        "4d664562-c333-4aaf-bb8b-641e0568733e",
-                        "b533685d-3c60-4483-841b-a054f0a69fec",
-                        "3f14c88e-58db-4f76-b6e0-4b483ded1ca3",
-                        "32d0b267-f399-408a-b35f-f1ebc7d0fc1f",
-                        "3e8510c9-7e31-49bd-bb90-cb55577c2f25",
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+                    "2d2e58c6-7c24-4089-bbe9-d47b7482be46",
+                    "e4ce035a-f9e2-459f-8ecf-ce138ea00b34",
+                    "81214e49-318f-4221-bf2c-4ef00cfa916b",
+                    "7fc97754-1121-468b-b1e4-839bde86b6c8",
+                    "7d70d44c-b5d7-47be-9687-e9a775e86251",
+                    "ddb4f9d4-f2a1-42a5-87fa-e818071a5b33",
+                    "b7607809-e975-4c32-bff7-375cb2d8276f",
+                    "b8a6c863-626d-4fbf-863b-610cffaac37d",
+                    "45077a5c-ee96-47c0-a84f-9d46cf799338",
+                    "49d82b74-6f1a-415c-93ab-958c60f083b6",
+                    "753b51b7-a909-44e7-bb21-cf2cd18328f8",
+                    "c7ab6349-b2bb-4ba3-9c9b-27d270550052",
+                    "7be770fc-4a56-4f82-a4cf-3cf908d54dca",
+                    "3f5f8537-c1af-4d2e-a732-53b6d4275588",
+                    "3820feac-72c4-49c5-a5a0-773f4e5ee3c1",
+                    "f986c2c2-2823-45a0-80cf-5e6f67958afb",
+                    "7d17d6d6-d038-40c6-b965-6de41ce9c931",
+                    "3d208b38-62c8-492d-9434-21bb66ead16e",
+                    "9a982898-77c6-4a56-8e54-9cb83ff0b235",
+                    "1bdd91d7-0a1a-488d-ab9c-78eba7a6daa3",
+                    "24b6366f-03ce-4e4d-b50f-90687f3e2b94",
+                    "ec1d0987-fb49-48b8-aaeb-321c659fb67f",
+                    "e756ce65-ad72-42e6-a8cc-9c1bac781ce5",
+                    "6fbcb1c7-ce98-46db-8054-b451b6bca205",
+                    "c225fa8c-e8c8-46a4-bf23-720e2cf1c9ac",
+                    "aa6fca0d-6a70-4016-a0e4-307878e9ff45",
+                    "ee62cd8d-fb93-4082-980b-213c7a8a0c47",
+                    "bbd60a79-3572-42c0-8e53-b0c566a72f06",
+                    "bf585666-2fb4-4ad5-a9b3-b268a9953ed9",
+                    "52548ff8-5bbd-4b1c-9c52-4e5d82f846e2",
+                    "240a67cc-e827-41bf-8ac8-a66bc2797f13",
+                    "7a9b6534-fa1d-4282-a064-11e60e57a322",
+                    "b0af6371-4379-45f0-8c09-f6610833fc46",
+                    "f5ce7a96-cfc0-42c4-852b-386f9a27111d",
+                    "8bc05db7-bd23-4a10-9761-96be7b8ef9ee",
+                    "3dff4add-7d6f-418c-afba-e46864af51d2",
+                    "ab2b7c67-8f13-4388-acd7-e2abb0091f30",
+                    "d9912d93-3d92-48d2-9f75-826fbba3d94e",
+                    "8b37aba2-be5e-4963-8e6f-51a2df8e143e",
+                    "81c0e4e2-9021-4c4d-9876-1ed5b78ca7a7",
+                    "2d7e88dd-bddd-4289-9556-27d301be0b83",
+                    "0c1c578d-d4cc-40bb-a54d-d1d4d004373f",
+                    "9dc0ead3-f17a-4bb8-88e2-87f779029ff8",
+                    "f618a8bc-5e07-477f-a6d3-1b0af8c81ff0",
+                    "e834d3df-8432-40ba-b67d-c7cd0bd7328d",
+                    "d8908d6d-5daa-454d-9082-726054cfddc1",
+                    "c5a7142e-4702-4e84-b7aa-239df2a71ba8",
+                    "f69e44ef-cf23-4571-8dad-e44222697974",
+                    "ea72f81c-2c58-43e2-acca-294254f470f7",
+                    "89d1d2b5-81d3-487d-9fc1-d8b1d8ac34ab",
+                    "6928ac1b-fd1d-436c-bfc6-4087c65809d7",
+                    "07a7b938-435b-4804-b140-c255957b6532",
+                    "3d532a7b-55e7-4461-afbc-65ef76403384",
+                    "bab40245-28bd-49a2-8be0-ba109fe41c91",
+                    "9d577bd4-3a27-48be-ad7c-8c44cf803cda",
+                    "c4de7605-fec5-4389-bb9e-f2ea0c41cdef",
+                    "21a043b6-6dde-41b9-b20e-74b961da8b88",
+                    "11280200-1803-4110-aa84-2808776c2d50",
+                    "86df5269-576b-4d18-a0ce-6e2b2a36d51b",
+                    "e524ff4e-95fa-4561-bfd3-276cba79e664",
+                    "3d5737da-b1ab-48cb-a26f-d420e53edccd",
+                    "44cf15ec-3d4e-4698-bb14-107c34891191",
+                    "6242cdf3-fd6d-4479-a08a-1747818fd978",
+                    "bc60bbd4-8b09-425c-b507-9da24a84f412",
+                    "1f054ccf-f8dd-4127-a6f8-c577d7dd93dc",
+                    "9954cb4b-b0a4-4479-b31d-0bee1e75d9c7",
+                    "5f67c32c-a154-4620-8603-0b64979b04a4",
+                    "7d5bffb2-8bf9-4366-a8b2-762ebb4d6c5d",
+                    "dcee6df0-9e87-4935-8873-f8d30d449d76",
+                    "7d6bdde6-523f-46cb-bed5-d6cfa8fea80c",
+                    "e6d00b0c-3641-4ec4-a553-8fd742193dba",
+                    "e5034863-0528-4f55-be95-c8501c29f9fe",
+                    "cc61b14a-59d9-477b-8cb1-43c4ee4cf434",
+                    "33d332c9-aefe-4db5-8830-b8daddaed0d2",
+                    "bb3b6fc7-0902-432d-bad1-6b3f61951314",
+                    "2b734e88-3a33-4c73-92bb-82e0b8f8c13b"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "imaging_protocol",
+                        "protocol_id": "96ecb94d-e848-4d7b-8df9-f19af6ab17b8"
+                    }
+                ]
+            },
+            {
+                "process": "07acb7d0-3f1c-47f7-9ef9-851c4f1caaec",
+                "inputs": [
+                    "edd1d525-a6ae-4658-a6bf-6c31d7ab6948"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "87f58f88-ef8b-4323-bd19-cde1a2497b59"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "imaging_preparation_protocol",
+                        "protocol_id": "a6d431b0-4373-4eaf-a3af-8c3fe461ab38"
+                    }
+                ]
+            },
+            {
+                "process": "fee8a188-5783-44cd-a1c1-ed9d5d7c32a9",
+                "inputs": [
+                    "6cb9fc09-7755-4a35-b6b1-0d6fe696b2d4"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "edd1d525-a6ae-4658-a6bf-6c31d7ab6948"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "caf94c25-8327-4379-b88e-2a6642cd7513"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
index 28629f6db..82b13a528 100644
--- a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
+++ b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
@@ -858,73 +858,73 @@
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.5",
-            "links": [
-                {
-                    "process": "bf65ea92-6949-491d-b25b-52d06045044a",
-                    "inputs": [
-                        "5ea17576-5f1d-4879-97a1-6a868ccb2b0b"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "430755e7-2263-4b5b-ad65-b3231c0eb61d",
-                        "d53454df-9542-4c64-9f84-0d798d923777"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "58df9607-ab66-48e0-a47b-1f897baae139"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "6282594c-1b9d-4f26-a4f3-a26066878740"
-                        }
-                    ]
-                },
-                {
-                    "process": "11b9ffae-0643-425b-b120-85a7bd46c057",
-                    "inputs": [
-                        "d9b27804-1763-410b-9f19-995a363fe488"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "5ea17576-5f1d-4879-97a1-6a868ccb2b0b"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "3f9fda53-2b30-47bb-8c92-4e131920b2e3"
-                        }
-                    ]
-                },
-                {
-                    "process": "4c6d81f9-4f12-457e-89cd-6efb297ca848",
-                    "inputs": [
-                        "587d1170-aa27-4b06-9c15-b51846d14588"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "d9b27804-1763-410b-9f19-995a363fe488"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "e95ebc23-53b9-48a0-acd4-185969122f2d"
-                        },
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "4dfda495-6aeb-41d9-b995-04da33cd2810"
-                        }
-                    ]
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.5",
+        "links": [
+            {
+                "process": "bf65ea92-6949-491d-b25b-52d06045044a",
+                "inputs": [
+                    "5ea17576-5f1d-4879-97a1-6a868ccb2b0b"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "430755e7-2263-4b5b-ad65-b3231c0eb61d",
+                    "d53454df-9542-4c64-9f84-0d798d923777"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "58df9607-ab66-48e0-a47b-1f897baae139"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "6282594c-1b9d-4f26-a4f3-a26066878740"
+                    }
+                ]
+            },
+            {
+                "process": "11b9ffae-0643-425b-b120-85a7bd46c057",
+                "inputs": [
+                    "d9b27804-1763-410b-9f19-995a363fe488"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "5ea17576-5f1d-4879-97a1-6a868ccb2b0b"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "3f9fda53-2b30-47bb-8c92-4e131920b2e3"
+                    }
+                ]
+            },
+            {
+                "process": "4c6d81f9-4f12-457e-89cd-6efb297ca848",
+                "inputs": [
+                    "587d1170-aa27-4b06-9c15-b51846d14588"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "d9b27804-1763-410b-9f19-995a363fe488"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "e95ebc23-53b9-48a0-acd4-185969122f2d"
+                    },
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "4dfda495-6aeb-41d9-b995-04da33cd2810"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json b/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
index 57d87c415..b197d3ad9 100644
--- a/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
+++ b/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
@@ -357,121 +357,6 @@
                 "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
             }
         },
-        "links.json": {
-            "links": [
-                {
-                    "source_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
-                    "source_type": "biomaterial",
-                    "destination_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "source_type": "dissociation_process",
-                    "destination_id": "f59292f0-318f-40d0-bce5-29413b59a790",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "source_type": "dissociation_process",
-                    "destination_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
-                    "source_type": "process",
-                    "destination_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "689311a2-bfaf-4196-a753-554e69ab59b2",
-                    "source_type": "biomaterial",
-                    "destination_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
-                    "source_type": "biomaterial",
-                    "destination_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4",
-                    "destination_type": "enrichment_process"
-                },
-                {
-                    "source_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4",
-                    "source_type": "enrichment_process",
-                    "destination_id": "f59292f0-318f-40d0-bce5-29413b59a790",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4",
-                    "source_type": "enrichment_process",
-                    "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
-                    "source_type": "process",
-                    "destination_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "689311a2-bfaf-4196-a753-554e69ab59b2",
-                    "source_type": "biomaterial",
-                    "destination_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "f59292f0-318f-40d0-bce5-29413b59a790",
-                    "source_type": "biomaterial",
-                    "destination_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "destination_type": "library_preparation_process"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "e080459e-e4ab-40ea-ab75-a2646b5fdd29",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "3417cdb5-5618-4c0c-bc27-62a4eb78916a",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "f59292f0-318f-40d0-bce5-29413b59a790",
-                    "source_type": "biomaterial",
-                    "destination_id": "b8a6acbe-6b57-4efb-b6c7-bceaa6d9924d",
-                    "destination_type": "sequencing_process"
-                },
-                {
-                    "source_id": "b8a6acbe-6b57-4efb-b6c7-bceaa6d9924d",
-                    "source_type": "sequencing_process",
-                    "destination_id": "e080459e-e4ab-40ea-ab75-a2646b5fdd29",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "b8a6acbe-6b57-4efb-b6c7-bceaa6d9924d",
-                    "source_type": "sequencing_process",
-                    "destination_id": "3417cdb5-5618-4c0c-bc27-62a4eb78916a",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "b8a6acbe-6b57-4efb-b6c7-bceaa6d9924d",
-                    "source_type": "sequencing_process",
-                    "destination_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9",
-                    "destination_type": "protocol"
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
-            "schema_version": "1.0.0",
-            "schema_type": "link_bundle"
-        },
         "cell_suspension_0.json": {
             "content": {
                 "genus_species": [
@@ -580,5 +465,120 @@
                 "document_id": "689311a2-bfaf-4196-a753-554e69ab59b2"
             }
         }
+    },
+    "links": {
+        "links": [
+            {
+                "source_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
+                "source_type": "biomaterial",
+                "destination_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "destination_type": "dissociation_process"
+            },
+            {
+                "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "source_type": "dissociation_process",
+                "destination_id": "f59292f0-318f-40d0-bce5-29413b59a790",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "source_type": "dissociation_process",
+                "destination_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
+                "source_type": "process",
+                "destination_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "689311a2-bfaf-4196-a753-554e69ab59b2",
+                "source_type": "biomaterial",
+                "destination_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
+                "source_type": "biomaterial",
+                "destination_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4",
+                "destination_type": "enrichment_process"
+            },
+            {
+                "source_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4",
+                "source_type": "enrichment_process",
+                "destination_id": "f59292f0-318f-40d0-bce5-29413b59a790",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4",
+                "source_type": "enrichment_process",
+                "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
+                "source_type": "process",
+                "destination_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "689311a2-bfaf-4196-a753-554e69ab59b2",
+                "source_type": "biomaterial",
+                "destination_id": "0763320a-e0c4-4c07-b150-b83650fbef68",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "f59292f0-318f-40d0-bce5-29413b59a790",
+                "source_type": "biomaterial",
+                "destination_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "destination_type": "library_preparation_process"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "e080459e-e4ab-40ea-ab75-a2646b5fdd29",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "3417cdb5-5618-4c0c-bc27-62a4eb78916a",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "f59292f0-318f-40d0-bce5-29413b59a790",
+                "source_type": "biomaterial",
+                "destination_id": "b8a6acbe-6b57-4efb-b6c7-bceaa6d9924d",
+                "destination_type": "sequencing_process"
+            },
+            {
+                "source_id": "b8a6acbe-6b57-4efb-b6c7-bceaa6d9924d",
+                "source_type": "sequencing_process",
+                "destination_id": "e080459e-e4ab-40ea-ab75-a2646b5fdd29",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "b8a6acbe-6b57-4efb-b6c7-bceaa6d9924d",
+                "source_type": "sequencing_process",
+                "destination_id": "3417cdb5-5618-4c0c-bc27-62a4eb78916a",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "b8a6acbe-6b57-4efb-b6c7-bceaa6d9924d",
+                "source_type": "sequencing_process",
+                "destination_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9",
+                "destination_type": "protocol"
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
+        "schema_version": "1.0.0",
+        "schema_type": "link_bundle"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
index bbd43843e..7988bc571 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
@@ -524,68 +524,68 @@
                 "submission_date": "2018-11-02T10:05:05.605Z",
                 "update_date": "2018-11-02T10:12:03.520Z"
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.3/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.3",
-            "links": [
-                {
-                    "process": "771ddaf6-3a4f-4314-97fe-6294ff8e25a4",
-                    "inputs": [
-                        "412898c5-5b9b-4907-b07c-e9b89666e204"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "70d1af4a-82c8-478a-8960-e9028b3616ca",
-                        "0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "9c32cf70-3ed7-4720-badc-5ee71e8a38af"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "61e629ed-0135-4492-ac8a-5c4ab3ccca8a"
-                        }
-                    ]
-                },
-                {
-                    "process": "4c28e079-59af-4bd3-8c8b-763ea0beba98",
-                    "inputs": [
-                        "a21dc760-a500-4236-bcff-da34a0e873d2"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "412898c5-5b9b-4907-b07c-e9b89666e204"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "31e708d3-79df-49b8-a3df-b1d694963468"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "5bd4ba68-4c0e-4d22-840d-afc025e7badc"
-                        }
-                    ]
-                },
-                {
-                    "process": "4674255d-5ecd-4860-9b8d-beae98772cd9",
-                    "inputs": [
-                        "7b07b9d0-cc0e-4098-9f64-f4a569f7d746"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "a21dc760-a500-4236-bcff-da34a0e873d2"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.3/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.3",
+        "links": [
+            {
+                "process": "771ddaf6-3a4f-4314-97fe-6294ff8e25a4",
+                "inputs": [
+                    "412898c5-5b9b-4907-b07c-e9b89666e204"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "70d1af4a-82c8-478a-8960-e9028b3616ca",
+                    "0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "9c32cf70-3ed7-4720-badc-5ee71e8a38af"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "61e629ed-0135-4492-ac8a-5c4ab3ccca8a"
+                    }
+                ]
+            },
+            {
+                "process": "4c28e079-59af-4bd3-8c8b-763ea0beba98",
+                "inputs": [
+                    "a21dc760-a500-4236-bcff-da34a0e873d2"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "412898c5-5b9b-4907-b07c-e9b89666e204"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "31e708d3-79df-49b8-a3df-b1d694963468"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "5bd4ba68-4c0e-4d22-840d-afc025e7badc"
+                    }
+                ]
+            },
+            {
+                "process": "4674255d-5ecd-4860-9b8d-beae98772cd9",
+                "inputs": [
+                    "7b07b9d0-cc0e-4098-9f64-f4a569f7d746"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "a21dc760-a500-4236-bcff-da34a0e873d2"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
index b624f9147..1bf0a58dc 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
@@ -524,68 +524,68 @@
                 "submission_date": "2018-11-04T10:05:05.605Z",
                 "update_date": "2018-11-04T10:12:03.520Z"
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.3/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.3",
-            "links": [
-                {
-                    "process": "771ddaf6-3a4f-4314-97fe-6294ff8e25a4",
-                    "inputs": [
-                        "412898c5-5b9b-4907-b07c-e9b89666e204"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "70d1af4a-82c8-478a-8960-e9028b3616ca",
-                        "0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "9c32cf70-3ed7-4720-badc-5ee71e8a38af"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "61e629ed-0135-4492-ac8a-5c4ab3ccca8a"
-                        }
-                    ]
-                },
-                {
-                    "process": "4c28e079-59af-4bd3-8c8b-763ea0beba98",
-                    "inputs": [
-                        "a21dc760-a500-4236-bcff-da34a0e873d2"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "412898c5-5b9b-4907-b07c-e9b89666e204"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "31e708d3-79df-49b8-a3df-b1d694963468"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "5bd4ba68-4c0e-4d22-840d-afc025e7badc"
-                        }
-                    ]
-                },
-                {
-                    "process": "4674255d-5ecd-4860-9b8d-beae98772cd9",
-                    "inputs": [
-                        "7b07b9d0-cc0e-4098-9f64-f4a569f7d746"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "a21dc760-a500-4236-bcff-da34a0e873d2"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.3/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.3",
+        "links": [
+            {
+                "process": "771ddaf6-3a4f-4314-97fe-6294ff8e25a4",
+                "inputs": [
+                    "412898c5-5b9b-4907-b07c-e9b89666e204"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "70d1af4a-82c8-478a-8960-e9028b3616ca",
+                    "0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "9c32cf70-3ed7-4720-badc-5ee71e8a38af"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "61e629ed-0135-4492-ac8a-5c4ab3ccca8a"
+                    }
+                ]
+            },
+            {
+                "process": "4c28e079-59af-4bd3-8c8b-763ea0beba98",
+                "inputs": [
+                    "a21dc760-a500-4236-bcff-da34a0e873d2"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "412898c5-5b9b-4907-b07c-e9b89666e204"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "31e708d3-79df-49b8-a3df-b1d694963468"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "5bd4ba68-4c0e-4d22-840d-afc025e7badc"
+                    }
+                ]
+            },
+            {
+                "process": "4674255d-5ecd-4860-9b8d-beae98772cd9",
+                "inputs": [
+                    "7b07b9d0-cc0e-4098-9f64-f4a569f7d746"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "a21dc760-a500-4236-bcff-da34a0e873d2"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json b/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
index 7de7ec75a..5c4c24ec6 100644
--- a/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
+++ b/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
@@ -9128,3673 +9128,3673 @@
                 "updateDate": "2018-03-26T16:59:27.537Z",
                 "document_id": "e99eed63-5794-4d8d-baf9-9c6888e91e6d"
             }
-        },
-        "links.json": {
-            "links": [
-                {
-                    "source_id": "763da7c3-cf84-4dd1-9816-99387476f439",
-                    "source_type": "biomaterial",
-                    "destination_id": "6f8cc2d1-6884-4ac7-81b3-bca185e1b8ae",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "6f8cc2d1-6884-4ac7-81b3-bca185e1b8ae",
-                    "source_type": "dissociation_process",
-                    "destination_id": "81bdd959-6a0c-45e8-a95f-9e94362ac234",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "6f8cc2d1-6884-4ac7-81b3-bca185e1b8ae",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "de4fc3e2-cf67-4915-a096-5b87a4e95e69",
-                    "source_type": "process",
-                    "destination_id": "763da7c3-cf84-4dd1-9816-99387476f439",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "50df319c-ce04-45d3-bf61-72017700f4c7",
-                    "source_type": "biomaterial",
-                    "destination_id": "de4fc3e2-cf67-4915-a096-5b87a4e95e69",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "ea978eed-c518-421b-9ff1-e9946e79285d",
-                    "source_type": "biomaterial",
-                    "destination_id": "d44b888c-d44f-4f2f-bfe9-f2692d976153",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "d44b888c-d44f-4f2f-bfe9-f2692d976153",
-                    "source_type": "dissociation_process",
-                    "destination_id": "8a5f6526-b075-4dc6-911a-094c9e9df5b8",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "d44b888c-d44f-4f2f-bfe9-f2692d976153",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "d5c49bcf-d959-4143-8ab4-2da4bdcf039c",
-                    "source_type": "process",
-                    "destination_id": "ea978eed-c518-421b-9ff1-e9946e79285d",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "dc6819c9-6df9-4028-9a27-d4b4051475ae",
-                    "source_type": "biomaterial",
-                    "destination_id": "d5c49bcf-d959-4143-8ab4-2da4bdcf039c",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "78dc08e0-7fe8-4f1d-a5cb-b11634010810",
-                    "source_type": "biomaterial",
-                    "destination_id": "b365f021-1729-4735-a1f2-504bbd9c7f56",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "b365f021-1729-4735-a1f2-504bbd9c7f56",
-                    "source_type": "dissociation_process",
-                    "destination_id": "572da738-8893-43d6-b437-97b57372f0aa",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "b365f021-1729-4735-a1f2-504bbd9c7f56",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "9a967de7-3113-4a14-b586-5f387810cc50",
-                    "source_type": "process",
-                    "destination_id": "78dc08e0-7fe8-4f1d-a5cb-b11634010810",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "314393db-9a5f-45f8-95e3-cafb4006484c",
-                    "source_type": "biomaterial",
-                    "destination_id": "9a967de7-3113-4a14-b586-5f387810cc50",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "d1c9cf7c-021d-48a2-84f9-17f92358d6e7",
-                    "source_type": "biomaterial",
-                    "destination_id": "d5fd4a48-75f1-476d-a4b5-ecdf96fe10bc",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "d5fd4a48-75f1-476d-a4b5-ecdf96fe10bc",
-                    "source_type": "dissociation_process",
-                    "destination_id": "71736a6a-0d29-4abe-a0d8-c2cb9d8b010d",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "d5fd4a48-75f1-476d-a4b5-ecdf96fe10bc",
-                    "source_type": "dissociation_process",
-                    "destination_id": "3cbebf0a-4aab-4525-80f4-222703d14b98",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "fb846e68-7d02-4299-8b6b-7ea1a7dc3f5d",
-                    "source_type": "process",
-                    "destination_id": "d1c9cf7c-021d-48a2-84f9-17f92358d6e7",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "db47eeb1-619b-4b97-b5a6-f7e8c7b316aa",
-                    "source_type": "biomaterial",
-                    "destination_id": "fb846e68-7d02-4299-8b6b-7ea1a7dc3f5d",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "d3e0f71e-4d00-4567-88af-d797365a7544",
-                    "source_type": "biomaterial",
-                    "destination_id": "1296a80d-a0e9-420f-ba0b-42b361cd6174",
-                    "destination_type": "dissociation_process"
-                },
-                {
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+                "source_type": "sequencing_process",
+                "destination_id": "e99eed63-5794-4d8d-baf9-9c6888e91e6d",
+                "destination_type": "protocol"
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
+        "schema_version": "1.0.0",
+        "schema_type": "link_bundle"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json b/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
index 50e8ccded..a494c951c 100644
--- a/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
+++ b/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
@@ -481,151 +481,151 @@
                 "updateDate": "2018-03-28T14:30:39.321Z",
                 "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
             }
-        },
-        "links.json": {
-            "links": [
-                {
-                    "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
-                    "source_type": "biomaterial",
-                    "destination_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "destination_type": "dissociation_process"
-                },
-                {
-                    "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "source_type": "dissociation_process",
-                    "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
-                    "source_type": "dissociation_process",
-                    "destination_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
-                    "source_type": "process",
-                    "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
-                    "source_type": "biomaterial",
-                    "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
-                    "source_type": "biomaterial",
-                    "destination_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
-                    "destination_type": "enrichment_process"
-                },
-                {
-                    "source_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
-                    "source_type": "enrichment_process",
-                    "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
-                    "source_type": "enrichment_process",
-                    "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
-                    "source_type": "process",
-                    "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
-                    "source_type": "biomaterial",
-                    "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
-                    "source_type": "biomaterial",
-                    "destination_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
-                    "destination_type": "enrichment_process"
-                },
-                {
-                    "source_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
-                    "source_type": "enrichment_process",
-                    "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
-                    "source_type": "enrichment_process",
-                    "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
-                    "source_type": "process",
-                    "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
-                    "destination_type": "biomaterial"
-                },
-                {
-                    "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
-                    "source_type": "biomaterial",
-                    "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
-                    "destination_type": "process"
-                },
-                {
-                    "source_id": "603a818f-dbe7-466a-8241-58b9c1618846",
-                    "source_type": "biomaterial",
-                    "destination_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "destination_type": "library_preparation_process"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "aa662c76-d220-49f4-8316-f4af5820d60b",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
-                    "source_type": "library_preparation_process",
-                    "destination_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643",
-                    "destination_type": "protocol"
-                },
-                {
-                    "source_id": "603a818f-dbe7-466a-8241-58b9c1618846",
-                    "source_type": "biomaterial",
-                    "destination_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
-                    "destination_type": "sequencing_process"
-                },
-                {
-                    "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
-                    "source_type": "sequencing_process",
-                    "destination_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
-                    "source_type": "sequencing_process",
-                    "destination_id": "aa662c76-d220-49f4-8316-f4af5820d60b",
-                    "destination_type": "file"
-                },
-                {
-                    "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
-                    "source_type": "sequencing_process",
-                    "destination_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9",
-                    "destination_type": "protocol"
-                }
-            ],
-            "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
-            "schema_version": "1.0.0",
-            "schema_type": "link_bundle"
         }
+    },
+    "links": {
+        "links": [
+            {
+                "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                "source_type": "biomaterial",
+                "destination_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "destination_type": "dissociation_process"
+            },
+            {
+                "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "source_type": "dissociation_process",
+                "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902",
+                "source_type": "dissociation_process",
+                "destination_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                "source_type": "process",
+                "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
+                "source_type": "biomaterial",
+                "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                "source_type": "biomaterial",
+                "destination_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
+                "destination_type": "enrichment_process"
+            },
+            {
+                "source_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
+                "source_type": "enrichment_process",
+                "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78",
+                "source_type": "enrichment_process",
+                "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                "source_type": "process",
+                "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
+                "source_type": "biomaterial",
+                "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                "source_type": "biomaterial",
+                "destination_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
+                "destination_type": "enrichment_process"
+            },
+            {
+                "source_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
+                "source_type": "enrichment_process",
+                "destination_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215",
+                "source_type": "enrichment_process",
+                "destination_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                "source_type": "process",
+                "destination_id": "4e41a067-dbb7-439f-b72f-80240ce858f6",
+                "destination_type": "biomaterial"
+            },
+            {
+                "source_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410",
+                "source_type": "biomaterial",
+                "destination_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9",
+                "destination_type": "process"
+            },
+            {
+                "source_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                "source_type": "biomaterial",
+                "destination_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "destination_type": "library_preparation_process"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "aa662c76-d220-49f4-8316-f4af5820d60b",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "687065f3-c70f-46c3-8452-a5eead33a1bf",
+                "source_type": "library_preparation_process",
+                "destination_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643",
+                "destination_type": "protocol"
+            },
+            {
+                "source_id": "603a818f-dbe7-466a-8241-58b9c1618846",
+                "source_type": "biomaterial",
+                "destination_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
+                "destination_type": "sequencing_process"
+            },
+            {
+                "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
+                "source_type": "sequencing_process",
+                "destination_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
+                "source_type": "sequencing_process",
+                "destination_id": "aa662c76-d220-49f4-8316-f4af5820d60b",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "2580dcf9-3f7d-4421-b962-ab860e10d072",
+                "source_type": "sequencing_process",
+                "destination_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9",
+                "destination_type": "protocol"
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
+        "schema_version": "1.0.0",
+        "schema_type": "link_bundle"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
index ae2cf7e90..b29f6b7b8 100644
--- a/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
+++ b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
@@ -606,89 +606,89 @@
                 "submission_date": "2018-09-11T16:40:39.858Z",
                 "update_date": "2018-09-11T17:05:50.168Z"
             }
-        },
-        "links.json": {
-            "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.1/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.1",
-            "links": [
-                {
-                    "process": "78e53890-4a5c-423b-a7b9-aa3247ecf98b",
-                    "inputs": [
-                        "1e07c7cf-66c3-4cd5-a061-71f3e89489ff"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "211d3f25-1253-4a01-aadf-08b6452de585"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "3720c08b-f4b6-4bc7-a889-d4d3db602e7d"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "3e11dd06-396b-4aaa-a6ae-3b6a26a1d9f0"
-                        }
-                    ]
-                },
-                {
-                    "process": "427f77a0-9fc5-4fea-a9bb-d05841fad71c",
-                    "inputs": [
-                        "39a16395-6e12-4ec1-8cff-b77dd23f7024",
-                        "1fe5d2c3-cf34-45ce-b1e4-dc8568ca5ab2",
-                        "02f67508-6e87-42cf-9588-df49a4250a95"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "1e07c7cf-66c3-4cd5-a061-71f3e89489ff"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "f90527fc-d710-414b-b185-0e9c5b4138af"
-                        }
-                    ]
-                },
-                {
-                    "process": "677e65b8-5a0d-4f5a-af89-7cca51bcd6c3",
-                    "inputs": [
-                        "ff15c305-fc63-419f-a0fd-84d123f9b975"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "39a16395-6e12-4ec1-8cff-b77dd23f7024"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "ac321e06-ec12-423a-bf12-5e0ec97f0fb1",
-                    "inputs": [
-                        "ff15c305-fc63-419f-a0fd-84d123f9b975"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "1fe5d2c3-cf34-45ce-b1e4-dc8568ca5ab2"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "34aa8a89-27d0-4a03-8196-72da4d701efb",
-                    "inputs": [
-                        "ff15c305-fc63-419f-a0fd-84d123f9b975"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "02f67508-6e87-42cf-9588-df49a4250a95"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.1/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.1",
+        "links": [
+            {
+                "process": "78e53890-4a5c-423b-a7b9-aa3247ecf98b",
+                "inputs": [
+                    "1e07c7cf-66c3-4cd5-a061-71f3e89489ff"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "211d3f25-1253-4a01-aadf-08b6452de585"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "3720c08b-f4b6-4bc7-a889-d4d3db602e7d"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "3e11dd06-396b-4aaa-a6ae-3b6a26a1d9f0"
+                    }
+                ]
+            },
+            {
+                "process": "427f77a0-9fc5-4fea-a9bb-d05841fad71c",
+                "inputs": [
+                    "39a16395-6e12-4ec1-8cff-b77dd23f7024",
+                    "1fe5d2c3-cf34-45ce-b1e4-dc8568ca5ab2",
+                    "02f67508-6e87-42cf-9588-df49a4250a95"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "1e07c7cf-66c3-4cd5-a061-71f3e89489ff"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "f90527fc-d710-414b-b185-0e9c5b4138af"
+                    }
+                ]
+            },
+            {
+                "process": "677e65b8-5a0d-4f5a-af89-7cca51bcd6c3",
+                "inputs": [
+                    "ff15c305-fc63-419f-a0fd-84d123f9b975"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "39a16395-6e12-4ec1-8cff-b77dd23f7024"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "ac321e06-ec12-423a-bf12-5e0ec97f0fb1",
+                "inputs": [
+                    "ff15c305-fc63-419f-a0fd-84d123f9b975"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "1fe5d2c3-cf34-45ce-b1e4-dc8568ca5ab2"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "34aa8a89-27d0-4a03-8196-72da4d701efb",
+                "inputs": [
+                    "ff15c305-fc63-419f-a0fd-84d123f9b975"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "02f67508-6e87-42cf-9588-df49a4250a95"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json b/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
index 4efdb0de7..0ac584027 100644
--- a/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
+++ b/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
@@ -8855,3559 +8855,3559 @@
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+                "destination_id": "f2edefd2-c29c-470d-8879-3d480a6c55f9",
+                "destination_type": "file"
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+                "destination_type": "file"
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+                "source_type": "sequencing_process",
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+                "destination_type": "file"
+            },
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+                "destination_type": "file"
+            },
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+                "source_type": "sequencing_process",
+                "destination_id": "f0b940a1-de2c-461e-a40d-7a5b0c11ca40",
+                "destination_type": "file"
+            },
+            {
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+                "destination_id": "04e94fd5-49df-4149-9da5-ff9c86a2e494",
+                "destination_type": "file"
+            },
+            {
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+                "source_type": "sequencing_process",
+                "destination_id": "5675b050-9c66-4c34-803f-3e6e0ea0af3f",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "d889a2da-2b28-4553-9045-fe9c958b4616",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "4d7b8243-f099-4eab-a5a4-1e6c359f999d",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "462d6d7c-8c83-4e91-b851-4ebe7f04ed4a",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "d7bbc88d-ea41-483f-940a-332989f6dd75",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "2ff31790-2e31-4056-ade6-a40b3333efbe",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "e4e33817-0d2c-4e42-8d10-17cba4b3c1d8",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "aa24229f-3be5-495b-9989-d9e793056993",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "9b34f6ca-9952-4fbd-b55b-e06e44094463",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "eb21d839-7f51-4781-bf46-886fc6d82a11",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "0bb11e93-d9c6-411e-a614-e38252775d75",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "2320aa06-7d82-46ec-ad6d-a1c9fd280cde",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "1f650fa2-e91a-4cde-8ff5-ad2738f0d3cc",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "b692d3f7-0e85-4e18-9373-214300cc0293",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "c9a2b54f-1316-4463-8f0b-9061bb4b51cd",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "87e595d8-7285-4067-a73f-e80944ffae3c",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "38cef0ea-3ef8-45cd-aadc-5e8e64319cf0",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "29b8c167-5542-47bd-85a8-926645d7846a",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "312522d0-f218-4304-8376-d6f1feeb7553",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "ca1ca1f1-f0ab-4224-8422-d5345ccab557",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "124dc699-f389-4462-9c29-41a091d5cc04",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "abb46e44-0aba-4814-a7f4-b9b62fb5f6ad",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "8f4e5133-7aa0-468d-b13c-6fa23cdaf407",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "d8e59dbd-2add-4514-ae3e-9fac8ae902f5",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "4fa725fa-23c0-4b9b-9c0d-92b82aa75919",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "da84551f-0859-46fd-aaa2-4797cd373991",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "b63d119a-2496-4d92-9bab-e67e85914708",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "274e4b04-3174-46f1-bba5-004bb1ed2cc5",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "86d25b68-ffb0-4fd4-bf48-10f6c3c184a5",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "8bea9251-da22-4f68-91a4-1e60c4af956f",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "487e2d7f-320d-4d75-9d34-3a0fb791c553",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "31ad52e7-70e8-4e3e-9cd7-0d8d8b1b4331",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "3fed1e54-3bf7-46fc-829a-f538a092d774",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "5e31c504-cb51-459e-a939-d49bc83d5d44",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "9e7ac38d-b196-4e80-a59c-0d630d725745",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "93e242a1-3d4b-491b-9d5f-02e038e212cb",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "709da3b4-e8a0-431d-b082-8530ffae33f8",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "b8a56d3f-9910-44a0-a9c0-bb7d51705792",
+                "destination_type": "file"
+            },
+            {
+                "source_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1",
+                "source_type": "sequencing_process",
+                "destination_id": "e99eed63-5794-4d8d-baf9-9c6888e91e6d",
+                "destination_type": "protocol"
+            }
+        ],
+        "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
+        "schema_version": "1.0.0",
+        "schema_type": "link_bundle"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
index d3d010a16..0b5d0344b 100644
--- a/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
+++ b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
@@ -688,80 +688,80 @@
                 "submission_date": "2019-07-18T21:12:40.114Z",
                 "update_date": "2019-07-18T21:12:44.455Z"
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.5",
-            "links": [
-                {
-                    "process": "f59c9106-16a8-47f8-b681-490d23ee09de",
-                    "inputs": [
-                        "13eab62e-0038-4997-aeab-aa3192cc090e"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "3f193e72-8efe-4c2a-ace1-79140ca36477",
-                        "078b71eb-220a-43e5-a0fc-4f231e90f85f"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "dc19bb22-ae7b-431b-9b8b-7b49799a8fcd"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "461851b8-55a5-4ae6-a52a-5bca71a00beb"
-                        }
-                    ]
-                },
-                {
-                    "process": "a03f7164-419b-4792-9a52-e6dda08b85bc",
-                    "inputs": [
-                        "4ccd163e-a630-4ede-bc0c-336ba044b783"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "13eab62e-0038-4997-aeab-aa3192cc090e"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "57d2c83d-cd8b-44c9-9644-c3475a44b0a7",
-                    "inputs": [
-                        "92254a9e-3a14-4760-b229-d914f3e8973f"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "4ccd163e-a630-4ede-bc0c-336ba044b783"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "8b1f44be-7eaa-4030-b6c5-697c5fc388eb",
-                    "inputs": [
-                        "39d1a24f-1785-476d-9c04-065be917e3ff"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "92254a9e-3a14-4760-b229-d914f3e8973f"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "79f7c6ac-ada8-4c17-86ec-e73e87b94374"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "5d9fc5a2-5516-4205-9d6e-8d0d674f146f"
-                        }
-                    ]
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.5",
+        "links": [
+            {
+                "process": "f59c9106-16a8-47f8-b681-490d23ee09de",
+                "inputs": [
+                    "13eab62e-0038-4997-aeab-aa3192cc090e"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "3f193e72-8efe-4c2a-ace1-79140ca36477",
+                    "078b71eb-220a-43e5-a0fc-4f231e90f85f"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "dc19bb22-ae7b-431b-9b8b-7b49799a8fcd"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "461851b8-55a5-4ae6-a52a-5bca71a00beb"
+                    }
+                ]
+            },
+            {
+                "process": "a03f7164-419b-4792-9a52-e6dda08b85bc",
+                "inputs": [
+                    "4ccd163e-a630-4ede-bc0c-336ba044b783"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "13eab62e-0038-4997-aeab-aa3192cc090e"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "57d2c83d-cd8b-44c9-9644-c3475a44b0a7",
+                "inputs": [
+                    "92254a9e-3a14-4760-b229-d914f3e8973f"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "4ccd163e-a630-4ede-bc0c-336ba044b783"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "8b1f44be-7eaa-4030-b6c5-697c5fc388eb",
+                "inputs": [
+                    "39d1a24f-1785-476d-9c04-065be917e3ff"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "92254a9e-3a14-4760-b229-d914f3e8973f"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "79f7c6ac-ada8-4c17-86ec-e73e87b94374"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "5d9fc5a2-5516-4205-9d6e-8d0d674f146f"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
index cfdb0d0b0..cd2ef9a55 100644
--- a/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
+++ b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
@@ -27427,15010 +27427,15010 @@
                 "submission_date": "2018-10-01T14:31:17.397Z",
                 "update_date": "2018-10-01T20:13:06.669Z"
             }
-        },
-        "links.json": {
-            "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.3/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.3",
-            "links": [
-                {
-                    "process": "f8dfb127-a6db-4e3a-b1d7-ceff08c70594",
-                    "inputs": [
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-                        "462505d7-48e1-4d85-92e3-f768a93d4fca",
-                        "090682b0-dc11-43d0-b6f5-cf3dee18533a",
-                        "e67853b9-dc53-4b5f-8693-8ad4e3a4d5d2",
-                        "69dbf7cd-c728-41d3-9851-916dc64e07c2",
-                        "1a6292df-a383-40c7-bc28-b8bf63e03967",
-                        "4aad31c4-06fc-4af6-804b-f10afa1cae1d",
-                        "2a630ecd-440d-43c3-9c9a-2a8ec98a1784",
-                        "b60a1acf-24f7-46a7-b276-39c48f3460e9",
-                        "5db6e3cf-bb9a-430d-8e5a-1499088526fc",
-                        "6ff20c11-cb2e-4ace-9b3a-48094ce7a231",
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+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "9e9d6f8e-64e9-4d7a-94b2-3ae052dfaf6f"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "9b361ad6-2028-41a0-a601-c59585ba157a"
+                    }
+                ]
+            },
+            {
+                "process": "9c0c0d02-ad7f-43d4-bf36-52deb0cb3c1f",
+                "inputs": [
+                    "79682426-b813-4f69-8c9c-2764ffac5dc1"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "4e43967a-bd73-4d99-8339-cc5d72622916"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "9b361ad6-2028-41a0-a601-c59585ba157a"
+                    }
+                ]
+            },
+            {
+                "process": "2d38bafa-8d98-4f45-91cc-272c7682fa18",
+                "inputs": [
+                    "35479c97-1a62-4d90-b057-49c1a518e0c8"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "79682426-b813-4f69-8c9c-2764ffac5dc1"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "9e9d6f8e-64e9-4d7a-94b2-3ae052dfaf6f"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "9b361ad6-2028-41a0-a601-c59585ba157a"
+                    }
+                ]
+            },
+            {
+                "process": "a74926cf-9c9a-4faf-8a01-3915b5021c9f",
+                "inputs": [
+                    "79682426-b813-4f69-8c9c-2764ffac5dc1"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "40482eca-921a-4d5a-907d-876f3c8c6d40"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "9b361ad6-2028-41a0-a601-c59585ba157a"
+                    }
+                ]
+            },
+            {
+                "process": "2d38bafa-8d98-4f45-91cc-272c7682fa18",
+                "inputs": [
+                    "35479c97-1a62-4d90-b057-49c1a518e0c8"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "79682426-b813-4f69-8c9c-2764ffac5dc1"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "9e9d6f8e-64e9-4d7a-94b2-3ae052dfaf6f"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "9b361ad6-2028-41a0-a601-c59585ba157a"
+                    }
+                ]
+            },
+            {
+                "process": "70b726b0-8e2a-4040-9006-8357e300fbd4",
+                "inputs": [
+                    "79682426-b813-4f69-8c9c-2764ffac5dc1"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "4c8ec421-0ec0-4097-afa3-4a87263e7d87"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "9b361ad6-2028-41a0-a601-c59585ba157a"
+                    }
+                ]
+            },
+            {
+                "process": "2d38bafa-8d98-4f45-91cc-272c7682fa18",
+                "inputs": [
+                    "35479c97-1a62-4d90-b057-49c1a518e0c8"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "79682426-b813-4f69-8c9c-2764ffac5dc1"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "9e9d6f8e-64e9-4d7a-94b2-3ae052dfaf6f"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "9b361ad6-2028-41a0-a601-c59585ba157a"
+                    }
+                ]
+            },
+            {
+                "process": "02cea5bd-bb23-45d8-a1f0-9f46dd1974be",
+                "inputs": [
+                    "79682426-b813-4f69-8c9c-2764ffac5dc1"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "04ef0085-f955-46ce-8876-28e06a1301f8"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "9b361ad6-2028-41a0-a601-c59585ba157a"
+                    }
+                ]
+            },
+            {
+                "process": "2d38bafa-8d98-4f45-91cc-272c7682fa18",
+                "inputs": [
+                    "35479c97-1a62-4d90-b057-49c1a518e0c8"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "79682426-b813-4f69-8c9c-2764ffac5dc1"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "9e9d6f8e-64e9-4d7a-94b2-3ae052dfaf6f"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "9b361ad6-2028-41a0-a601-c59585ba157a"
+                    }
+                ]
+            },
+            {
+                "process": "3197c12d-693c-49c9-992b-9051a4794814",
+                "inputs": [
+                    "79682426-b813-4f69-8c9c-2764ffac5dc1"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "892ec3fd-5b6a-4079-92a5-9362ee64c650"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "9b361ad6-2028-41a0-a601-c59585ba157a"
+                    }
+                ]
+            },
+            {
+                "process": "2d38bafa-8d98-4f45-91cc-272c7682fa18",
+                "inputs": [
+                    "35479c97-1a62-4d90-b057-49c1a518e0c8"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "79682426-b813-4f69-8c9c-2764ffac5dc1"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "9e9d6f8e-64e9-4d7a-94b2-3ae052dfaf6f"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "9b361ad6-2028-41a0-a601-c59585ba157a"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
index 833ab0476..ddb6fed8b 100644
--- a/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
+++ b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
@@ -2014,158 +2014,158 @@
                 "submission_date": "2018-09-06T17:43:15.801Z",
                 "update_date": "2018-09-06T17:43:54.690Z"
             }
-        },
-        "links.json": {
-            "describedBy": "http://schema.integration.data.humancellatlas.org/system/1.1.1/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.1",
-            "links": [
-                {
-                    "process": "2a4e1440-dab6-4b0b-8204-ebb270613cc1",
-                    "inputs": [
-                        "c5d76832-f738-43a0-afe7-f62aa53a7824",
-                        "be1f1c69-5ad5-4d2c-a86f-c43f1f003210"
-                    ],
-                    "input_type": "file",
-                    "outputs": [
-                        "84d27b0a-348e-4af2-82cb-c37973a9fe17",
-                        "36671cf7-ab85-409f-a28b-27c489e2ab51",
-                        "4ba5d8f9-2d1c-432d-9fa5-7e22eff732f1",
-                        "f71ca185-a4d4-42ec-b6f0-dbb140cb2f23",
-                        "a0521704-08fa-4594-90da-0b29ee40dc0a",
-                        "8dfb781a-9fa1-488d-9ddc-e8272bef5fe0",
-                        "e80fdd63-3c87-45f9-b1f7-9d7b7122dfdf",
-                        "29164286-43cf-43ca-b3b9-ad61f2e7a1c8",
-                        "46dc4f0d-11c0-4000-b6e9-710553a2a9cc",
-                        "b78926da-4a2c-4af9-8cd8-4ae337336ccc",
-                        "a002691d-8568-40a3-9fd2-bae403916e08",
-                        "0963c920-cd31-45bd-8844-ff0200ff1667",
-                        "fff7c188-ff07-4014-83a5-3f90dfafc09a",
-                        "cf4782d0-79e1-43dc-8313-93447a35620b",
-                        "63cb3d77-fded-4235-87a2-50e5f756826b",
-                        "140c27ca-12de-4425-953b-b1d4c2c918fc",
-                        "38c67a5f-db0c-4d5f-839b-b061709d8be9",
-                        "9efb3c26-4fd8-4986-8a72-1507880e6ab7",
-                        "fff934f7-4a3e-442b-99b2-3479762db53c",
-                        "3268e4bf-591a-4ca3-b7ad-440f61460610",
-                        "68b243fc-c128-40ac-8e51-0383b4860c29",
-                        "4448df34-27c1-413d-bfc1-a508f238e2ed",
-                        "c2c8aec7-489b-4c2b-9b79-dc9f9a6d2d1d",
-                        "b4b3e436-19f2-4b56-b30c-dd22682e94fe",
-                        "477b3e82-552d-47dc-a27b-22d242298362",
-                        "e274e132-3fe1-44e9-879b-d6bc22cba2ab",
-                        "2c11a11d-840c-4a3d-b811-e0e03c2e0976",
-                        "f3ca70e5-f530-4890-be95-e3635dcf164a",
-                        "12bcb6de-0f5b-4581-8d02-4ed3c59c13ab",
-                        "e3a50ba8-8e82-4b7f-89de-b6f512037e3d",
-                        "cf3a255f-e731-4912-a7b1-cbec1b0d5239"
-                    ],
-                    "output_type": "file",
-                    "protocols": []
-                },
-                {
-                    "process": "c8ac10c7-fa3a-4fbc-a9bd-55e767444773",
-                    "inputs": [
-                        "13b00a71-4916-441c-a863-0204b40ba127"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "c5d76832-f738-43a0-afe7-f62aa53a7824",
-                        "be1f1c69-5ad5-4d2c-a86f-c43f1f003210"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "237048e6-dbd9-4a0b-b0cc-8085513c2944"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "f6527c69-b8bb-467a-af22-32a1b7863c65"
-                        }
-                    ]
-                },
-                {
-                    "process": "94510a2b-edc8-4f14-ab1e-494732ccf80a",
-                    "inputs": [
-                        "131f2ca9-0a3e-4794-a6f6-0170884de3bf"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "13b00a71-4916-441c-a863-0204b40ba127"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "babc8692-6932-4c29-b33d-4d7b4deebe54"
-                        }
-                    ]
-                },
-                {
-                    "process": "44edcce5-152d-401c-ba29-ed73cd9ec57f",
-                    "inputs": [
-                        "651a2e3a-80a6-4e3a-99d0-63224ee2ef02"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "131f2ca9-0a3e-4794-a6f6-0170884de3bf"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "c8ac10c7-fa3a-4fbc-a9bd-55e767444773",
-                    "inputs": [
-                        "13b00a71-4916-441c-a863-0204b40ba127"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "c5d76832-f738-43a0-afe7-f62aa53a7824",
-                        "be1f1c69-5ad5-4d2c-a86f-c43f1f003210"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "237048e6-dbd9-4a0b-b0cc-8085513c2944"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "f6527c69-b8bb-467a-af22-32a1b7863c65"
-                        }
-                    ]
-                },
-                {
-                    "process": "94510a2b-edc8-4f14-ab1e-494732ccf80a",
-                    "inputs": [
-                        "131f2ca9-0a3e-4794-a6f6-0170884de3bf"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "13b00a71-4916-441c-a863-0204b40ba127"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "babc8692-6932-4c29-b33d-4d7b4deebe54"
-                        }
-                    ]
-                },
-                {
-                    "process": "44edcce5-152d-401c-ba29-ed73cd9ec57f",
-                    "inputs": [
-                        "651a2e3a-80a6-4e3a-99d0-63224ee2ef02"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "131f2ca9-0a3e-4794-a6f6-0170884de3bf"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "http://schema.integration.data.humancellatlas.org/system/1.1.1/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.1",
+        "links": [
+            {
+                "process": "2a4e1440-dab6-4b0b-8204-ebb270613cc1",
+                "inputs": [
+                    "c5d76832-f738-43a0-afe7-f62aa53a7824",
+                    "be1f1c69-5ad5-4d2c-a86f-c43f1f003210"
+                ],
+                "input_type": "file",
+                "outputs": [
+                    "84d27b0a-348e-4af2-82cb-c37973a9fe17",
+                    "36671cf7-ab85-409f-a28b-27c489e2ab51",
+                    "4ba5d8f9-2d1c-432d-9fa5-7e22eff732f1",
+                    "f71ca185-a4d4-42ec-b6f0-dbb140cb2f23",
+                    "a0521704-08fa-4594-90da-0b29ee40dc0a",
+                    "8dfb781a-9fa1-488d-9ddc-e8272bef5fe0",
+                    "e80fdd63-3c87-45f9-b1f7-9d7b7122dfdf",
+                    "29164286-43cf-43ca-b3b9-ad61f2e7a1c8",
+                    "46dc4f0d-11c0-4000-b6e9-710553a2a9cc",
+                    "b78926da-4a2c-4af9-8cd8-4ae337336ccc",
+                    "a002691d-8568-40a3-9fd2-bae403916e08",
+                    "0963c920-cd31-45bd-8844-ff0200ff1667",
+                    "fff7c188-ff07-4014-83a5-3f90dfafc09a",
+                    "cf4782d0-79e1-43dc-8313-93447a35620b",
+                    "63cb3d77-fded-4235-87a2-50e5f756826b",
+                    "140c27ca-12de-4425-953b-b1d4c2c918fc",
+                    "38c67a5f-db0c-4d5f-839b-b061709d8be9",
+                    "9efb3c26-4fd8-4986-8a72-1507880e6ab7",
+                    "fff934f7-4a3e-442b-99b2-3479762db53c",
+                    "3268e4bf-591a-4ca3-b7ad-440f61460610",
+                    "68b243fc-c128-40ac-8e51-0383b4860c29",
+                    "4448df34-27c1-413d-bfc1-a508f238e2ed",
+                    "c2c8aec7-489b-4c2b-9b79-dc9f9a6d2d1d",
+                    "b4b3e436-19f2-4b56-b30c-dd22682e94fe",
+                    "477b3e82-552d-47dc-a27b-22d242298362",
+                    "e274e132-3fe1-44e9-879b-d6bc22cba2ab",
+                    "2c11a11d-840c-4a3d-b811-e0e03c2e0976",
+                    "f3ca70e5-f530-4890-be95-e3635dcf164a",
+                    "12bcb6de-0f5b-4581-8d02-4ed3c59c13ab",
+                    "e3a50ba8-8e82-4b7f-89de-b6f512037e3d",
+                    "cf3a255f-e731-4912-a7b1-cbec1b0d5239"
+                ],
+                "output_type": "file",
+                "protocols": []
+            },
+            {
+                "process": "c8ac10c7-fa3a-4fbc-a9bd-55e767444773",
+                "inputs": [
+                    "13b00a71-4916-441c-a863-0204b40ba127"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "c5d76832-f738-43a0-afe7-f62aa53a7824",
+                    "be1f1c69-5ad5-4d2c-a86f-c43f1f003210"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "237048e6-dbd9-4a0b-b0cc-8085513c2944"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "f6527c69-b8bb-467a-af22-32a1b7863c65"
+                    }
+                ]
+            },
+            {
+                "process": "94510a2b-edc8-4f14-ab1e-494732ccf80a",
+                "inputs": [
+                    "131f2ca9-0a3e-4794-a6f6-0170884de3bf"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "13b00a71-4916-441c-a863-0204b40ba127"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "babc8692-6932-4c29-b33d-4d7b4deebe54"
+                    }
+                ]
+            },
+            {
+                "process": "44edcce5-152d-401c-ba29-ed73cd9ec57f",
+                "inputs": [
+                    "651a2e3a-80a6-4e3a-99d0-63224ee2ef02"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "131f2ca9-0a3e-4794-a6f6-0170884de3bf"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "c8ac10c7-fa3a-4fbc-a9bd-55e767444773",
+                "inputs": [
+                    "13b00a71-4916-441c-a863-0204b40ba127"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "c5d76832-f738-43a0-afe7-f62aa53a7824",
+                    "be1f1c69-5ad5-4d2c-a86f-c43f1f003210"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "237048e6-dbd9-4a0b-b0cc-8085513c2944"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "f6527c69-b8bb-467a-af22-32a1b7863c65"
+                    }
+                ]
+            },
+            {
+                "process": "94510a2b-edc8-4f14-ab1e-494732ccf80a",
+                "inputs": [
+                    "131f2ca9-0a3e-4794-a6f6-0170884de3bf"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "13b00a71-4916-441c-a863-0204b40ba127"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "babc8692-6932-4c29-b33d-4d7b4deebe54"
+                    }
+                ]
+            },
+            {
+                "process": "44edcce5-152d-401c-ba29-ed73cd9ec57f",
+                "inputs": [
+                    "651a2e3a-80a6-4e3a-99d0-63224ee2ef02"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "131f2ca9-0a3e-4794-a6f6-0170884de3bf"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json b/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
index 374909aa4..0c4e3609b 100644
--- a/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
+++ b/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
@@ -194,109 +194,6 @@
         }
     ],
     "metadata": {
-        "links.json": {
-            "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
-            "links": [
-                {
-                    "inputs": [
-                        {
-                            "input_id": "af3549f4-8632-58c2-9821-c6249c622b0a",
-                            "input_type": "cell_suspension"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "f0c8ac7c-1c4a-5c9c-9286-c8b16208f9ae",
-                            "output_type": "analysis_file"
-                        }
-                    ],
-                    "process_id": "d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "811adf54-7f27-5aec-9ed7-c6084c4c3a1b",
-                            "protocol_type": "analysis_protocol"
-                        },
-                        {
-                            "protocol_id": "767282b2-2fc1-5559-b020-29686b810206",
-                            "protocol_type": "library_preparation_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "119c4135-7b77-5003-a150-f052e22c6834",
-                            "input_type": "cell_suspension"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "af3549f4-8632-58c2-9821-c6249c622b0a",
-                            "output_type": "cell_suspension"
-                        }
-                    ],
-                    "process_id": "b8ec88d7-675c-54ff-8071-63255adc181b",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "0f959f0b-5efa-5cc8-9c46-097b0cb574d5",
-                            "protocol_type": "treatment_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "3bee0c9a-aced-52f2-b97f-89518f826b36",
-                            "input_type": "specimen_from_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "119c4135-7b77-5003-a150-f052e22c6834",
-                            "output_type": "cell_suspension"
-                        }
-                    ],
-                    "process_id": "bd6a4a38-c44b-5d17-b2b1-d0d4c4531bf0",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "46435803-7ee8-5157-8569-8a61ad50c315",
-                            "protocol_type": "enrichment_protocol"
-                        }
-                    ]
-                },
-                {
-                    "inputs": [
-                        {
-                            "input_id": "5bc2bf2f-eb98-5510-a386-172cef38f2f2",
-                            "input_type": "donor_organism"
-                        }
-                    ],
-                    "link_type": "process_link",
-                    "outputs": [
-                        {
-                            "output_id": "3bee0c9a-aced-52f2-b97f-89518f826b36",
-                            "output_type": "specimen_from_organism"
-                        }
-                    ],
-                    "process_id": "37e91a9f-b04e-5313-bbc0-4c394406247e",
-                    "process_type": "process",
-                    "protocols": [
-                        {
-                            "protocol_id": "e7f864e3-6ba7-53c8-842f-2a05cb90e1b7",
-                            "protocol_type": "collection_protocol"
-                        }
-                    ]
-                }
-            ],
-            "schema_type": "links",
-            "schema_version": "3.1.0"
-        },
         "project_0.json": {
             "array_express_accessions": [
                 "E-MTAB-10026"
@@ -779,5 +676,108 @@
             },
             "schema_type": "protocol"
         }
+    },
+    "links": {
+        "describedBy": "https://schema.staging.data.humancellatlas.org/system/3.1.0/links",
+        "links": [
+            {
+                "inputs": [
+                    {
+                        "input_id": "af3549f4-8632-58c2-9821-c6249c622b0a",
+                        "input_type": "cell_suspension"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "f0c8ac7c-1c4a-5c9c-9286-c8b16208f9ae",
+                        "output_type": "analysis_file"
+                    }
+                ],
+                "process_id": "d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "811adf54-7f27-5aec-9ed7-c6084c4c3a1b",
+                        "protocol_type": "analysis_protocol"
+                    },
+                    {
+                        "protocol_id": "767282b2-2fc1-5559-b020-29686b810206",
+                        "protocol_type": "library_preparation_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "119c4135-7b77-5003-a150-f052e22c6834",
+                        "input_type": "cell_suspension"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "af3549f4-8632-58c2-9821-c6249c622b0a",
+                        "output_type": "cell_suspension"
+                    }
+                ],
+                "process_id": "b8ec88d7-675c-54ff-8071-63255adc181b",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "0f959f0b-5efa-5cc8-9c46-097b0cb574d5",
+                        "protocol_type": "treatment_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "3bee0c9a-aced-52f2-b97f-89518f826b36",
+                        "input_type": "specimen_from_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "119c4135-7b77-5003-a150-f052e22c6834",
+                        "output_type": "cell_suspension"
+                    }
+                ],
+                "process_id": "bd6a4a38-c44b-5d17-b2b1-d0d4c4531bf0",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "46435803-7ee8-5157-8569-8a61ad50c315",
+                        "protocol_type": "enrichment_protocol"
+                    }
+                ]
+            },
+            {
+                "inputs": [
+                    {
+                        "input_id": "5bc2bf2f-eb98-5510-a386-172cef38f2f2",
+                        "input_type": "donor_organism"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "3bee0c9a-aced-52f2-b97f-89518f826b36",
+                        "output_type": "specimen_from_organism"
+                    }
+                ],
+                "process_id": "37e91a9f-b04e-5313-bbc0-4c394406247e",
+                "process_type": "process",
+                "protocols": [
+                    {
+                        "protocol_id": "e7f864e3-6ba7-53c8-842f-2a05cb90e1b7",
+                        "protocol_type": "collection_protocol"
+                    }
+                ]
+            }
+        ],
+        "schema_type": "links",
+        "schema_version": "3.1.0"
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
index 8d7d20190..d632a9c69 100644
--- a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
+++ b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
@@ -2392,723 +2392,723 @@
                 "submission_date": "2018-10-11T21:18:03.026Z",
                 "update_date": "2018-10-11T21:18:10.586Z"
             }
-        },
-        "links.json": {
-            "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.3/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.3",
-            "links": [
-                {
-                    "process": "228fd33a-3627-4dea-bda9-e9cdc3b924b6",
-                    "inputs": [
-                        "281c2d08-9e43-47f9-b937-e733e3ba3322",
-                        "ae1d6fa7-964f-465a-8c78-565206827434",
-                        "f518a8cc-e1d9-4fc9-bc32-491dd8543902",
-                        "213381ea-6161-4159-853e-cfcae4968001",
-                        "9ee3da9e-83ca-4c02-84d6-ac09702b12ba",
-                        "330a08ca-ae8e-4f1f-aa03-970abcd27f39"
-                    ],
-                    "input_type": "file",
-                    "outputs": [
-                        "cf93f747-1392-4670-8eb3-3ac60a96855e",
-                        "477c0b3e-4a06-4214-8f27-58199ba63528",
-                        "ad6d5170-d74b-408c-af6b-25a14315c9da",
-                        "50be9b67-fae5-4472-9719-478dd1303d6e",
-                        "fd16b62e-e540-4f03-8ba0-07d0c204e3c8",
-                        "3c41b5b6-f480-4d47-8c5e-155e7c1adf54",
-                        "022a217c-384d-4d9d-8631-6397b6838e3a",
-                        "9b778e46-0c51-4260-8e3f-000ecc145f0a",
-                        "af025a74-53f1-4972-b50d-53095b5ffac2",
-                        "e8395271-7c8e-4ec4-9598-495df43fe5fd",
-                        "211a8fbf-b190-4576-ac2f-2b1a91743abb",
-                        "17222e3a-5757-45e9-9dfe-c4b6aa10f28a",
-                        "2fb8a975-b50c-4528-b850-838a19e19a1e"
-                    ],
-                    "output_type": "file",
-                    "protocols": []
-                },
-                {
-                    "process": "a2510b8c-8c92-4fe4-bc06-5e4e92093545",
-                    "inputs": [
-                        "803fd65a-c578-4c4f-a39e-bedec24e2578"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "213381ea-6161-4159-853e-cfcae4968001",
-                        "9ee3da9e-83ca-4c02-84d6-ac09702b12ba",
-                        "330a08ca-ae8e-4f1f-aa03-970abcd27f39"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "92277226-bf78-4df9-a594-5190a8790a14"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "102cdbf3-b0e5-4dd5-9168-51150a9ebb6b"
-                        }
-                    ]
-                },
-                {
-                    "process": "c7b6e9fe-6f08-41a9-8907-9c0347e6d604",
-                    "inputs": [
-                        "2d8282f0-6cbb-4d5a-822c-4b01718b4d0d",
-                        "b7214641-1ac5-4f60-b795-cb33a7c25434",
-                        "308eea51-d14b-4036-8cd1-cfd81d7532c3",
-                        "73f10dad-afc5-4d1d-a71c-4a8b6fff9172"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "803fd65a-c578-4c4f-a39e-bedec24e2578"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "755762e0-7aff-48ed-a7d4-d3ea4005758f"
-                        }
-                    ]
-                },
-                {
-                    "process": "0d1d507d-4246-4b1c-8836-261d42f784eb",
-                    "inputs": [
-                        "c532cca7-67c6-4617-ac47-5b91652621a5"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "2d8282f0-6cbb-4d5a-822c-4b01718b4d0d"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "8f4a8e7c-e7ee-44dc-8e09-f4012355060f"
-                        }
-                    ]
-                },
-                {
-                    "process": "5fcbd4b3-6ad0-434a-bf84-19c33c2d7dc0",
-                    "inputs": [
-                        "c8e14a8e-81f9-4109-bb27-4bb3029240c1"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "c532cca7-67c6-4617-ac47-5b91652621a5"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "ipsc_induction_protocol",
-                            "protocol_id": "cdfe38f2-1d90-4700-a199-d8105ce299df"
-                        }
-                    ]
-                },
-                {
-                    "process": "54760853-d6ed-4149-9a49-53c4cddfd93c",
-                    "inputs": [
-                        "d4c29b1a-f23c-4511-a2ae-097772d90254"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "c8e14a8e-81f9-4109-bb27-4bb3029240c1"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "d5ac7f5f-9a50-403e-9b8d-6e983a099826",
-                    "inputs": [
-                        "e924c114-e3cd-4060-9c8e-3d980ec7fcbe"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "b7214641-1ac5-4f60-b795-cb33a7c25434"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "8f4a8e7c-e7ee-44dc-8e09-f4012355060f"
-                        }
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-                {
-                    "process": "53f025f5-931a-4b6e-9a9b-545b5b881710",
-                    "inputs": [
-                        "5bd6106c-0158-4c2c-8c60-32019c599c83"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "e924c114-e3cd-4060-9c8e-3d980ec7fcbe"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "ipsc_induction_protocol",
-                            "protocol_id": "cdfe38f2-1d90-4700-a199-d8105ce299df"
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-                {
-                    "process": "45c67d31-0b05-4d5e-b215-e50e1b2b125c",
-                    "inputs": [
-                        "ef7e6ac7-172a-4b24-9620-fc909a5e9c6c"
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-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "5bd6106c-0158-4c2c-8c60-32019c599c83"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "fe0d9d3a-56be-41ca-9fdf-70c8c637fd62",
-                    "inputs": [
-                        "a3651f83-dee6-49b2-ba4e-0ce20f02467d"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "308eea51-d14b-4036-8cd1-cfd81d7532c3"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "8f4a8e7c-e7ee-44dc-8e09-f4012355060f"
-                        }
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-                {
-                    "process": "4ed306ec-5cf1-49ed-a17a-00f9a0fc38bc",
-                    "inputs": [
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-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "a3651f83-dee6-49b2-ba4e-0ce20f02467d"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "ipsc_induction_protocol",
-                            "protocol_id": "cdfe38f2-1d90-4700-a199-d8105ce299df"
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-                {
-                    "process": "76e685c9-fcf2-4582-bbfa-5e0369eb5bdb",
-                    "inputs": [
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-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "8f328973-9bc0-46b9-8a1f-38893e77b3b5"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "bce97917-252e-40f2-af8e-df591099acd8",
-                    "inputs": [
-                        "6a16de30-176d-4488-81de-9337a1a6d8c5"
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-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "73f10dad-afc5-4d1d-a71c-4a8b6fff9172"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "8f4a8e7c-e7ee-44dc-8e09-f4012355060f"
-                        }
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-                    "inputs": [
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-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "6a16de30-176d-4488-81de-9337a1a6d8c5"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "ipsc_induction_protocol",
-                            "protocol_id": "cdfe38f2-1d90-4700-a199-d8105ce299df"
-                        }
-                    ]
-                },
-                {
-                    "process": "bb2365b9-5a5b-436f-92e3-4fc6d86a9efd",
-                    "inputs": [
-                        "96757312-0221-447a-84f1-7a737b5afd01"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "82368936-7b99-4864-9f49-b8fee3906d47"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "a2510b8c-8c92-4fe4-bc06-5e4e92093545",
-                    "inputs": [
-                        "803fd65a-c578-4c4f-a39e-bedec24e2578"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "213381ea-6161-4159-853e-cfcae4968001",
-                        "9ee3da9e-83ca-4c02-84d6-ac09702b12ba",
-                        "330a08ca-ae8e-4f1f-aa03-970abcd27f39"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "92277226-bf78-4df9-a594-5190a8790a14"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "102cdbf3-b0e5-4dd5-9168-51150a9ebb6b"
-                        }
-                    ]
-                },
-                {
-                    "process": "c7b6e9fe-6f08-41a9-8907-9c0347e6d604",
-                    "inputs": [
-                        "2d8282f0-6cbb-4d5a-822c-4b01718b4d0d",
-                        "b7214641-1ac5-4f60-b795-cb33a7c25434",
-                        "308eea51-d14b-4036-8cd1-cfd81d7532c3",
-                        "73f10dad-afc5-4d1d-a71c-4a8b6fff9172"
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-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "803fd65a-c578-4c4f-a39e-bedec24e2578"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "755762e0-7aff-48ed-a7d4-d3ea4005758f"
-                        }
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+                "protocols": []
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     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
index 2e9d79780..b269b25d5 100644
--- a/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
+++ b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
@@ -720,97 +720,97 @@
                 "document_id": "84d06811-a6b5-4a37-809c-842b0ca9e093",
                 "submission_date": "2018-12-04T16:22:46.435Z"
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.3/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.3",
-            "links": [
-                {
-                    "process": "c124da1f-12bf-48c6-baf5-95aa74439a3a",
-                    "inputs": [
-                        "d29c64bd-b8d2-4e72-abbc-5536a44eac12"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "12b25cbd-8cfa-4f0e-818f-d6ba3e823af4",
-                        "65d3d936-ae9d-4a18-a8c7-73ce6132355e"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "7a7788ce-ba24-431b-bd4b-dc02dcee1547"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "2ea1f5b3-d137-43f5-98b6-268d82f682aa"
-                        }
-                    ]
-                },
-                {
-                    "process": "e2144c69-dbdd-485a-834b-5d05ba06b3fc",
-                    "inputs": [
-                        "195b2621-ec05-4618-9063-c56048de97d1"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "d29c64bd-b8d2-4e72-abbc-5536a44eac12"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "028e8015-e9b6-4593-8cb8-59357085a746"
-                        }
-                    ]
-                },
-                {
-                    "process": "7b7c1273-3e0f-4f77-af53-721807a6af85",
-                    "inputs": [
-                        "c737000c-60d3-43c6-9017-16de92294529"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "195b2621-ec05-4618-9063-c56048de97d1"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "ipsc_induction_protocol",
-                            "protocol_id": "de1be240-5ac5-4b6d-8294-ae0c58e0e289"
-                        },
-                        {
-                            "protocol_type": "differentiation_protocol",
-                            "protocol_id": "944f1bef-a1af-4a88-a6af-e8eec48172a3"
-                        }
-                    ]
-                },
-                {
-                    "process": "e1c9e3e3-fa47-49bc-b718-33ca9b89eea9",
-                    "inputs": [
-                        "50eec9fe-0138-458a-a946-9eec1403eb80"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "c737000c-60d3-43c6-9017-16de92294529"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "84d06811-a6b5-4a37-809c-842b0ca9e093",
-                    "inputs": [
-                        "c4cfe441-ae72-4539-a23b-fac1fb61103e"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "50eec9fe-0138-458a-a946-9eec1403eb80"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.3/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.3",
+        "links": [
+            {
+                "process": "c124da1f-12bf-48c6-baf5-95aa74439a3a",
+                "inputs": [
+                    "d29c64bd-b8d2-4e72-abbc-5536a44eac12"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "12b25cbd-8cfa-4f0e-818f-d6ba3e823af4",
+                    "65d3d936-ae9d-4a18-a8c7-73ce6132355e"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "7a7788ce-ba24-431b-bd4b-dc02dcee1547"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "2ea1f5b3-d137-43f5-98b6-268d82f682aa"
+                    }
+                ]
+            },
+            {
+                "process": "e2144c69-dbdd-485a-834b-5d05ba06b3fc",
+                "inputs": [
+                    "195b2621-ec05-4618-9063-c56048de97d1"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "d29c64bd-b8d2-4e72-abbc-5536a44eac12"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "028e8015-e9b6-4593-8cb8-59357085a746"
+                    }
+                ]
+            },
+            {
+                "process": "7b7c1273-3e0f-4f77-af53-721807a6af85",
+                "inputs": [
+                    "c737000c-60d3-43c6-9017-16de92294529"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "195b2621-ec05-4618-9063-c56048de97d1"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "ipsc_induction_protocol",
+                        "protocol_id": "de1be240-5ac5-4b6d-8294-ae0c58e0e289"
+                    },
+                    {
+                        "protocol_type": "differentiation_protocol",
+                        "protocol_id": "944f1bef-a1af-4a88-a6af-e8eec48172a3"
+                    }
+                ]
+            },
+            {
+                "process": "e1c9e3e3-fa47-49bc-b718-33ca9b89eea9",
+                "inputs": [
+                    "50eec9fe-0138-458a-a946-9eec1403eb80"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "c737000c-60d3-43c6-9017-16de92294529"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "84d06811-a6b5-4a37-809c-842b0ca9e093",
+                "inputs": [
+                    "c4cfe441-ae72-4539-a23b-fac1fb61103e"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "50eec9fe-0138-458a-a946-9eec1403eb80"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
index aaeaf6953..10c5888fd 100644
--- a/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
+++ b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
@@ -2218,173 +2218,173 @@
                 "submission_date": "2018-10-16T07:53:53.709Z",
                 "update_date": "2018-10-16T08:06:34.625Z"
             }
-        },
-        "links.json": {
-            "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.3/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.3",
-            "links": [
-                {
-                    "process": "1c1d9a13-1132-4f64-aaa9-86ecac56c9f0",
-                    "inputs": [
-                        "c8ed5871-28e6-42e2-8ccf-caa586a72c9e",
-                        "6291c2e7-3cc4-4d87-9bf6-2d6f6b131628"
-                    ],
-                    "input_type": "file",
-                    "outputs": [
-                        "f5f82e76-173c-4f95-b25a-4ddc80bd1f86",
-                        "9b32ad49-e38d-458c-8976-668daa24c30e",
-                        "479b4d96-b76b-41a7-9606-a523d701ce0c",
-                        "f0b686e9-7a26-40f1-bdb2-58a1414d77eb",
-                        "30f8d79e-8a4d-4fd3-93af-b5346f16b640",
-                        "20a011f9-e862-413b-bf1c-b43f3c64b874",
-                        "c8caa0c3-7e78-40ac-a7f9-6219cbc2ee50",
-                        "bdea53d3-49a6-4f5c-8504-d74996fe0745",
-                        "0d27455f-d951-472a-849a-e234efca42d6",
-                        "2da7e3ba-23f5-4e81-9c36-5106b55bcdce",
-                        "8776d7ea-5e3e-49a0-bd97-a713e9a14f3e",
-                        "4fb97024-86ac-4d01-907d-d9b3159cf4be",
-                        "e1982adb-80b9-4ea6-a616-9206b0846afd",
-                        "b9254ef6-3f3a-4259-8829-01a6006fe5e3",
-                        "4bdb540a-7189-490a-9823-0f5c67e146d4",
-                        "02e4b9e0-0750-4a21-8b18-46df9f7c86b5",
-                        "55a4c327-4ca0-400d-88b9-91ccd89cad31",
-                        "dd5a65c4-23fc-40ba-8caf-37393a059e0f",
-                        "bc051b66-16fd-49b0-aca7-d6b29c445f61",
-                        "b104083d-c607-4ad5-993e-e97632c9e4d9",
-                        "b6576e30-18a2-412c-846d-377ad50cceed",
-                        "544245b6-180b-4765-b8d2-db9a07fd2790",
-                        "bdfc95f5-452d-45f0-a539-03e70be04d73",
-                        "46742270-3e39-45a2-99d6-50c2e1277045",
-                        "1251ee1c-3f6f-43ef-b540-c4a3f3461e78",
-                        "ad5a0217-3f5e-4293-bf4e-d56f55453dd5",
-                        "fc842ec4-3fdc-447c-82a3-b59584f6509f",
-                        "858b76ef-bb5b-44e2-b6fa-09efd3430a98",
-                        "8c4c53c9-87a3-4f28-8c65-57090360a9dc",
-                        "ec81ed84-ba61-4361-b611-c2ab3bf3f08e",
-                        "51adec61-135c-4a93-b3d2-50019c0f58ad",
-                        "abfb543f-345d-4f01-8a3d-c9c02b87cd0b",
-                        "1afd626b-6730-4cb6-92c1-3379e7944f66"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "analysis_protocol",
-                            "protocol_id": "7770a568-a5e5-4767-8e85-69ac1574a190"
-                        }
-                    ]
-                },
-                {
-                    "process": "30031d43-a8ee-465a-b015-bfae1d762b67",
-                    "inputs": [
-                        "75d0f208-d856-4e12-8916-a84f8f0e5338"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "c8ed5871-28e6-42e2-8ccf-caa586a72c9e",
-                        "6291c2e7-3cc4-4d87-9bf6-2d6f6b131628"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "7faadd95-bcee-4627-8990-04b79cf617f9"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "dcf48263-da0f-4fb8-9af7-2cb0e3af5b09"
-                        }
-                    ]
-                },
-                {
-                    "process": "0c56f1fe-3ba6-4e09-9c91-ee1cdb97afdc",
-                    "inputs": [
-                        "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "75d0f208-d856-4e12-8916-a84f8f0e5338"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "2f0c9a0e-bf38-4df9-ba9c-d3502b843e2b"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "d9fdfade-52d2-40df-b299-e9aa292ea120"
-                        }
-                    ]
-                },
-                {
-                    "process": "4a1432a1-ae18-45f2-b574-9869b7242289",
-                    "inputs": [
-                        "d919428e-d58b-4815-b36a-c9f186df6582"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                },
-                {
-                    "process": "30031d43-a8ee-465a-b015-bfae1d762b67",
-                    "inputs": [
-                        "75d0f208-d856-4e12-8916-a84f8f0e5338"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "c8ed5871-28e6-42e2-8ccf-caa586a72c9e",
-                        "6291c2e7-3cc4-4d87-9bf6-2d6f6b131628"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "7faadd95-bcee-4627-8990-04b79cf617f9"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "dcf48263-da0f-4fb8-9af7-2cb0e3af5b09"
-                        }
-                    ]
-                },
-                {
-                    "process": "0c56f1fe-3ba6-4e09-9c91-ee1cdb97afdc",
-                    "inputs": [
-                        "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "75d0f208-d856-4e12-8916-a84f8f0e5338"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "2f0c9a0e-bf38-4df9-ba9c-d3502b843e2b"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "d9fdfade-52d2-40df-b299-e9aa292ea120"
-                        }
-                    ]
-                },
-                {
-                    "process": "4a1432a1-ae18-45f2-b574-9869b7242289",
-                    "inputs": [
-                        "d919428e-d58b-4815-b36a-c9f186df6582"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.3/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.3",
+        "links": [
+            {
+                "process": "1c1d9a13-1132-4f64-aaa9-86ecac56c9f0",
+                "inputs": [
+                    "c8ed5871-28e6-42e2-8ccf-caa586a72c9e",
+                    "6291c2e7-3cc4-4d87-9bf6-2d6f6b131628"
+                ],
+                "input_type": "file",
+                "outputs": [
+                    "f5f82e76-173c-4f95-b25a-4ddc80bd1f86",
+                    "9b32ad49-e38d-458c-8976-668daa24c30e",
+                    "479b4d96-b76b-41a7-9606-a523d701ce0c",
+                    "f0b686e9-7a26-40f1-bdb2-58a1414d77eb",
+                    "30f8d79e-8a4d-4fd3-93af-b5346f16b640",
+                    "20a011f9-e862-413b-bf1c-b43f3c64b874",
+                    "c8caa0c3-7e78-40ac-a7f9-6219cbc2ee50",
+                    "bdea53d3-49a6-4f5c-8504-d74996fe0745",
+                    "0d27455f-d951-472a-849a-e234efca42d6",
+                    "2da7e3ba-23f5-4e81-9c36-5106b55bcdce",
+                    "8776d7ea-5e3e-49a0-bd97-a713e9a14f3e",
+                    "4fb97024-86ac-4d01-907d-d9b3159cf4be",
+                    "e1982adb-80b9-4ea6-a616-9206b0846afd",
+                    "b9254ef6-3f3a-4259-8829-01a6006fe5e3",
+                    "4bdb540a-7189-490a-9823-0f5c67e146d4",
+                    "02e4b9e0-0750-4a21-8b18-46df9f7c86b5",
+                    "55a4c327-4ca0-400d-88b9-91ccd89cad31",
+                    "dd5a65c4-23fc-40ba-8caf-37393a059e0f",
+                    "bc051b66-16fd-49b0-aca7-d6b29c445f61",
+                    "b104083d-c607-4ad5-993e-e97632c9e4d9",
+                    "b6576e30-18a2-412c-846d-377ad50cceed",
+                    "544245b6-180b-4765-b8d2-db9a07fd2790",
+                    "bdfc95f5-452d-45f0-a539-03e70be04d73",
+                    "46742270-3e39-45a2-99d6-50c2e1277045",
+                    "1251ee1c-3f6f-43ef-b540-c4a3f3461e78",
+                    "ad5a0217-3f5e-4293-bf4e-d56f55453dd5",
+                    "fc842ec4-3fdc-447c-82a3-b59584f6509f",
+                    "858b76ef-bb5b-44e2-b6fa-09efd3430a98",
+                    "8c4c53c9-87a3-4f28-8c65-57090360a9dc",
+                    "ec81ed84-ba61-4361-b611-c2ab3bf3f08e",
+                    "51adec61-135c-4a93-b3d2-50019c0f58ad",
+                    "abfb543f-345d-4f01-8a3d-c9c02b87cd0b",
+                    "1afd626b-6730-4cb6-92c1-3379e7944f66"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "analysis_protocol",
+                        "protocol_id": "7770a568-a5e5-4767-8e85-69ac1574a190"
+                    }
+                ]
+            },
+            {
+                "process": "30031d43-a8ee-465a-b015-bfae1d762b67",
+                "inputs": [
+                    "75d0f208-d856-4e12-8916-a84f8f0e5338"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "c8ed5871-28e6-42e2-8ccf-caa586a72c9e",
+                    "6291c2e7-3cc4-4d87-9bf6-2d6f6b131628"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "7faadd95-bcee-4627-8990-04b79cf617f9"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "dcf48263-da0f-4fb8-9af7-2cb0e3af5b09"
+                    }
+                ]
+            },
+            {
+                "process": "0c56f1fe-3ba6-4e09-9c91-ee1cdb97afdc",
+                "inputs": [
+                    "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "75d0f208-d856-4e12-8916-a84f8f0e5338"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "2f0c9a0e-bf38-4df9-ba9c-d3502b843e2b"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "d9fdfade-52d2-40df-b299-e9aa292ea120"
+                    }
+                ]
+            },
+            {
+                "process": "4a1432a1-ae18-45f2-b574-9869b7242289",
+                "inputs": [
+                    "d919428e-d58b-4815-b36a-c9f186df6582"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "30031d43-a8ee-465a-b015-bfae1d762b67",
+                "inputs": [
+                    "75d0f208-d856-4e12-8916-a84f8f0e5338"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "c8ed5871-28e6-42e2-8ccf-caa586a72c9e",
+                    "6291c2e7-3cc4-4d87-9bf6-2d6f6b131628"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "7faadd95-bcee-4627-8990-04b79cf617f9"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "dcf48263-da0f-4fb8-9af7-2cb0e3af5b09"
+                    }
+                ]
+            },
+            {
+                "process": "0c56f1fe-3ba6-4e09-9c91-ee1cdb97afdc",
+                "inputs": [
+                    "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "75d0f208-d856-4e12-8916-a84f8f0e5338"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "2f0c9a0e-bf38-4df9-ba9c-d3502b843e2b"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "d9fdfade-52d2-40df-b299-e9aa292ea120"
+                    }
+                ]
+            },
+            {
+                "process": "4a1432a1-ae18-45f2-b574-9869b7242289",
+                "inputs": [
+                    "d919428e-d58b-4815-b36a-c9f186df6582"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "4c2b6ea0-43eb-4e37-b973-f2bdbc724e92"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
index 2990aa646..31e7ea289 100644
--- a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
+++ b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
@@ -11517,380 +11517,380 @@
                 "submission_date": "2019-07-18T21:12:40.114Z",
                 "update_date": "2019-07-18T21:12:44.455Z"
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.5",
-            "links": [
-                {
-                    "process": "af6dce39-9d35-4299-8239-03ba1d513342",
-                    "inputs": [
-                        "3f193e72-8efe-4c2a-ace1-79140ca36477",
-                        "078b71eb-220a-43e5-a0fc-4f231e90f85f"
-                    ],
-                    "input_type": "file",
-                    "outputs": [
-                        "2afae9e4-be02-4d57-bc44-24931f71d54c",
-                        "7a42f079-a318-4975-9d91-8f1e816531de",
-                        "aaaf3d7b-9602-4d74-aa6f-b429e1e8b8ef",
-                        "433f86ab-0a07-4f8c-ac18-b4dec37fa434",
-                        "5ec54ddd-c6d7-4ae6-a822-94720c7bdbd1",
-                        "b7890117-4733-4979-91ec-ba0208e088e9",
-                        "5350b852-077e-43e3-885b-d1b37b3d7a6e",
-                        "2c0bc0eb-739f-42ea-a5df-7d2943977fab",
-                        "93153632-bf8c-49bb-a283-00957c7f853c",
-                        "01d206e5-47b4-48dd-b823-74e62e2325d1",
-                        "752857d0-35f9-46fa-9888-fde25f21195b",
-                        "ded3278c-98d4-43d1-81ce-5233f7123842",
-                        "2e205f24-56cc-40ec-81b1-c17ebd0a5047",
-                        "cc486886-d9a2-44e6-8bf3-84a84c035ff6",
-                        "20ac4de0-bb12-4f99-9e54-bd6f284c741a",
-                        "d6ccfc37-bccb-463f-bd96-53accf9b5803",
-                        "12c88fdb-2350-498c-a51c-6f93fad50621",
-                        "bf4431ba-80da-468c-852b-7dbe008519f6",
-                        "4018b8da-201c-423b-a26a-737549674742",
-                        "8be955e9-eb4e-4834-8576-0fd7ba1c672d",
-                        "291bc053-766d-4b04-aa69-53a7d6a05366",
-                        "80b4596c-4047-40f7-8e90-d7ba13c3aba4",
-                        "bd8f069d-1b75-4f7d-b10a-55efe37e4625",
-                        "287203a8-b15c-4fc9-ade7-4bfa9b4928e7",
-                        "3574966b-2810-45e2-8a1f-bb20a183d9c2",
-                        "5a2aa294-f923-4331-98c0-e9556263252e",
-                        "1e84fd86-6cd6-4533-8b48-cd314820e9a9",
-                        "058de439-51f8-47d4-8e63-c98ea902e527",
-                        "f7ab60fb-4ffb-43d5-8ce3-1ce6559d97b5",
-                        "f42e5e79-a8a9-425d-a4bb-b1e3b166f3d4",
-                        "2c0a6b30-a4f7-4edf-86b3-bf344e895893",
-                        "80224b34-0cab-4b02-95db-99573c3aaf4d",
-                        "48ca6e39-74f8-458e-8233-7e310a873f1d",
-                        "0e722000-9c5a-409e-b113-6f1382317a61",
-                        "b4038c93-a07c-4573-8d5a-0428fb766db0",
-                        "c847ae70-af73-4294-bbdc-b0ac1f10fcc3",
-                        "0074fd7c-1c4a-45bb-9a3e-f27f4d66d9d8",
-                        "fb66bdf7-df50-4ef1-8c11-e643afc4e1a2",
-                        "981391eb-6ed5-4f38-8b50-99c49db205dc",
-                        "7f9e2c6c-abfa-46f6-84bf-c7957c2e25b5",
-                        "182fa5c6-b762-414d-8117-d1b7fd6b554a",
-                        "00689444-5c04-4d33-bc48-bf9412382086",
-                        "80168b45-6e50-4385-902a-b9da569f272b",
-                        "63731ed9-61dd-4e32-9696-89b7c4778819",
-                        "cd4c3355-1e7f-4e6f-989b-b067bcd257d9",
-                        "12499e08-3eda-42f6-97f1-bb5e6d6b2dc4",
-                        "d0247302-2653-423d-9945-b160f29a6658",
-                        "fe8110a2-8616-4bdd-a867-b44612f7904f",
-                        "a3c971eb-dd56-4dcd-adb1-530ac7fefca2",
-                        "ea51d2fb-3e38-45b4-b547-683068565fb4",
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-                        "05d16edd-0757-4497-804a-2d540f280f5f",
-                        "e8876fea-5529-4e3c-8a1f-6cd0351d95fc",
-                        "97c23453-969b-4603-8118-6dfed4c48f67",
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+                    "f719374f-7e9d-4aa0-a135-37d378018385",
+                    "df814431-6493-4c7a-ae77-f615174cc8f0",
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+                    "a4ebbbda-8cf0-4dd3-acf2-935d4b21e635",
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+                    "8248bc28-ed8e-4445-a3c9-8d86dbef1c33",
+                    "28dc1d99-864a-40f3-b352-091bfa830f44",
+                    "2054c82b-ab2d-4f2b-b36d-474ee1967db6",
+                    "2e3fff44-0895-41ee-9fc2-392c60970871",
+                    "4b65b43d-3f81-480d-9b56-64f32f05ae4a",
+                    "f3a76c83-575b-4632-a199-79d224a41491",
+                    "834a3d7f-03c5-4b80-b812-e46c7a41ea85",
+                    "b96baaa5-a935-4613-a57a-d46680d65024",
+                    "0de7c34d-c46d-451c-9cce-456604ff8098",
+                    "27c0877d-17d8-4f7d-8f29-cac03169a134",
+                    "0c1db26c-7b42-425a-bdc2-e0939594874b",
+                    "3edd2d04-d41a-4877-92c0-79f9b81b9d46",
+                    "1874790c-9a17-48ae-ab4f-5608979d337a",
+                    "270f194e-991f-4eee-a3bf-f3558e0875a7",
+                    "d71b2d27-6a8c-4b86-93a8-4c8ed27de03d",
+                    "b4eaf58e-77f5-4876-9116-8377b7768301",
+                    "2c10bd25-0258-4c0f-891b-27e5335aec37",
+                    "e05803d2-29fb-4a42-afe1-9eb173d9f175",
+                    "6d20852c-06d3-4187-be32-a6e654480e77",
+                    "a47f0826-d375-4c36-8dfe-e6c7c32f70ac",
+                    "522e0dca-0892-4f00-9dde-195b754cb0b8",
+                    "b1217476-441a-44de-ab1b-fbe20d24c3ec",
+                    "4694137c-7509-4762-bcc0-f930d1e5a271",
+                    "32cc38e3-118e-40e2-96e1-cd92fe3e11aa",
+                    "b72b09fc-9e76-40b4-99fe-8227504be200",
+                    "a5e57712-e3c6-43ec-b0fc-869d9b66396e",
+                    "080a1ebc-6d00-48ef-b293-138ef083f47d",
+                    "9b65eed3-eb7a-4c63-9e8f-aeffa81f1e23",
+                    "0919427e-9f5f-4ce3-baf4-e825f86adbec",
+                    "890b6a2a-99cc-4e0f-b561-45469acce96f",
+                    "33c48f1d-0909-4e5f-9b41-422c6ab92406",
+                    "c8424e37-f930-4b5c-91b1-93d220968718",
+                    "263cef0c-aac2-4dee-861d-50c74a116b97",
+                    "8bbac3b8-17b8-48cb-8a08-4bd10da0d852",
+                    "ed54d68f-ec20-4925-8096-1aa7a2219166",
+                    "26e09825-41c0-47a3-b88e-b3bdda55a64d",
+                    "624ae45a-e684-484f-b35c-96c68f1c2818",
+                    "fe5c88b4-687b-4b66-87f0-271deb195aaf",
+                    "1ff25469-3040-497c-a2ad-ddfcbfa56e81",
+                    "a4e098fe-d251-4eff-a6c4-1516c3db5f45",
+                    "45c524c7-9f61-4fd7-a188-73f2b2f222fe",
+                    "a66b12e3-22e0-46b5-8431-49cae2781fa3",
+                    "d4c479b7-3fa9-45f9-b5dd-d566c069e0b0",
+                    "9ea49dbc-aeec-4c23-89ad-6bb19dc4f3f8",
+                    "0a06b519-54a2-4fe6-a0b9-ced484f2ee88",
+                    "09e2872a-e14e-4278-90d9-0272bf674ade",
+                    "4531af8b-472e-4305-8584-136a6139136e",
+                    "a21642da-c606-4318-9923-04fef26563c7",
+                    "cfe7e5fb-90ab-4a31-990f-ebae50e1ac55",
+                    "9e37e92f-fc60-4b1b-807a-b68b332ec42e",
+                    "0a138e45-159d-45ff-afe2-5615cd29e0c3",
+                    "4a4baaee-a014-4f01-8796-a78c53d26ff3",
+                    "ddb54f6b-6286-443d-854e-5cbdd3e73ac9",
+                    "82bdd527-5c90-4baa-9970-9067a2c1f7d1",
+                    "c3feea3c-fcf6-46f5-93db-dd54433e3cf4",
+                    "ff3620c9-5c36-48c0-a4ec-937fd585636e",
+                    "e727ebf7-276b-4704-801d-cd2f3b81a5c5",
+                    "fab74ba6-81c8-4d8c-b8c3-9b82e31f5b9f",
+                    "2b264ded-d29d-43e2-8288-26ab7ab1406b",
+                    "86db2ba1-16df-4d73-afea-18148d4e7faa"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "analysis_protocol",
+                        "protocol_id": "d3e7bf92-3c6b-433d-a4ac-488b9d099a74"
+                    }
+                ]
+            },
+            {
+                "process": "f59c9106-16a8-47f8-b681-490d23ee09de",
+                "inputs": [
+                    "13eab62e-0038-4997-aeab-aa3192cc090e"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "3f193e72-8efe-4c2a-ace1-79140ca36477",
+                    "078b71eb-220a-43e5-a0fc-4f231e90f85f"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "dc19bb22-ae7b-431b-9b8b-7b49799a8fcd"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "461851b8-55a5-4ae6-a52a-5bca71a00beb"
+                    }
+                ]
+            },
+            {
+                "process": "a03f7164-419b-4792-9a52-e6dda08b85bc",
+                "inputs": [
+                    "4ccd163e-a630-4ede-bc0c-336ba044b783"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "13eab62e-0038-4997-aeab-aa3192cc090e"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "57d2c83d-cd8b-44c9-9644-c3475a44b0a7",
+                "inputs": [
+                    "92254a9e-3a14-4760-b229-d914f3e8973f"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "4ccd163e-a630-4ede-bc0c-336ba044b783"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            },
+            {
+                "process": "8b1f44be-7eaa-4030-b6c5-697c5fc388eb",
+                "inputs": [
+                    "39d1a24f-1785-476d-9c04-065be917e3ff"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "92254a9e-3a14-4760-b229-d914f3e8973f"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "79f7c6ac-ada8-4c17-86ec-e73e87b94374"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "5d9fc5a2-5516-4205-9d6e-8d0d674f146f"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
index 1368f8265..caff9c466 100644
--- a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
+++ b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
@@ -743,72 +743,72 @@
                 "submission_date": "2018-09-13T18:05:04.998Z",
                 "update_date": "2018-09-13T18:41:19.322Z"
             }
-        },
-        "links.json": {
-            "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.1/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.1",
-            "links": [
-                {
-                    "process": "72732ed3-7b71-47df-bcec-c765ef7ea758",
-                    "inputs": [
-                        "0037c9eb-8038-432f-8d9d-13ee094e54ab",
-                        "aaaaaaaa-8038-432f-8d9d-13ee094e54ab"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "6c946b6c-040e-45cc-9114-a8b1454c8d20",
-                        "c86e42d7-854a-479b-a627-6be1b49c980c"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "0076f0aa-14c6-4cb9-93f8-97229787be21"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "362d9c34-f5c0-4906-955b-61ba0aac58cc"
-                        }
-                    ]
-                },
-                {
-                    "process": "6d77eef9-96cf-410e-8bbc-a83430267b61",
-                    "inputs": [
-                        "b4e55fe1-7bab-44ba-a81d-3d8cb3873244",
-                        "aaaaaaaa-7bab-44ba-a81d-3d8cb3873244"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "0037c9eb-8038-432f-8d9d-13ee094e54ab",
-                        "aaaaaaaa-8038-432f-8d9d-13ee094e54ab"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "40056e47-131d-4c6e-a884-a927bfccf8ce"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "d3287615-b97a-4984-a8cf-30a1c30e4773"
-                        }
-                    ]
-                },
-                {
-                    "process": "c0f05fdb-8375-4c39-adba-24a63c004b9d",
-                    "inputs": [
-                        "89b50434-f831-4e15-a8c0-0d57e6baa94c"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "b4e55fe1-7bab-44ba-a81d-3d8cb3873244",
-                        "aaaaaaaa-7bab-44ba-a81d-3d8cb3873244"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": []
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "http://schema.staging.data.humancellatlas.org/system/1.1.1/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.1",
+        "links": [
+            {
+                "process": "72732ed3-7b71-47df-bcec-c765ef7ea758",
+                "inputs": [
+                    "0037c9eb-8038-432f-8d9d-13ee094e54ab",
+                    "aaaaaaaa-8038-432f-8d9d-13ee094e54ab"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "6c946b6c-040e-45cc-9114-a8b1454c8d20",
+                    "c86e42d7-854a-479b-a627-6be1b49c980c"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "0076f0aa-14c6-4cb9-93f8-97229787be21"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "362d9c34-f5c0-4906-955b-61ba0aac58cc"
+                    }
+                ]
+            },
+            {
+                "process": "6d77eef9-96cf-410e-8bbc-a83430267b61",
+                "inputs": [
+                    "b4e55fe1-7bab-44ba-a81d-3d8cb3873244",
+                    "aaaaaaaa-7bab-44ba-a81d-3d8cb3873244"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "0037c9eb-8038-432f-8d9d-13ee094e54ab",
+                    "aaaaaaaa-8038-432f-8d9d-13ee094e54ab"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "40056e47-131d-4c6e-a884-a927bfccf8ce"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "d3287615-b97a-4984-a8cf-30a1c30e4773"
+                    }
+                ]
+            },
+            {
+                "process": "c0f05fdb-8375-4c39-adba-24a63c004b9d",
+                "inputs": [
+                    "89b50434-f831-4e15-a8c0-0d57e6baa94c"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "b4e55fe1-7bab-44ba-a81d-3d8cb3873244",
+                    "aaaaaaaa-7bab-44ba-a81d-3d8cb3873244"
+                ],
+                "output_type": "biomaterial",
+                "protocols": []
+            }
+        ]
     }
 }
diff --git a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
index b7df8b085..90063e3b0 100644
--- a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
+++ b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
@@ -1389,227 +1389,227 @@
                 "submission_date": "2019-02-14T18:29:42.635Z",
                 "update_date": "2019-02-14T18:29:48.758Z"
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.staging.data.humancellatlas.org/system/1.1.5/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.5",
-            "links": [
-                {
-                    "process": "4b6534a8-7fe7-4792-9ae9-7e87effe458b",
-                    "inputs": [
-                        "7df5d656-43cb-49f9-b81d-86cca3c44a65",
-                        "acd7d986-73ab-4d0b-9ead-377f3a2d646d",
-                        "f9a78d6a-7c80-4c45-bedf-4bc152dc172d"
-                    ],
-                    "input_type": "file",
-                    "outputs": [
-                        "bd1307b9-70b5-49e4-8e02-9d4ca0d64747",
-                        "cf3453a3-68fb-4156-bc3e-0f08f7e6512c",
-                        "234b0359-3853-4df4-898f-5182f698d48b",
-                        "d95392c5-1958-4825-9076-2a9c130c53f3",
-                        "b9609367-7006-4055-8815-1bad881a1502",
-                        "ebb2ec91-2cd0-4ec4-ba2b-5a6d6630bc5a",
-                        "1ab612ca-2a5a-4443-8004-bb5f0f784c67",
-                        "34c64244-d3ed-4841-84b7-aa4cbb9d794b",
-                        "71710439-3864-4fc6-bc48-ca2ac90f7ccf",
-                        "2ab5242e-f118-48e3-afe5-c2287fa2e2b1",
-                        "6da39577-256d-43fd-97c4-a3bedaa54273",
-                        "86a93e19-eb89-4c27-8b64-006f96bb2c83",
-                        "0f858ddb-6d93-404e-95fd-0c200921dd40"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "analysis_protocol",
-                            "protocol_id": "71470c53-1b86-4e6d-9707-55a0f70745a4"
-                        }
-                    ]
-                },
-                {
-                    "process": "67be2852-4657-43ce-a4eb-a323de228355",
-                    "inputs": [
-                        "a9ae9936-c11b-4195-b63a-fa6cb9c78e4c"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "7df5d656-43cb-49f9-b81d-86cca3c44a65",
-                        "acd7d986-73ab-4d0b-9ead-377f3a2d646d",
-                        "f9a78d6a-7c80-4c45-bedf-4bc152dc172d"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "b7519a0c-957e-48b5-a416-a7c1115d2963"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "f34c4543-4f98-49ce-b8a0-798ec96d5059"
-                        }
-                    ]
-                },
-                {
-                    "process": "10b0325b-45cc-4f27-929c-30e46fec23b6",
-                    "inputs": [
-                        "58c60e15-e07c-4875-ac34-f026d6912f1c"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "a9ae9936-c11b-4195-b63a-fa6cb9c78e4c"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "0fa5708b-b5fb-4cf6-becb-ad48f3f8e7fa"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
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-                        "acd7d986-73ab-4d0b-9ead-377f3a2d646d",
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-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "58c60e15-e07c-4875-ac34-f026d6912f1c"
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-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
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-                    ]
-                }
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+                "process": "4b6534a8-7fe7-4792-9ae9-7e87effe458b",
+                "inputs": [
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+                    "acd7d986-73ab-4d0b-9ead-377f3a2d646d",
+                    "f9a78d6a-7c80-4c45-bedf-4bc152dc172d"
+                ],
+                "input_type": "file",
+                "outputs": [
+                    "bd1307b9-70b5-49e4-8e02-9d4ca0d64747",
+                    "cf3453a3-68fb-4156-bc3e-0f08f7e6512c",
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+                    "86a93e19-eb89-4c27-8b64-006f96bb2c83",
+                    "0f858ddb-6d93-404e-95fd-0c200921dd40"
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+                    {
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+                        "protocol_id": "71470c53-1b86-4e6d-9707-55a0f70745a4"
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+                "process": "67be2852-4657-43ce-a4eb-a323de228355",
+                "inputs": [
+                    "a9ae9936-c11b-4195-b63a-fa6cb9c78e4c"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "7df5d656-43cb-49f9-b81d-86cca3c44a65",
+                    "acd7d986-73ab-4d0b-9ead-377f3a2d646d",
+                    "f9a78d6a-7c80-4c45-bedf-4bc152dc172d"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "b7519a0c-957e-48b5-a416-a7c1115d2963"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "f34c4543-4f98-49ce-b8a0-798ec96d5059"
+                    }
+                ]
+            },
+            {
+                "process": "10b0325b-45cc-4f27-929c-30e46fec23b6",
+                "inputs": [
+                    "58c60e15-e07c-4875-ac34-f026d6912f1c"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "a9ae9936-c11b-4195-b63a-fa6cb9c78e4c"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "0fa5708b-b5fb-4cf6-becb-ad48f3f8e7fa"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "469fa0db-f00b-4352-a2e2-753733a38e8b"
+                    }
+                ]
+            },
+            {
+                "process": "85b60548-5e15-4efa-8baa-966f0de7d11c",
+                "inputs": [
+                    "fad95a8a-4156-4631-95d4-a1c99b001dbd"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "58c60e15-e07c-4875-ac34-f026d6912f1c"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "c5d77e53-9016-4ed8-96ca-ad0eeb355d3a"
+                    }
+                ]
+            },
+            {
+                "process": "67be2852-4657-43ce-a4eb-a323de228355",
+                "inputs": [
+                    "a9ae9936-c11b-4195-b63a-fa6cb9c78e4c"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "7df5d656-43cb-49f9-b81d-86cca3c44a65",
+                    "acd7d986-73ab-4d0b-9ead-377f3a2d646d",
+                    "f9a78d6a-7c80-4c45-bedf-4bc152dc172d"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "b7519a0c-957e-48b5-a416-a7c1115d2963"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "f34c4543-4f98-49ce-b8a0-798ec96d5059"
+                    }
+                ]
+            },
+            {
+                "process": "10b0325b-45cc-4f27-929c-30e46fec23b6",
+                "inputs": [
+                    "58c60e15-e07c-4875-ac34-f026d6912f1c"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "a9ae9936-c11b-4195-b63a-fa6cb9c78e4c"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "0fa5708b-b5fb-4cf6-becb-ad48f3f8e7fa"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "469fa0db-f00b-4352-a2e2-753733a38e8b"
+                    }
+                ]
+            },
+            {
+                "process": "85b60548-5e15-4efa-8baa-966f0de7d11c",
+                "inputs": [
+                    "fad95a8a-4156-4631-95d4-a1c99b001dbd"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "58c60e15-e07c-4875-ac34-f026d6912f1c"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "c5d77e53-9016-4ed8-96ca-ad0eeb355d3a"
+                    }
+                ]
+            },
+            {
+                "process": "67be2852-4657-43ce-a4eb-a323de228355",
+                "inputs": [
+                    "a9ae9936-c11b-4195-b63a-fa6cb9c78e4c"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "7df5d656-43cb-49f9-b81d-86cca3c44a65",
+                    "acd7d986-73ab-4d0b-9ead-377f3a2d646d",
+                    "f9a78d6a-7c80-4c45-bedf-4bc152dc172d"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "b7519a0c-957e-48b5-a416-a7c1115d2963"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "f34c4543-4f98-49ce-b8a0-798ec96d5059"
+                    }
+                ]
+            },
+            {
+                "process": "10b0325b-45cc-4f27-929c-30e46fec23b6",
+                "inputs": [
+                    "58c60e15-e07c-4875-ac34-f026d6912f1c"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "a9ae9936-c11b-4195-b63a-fa6cb9c78e4c"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "0fa5708b-b5fb-4cf6-becb-ad48f3f8e7fa"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "469fa0db-f00b-4352-a2e2-753733a38e8b"
+                    }
+                ]
+            },
+            {
+                "process": "85b60548-5e15-4efa-8baa-966f0de7d11c",
+                "inputs": [
+                    "fad95a8a-4156-4631-95d4-a1c99b001dbd"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "58c60e15-e07c-4875-ac34-f026d6912f1c"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "c5d77e53-9016-4ed8-96ca-ad0eeb355d3a"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
index acabe1388..da70bd714 100644
--- a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
+++ b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
@@ -7208,5144 +7208,6 @@
         }
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@@ -13222,84 +8084,258 @@
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@@ -13309,16 +8345,16 @@
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@@ -13328,17 +8364,16 @@
                         "text": "DCP/2-generated matrix"
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@@ -13348,42 +8383,48 @@
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+                    "project_role": {
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+                    "laboratory": "Institute of Cellular Medicine",
+                    "address": "Newcastle upon Tyne, NE2 4HH",
+                    "country": "UK",
+                    "corresponding_contributor": true,
+                    "project_role": {
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+                        "ontology": "EFO:0009736",
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+                    "country": "UK",
+                    "corresponding_contributor": false,
+                    "project_role": {
+                        "text": "Human Cell Atlas wrangler",
+                        "ontology": "EFO:0009737",
+                        "ontology_label": "data curator"
+                    },
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+                    "address": "Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA",
+                    "country": "UK",
+                    "corresponding_contributor": false,
+                    "project_role": {
+                        "text": "ArrayExpress Data curator",
+                        "ontology": "EFO:0009737",
+                        "ontology_label": "data curator"
+                    }
+                }
+            ],
+            "publications": [
+                {
+                    "authors": [
+                        "Popescu D-M",
+                        "Botting RA",
+                        "Stephenson E",
+                        "Green K",
+                        "Jardine L",
+                        "Calderbank EF",
+                        "Efremova M",
+                        "Acres M",
+                        "Maunder D",
+                        "Vegh P",
+                        "Goh I",
+                        "Gitton Y",
+                        "Park J",
+                        "Polanski K",
+                        "Vento-Tormo R",
+                        "Miao Z",
+                        "Rowell R",
+                        "McDonald D",
+                        "Fletcher J",
+                        "Dixon D",
+                        "Poyner E",
+                        "Reynolds G",
+                        "Mather M",
+                        "Moldovan C",
+                        "Mamanova L",
+                        "Greig F",
+                        "Young M",
+                        "Meyer K",
+                        "Lisgo S",
+                        "Bacardit J",
+                        "Fuller A",
+                        "Millar B",
+                        "Innes B",
+                        "Lindsay S",
+                        "Stubbington MJT",
+                        "Kowalczyk MS",
+                        "Li B",
+                        "Ashenbrg O",
+                        "Tabaka M",
+                        "Dionne D",
+                        "Tickle TL",
+                        "Slyper M",
+                        "Rozenblatt-Rosen O",
+                        "Filby A",
+                        "Villani A-C",
+                        "Roy A",
+                        "Regev A",
+                        "Chedotal A",
+                        "Roberts I",
+                        "G\u00f6ttgens B",
+                        "Laurenti E",
+                        "Behjati S",
+                        "Teichmann SA",
+                        "Haniffa M"
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@@ -14152,11 +11114,11 @@
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@@ -14164,11 +11126,11 @@
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@@ -14176,11 +11138,11 @@
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@@ -14188,11 +11150,11 @@
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@@ -14200,11 +11162,11 @@
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@@ -14212,47 +11174,47 @@
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                     "task_name": "PreUMISort",
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@@ -14260,11 +11222,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/2096cc65-c180-45f2-93b7-fcc5c21db3a1/call-RunEmptyDrops/stderr",
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                     "memory": "15.625 GB",
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-                    "stop_time": "2021-02-09T07:22:50.470Z",
+                    "start_time": "2021-02-09T07:25:30.990Z",
+                    "stop_time": "2021-02-09T07:36:12.306Z",
                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -14272,11 +11234,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/2096cc65-c180-45f2-93b7-fcc5c21db3a1/call-StarAlign/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/2096cc65-c180-45f2-93b7-fcc5c21db3a1/call-StarAlign/shard-0/stdout",
                     "memory": "36.5234375 GB",
-                    "start_time": "2021-02-08T21:15:01.766Z",
-                    "stop_time": "2021-02-08T22:06:44.520Z",
+                    "start_time": "2021-02-08T21:11:33.616Z",
+                    "stop_time": "2021-02-08T23:17:50.324Z",
                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -14284,11 +11246,11 @@
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@@ -14296,36 +11258,36 @@
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+                    "start_time": "2021-02-08T21:11:24.403Z",
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                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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-            "timestamp_start_utc": "2021-02-08T21:12:25.667Z",
-            "timestamp_stop_utc": "2021-02-09T08:53:55.314Z",
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             "type": {
                 "text": "analysis"
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         },
-        "analysis_process_1.json": {
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             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_3c6fddd8-d7d5-4b6a-96ec-7ff0884bc7fa']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -14333,7 +11295,7 @@
                 },
                 {
                     "parameter_name": "input_id",
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+                    "parameter_value": "1d732738-9b3b-4393-920a-a3dd2ff6f7e1"
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                 {
                     "parameter_name": "tar_star_reference",
@@ -14353,10 +11315,10 @@
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             ],
             "process_core": {
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+                "process_id": "20eaba77-49c4-4d9e-9e82-fb6351a9012a"
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@@ -14368,11 +11330,11 @@
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@@ -14380,11 +11342,11 @@
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@@ -14392,23 +11354,23 @@
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                 {
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@@ -14416,11 +11378,11 @@
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@@ -14428,11 +11390,11 @@
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+                    "start_time": "2021-02-08T21:11:21.883Z",
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@@ -14440,11 +11402,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/20eaba77-49c4-4d9e-9e82-fb6351a9012a/call-GeneSortBam/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/20eaba77-49c4-4d9e-9e82-fb6351a9012a/call-GeneSortBam/shard-0/stdout",
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-                    "stop_time": "2021-02-09T06:55:38.317Z",
+                    "start_time": "2021-02-09T06:05:35.675Z",
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                     "task_name": "GeneSortBam",
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@@ -14452,11 +11414,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/20eaba77-49c4-4d9e-9e82-fb6351a9012a/call-MergeCellMetrics/stderr",
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-                    "start_time": "2021-02-09T08:17:17.020Z",
-                    "stop_time": "2021-02-09T08:22:59.307Z",
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@@ -14464,11 +11426,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/20eaba77-49c4-4d9e-9e82-fb6351a9012a/call-MergeCountFiles/stderr",
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@@ -14476,11 +11438,11 @@
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                     "task_name": "MergeGeneMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -14488,11 +11450,11 @@
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+                    "stop_time": "2021-02-09T08:10:16.250Z",
                     "task_name": "MergeSorted",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -14500,11 +11462,11 @@
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                     "task_name": "ModifyGtf",
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@@ -14512,11 +11474,11 @@
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                     "memory": "18 GB",
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+                    "stop_time": "2021-02-09T07:29:34.252Z",
                     "task_name": "OptimusLoomGeneration",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -14524,11 +11486,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/20eaba77-49c4-4d9e-9e82-fb6351a9012a/call-PreCountSort/shard-0/stderr",
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                     "memory": "8.056640625 GB",
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                     "task_name": "PreCountSort",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -14536,11 +11498,11 @@
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                     "memory": "8.056640625 GB",
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                     "task_name": "PreMergeSort",
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@@ -14548,11 +11510,11 @@
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                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T03:46:47.208Z",
-                    "stop_time": "2021-02-09T05:48:05.698Z",
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+                    "stop_time": "2021-02-09T05:45:40.262Z",
                     "task_name": "PreUMISort",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -14560,11 +11522,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/20eaba77-49c4-4d9e-9e82-fb6351a9012a/call-RunEmptyDrops/stderr",
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                     "memory": "15.625 GB",
-                    "start_time": "2021-02-09T08:06:22.120Z",
-                    "stop_time": "2021-02-09T08:17:44.307Z",
+                    "start_time": "2021-02-09T06:32:17.308Z",
+                    "stop_time": "2021-02-09T06:42:19.254Z",
                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -14572,11 +11534,11 @@
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                     "docker_image": "quay.io/humancellatlas/secondary-analysis-star:v0.2.2-2.5.3a-40ead6e",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/20eaba77-49c4-4d9e-9e82-fb6351a9012a/call-StarAlign/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/20eaba77-49c4-4d9e-9e82-fb6351a9012a/call-StarAlign/shard-0/stdout",
                     "memory": "36.5234375 GB",
-                    "start_time": "2021-02-08T21:11:32.638Z",
-                    "stop_time": "2021-02-09T00:51:20.333Z",
+                    "start_time": "2021-02-08T19:06:12.755Z",
+                    "stop_time": "2021-02-09T02:43:22.275Z",
                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -14584,11 +11546,11 @@
                     "cpus": 1,
                     "disk_size": "local-disk 25 HDD",
                     "docker_image": "quay.io/humancellatlas/secondary-analysis-dropseqtools:v0.2.2-1.13",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/20eaba77-49c4-4d9e-9e82-fb6351a9012a/call-TagGenes/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/20eaba77-49c4-4d9e-9e82-fb6351a9012a/call-TagGenes/shard-0/stdout",
                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T00:51:21.819Z",
-                    "stop_time": "2021-02-09T02:05:42.307Z",
+                    "start_time": "2021-02-09T02:43:24.306Z",
+                    "stop_time": "2021-02-09T05:33:55.253Z",
                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -14596,36 +11558,36 @@
                     "cpus": 1,
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                     "docker_image": "ubuntu:18.04",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/20eaba77-49c4-4d9e-9e82-fb6351a9012a/call-checkOptimusInput/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/20eaba77-49c4-4d9e-9e82-fb6351a9012a/call-checkOptimusInput/stdout",
                     "memory": "1 GB",
-                    "start_time": "2021-02-08T21:11:24.409Z",
-                    "stop_time": "2021-02-08T21:11:38.623Z",
+                    "start_time": "2021-02-08T21:11:21.883Z",
+                    "stop_time": "2021-02-08T17:21:23.962Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 }
             ],
-            "timestamp_start_utc": "2021-02-08T21:11:17.162Z",
-            "timestamp_stop_utc": "2021-02-09T09:42:45.779Z",
+            "timestamp_start_utc": "2021-02-08T21:11:18.774Z",
+            "timestamp_stop_utc": "2021-02-09T08:10:17.385Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_2.json": {
+        "analysis_process_9.json": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
                 {
                     "parameter_name": "r1_fastq",
-                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_7174b07a-bbc1-4796-9071-a52800c2db12']"
+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_7e29e017-abc0-418b-a687-6f045dbb771a']"
                 },
                 {
                     "parameter_name": "r2_fastq",
-                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_746bffff-170c-441b-a24f-08b86f5a5d20']"
+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_cf1332d5-400f-4a8e-b180-a95a6deffb8d']"
                 },
                 {
                     "parameter_name": "i1_fastq",
-                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_38ef4491-9ec7-4149-8a67-70cf17488149']"
+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_da792aa3-34c0-4be2-bb8c-ea92ab43bc19']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -14633,7 +11595,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "232174af-3ebf-4b3b-97fd-35547950c4c8"
+                    "parameter_value": "27e030cc-b89e-41fc-b0c8-c3258a4b2c6e"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -14653,10 +11615,10 @@
                 }
             ],
             "process_core": {
-                "process_id": "0c75f376-4092-403f-8b91-dbb19b4fdf94"
+                "process_id": "21581af6-c4c4-4268-9d63-cf5a3a7f5058"
             },
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@@ -14666,85 +11628,85 @@
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@@ -14752,11 +11714,11 @@
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@@ -14764,11 +11726,11 @@
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@@ -14812,47 +11774,47 @@
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@@ -14872,23 +11834,23 @@
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@@ -14896,36 +11858,36 @@
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                     "task_name": "checkOptimusInput",
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-            "timestamp_start_utc": "2021-02-08T21:12:25.668Z",
-            "timestamp_stop_utc": "2021-02-09T09:59:36.787Z",
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+            "timestamp_stop_utc": "2021-02-09T10:43:51.581Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_3.json": {
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             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
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@@ -14933,7 +11895,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "b7914794-f8a7-4fba-bb5b-10536eac7d8b"
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                 {
                     "parameter_name": "tar_star_reference",
@@ -14953,10 +11915,10 @@
                 }
             ],
             "process_core": {
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+                "process_id": "223980cd-b247-415a-bb6d-41ed360837f2"
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             "provenance": {
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@@ -14968,11 +11930,11 @@
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                     "task_name": "CalculateCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -14980,23 +11942,23 @@
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                     "memory": "29.296875 GB",
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+                    "start_time": "2021-02-09T01:59:33.865Z",
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                     "task_name": "CalculateGeneMetrics",
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                 {
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@@ -15052,11 +12014,11 @@
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@@ -15064,11 +12026,11 @@
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@@ -15100,11 +12062,11 @@
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@@ -15112,11 +12074,11 @@
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+                    "stop_time": "2021-02-09T07:44:47.471Z",
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@@ -15124,11 +12086,11 @@
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@@ -15136,23 +12098,23 @@
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@@ -15172,11 +12134,11 @@
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@@ -15184,11 +12146,11 @@
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@@ -15196,36 +12158,36 @@
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-            "timestamp_start_utc": "2021-02-08T21:11:17.162Z",
-            "timestamp_stop_utc": "2021-02-09T09:43:51.889Z",
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             "type": {
                 "text": "analysis"
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         },
-        "analysis_process_4.json": {
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@@ -15233,7 +12195,7 @@
                 },
                 {
                     "parameter_name": "input_id",
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                 {
                     "parameter_name": "tar_star_reference",
@@ -15253,10 +12215,10 @@
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@@ -15268,35 +12230,35 @@
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@@ -15304,11 +12266,11 @@
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                     "task_name": "CorrectUMItools",
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@@ -15316,35 +12278,35 @@
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+                    "start_time": "2021-02-09T06:47:32.375Z",
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@@ -15352,11 +12314,11 @@
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@@ -15364,11 +12326,11 @@
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@@ -15376,11 +12338,11 @@
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@@ -15388,11 +12350,11 @@
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@@ -15400,11 +12362,11 @@
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@@ -15412,47 +12374,47 @@
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@@ -15460,11 +12422,11 @@
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-                    "stop_time": "2021-02-09T07:49:50.308Z",
+                    "start_time": "2021-02-09T07:15:41.865Z",
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                     "task_name": "RunEmptyDrops",
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@@ -15472,11 +12434,11 @@
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                     "memory": "36.5234375 GB",
-                    "start_time": "2021-02-08T21:11:32.604Z",
-                    "stop_time": "2021-02-08T21:16:25.648Z",
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+                    "stop_time": "2021-02-09T05:58:25.273Z",
                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -15484,11 +12446,11 @@
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                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -15496,36 +12458,36 @@
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                     "memory": "1 GB",
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+                    "start_time": "2021-02-08T17:21:06.277Z",
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                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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-            "timestamp_start_utc": "2021-02-08T21:11:17.160Z",
-            "timestamp_stop_utc": "2021-02-09T09:19:22.078Z",
+            "timestamp_start_utc": "2021-02-08T21:12:19.623Z",
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             "type": {
                 "text": "analysis"
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         },
-        "analysis_process_5.json": {
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             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
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                 {
                     "parameter_name": "whitelist",
@@ -15533,7 +12495,7 @@
                 },
                 {
                     "parameter_name": "input_id",
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+                    "parameter_value": "536ba4f7-6694-4a31-8df1-0e6668ed10da"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -15553,10 +12515,10 @@
                 }
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             "process_core": {
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+                "process_id": "39c38ab6-dd8a-4098-87a8-8a861d55b7fb"
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                 "submission_date": "2021-02-09T01:30:00.000000Z"
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@@ -15568,47 +12530,47 @@
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@@ -15616,35 +12578,35 @@
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+                    "start_time": "2021-02-09T07:09:01.239Z",
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                     "task_name": "GeneSortBam",
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@@ -15652,11 +12614,11 @@
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@@ -15664,11 +12626,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/39c38ab6-dd8a-4098-87a8-8a861d55b7fb/call-MergeCountFiles/stderr",
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@@ -15676,11 +12638,11 @@
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@@ -15688,11 +12650,11 @@
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@@ -15700,11 +12662,11 @@
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@@ -15712,47 +12674,47 @@
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@@ -15760,11 +12722,11 @@
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                     "memory": "15.625 GB",
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                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -15772,11 +12734,11 @@
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                     "memory": "36.5234375 GB",
-                    "start_time": "2021-02-08T21:11:41.064Z",
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+                    "stop_time": "2021-02-09T02:33:53.348Z",
                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -15784,11 +12746,11 @@
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                     "memory": "8.056640625 GB",
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-                    "stop_time": "2021-02-09T05:31:20.334Z",
+                    "start_time": "2021-02-09T02:33:54.520Z",
+                    "stop_time": "2021-02-09T05:30:44.334Z",
                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -15796,36 +12758,56 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/39c38ab6-dd8a-4098-87a8-8a861d55b7fb/call-checkOptimusInput/stderr",
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                     "memory": "1 GB",
-                    "start_time": "2021-02-08T21:11:24.405Z",
-                    "stop_time": "2021-02-08T21:11:24.653Z",
+                    "start_time": "2021-02-08T21:11:24.404Z",
+                    "stop_time": "2021-02-08T21:11:25.620Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 }
             ],
-            "timestamp_start_utc": "2021-02-08T21:11:17.166Z",
-            "timestamp_stop_utc": "2021-02-09T09:24:51.538Z",
+            "timestamp_start_utc": "2021-02-08T21:11:17.161Z",
+            "timestamp_stop_utc": "2021-02-09T09:14:30.429Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_6.json": {
+        "analysis_process_13.json": {
+            "analysis_run_type": "run",
+            "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
+            "inputs": [],
+            "process_core": {
+                "process_id": "46dc43b4-19e7-475f-a015-157436454de4"
+            },
+            "provenance": {
+                "document_id": "46dc43b4-19e7-475f-a015-157436454de4",
+                "submission_date": "2021-02-09T01:30:00.000000Z"
+            },
+            "reference_files": [],
+            "schema_type": "process",
+            "tasks": [],
+            "timestamp_start_utc": "2021-02-16T04:18:18.000000Z",
+            "timestamp_stop_utc": "2021-02-16T04:18:18.000000Z",
+            "type": {
+                "text": "analysis; merge matrices"
+            }
+        },
+        "analysis_process_14.json": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
                 {
                     "parameter_name": "r1_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_a8b799b5-daf4-44ae-87f6-fdd330abd6f8']"
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                 },
                 {
                     "parameter_name": "whitelist",
@@ -15833,7 +12815,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "3381994d-5624-4f5f-a574-01ad099c448c"
+                    "parameter_value": "e23d96b7-a271-403e-a29e-b2bdb1949070"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -15853,10 +12835,10 @@
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+                "process_id": "4ae55a6b-6e40-4300-b2a7-7e8c72c285de"
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@@ -15868,23 +12850,23 @@
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@@ -15892,11 +12874,11 @@
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@@ -15904,11 +12886,11 @@
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@@ -15916,23 +12898,23 @@
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@@ -15940,11 +12922,11 @@
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@@ -15952,11 +12934,11 @@
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@@ -15964,11 +12946,11 @@
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@@ -15976,11 +12958,11 @@
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@@ -15988,11 +12970,11 @@
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+                    "start_time": "2021-02-09T05:59:17.305Z",
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                     "task_name": "MergeSorted",
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@@ -16000,11 +12982,11 @@
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-                    "start_time": "2021-02-08T21:11:24.421Z",
-                    "stop_time": "2021-02-08T21:11:24.797Z",
+                    "start_time": "2021-02-08T21:12:28.752Z",
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                     "task_name": "ModifyGtf",
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@@ -16012,11 +12994,11 @@
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@@ -16024,11 +13006,11 @@
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@@ -16060,11 +13042,11 @@
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@@ -16072,11 +13054,11 @@
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                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -16084,11 +13066,11 @@
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+                    "start_time": "2021-02-08T21:17:54.614Z",
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                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -16096,36 +13078,36 @@
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                     "memory": "1 GB",
-                    "start_time": "2021-02-08T21:11:24.404Z",
-                    "stop_time": "2021-02-08T21:11:48.591Z",
+                    "start_time": "2021-02-08T21:12:28.751Z",
+                    "stop_time": "2021-02-08T21:14:59.833Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 }
             ],
-            "timestamp_start_utc": "2021-02-08T21:11:17.161Z",
-            "timestamp_stop_utc": "2021-02-09T09:06:09.558Z",
+            "timestamp_start_utc": "2021-02-08T21:12:25.709Z",
+            "timestamp_stop_utc": "2021-02-09T07:43:03.628Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_7.json": {
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             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_4cccdd0c-adeb-4d23-8abb-cb9f91f9d4fc']"
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_a03cb9df-dc59-4a0b-b44c-82d774fca5a3']"
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_9d24fef4-d7ac-42bd-8754-376642d97679']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -16133,7 +13115,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "37925a3b-3bce-4876-bb29-745922b2c972"
+                    "parameter_value": "cfa1e5da-607e-49b6-aa0d-8f43702b971f"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -16153,10 +13135,10 @@
                 }
             ],
             "process_core": {
-                "process_id": "2096cc65-c180-45f2-93b7-fcc5c21db3a1"
+                "process_id": "4c1d363b-0560-49f2-addd-aaa879db3d30"
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             "provenance": {
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+                "document_id": "4c1d363b-0560-49f2-addd-aaa879db3d30",
                 "submission_date": "2021-02-09T01:30:00.000000Z"
             },
             "reference_files": [
@@ -16168,23 +13150,23 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-CalculateCellMetrics/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-CalculateCellMetrics/shard-0/stdout",
                     "memory": "43.9453125 GB",
-                    "start_time": "2021-02-09T06:04:24.659Z",
-                    "stop_time": "2021-02-09T06:44:08.322Z",
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+                    "stop_time": "2021-02-09T05:16:38.320Z",
                     "task_name": "CalculateCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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                 {
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-CalculateGeneMetrics/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-CalculateGeneMetrics/shard-0/stdout",
                     "memory": "29.296875 GB",
-                    "start_time": "2021-02-09T06:01:54.549Z",
-                    "stop_time": "2021-02-09T06:34:35.317Z",
+                    "start_time": "2021-02-09T03:32:51.631Z",
+                    "stop_time": "2021-02-09T05:52:59.336Z",
                     "task_name": "CalculateGeneMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -16192,11 +13174,11 @@
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@@ -16264,11 +13246,11 @@
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@@ -16300,11 +13282,11 @@
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@@ -16312,11 +13294,11 @@
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+                    "stop_time": "2021-02-09T08:44:50.311Z",
                     "task_name": "OptimusLoomGeneration",
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@@ -16324,11 +13306,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-PreCountSort/shard-0/stderr",
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@@ -16336,23 +13318,23 @@
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@@ -16360,11 +13342,11 @@
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                     "task_name": "RunEmptyDrops",
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@@ -16372,11 +13354,11 @@
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@@ -16384,11 +13366,11 @@
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+                    "start_time": "2021-02-08T21:59:39.581Z",
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                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -16396,36 +13378,36 @@
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                     "memory": "1 GB",
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+                    "start_time": "2021-02-08T21:11:24.406Z",
+                    "stop_time": "2021-02-08T21:11:49.539Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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             ],
-            "timestamp_start_utc": "2021-02-08T21:11:17.160Z",
-            "timestamp_stop_utc": "2021-02-09T08:26:01.299Z",
+            "timestamp_start_utc": "2021-02-08T21:11:17.161Z",
+            "timestamp_stop_utc": "2021-02-09T10:03:40.170Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_8.json": {
+        "analysis_process_16.json": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_6e664e9a-7344-4809-a48d-4aff34415976']"
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_7a17314a-d973-4b75-a978-8935b3a71e01']"
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_b99bed54-1eda-46d1-9cef-bf42af726cdd']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -16433,7 +13415,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "1d732738-9b3b-4393-920a-a3dd2ff6f7e1"
+                    "parameter_value": "62a131e1-c415-460e-bc5b-75cca5d3323b"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -16453,10 +13435,10 @@
                 }
             ],
             "process_core": {
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+                "process_id": "58d03b27-9049-444e-a337-3491a5d715e1"
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             "provenance": {
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                 "submission_date": "2021-02-09T01:30:00.000000Z"
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@@ -16468,11 +13450,11 @@
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                     "task_name": "CalculateCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -16480,11 +13462,11 @@
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+                    "start_time": "2021-02-09T03:47:52.070Z",
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                     "task_name": "CalculateGeneMetrics",
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@@ -16492,23 +13474,23 @@
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                     "memory": "97.65625 GB",
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+                    "stop_time": "2021-02-09T02:24:35.331Z",
                     "task_name": "CellSortBam",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/58d03b27-9049-444e-a337-3491a5d715e1/call-CorrectUMItools/shard-0/stderr",
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                     "task_name": "CorrectUMItools",
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@@ -16516,23 +13498,23 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/58d03b27-9049-444e-a337-3491a5d715e1/call-CreateSparseCountMatrix/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/58d03b27-9049-444e-a337-3491a5d715e1/call-CreateSparseCountMatrix/shard-0/stdout",
                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T06:19:02.505Z",
-                    "stop_time": "2021-02-09T06:26:49.273Z",
+                    "start_time": "2021-02-09T02:17:55.071Z",
+                    "stop_time": "2021-02-09T03:42:08.333Z",
                     "task_name": "CreateSparseCountMatrix",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
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-                    "disk_size": "local-disk 606 HDD",
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@@ -16540,11 +13522,11 @@
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@@ -16552,11 +13534,11 @@
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@@ -16564,11 +13546,11 @@
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@@ -16576,11 +13558,11 @@
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@@ -16588,11 +13570,11 @@
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@@ -16600,11 +13582,11 @@
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@@ -16612,11 +13594,11 @@
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+                    "stop_time": "2021-02-09T08:30:08.309Z",
                     "task_name": "OptimusLoomGeneration",
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@@ -16624,11 +13606,11 @@
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@@ -16636,23 +13618,23 @@
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                 {
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-                    "stop_time": "2021-02-09T05:45:40.262Z",
+                    "start_time": "2021-02-08T22:12:01.379Z",
+                    "stop_time": "2021-02-08T23:40:35.334Z",
                     "task_name": "PreUMISort",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -16660,11 +13642,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/58d03b27-9049-444e-a337-3491a5d715e1/call-RunEmptyDrops/stderr",
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                     "memory": "15.625 GB",
-                    "start_time": "2021-02-09T06:32:17.308Z",
-                    "stop_time": "2021-02-09T06:42:19.254Z",
+                    "start_time": "2021-02-09T07:34:00.989Z",
+                    "stop_time": "2021-02-09T07:46:50.313Z",
                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -16672,11 +13654,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/58d03b27-9049-444e-a337-3491a5d715e1/call-StarAlign/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/58d03b27-9049-444e-a337-3491a5d715e1/call-StarAlign/shard-0/stdout",
                     "memory": "36.5234375 GB",
-                    "start_time": "2021-02-08T19:06:12.755Z",
-                    "stop_time": "2021-02-09T02:43:22.275Z",
+                    "start_time": "2021-02-08T21:11:29.657Z",
+                    "stop_time": "2021-02-08T21:13:50.553Z",
                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -16684,11 +13666,11 @@
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                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -16696,36 +13678,36 @@
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                     "memory": "1 GB",
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+                    "start_time": "2021-02-08T21:11:24.403Z",
+                    "stop_time": "2021-02-08T21:11:47.724Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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             ],
-            "timestamp_start_utc": "2021-02-08T21:11:18.774Z",
-            "timestamp_stop_utc": "2021-02-09T08:10:17.385Z",
+            "timestamp_start_utc": "2021-02-08T21:11:17.166Z",
+            "timestamp_stop_utc": "2021-02-09T09:12:00.459Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_9.json": {
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             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
                 {
                     "parameter_name": "r1_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_01b73e38-a2b2-4ec6-b4a0-831e1258c3ea']"
                 },
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                     "parameter_name": "r2_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_0e8d3673-5109-41ee-9092-8b79baa6d3b1']"
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                     "parameter_name": "i1_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_94f359a4-7b77-4eb1-b94a-703a35644886']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -16733,7 +13715,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "27e030cc-b89e-41fc-b0c8-c3258a4b2c6e"
+                    "parameter_value": "ded9b30e-12df-4998-846a-7cef685e4bd6"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -16753,10 +13735,10 @@
                 }
             ],
             "process_core": {
-                "process_id": "21581af6-c4c4-4268-9d63-cf5a3a7f5058"
+                "process_id": "725cbe75-92a1-46dc-862a-1b9d012e0fc1"
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             "provenance": {
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+                "document_id": "725cbe75-92a1-46dc-862a-1b9d012e0fc1",
                 "submission_date": "2021-02-09T01:30:00.000000Z"
             },
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@@ -16766,85 +13748,85 @@
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@@ -16852,11 +13834,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/725cbe75-92a1-46dc-862a-1b9d012e0fc1/call-MergeCellMetrics/stderr",
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+                    "stop_time": "2021-02-09T08:10:38.307Z",
                     "task_name": "MergeCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -16864,11 +13846,11 @@
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                     "task_name": "MergeCountFiles",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -16876,11 +13858,11 @@
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                     "task_name": "MergeGeneMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -16888,11 +13870,11 @@
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                     "task_name": "MergeSorted",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -16900,11 +13882,11 @@
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@@ -16912,47 +13894,47 @@
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+                    "stop_time": "2021-02-09T08:59:53.307Z",
                     "task_name": "OptimusLoomGeneration",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
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-                    "disk_size": "local-disk 203 HDD",
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                     "task_name": "PreUMISort",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -16960,35 +13942,35 @@
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                     "memory": "15.625 GB",
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+                    "stop_time": "2021-02-09T08:07:44.306Z",
                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
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-                    "disk_size": "local-disk 71 SSD",
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                     "memory": "36.5234375 GB",
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                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
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                     "docker_image": "quay.io/humancellatlas/secondary-analysis-dropseqtools:v0.2.2-1.13",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/725cbe75-92a1-46dc-862a-1b9d012e0fc1/call-TagGenes/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/725cbe75-92a1-46dc-862a-1b9d012e0fc1/call-TagGenes/shard-0/stdout",
                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T05:12:24.512Z",
-                    "stop_time": "2021-02-09T05:50:14.330Z",
+                    "start_time": "2021-02-09T00:44:52.001Z",
+                    "stop_time": "2021-02-09T01:46:35.318Z",
                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -16996,36 +13978,36 @@
                     "cpus": 1,
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                     "docker_image": "ubuntu:18.04",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/725cbe75-92a1-46dc-862a-1b9d012e0fc1/call-checkOptimusInput/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/725cbe75-92a1-46dc-862a-1b9d012e0fc1/call-checkOptimusInput/stdout",
                     "memory": "1 GB",
-                    "start_time": "2021-02-08T21:11:24.404Z",
-                    "stop_time": "2021-02-08T21:11:40.125Z",
+                    "start_time": "2021-02-08T21:11:24.403Z",
+                    "stop_time": "2021-02-08T21:11:28.080Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 }
             ],
-            "timestamp_start_utc": "2021-02-08T21:11:17.160Z",
-            "timestamp_stop_utc": "2021-02-09T10:43:51.581Z",
+            "timestamp_start_utc": "2021-02-08T21:11:17.167Z",
+            "timestamp_stop_utc": "2021-02-09T09:51:09.469Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_10.json": {
+        "analysis_process_18.json": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
                 {
                     "parameter_name": "r1_fastq",
-                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_aa0d9a26-ec62-433f-8c07-543ae8188389']"
+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_73a0e7a2-e7a5-43c7-8439-e6d2f3d3fd24']"
                 },
                 {
                     "parameter_name": "r2_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_0f549aae-515b-4504-9e85-07269eb59db0']"
                 },
                 {
                     "parameter_name": "i1_fastq",
-                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_54858ab1-fe9e-4891-97dd-bf5ada0b5bb6']"
+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_5e2dbfa6-a1fd-42de-9b00-184e6ba13c28']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -17033,7 +14015,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "10a02923-b945-43fe-97db-c984e06dc5a7"
+                    "parameter_value": "e7b60260-7ae4-4d5a-b1a4-51622467e4b3"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -17053,10 +14035,10 @@
                 }
             ],
             "process_core": {
-                "process_id": "223980cd-b247-415a-bb6d-41ed360837f2"
+                "process_id": "82c03181-f541-4770-8bad-5fb68bf221b2"
             },
             "provenance": {
-                "document_id": "223980cd-b247-415a-bb6d-41ed360837f2",
+                "document_id": "82c03181-f541-4770-8bad-5fb68bf221b2",
                 "submission_date": "2021-02-09T01:30:00.000000Z"
             },
             "reference_files": [
@@ -17066,49 +14048,49 @@
             "tasks": [
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                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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                     "task_name": "CorrectUMItools",
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@@ -17116,35 +14098,35 @@
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                     "task_name": "GeneSortBam",
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@@ -17152,11 +14134,11 @@
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                     "memory": "3.759765625 GB",
-                    "start_time": "2021-02-09T07:00:49.804Z",
-                    "stop_time": "2021-02-09T07:05:50.470Z",
+                    "start_time": "2021-02-09T08:01:23.269Z",
+                    "stop_time": "2021-02-09T08:06:20.307Z",
                     "task_name": "MergeCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -17164,11 +14146,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/82c03181-f541-4770-8bad-5fb68bf221b2/call-MergeCountFiles/stderr",
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-                    "start_time": "2021-02-09T06:46:31.734Z",
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+                    "start_time": "2021-02-09T07:41:22.779Z",
+                    "stop_time": "2021-02-09T07:47:05.314Z",
                     "task_name": "MergeCountFiles",
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@@ -17176,11 +14158,11 @@
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@@ -17188,11 +14170,11 @@
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-                    "start_time": "2021-02-09T06:38:23.074Z",
-                    "stop_time": "2021-02-09T08:10:41.467Z",
+                    "start_time": "2021-02-09T07:34:56.080Z",
+                    "stop_time": "2021-02-09T09:24:08.308Z",
                     "task_name": "MergeSorted",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -17200,11 +14182,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/82c03181-f541-4770-8bad-5fb68bf221b2/call-ModifyGtf/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/82c03181-f541-4770-8bad-5fb68bf221b2/call-ModifyGtf/stdout",
                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-08T21:12:28.752Z",
-                    "stop_time": "2021-02-08T21:15:05.882Z",
+                    "start_time": "2021-02-08T21:11:24.418Z",
+                    "stop_time": "2021-02-08T21:11:25.684Z",
                     "task_name": "ModifyGtf",
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@@ -17212,47 +14194,47 @@
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@@ -17260,11 +14242,11 @@
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@@ -17272,23 +14254,23 @@
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@@ -17296,36 +14278,36 @@
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-            "timestamp_start_utc": "2021-02-08T21:12:25.667Z",
-            "timestamp_stop_utc": "2021-02-09T08:10:43.263Z",
+            "timestamp_start_utc": "2021-02-08T21:11:17.167Z",
+            "timestamp_stop_utc": "2021-02-09T09:24:09.629Z",
             "type": {
                 "text": "analysis"
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         },
-        "analysis_process_11.json": {
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             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
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                 {
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@@ -17333,7 +14315,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "b1883730-3304-48c1-904b-eb90ab226168"
+                    "parameter_value": "951a8ffc-69c5-4f7c-8ee8-39b76171f630"
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                 {
                     "parameter_name": "tar_star_reference",
@@ -17353,10 +14335,10 @@
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+                "process_id": "98f74c7b-abd8-4adc-b68f-f68aa5d3e58c"
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             "provenance": {
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                 "submission_date": "2021-02-09T01:30:00.000000Z"
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@@ -17368,11 +14350,11 @@
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                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -17380,11 +14362,11 @@
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                     "memory": "29.296875 GB",
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-                    "stop_time": "2021-02-09T07:03:25.251Z",
+                    "start_time": "2021-02-09T05:51:37.070Z",
+                    "stop_time": "2021-02-09T06:24:38.318Z",
                     "task_name": "CalculateGeneMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -17392,11 +14374,11 @@
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                     "memory": "97.65625 GB",
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+                    "start_time": "2021-02-09T05:05:51.639Z",
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                     "task_name": "CellSortBam",
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@@ -17404,11 +14386,11 @@
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                     "task_name": "CorrectUMItools",
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@@ -17416,23 +14398,23 @@
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@@ -17440,11 +14422,11 @@
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@@ -17452,11 +14434,11 @@
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@@ -17464,11 +14446,11 @@
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@@ -17476,11 +14458,11 @@
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@@ -17488,11 +14470,11 @@
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@@ -17500,11 +14482,11 @@
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-                    "stop_time": "2021-02-08T21:21:54.502Z",
+                    "start_time": "2021-02-08T21:11:24.433Z",
+                    "stop_time": "2021-02-08T21:11:30.719Z",
                     "task_name": "ModifyGtf",
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@@ -17512,11 +14494,11 @@
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                     "memory": "18 GB",
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+                    "start_time": "2021-02-09T08:07:07.089Z",
+                    "stop_time": "2021-02-09T08:32:38.309Z",
                     "task_name": "OptimusLoomGeneration",
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                 },
@@ -17524,11 +14506,11 @@
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-                    "stop_time": "2021-02-09T06:47:31.257Z",
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                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -17536,23 +14518,23 @@
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-                    "start_time": "2021-02-09T06:35:11.736Z",
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@@ -17560,11 +14542,11 @@
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@@ -17572,23 +14554,23 @@
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@@ -17596,36 +14578,36 @@
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-            "timestamp_start_utc": "2021-02-08T21:12:19.623Z",
-            "timestamp_stop_utc": "2021-02-09T08:44:56.305Z",
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             "type": {
                 "text": "analysis"
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         },
-        "analysis_process_12.json": {
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                 {
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@@ -17633,7 +14615,7 @@
                 },
                 {
                     "parameter_name": "input_id",
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                 {
                     "parameter_name": "tar_star_reference",
@@ -17653,10 +14635,10 @@
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                 "submission_date": "2021-02-09T01:30:00.000000Z"
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@@ -17668,11 +14650,11 @@
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@@ -17680,11 +14662,11 @@
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@@ -17692,11 +14674,11 @@
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@@ -17704,11 +14686,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/997fecc1-cc72-4357-9a33-8aa2be30d96b/call-CorrectUMItools/shard-0/stderr",
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                     "task_name": "CorrectUMItools",
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@@ -17716,23 +14698,23 @@
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+                    "start_time": "2021-02-09T07:08:10.052Z",
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                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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                 {
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@@ -17740,11 +14722,11 @@
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                     "task_name": "GeneSortBam",
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@@ -17752,11 +14734,11 @@
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                     "task_name": "MergeCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -17764,11 +14746,11 @@
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@@ -17776,11 +14758,11 @@
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@@ -17788,11 +14770,11 @@
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@@ -17800,11 +14782,11 @@
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@@ -17812,11 +14794,11 @@
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+                    "stop_time": "2021-02-09T09:22:14.307Z",
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@@ -17824,11 +14806,11 @@
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@@ -17836,11 +14818,11 @@
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-                    "stop_time": "2021-02-09T07:09:44.316Z",
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@@ -17848,11 +14830,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/997fecc1-cc72-4357-9a33-8aa2be30d96b/call-PreUMISort/shard-0/stderr",
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                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T05:30:46.869Z",
-                    "stop_time": "2021-02-09T06:05:38.324Z",
+                    "start_time": "2021-02-09T05:34:26.162Z",
+                    "stop_time": "2021-02-09T06:07:59.331Z",
                     "task_name": "PreUMISort",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -17860,11 +14842,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/997fecc1-cc72-4357-9a33-8aa2be30d96b/call-RunEmptyDrops/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/997fecc1-cc72-4357-9a33-8aa2be30d96b/call-RunEmptyDrops/stdout",
                     "memory": "15.625 GB",
-                    "start_time": "2021-02-09T07:32:22.050Z",
-                    "stop_time": "2021-02-09T07:43:44.311Z",
+                    "start_time": "2021-02-09T07:42:00.523Z",
+                    "stop_time": "2021-02-09T07:52:53.309Z",
                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -17872,11 +14854,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/997fecc1-cc72-4357-9a33-8aa2be30d96b/call-StarAlign/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/997fecc1-cc72-4357-9a33-8aa2be30d96b/call-StarAlign/shard-0/stdout",
                     "memory": "36.5234375 GB",
-                    "start_time": "2021-02-08T21:11:33.662Z",
-                    "stop_time": "2021-02-09T02:33:53.348Z",
+                    "start_time": "2021-02-08T21:11:30.662Z",
+                    "stop_time": "2021-02-09T04:24:53.334Z",
                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -17884,11 +14866,11 @@
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             "type": {
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-            "type": {
-                "text": "analysis; merge matrices"
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@@ -17953,7 +14915,7 @@
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@@ -17973,10 +14935,10 @@
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@@ -18000,11 +14962,11 @@
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@@ -18012,11 +14974,11 @@
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@@ -18024,11 +14986,11 @@
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@@ -18036,23 +14998,23 @@
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@@ -18060,11 +15022,11 @@
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@@ -18072,11 +15034,11 @@
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@@ -18084,11 +15046,11 @@
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@@ -18108,11 +15070,11 @@
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@@ -18120,11 +15082,11 @@
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@@ -18144,11 +15106,11 @@
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@@ -18180,11 +15142,11 @@
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                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -18192,11 +15154,11 @@
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                     "memory": "36.5234375 GB",
-                    "start_time": "2021-02-08T21:15:04.826Z",
-                    "stop_time": "2021-02-08T21:17:53.476Z",
+                    "start_time": "2021-02-08T21:26:23.715Z",
+                    "stop_time": "2021-02-09T00:09:35.313Z",
                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -18204,11 +15166,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/a87c5838-140e-40f4-97b0-591aecbe1b3c/call-TagGenes/shard-0/stderr",
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                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-08T21:17:54.614Z",
-                    "stop_time": "2021-02-08T21:29:14.477Z",
+                    "start_time": "2021-02-09T00:09:36.910Z",
+                    "stop_time": "2021-02-09T03:56:59.322Z",
                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -18216,36 +15178,36 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/a87c5838-140e-40f4-97b0-591aecbe1b3c/call-checkOptimusInput/stderr",
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                     "memory": "1 GB",
-                    "start_time": "2021-02-08T21:12:28.751Z",
-                    "stop_time": "2021-02-08T21:14:59.833Z",
+                    "start_time": "2021-02-08T21:11:24.403Z",
+                    "stop_time": "2021-02-08T21:11:43.607Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 }
             ],
-            "timestamp_start_utc": "2021-02-08T21:12:25.709Z",
-            "timestamp_stop_utc": "2021-02-09T07:43:03.628Z",
+            "timestamp_start_utc": "2021-02-08T21:11:17.160Z",
+            "timestamp_stop_utc": "2021-02-09T09:39:55.259Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_15.json": {
+        "analysis_process_22.json": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
                 {
                     "parameter_name": "r1_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_509c3002-913e-4403-af5c-e9fdd912b383']"
                 },
                 {
                     "parameter_name": "r2_fastq",
-                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_a03cb9df-dc59-4a0b-b44c-82d774fca5a3']"
+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_0104fe7e-f505-4268-95e2-9b170c80b700']"
                 },
                 {
                     "parameter_name": "i1_fastq",
-                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_9d24fef4-d7ac-42bd-8754-376642d97679']"
+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_94040803-02b3-44a5-9a8a-0f068639032a']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -18253,7 +15215,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "cfa1e5da-607e-49b6-aa0d-8f43702b971f"
+                    "parameter_value": "b49fb5d4-6f31-4b7d-827e-bc09ed30a167"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -18273,10 +15235,10 @@
                 }
             ],
             "process_core": {
-                "process_id": "4c1d363b-0560-49f2-addd-aaa879db3d30"
+                "process_id": "b486e644-c56d-4209-b7c7-e56c527306b2"
             },
             "provenance": {
-                "document_id": "4c1d363b-0560-49f2-addd-aaa879db3d30",
+                "document_id": "b486e644-c56d-4209-b7c7-e56c527306b2",
                 "submission_date": "2021-02-09T01:30:00.000000Z"
             },
             "reference_files": [
@@ -18288,11 +15250,11 @@
                     "cpus": 1,
                     "disk_size": "local-disk 3 HDD",
                     "docker_image": "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11",
-                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-CalculateCellMetrics/shard-0/stderr",
-                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-CalculateCellMetrics/shard-0/stdout",
+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-CalculateCellMetrics/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-CalculateCellMetrics/shard-0/stdout",
                     "memory": "43.9453125 GB",
-                    "start_time": "2021-02-09T03:31:55.336Z",
-                    "stop_time": "2021-02-09T05:16:38.320Z",
+                    "start_time": "2021-02-09T05:56:52.230Z",
+                    "stop_time": "2021-02-09T06:33:44.309Z",
                     "task_name": "CalculateCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -18300,23 +15262,23 @@
                     "cpus": 1,
                     "disk_size": "local-disk 5 HDD",
                     "docker_image": "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11",
-                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-CalculateGeneMetrics/shard-0/stderr",
-                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-CalculateGeneMetrics/shard-0/stdout",
+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-CalculateGeneMetrics/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-CalculateGeneMetrics/shard-0/stdout",
                     "memory": "29.296875 GB",
-                    "start_time": "2021-02-09T03:32:51.631Z",
-                    "stop_time": "2021-02-09T05:52:59.336Z",
+                    "start_time": "2021-02-09T05:57:06.510Z",
+                    "stop_time": "2021-02-09T06:32:44.312Z",
                     "task_name": "CalculateGeneMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
                     "cpus": 2,
-                    "disk_size": "local-disk 8 HDD",
+                    "disk_size": "local-disk 9 HDD",
                     "docker_image": "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11",
-                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-CellSortBam/shard-0/stderr",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-CellSortBam/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-CellSortBam/shard-0/stdout",
                     "memory": "97.65625 GB",
-                    "start_time": "2021-02-09T01:59:36.502Z",
-                    "stop_time": "2021-02-09T03:31:53.333Z",
+                    "start_time": "2021-02-09T05:11:39.489Z",
+                    "stop_time": "2021-02-09T05:56:50.329Z",
                     "task_name": "CellSortBam",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -18324,11 +15286,11 @@
                     "cpus": 1,
                     "disk_size": "local-disk 56 HDD",
                     "docker_image": "quay.io/humancellatlas/secondary-analysis-umitools:0.0.1",
-                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-CorrectUMItools/shard-0/stderr",
-                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-CorrectUMItools/shard-0/stdout",
+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-CorrectUMItools/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-CorrectUMItools/shard-0/stdout",
                     "memory": "15.625 GB",
-                    "start_time": "2021-02-09T00:51:09.582Z",
-                    "stop_time": "2021-02-09T01:59:35.323Z",
+                    "start_time": "2021-02-09T03:19:01.119Z",
+                    "stop_time": "2021-02-09T05:11:38.334Z",
                     "task_name": "CorrectUMItools",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -18336,35 +15298,35 @@
                     "cpus": 1,
                     "disk_size": "local-disk 18 HDD",
                     "docker_image": "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11",
-                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-CreateSparseCountMatrix/shard-0/stderr",
-                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-CreateSparseCountMatrix/shard-0/stdout",
+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-CreateSparseCountMatrix/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-CreateSparseCountMatrix/shard-0/stdout",
                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T03:44:46.202Z",
-                    "stop_time": "2021-02-09T04:41:35.332Z",
+                    "start_time": "2021-02-09T05:56:07.350Z",
+                    "stop_time": "2021-02-09T06:21:59.310Z",
                     "task_name": "CreateSparseCountMatrix",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
                     "cpus": 16,
-                    "disk_size": "local-disk 709 HDD",
+                    "disk_size": "local-disk 600 HDD",
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-                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-FastqProcessing/stderr",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-FastqProcessing/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-FastqProcessing/stdout",
                     "memory": "39.0625 GB",
-                    "start_time": "2021-02-08T21:11:24.432Z",
-                    "stop_time": "2021-02-08T21:11:25.646Z",
+                    "start_time": "2021-02-08T21:11:24.418Z",
+                    "stop_time": "2021-02-08T21:11:25.666Z",
                     "task_name": "FastqProcessing",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
                     "cpus": 2,
-                    "disk_size": "local-disk 4 HDD",
+                    "disk_size": "local-disk 5 HDD",
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-                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-GeneSortBam/shard-0/stderr",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-GeneSortBam/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-GeneSortBam/shard-0/stdout",
                     "memory": "97.65625 GB",
-                    "start_time": "2021-02-09T01:59:36.502Z",
-                    "stop_time": "2021-02-09T03:32:50.367Z",
+                    "start_time": "2021-02-09T05:11:39.489Z",
+                    "stop_time": "2021-02-09T05:57:05.343Z",
                     "task_name": "GeneSortBam",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -18372,11 +15334,11 @@
                     "cpus": 1,
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                     "docker_image": "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11",
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-                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-MergeCellMetrics/stdout",
+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-MergeCellMetrics/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-MergeCellMetrics/stdout",
                     "memory": "3.759765625 GB",
-                    "start_time": "2021-02-09T07:58:31.913Z",
-                    "stop_time": "2021-02-09T08:03:53.307Z",
+                    "start_time": "2021-02-09T07:50:46.821Z",
+                    "stop_time": "2021-02-09T07:55:29.321Z",
                     "task_name": "MergeCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -18384,11 +15346,11 @@
                     "cpus": 1,
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                     "docker_image": "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11",
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-                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-MergeCountFiles/stdout",
+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-MergeCountFiles/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-MergeCountFiles/stdout",
                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T07:28:11.152Z",
-                    "stop_time": "2021-02-09T07:35:23.315Z",
+                    "start_time": "2021-02-09T07:32:07.719Z",
+                    "stop_time": "2021-02-09T07:37:08.308Z",
                     "task_name": "MergeCountFiles",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -18396,11 +15358,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-MergeGeneMetrics/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-MergeGeneMetrics/stdout",
                     "memory": "3.759765625 GB",
-                    "start_time": "2021-02-09T07:49:17.063Z",
-                    "stop_time": "2021-02-09T08:32:35.304Z",
+                    "start_time": "2021-02-09T07:42:01.530Z",
+                    "stop_time": "2021-02-09T08:06:35.310Z",
                     "task_name": "MergeGeneMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -18408,11 +15370,11 @@
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                     "docker_image": "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.3.3-1513176735",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-MergeSorted/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-MergeSorted/stdout",
                     "memory": "17.724609375 GB",
-                    "start_time": "2021-02-09T07:12:40.572Z",
-                    "stop_time": "2021-02-09T10:03:38.307Z",
+                    "start_time": "2021-02-09T07:24:31.639Z",
+                    "stop_time": "2021-02-09T09:09:59.309Z",
                     "task_name": "MergeSorted",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -18420,11 +15382,11 @@
                     "cpus": 1,
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                     "docker_image": "quay.io/humancellatlas/modify-gtf:0.1.0",
-                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/4c1d363b-0560-49f2-addd-aaa879db3d30/call-ModifyGtf/stderr",
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@@ -18432,47 +15394,47 @@
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+                    "start_time": "2021-02-09T08:06:36.399Z",
+                    "stop_time": "2021-02-09T08:32:53.310Z",
                     "task_name": "OptimusLoomGeneration",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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                 {
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@@ -18480,11 +15442,11 @@
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                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -18492,11 +15454,11 @@
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                     "memory": "36.5234375 GB",
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                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -18504,11 +15466,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-TagGenes/shard-0/stderr",
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-                    "start_time": "2021-02-08T21:59:39.581Z",
-                    "stop_time": "2021-02-08T23:32:20.316Z",
+                    "start_time": "2021-02-09T00:51:00.399Z",
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                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -18516,36 +15478,36 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b486e644-c56d-4209-b7c7-e56c527306b2/call-checkOptimusInput/stderr",
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                     "memory": "1 GB",
-                    "start_time": "2021-02-08T21:11:24.406Z",
-                    "stop_time": "2021-02-08T21:11:49.539Z",
+                    "start_time": "2021-02-08T21:11:24.405Z",
+                    "stop_time": "2021-02-08T21:11:24.614Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 }
             ],
-            "timestamp_start_utc": "2021-02-08T21:11:17.161Z",
-            "timestamp_stop_utc": "2021-02-09T10:03:40.170Z",
+            "timestamp_start_utc": "2021-02-08T21:11:17.166Z",
+            "timestamp_stop_utc": "2021-02-09T09:10:01.019Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_16.json": {
+        "analysis_process_23.json": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_c3cd00b7-9c8b-4cbb-adb4-4755d4271d5c']"
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_3b387d39-9f87-42c6-82d9-142abb485122']"
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_a903180c-2c06-4056-9f39-56992dba8c71']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -18553,7 +15515,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "62a131e1-c415-460e-bc5b-75cca5d3323b"
+                    "parameter_value": "f26c4715-5488-4d7f-ae0e-1c965128fbb1"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -18573,10 +15535,10 @@
                 }
             ],
             "process_core": {
-                "process_id": "58d03b27-9049-444e-a337-3491a5d715e1"
+                "process_id": "b9b49dd4-471a-4364-bc72-acaa1bcb633d"
             },
             "provenance": {
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+                "document_id": "b9b49dd4-471a-4364-bc72-acaa1bcb633d",
                 "submission_date": "2021-02-09T01:30:00.000000Z"
             },
             "reference_files": [
@@ -18588,47 +15550,47 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/b9b49dd4-471a-4364-bc72-acaa1bcb633d/call-CalculateCellMetrics/shard-0/stderr",
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                     "memory": "43.9453125 GB",
-                    "start_time": "2021-02-09T02:24:37.164Z",
-                    "stop_time": "2021-02-09T03:59:05.322Z",
+                    "start_time": "2021-02-09T06:52:06.559Z",
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                     "task_name": "CalculateCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
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-                    "start_time": "2021-02-09T03:47:52.070Z",
-                    "stop_time": "2021-02-09T05:26:14.328Z",
+                    "start_time": "2021-02-09T06:48:39.499Z",
+                    "stop_time": "2021-02-09T07:16:44.315Z",
                     "task_name": "CalculateGeneMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
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-                    "disk_size": "local-disk 9 HDD",
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@@ -18732,47 +15694,47 @@
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@@ -18780,11 +15742,11 @@
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                     "task_name": "RunEmptyDrops",
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@@ -18792,23 +15754,23 @@
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                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -18816,36 +15778,36 @@
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                     "memory": "1 GB",
-                    "start_time": "2021-02-08T21:11:24.403Z",
-                    "stop_time": "2021-02-08T21:11:47.724Z",
+                    "start_time": "2021-02-08T21:11:24.405Z",
+                    "stop_time": "2021-02-08T21:11:37.798Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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             ],
             "timestamp_start_utc": "2021-02-08T21:11:17.166Z",
-            "timestamp_stop_utc": "2021-02-09T09:12:00.459Z",
+            "timestamp_stop_utc": "2021-02-09T09:15:16.258Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_17.json": {
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             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
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                     "parameter_name": "r1_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_a6f3589a-6f4d-4cb7-a702-ea7b196d2c12']"
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                     "parameter_name": "r2_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_bd4156db-bab0-4f0c-8134-d8c55b18af26']"
                 },
                 {
                     "parameter_name": "i1_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_c2fdcc28-3eba-40f7-aa9b-41a7f2630879']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -18853,7 +15815,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "ded9b30e-12df-4998-846a-7cef685e4bd6"
+                    "parameter_value": "a0e661e2-dac9-4004-9605-8307c15f831d"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -18873,10 +15835,10 @@
                 }
             ],
             "process_core": {
-                "process_id": "725cbe75-92a1-46dc-862a-1b9d012e0fc1"
+                "process_id": "bc6bf485-351c-47c7-9837-d564bd32699b"
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             "provenance": {
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+                "document_id": "bc6bf485-351c-47c7-9837-d564bd32699b",
                 "submission_date": "2021-02-09T01:30:00.000000Z"
             },
             "reference_files": [
@@ -18886,49 +15848,49 @@
             "tasks": [
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                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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                 {
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                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
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                     "task_name": "CorrectUMItools",
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@@ -18936,35 +15898,35 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/bc6bf485-351c-47c7-9837-d564bd32699b/call-CreateSparseCountMatrix/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/bc6bf485-351c-47c7-9837-d564bd32699b/call-CreateSparseCountMatrix/shard-0/stdout",
                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T06:03:00.519Z",
-                    "stop_time": "2021-02-09T06:28:50.314Z",
+                    "start_time": "2021-02-09T03:47:21.979Z",
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                     "task_name": "CreateSparseCountMatrix",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
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@@ -18972,11 +15934,11 @@
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@@ -18984,11 +15946,11 @@
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@@ -18996,11 +15958,11 @@
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@@ -19008,11 +15970,11 @@
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@@ -19020,11 +15982,11 @@
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@@ -19032,35 +15994,35 @@
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@@ -19068,11 +16030,11 @@
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-                    "start_time": "2021-02-09T01:46:37.889Z",
-                    "stop_time": "2021-02-09T03:07:50.336Z",
+                    "start_time": "2021-02-08T23:45:56.179Z",
+                    "stop_time": "2021-02-09T01:03:05.342Z",
                     "task_name": "PreUMISort",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -19080,11 +16042,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/bc6bf485-351c-47c7-9837-d564bd32699b/call-RunEmptyDrops/stderr",
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                     "memory": "15.625 GB",
-                    "start_time": "2021-02-09T07:54:39.370Z",
-                    "stop_time": "2021-02-09T08:07:44.306Z",
+                    "start_time": "2021-02-09T07:31:00.460Z",
+                    "stop_time": "2021-02-09T07:44:14.315Z",
                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -19092,11 +16054,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/bc6bf485-351c-47c7-9837-d564bd32699b/call-StarAlign/shard-0/stderr",
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                     "memory": "36.5234375 GB",
-                    "start_time": "2021-02-08T21:14:26.671Z",
-                    "stop_time": "2021-02-09T00:44:50.342Z",
+                    "start_time": "2021-02-08T21:11:29.649Z",
+                    "stop_time": "2021-02-08T22:40:08.322Z",
                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -19104,11 +16066,11 @@
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-            "timestamp_start_utc": "2021-02-08T21:11:17.167Z",
-            "timestamp_stop_utc": "2021-02-09T09:51:09.469Z",
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             "type": {
                 "text": "analysis"
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         },
-        "analysis_process_18.json": {
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@@ -19153,7 +16115,7 @@
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                 {
                     "parameter_name": "input_id",
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@@ -19173,10 +16135,10 @@
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@@ -19200,11 +16162,11 @@
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@@ -19212,11 +16174,11 @@
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@@ -19224,11 +16186,11 @@
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@@ -19236,23 +16198,23 @@
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@@ -19260,11 +16222,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/bcee0e35-49c4-4af1-b202-eaf4df226025/call-GeneSortBam/shard-0/stderr",
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+                    "start_time": "2021-02-08T21:42:15.174Z",
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                     "task_name": "GeneSortBam",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -19272,11 +16234,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/bcee0e35-49c4-4af1-b202-eaf4df226025/call-MergeCellMetrics/stderr",
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-                    "start_time": "2021-02-09T08:01:23.269Z",
-                    "stop_time": "2021-02-09T08:06:20.307Z",
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+                    "stop_time": "2021-02-09T06:20:55.271Z",
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@@ -19284,11 +16246,11 @@
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@@ -19296,11 +16258,11 @@
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+                    "start_time": "2021-02-09T06:16:58.115Z",
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                     "task_name": "MergeGeneMetrics",
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@@ -19308,11 +16270,11 @@
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@@ -19320,11 +16282,11 @@
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@@ -19332,11 +16294,11 @@
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                     "task_name": "OptimusLoomGeneration",
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@@ -19344,11 +16306,11 @@
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@@ -19356,11 +16318,11 @@
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@@ -19368,11 +16330,11 @@
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@@ -19380,11 +16342,11 @@
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                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -19392,11 +16354,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/bcee0e35-49c4-4af1-b202-eaf4df226025/call-StarAlign/shard-0/stderr",
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                     "memory": "36.5234375 GB",
-                    "start_time": "2021-02-08T21:11:31.599Z",
-                    "stop_time": "2021-02-09T04:41:05.333Z",
+                    "start_time": "2021-02-08T21:22:13.983Z",
+                    "stop_time": "2021-02-08T21:30:02.566Z",
                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -19404,11 +16366,11 @@
                     "cpus": 1,
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/bcee0e35-49c4-4af1-b202-eaf4df226025/call-TagGenes/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/bcee0e35-49c4-4af1-b202-eaf4df226025/call-TagGenes/shard-0/stdout",
                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T04:41:06.823Z",
-                    "stop_time": "2021-02-09T05:38:53.321Z",
+                    "start_time": "2021-02-08T21:30:03.805Z",
+                    "stop_time": "2021-02-08T21:36:58.523Z",
                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -19416,36 +16378,36 @@
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                     "docker_image": "ubuntu:18.04",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/bcee0e35-49c4-4af1-b202-eaf4df226025/call-checkOptimusInput/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/bcee0e35-49c4-4af1-b202-eaf4df226025/call-checkOptimusInput/stdout",
                     "memory": "1 GB",
-                    "start_time": "2021-02-08T21:11:24.405Z",
-                    "stop_time": "2021-02-08T21:11:41.660Z",
+                    "start_time": "2021-02-08T17:21:06.277Z",
+                    "stop_time": "2021-02-08T17:21:14.389Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 }
             ],
-            "timestamp_start_utc": "2021-02-08T21:11:17.167Z",
-            "timestamp_stop_utc": "2021-02-09T09:24:09.629Z",
+            "timestamp_start_utc": "2021-02-08T21:12:19.626Z",
+            "timestamp_stop_utc": "2021-02-09T07:47:32.625Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_19.json": {
+        "analysis_process_26.json": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
                 {
                     "parameter_name": "r1_fastq",
-                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_64f727fd-cd90-415b-a166-ca45e660f835']"
+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_ae699a07-7b00-4967-b977-d86479e58249']"
                 },
                 {
                     "parameter_name": "r2_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_6e602e50-2565-4f5a-bee6-72888fc6ef14']"
                 },
                 {
                     "parameter_name": "i1_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_ed96c39c-ac5b-4265-854b-2773795406ac']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -19453,7 +16415,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "951a8ffc-69c5-4f7c-8ee8-39b76171f630"
+                    "parameter_value": "be7a2637-26cf-48ba-bfc5-52fa945d2d88"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -19473,10 +16435,10 @@
                 }
             ],
             "process_core": {
-                "process_id": "98f74c7b-abd8-4adc-b68f-f68aa5d3e58c"
+                "process_id": "c1ab22ca-2289-4384-82be-a3f16bdf113d"
             },
             "provenance": {
-                "document_id": "98f74c7b-abd8-4adc-b68f-f68aa5d3e58c",
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                 "submission_date": "2021-02-09T01:30:00.000000Z"
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             "type": {
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@@ -19753,7 +16715,7 @@
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@@ -19773,10 +16735,10 @@
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@@ -19788,11 +16750,11 @@
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@@ -19800,35 +16762,35 @@
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@@ -19992,11 +16954,11 @@
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@@ -20004,11 +16966,11 @@
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-            "timestamp_start_utc": "2021-02-08T21:11:17.167Z",
-            "timestamp_stop_utc": "2021-02-09T10:43:39.521Z",
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             "type": {
                 "text": "analysis"
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         },
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@@ -20053,7 +17015,7 @@
                 },
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                     "parameter_name": "input_id",
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@@ -20073,10 +17035,10 @@
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@@ -20100,11 +17062,11 @@
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@@ -20112,11 +17074,11 @@
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@@ -20124,11 +17086,11 @@
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                     "task_name": "CorrectUMItools",
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@@ -20136,23 +17098,23 @@
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+                    "start_time": "2021-02-09T05:20:27.589Z",
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@@ -20184,11 +17146,11 @@
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@@ -20232,11 +17194,11 @@
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@@ -20268,11 +17230,11 @@
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-                    "stop_time": "2021-02-09T05:31:20.335Z",
+                    "start_time": "2021-02-08T22:37:07.990Z",
+                    "stop_time": "2021-02-09T01:03:22.305Z",
                     "task_name": "PreUMISort",
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@@ -20280,11 +17242,11 @@
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                     "memory": "15.625 GB",
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-                    "stop_time": "2021-02-09T08:03:14.305Z",
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+                    "stop_time": "2021-02-09T07:51:59.310Z",
                     "task_name": "RunEmptyDrops",
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@@ -20292,11 +17254,11 @@
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                     "memory": "36.5234375 GB",
-                    "start_time": "2021-02-08T21:26:23.715Z",
-                    "stop_time": "2021-02-09T00:09:35.313Z",
+                    "start_time": "2021-02-08T21:11:30.644Z",
+                    "stop_time": "2021-02-08T21:15:35.320Z",
                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -20304,11 +17266,11 @@
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@@ -20316,36 +17278,36 @@
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                     "task_name": "checkOptimusInput",
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             "timestamp_start_utc": "2021-02-08T21:11:17.160Z",
-            "timestamp_stop_utc": "2021-02-09T09:39:55.259Z",
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             "type": {
                 "text": "analysis"
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         },
-        "analysis_process_22.json": {
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@@ -20353,7 +17315,7 @@
                 },
                 {
                     "parameter_name": "input_id",
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                     "parameter_name": "tar_star_reference",
@@ -20373,10 +17335,10 @@
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@@ -20386,49 +17348,49 @@
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@@ -20436,35 +17398,35 @@
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@@ -20472,11 +17434,11 @@
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@@ -20484,11 +17446,11 @@
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@@ -20508,11 +17470,11 @@
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@@ -20532,47 +17494,47 @@
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@@ -20580,11 +17542,11 @@
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                     "memory": "15.625 GB",
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                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -20592,23 +17554,23 @@
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                     "memory": "36.5234375 GB",
-                    "start_time": "2021-02-08T21:11:29.636Z",
-                    "stop_time": "2021-02-09T00:50:59.317Z",
+                    "start_time": "2021-02-08T21:15:02.786Z",
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                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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                 {
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-                    "disk_size": "local-disk 25 HDD",
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                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T00:51:00.399Z",
-                    "stop_time": "2021-02-09T01:51:53.323Z",
+                    "start_time": "2021-02-09T05:09:49.025Z",
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                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -20616,36 +17578,36 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/d09272b0-2827-4b7b-9a8c-a63fec7376ca/call-checkOptimusInput/stderr",
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                     "memory": "1 GB",
-                    "start_time": "2021-02-08T21:11:24.405Z",
-                    "stop_time": "2021-02-08T21:11:24.614Z",
+                    "start_time": "2021-02-08T21:12:28.751Z",
+                    "stop_time": "2021-02-08T21:15:04.889Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 }
             ],
-            "timestamp_start_utc": "2021-02-08T21:11:17.166Z",
-            "timestamp_stop_utc": "2021-02-09T09:10:01.019Z",
+            "timestamp_start_utc": "2021-02-08T21:12:25.668Z",
+            "timestamp_stop_utc": "2021-02-09T08:14:36.893Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_23.json": {
+        "analysis_process_30.json": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
                 {
                     "parameter_name": "r1_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_c23bd7fa-dd83-4b87-bf02-088f26b19201']"
                 },
                 {
                     "parameter_name": "r2_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_fd6f1c2d-4e3f-4c7a-9c6d-51edce6ca2a1']"
                 },
                 {
                     "parameter_name": "i1_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_692b6aec-9320-4e1d-bffb-6babf930040f']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -20653,7 +17615,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "f26c4715-5488-4d7f-ae0e-1c965128fbb1"
+                    "parameter_value": "f4183399-0e70-466e-8915-8e4481f9b7d1"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -20673,10 +17635,10 @@
                 }
             ],
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+                "process_id": "d2b4df36-221d-413d-8e9a-b233b72d3832"
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@@ -20688,11 +17650,11 @@
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@@ -20700,35 +17662,35 @@
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@@ -20736,23 +17698,23 @@
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@@ -20760,11 +17722,11 @@
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@@ -20772,11 +17734,11 @@
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@@ -20784,11 +17746,11 @@
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@@ -20796,11 +17758,11 @@
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@@ -20820,11 +17782,11 @@
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+                    "start_time": "2021-02-08T17:21:06.287Z",
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                     "task_name": "ModifyGtf",
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@@ -20832,11 +17794,11 @@
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                     "task_name": "OptimusLoomGeneration",
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@@ -20844,11 +17806,11 @@
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@@ -20856,23 +17818,23 @@
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@@ -20880,11 +17842,11 @@
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@@ -20892,23 +17854,23 @@
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                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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                 {
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-                    "disk_size": "local-disk 24 HDD",
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                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -20916,36 +17878,36 @@
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                     "memory": "1 GB",
-                    "start_time": "2021-02-08T21:11:24.405Z",
-                    "stop_time": "2021-02-08T21:11:37.798Z",
+                    "start_time": "2021-02-08T17:21:06.287Z",
+                    "stop_time": "2021-02-08T17:21:14.390Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 }
             ],
-            "timestamp_start_utc": "2021-02-08T21:11:17.166Z",
-            "timestamp_stop_utc": "2021-02-09T09:15:16.258Z",
+            "timestamp_start_utc": "2021-02-08T21:12:19.643Z",
+            "timestamp_stop_utc": "2021-02-09T07:52:21.285Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_24.json": {
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             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_058ef571-0842-4255-a4b2-290c6b20be84']"
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                 {
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_64e4b5f0-ef82-4314-acc5-01a695238d31']"
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_f114568a-30a8-4041-9dfc-eace4ecfdcf0']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -20953,7 +17915,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "a0e661e2-dac9-4004-9605-8307c15f831d"
+                    "parameter_value": "5d687d7c-8d96-4203-ad8e-d0668828ad37"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -20973,10 +17935,10 @@
                 }
             ],
             "process_core": {
-                "process_id": "bc6bf485-351c-47c7-9837-d564bd32699b"
+                "process_id": "d3c42b32-d484-458c-ad66-e7e9e7889ee9"
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             "provenance": {
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+                "document_id": "d3c42b32-d484-458c-ad66-e7e9e7889ee9",
                 "submission_date": "2021-02-09T01:30:00.000000Z"
             },
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@@ -20986,49 +17948,49 @@
             "tasks": [
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/d3c42b32-d484-458c-ad66-e7e9e7889ee9/call-CalculateCellMetrics/shard-0/stderr",
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-                    "start_time": "2021-02-09T03:50:40.241Z",
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                     "task_name": "CalculateCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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                 {
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-                    "stop_time": "2021-02-09T06:13:08.328Z",
+                    "start_time": "2021-02-09T04:43:48.427Z",
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                     "task_name": "CalculateGeneMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
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@@ -21132,47 +18094,47 @@
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@@ -21192,23 +18154,23 @@
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@@ -21216,36 +18178,36 @@
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-            "timestamp_start_utc": "2021-02-08T21:11:17.161Z",
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             "type": {
                 "text": "analysis"
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         },
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@@ -21253,7 +18215,7 @@
                 },
                 {
                     "parameter_name": "input_id",
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@@ -21273,10 +18235,10 @@
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@@ -21286,49 +18248,49 @@
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@@ -21336,23 +18298,23 @@
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@@ -21492,23 +18454,23 @@
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                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -21516,36 +18478,36 @@
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+                    "start_time": "2021-02-08T21:11:24.403Z",
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                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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-            "timestamp_start_utc": "2021-02-08T21:12:19.626Z",
-            "timestamp_stop_utc": "2021-02-09T07:47:32.625Z",
+            "timestamp_start_utc": "2021-02-08T21:11:17.160Z",
+            "timestamp_stop_utc": "2021-02-09T09:34:52.318Z",
             "type": {
                 "text": "analysis"
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         },
-        "analysis_process_26.json": {
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             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
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                     "parameter_name": "r1_fastq",
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                     "parameter_name": "r2_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_59075c99-0f72-4ffc-a598-5f1f7107c8fe']"
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_06f09e02-e0d9-43ce-80a3-8a572d61ec00']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -21553,7 +18515,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "be7a2637-26cf-48ba-bfc5-52fa945d2d88"
+                    "parameter_value": "1d5a282b-b4b5-41dc-ab46-862476a87c18"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -21573,10 +18535,10 @@
                 }
             ],
             "process_core": {
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+                "process_id": "e1b9ecf6-6fd8-4bc1-a28d-e9c9850055af"
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             "provenance": {
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                 "submission_date": "2021-02-09T01:30:00.000000Z"
             },
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@@ -21586,49 +18548,49 @@
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@@ -21636,35 +18598,35 @@
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@@ -21672,11 +18634,11 @@
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@@ -21684,11 +18646,11 @@
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                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -21696,11 +18658,11 @@
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                     "task_name": "MergeGeneMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -21708,11 +18670,11 @@
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                     "task_name": "MergeSorted",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -21720,11 +18682,11 @@
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                     "task_name": "ModifyGtf",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -21732,47 +18694,47 @@
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                     "memory": "18 GB",
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+                    "stop_time": "2021-02-09T08:36:38.307Z",
                     "task_name": "OptimusLoomGeneration",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
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-                    "disk_size": "local-disk 207 HDD",
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                     "task_name": "PreUMISort",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -21780,11 +18742,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/e1b9ecf6-6fd8-4bc1-a28d-e9c9850055af/call-RunEmptyDrops/stderr",
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                     "memory": "15.625 GB",
-                    "start_time": "2021-02-09T07:43:31.290Z",
-                    "stop_time": "2021-02-09T07:54:29.315Z",
+                    "start_time": "2021-02-09T07:37:25.090Z",
+                    "stop_time": "2021-02-09T07:47:44.307Z",
                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -21792,11 +18754,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/e1b9ecf6-6fd8-4bc1-a28d-e9c9850055af/call-StarAlign/shard-0/stderr",
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                     "memory": "36.5234375 GB",
-                    "start_time": "2021-02-08T21:11:37.707Z",
-                    "stop_time": "2021-02-08T21:17:29.357Z",
+                    "start_time": "2021-02-08T23:17:57.071Z",
+                    "stop_time": "2021-02-09T04:51:06.013Z",
                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -21804,11 +18766,11 @@
                     "cpus": 1,
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                     "docker_image": "quay.io/humancellatlas/secondary-analysis-dropseqtools:v0.2.2-1.13",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/e1b9ecf6-6fd8-4bc1-a28d-e9c9850055af/call-TagGenes/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/e1b9ecf6-6fd8-4bc1-a28d-e9c9850055af/call-TagGenes/shard-0/stdout",
                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-08T21:17:31.374Z",
-                    "stop_time": "2021-02-09T00:09:47.304Z",
+                    "start_time": "2021-02-09T04:51:07.669Z",
+                    "stop_time": "2021-02-09T05:43:59.324Z",
                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -21816,36 +18778,36 @@
                     "cpus": 1,
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                     "docker_image": "ubuntu:18.04",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/e1b9ecf6-6fd8-4bc1-a28d-e9c9850055af/call-checkOptimusInput/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/e1b9ecf6-6fd8-4bc1-a28d-e9c9850055af/call-checkOptimusInput/stdout",
                     "memory": "1 GB",
                     "start_time": "2021-02-08T21:11:24.404Z",
-                    "stop_time": "2021-02-08T21:11:47.542Z",
+                    "stop_time": "2021-02-08T21:11:28.130Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 }
             ],
-            "timestamp_start_utc": "2021-02-08T21:11:17.166Z",
-            "timestamp_stop_utc": "2021-02-09T09:26:22.248Z",
+            "timestamp_start_utc": "2021-02-08T21:11:17.162Z",
+            "timestamp_stop_utc": "2021-02-09T09:06:51.419Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_27.json": {
+        "analysis_process_34.json": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
                 {
                     "parameter_name": "r1_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_f400b4b8-1c0c-4071-87dc-739e412cf717']"
                 },
                 {
                     "parameter_name": "r2_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_b7e94aa3-02f4-40d2-9f1b-43928c817ffb']"
                 },
                 {
                     "parameter_name": "i1_fastq",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_053ddc57-64a6-4d71-9366-a398f6231137']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -21853,7 +18815,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "c301901f-95cd-4a3e-a4df-761fa21e92af"
+                    "parameter_value": "7f0f3ad8-9052-4003-ac7d-4e2e509b85f5"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -21873,10 +18835,10 @@
                 }
             ],
             "process_core": {
-                "process_id": "c6ca5e48-0be8-4b66-ac11-6e25511afe2a"
+                "process_id": "e607b72f-3024-4d7e-8292-19d2d53a3a95"
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+                "document_id": "e607b72f-3024-4d7e-8292-19d2d53a3a95",
                 "submission_date": "2021-02-09T01:30:00.000000Z"
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@@ -21888,23 +18850,23 @@
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@@ -21912,11 +18874,11 @@
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@@ -21924,11 +18886,11 @@
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                     "task_name": "CorrectUMItools",
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@@ -21936,23 +18898,23 @@
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@@ -21960,11 +18922,11 @@
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@@ -21972,11 +18934,11 @@
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@@ -21984,11 +18946,11 @@
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@@ -21996,11 +18958,11 @@
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@@ -22008,11 +18970,11 @@
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                     "task_name": "MergeSorted",
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@@ -22020,11 +18982,11 @@
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-                    "start_time": "2021-02-08T21:11:24.450Z",
-                    "stop_time": "2021-02-08T21:11:36.565Z",
+                    "start_time": "2021-02-08T21:11:24.424Z",
+                    "stop_time": "2021-02-08T21:11:26.684Z",
                     "task_name": "ModifyGtf",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -22032,11 +18994,11 @@
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@@ -22044,11 +19006,11 @@
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@@ -22056,23 +19018,23 @@
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@@ -22080,11 +19042,11 @@
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                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -22092,23 +19054,23 @@
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                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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                 {
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-                    "disk_size": "local-disk 25 HDD",
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                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -22116,36 +19078,36 @@
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                     "memory": "1 GB",
-                    "start_time": "2021-02-08T21:11:24.404Z",
-                    "stop_time": "2021-02-08T21:11:27.651Z",
+                    "start_time": "2021-02-08T21:11:24.411Z",
+                    "stop_time": "2021-02-08T21:11:28.663Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 }
             ],
-            "timestamp_start_utc": "2021-02-08T21:11:17.161Z",
-            "timestamp_stop_utc": "2021-02-09T08:57:06.839Z",
+            "timestamp_start_utc": "2021-02-08T21:11:17.160Z",
+            "timestamp_stop_utc": "2021-02-09T09:22:24.688Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_28.json": {
+        "analysis_process_35.json": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_4d25fa13-4b11-4c21-957c-e4ba8b261610']"
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_072ef189-77d1-4fe3-8fec-7d31575d2a1a']"
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                 {
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_68fa3fff-3e98-4d72-a60a-aec8bdb36396']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -22153,7 +19115,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "2e7e4b93-2d6c-4359-804c-f8ca1e21c31c"
+                    "parameter_value": "08b799a0-59d8-4c69-87b3-fd239aef4197"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -22173,10 +19135,10 @@
                 }
             ],
             "process_core": {
-                "process_id": "cdba26d8-9b1d-471f-9a08-875a09cbb96b"
+                "process_id": "e9de5082-46c8-4b26-83c0-7fd480dcb142"
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             "provenance": {
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+                "document_id": "e9de5082-46c8-4b26-83c0-7fd480dcb142",
                 "submission_date": "2021-02-09T01:30:00.000000Z"
             },
             "reference_files": [
@@ -22186,85 +19148,85 @@
             "tasks": [
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-                    "disk_size": "local-disk 3 HDD",
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+                    "start_time": "2021-02-09T05:32:35.917Z",
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                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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                 {
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+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/e9de5082-46c8-4b26-83c0-7fd480dcb142/call-CalculateGeneMetrics/shard-0/stdout",
                     "memory": "29.296875 GB",
-                    "start_time": "2021-02-09T05:06:31.121Z",
-                    "stop_time": "2021-02-09T05:50:50.327Z",
+                    "start_time": "2021-02-09T05:27:48.048Z",
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                     "task_name": "CalculateGeneMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
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@@ -22380,35 +19342,35 @@
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@@ -22416,36 +19378,36 @@
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-            "timestamp_start_utc": "2021-02-08T21:11:17.160Z",
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             "type": {
                 "text": "analysis"
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         },
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@@ -22453,7 +19415,7 @@
                 },
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                     "parameter_name": "input_id",
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                 {
                     "parameter_name": "tar_star_reference",
@@ -22473,10 +19435,10 @@
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@@ -22500,11 +19462,11 @@
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@@ -22512,11 +19474,11 @@
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@@ -22524,11 +19486,11 @@
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@@ -22536,23 +19498,23 @@
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@@ -22560,11 +19522,11 @@
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@@ -22572,11 +19534,11 @@
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@@ -22584,11 +19546,11 @@
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@@ -22596,11 +19558,11 @@
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@@ -22608,11 +19570,11 @@
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@@ -22620,11 +19582,11 @@
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@@ -22632,11 +19594,11 @@
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+                    "stop_time": "2021-02-09T08:59:35.308Z",
                     "task_name": "OptimusLoomGeneration",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -22644,11 +19606,11 @@
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@@ -22656,11 +19618,11 @@
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                     "task_name": "PreMergeSort",
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@@ -22668,11 +19630,11 @@
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                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T05:19:59.055Z",
-                    "stop_time": "2021-02-09T05:31:20.484Z",
+                    "start_time": "2021-02-09T00:13:38.319Z",
+                    "stop_time": "2021-02-09T01:18:53.350Z",
                     "task_name": "PreUMISort",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -22680,11 +19642,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/f1f25c56-1cd7-44e4-8e58-7adafd43529c/call-RunEmptyDrops/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/f1f25c56-1cd7-44e4-8e58-7adafd43529c/call-RunEmptyDrops/stdout",
                     "memory": "15.625 GB",
-                    "start_time": "2021-02-09T06:37:27.993Z",
-                    "stop_time": "2021-02-09T06:51:47.470Z",
+                    "start_time": "2021-02-09T07:59:40.250Z",
+                    "stop_time": "2021-02-09T08:10:05.306Z",
                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -22692,11 +19654,11 @@
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                     "task_name": "StarAlign",
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@@ -22704,11 +19666,11 @@
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                     "task_name": "TagGenes",
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@@ -22716,36 +19678,36 @@
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                     "memory": "1 GB",
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+                    "start_time": "2021-02-08T21:11:24.403Z",
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                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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-            "timestamp_start_utc": "2021-02-08T21:12:25.668Z",
-            "timestamp_stop_utc": "2021-02-09T08:14:36.893Z",
+            "timestamp_start_utc": "2021-02-08T21:11:17.161Z",
+            "timestamp_stop_utc": "2021-02-09T09:44:46.139Z",
             "type": {
                 "text": "analysis"
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         },
-        "analysis_process_30.json": {
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             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
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                     "parameter_name": "whitelist",
@@ -22753,7 +19715,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "f4183399-0e70-466e-8915-8e4481f9b7d1"
+                    "parameter_value": "bc5ba4f6-a3f1-4156-830f-11228df251bc"
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                 {
                     "parameter_name": "tar_star_reference",
@@ -22773,10 +19735,10 @@
                 }
             ],
             "process_core": {
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+                "process_id": "f3b53d83-7ee7-42db-b2d5-05a792204872"
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@@ -22788,11 +19750,11 @@
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@@ -22800,11 +19762,11 @@
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@@ -22812,11 +19774,11 @@
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@@ -22824,11 +19786,11 @@
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@@ -22836,23 +19798,23 @@
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-                    "stop_time": "2021-02-09T06:17:16.278Z",
+                    "start_time": "2021-02-09T02:37:15.754Z",
+                    "stop_time": "2021-02-09T02:44:20.489Z",
                     "task_name": "CreateSparseCountMatrix",
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                 },
                 {
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+                    "start_time": "2021-02-08T21:12:28.751Z",
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@@ -22860,11 +19822,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/f3b53d83-7ee7-42db-b2d5-05a792204872/call-GeneSortBam/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/f3b53d83-7ee7-42db-b2d5-05a792204872/call-GeneSortBam/shard-0/stdout",
                     "memory": "97.65625 GB",
-                    "start_time": "2021-02-09T05:56:12.005Z",
-                    "stop_time": "2021-02-09T06:10:31.263Z",
+                    "start_time": "2021-02-09T02:24:52.014Z",
+                    "stop_time": "2021-02-09T02:37:38.525Z",
                     "task_name": "GeneSortBam",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -22872,11 +19834,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/f3b53d83-7ee7-42db-b2d5-05a792204872/call-MergeCellMetrics/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/f3b53d83-7ee7-42db-b2d5-05a792204872/call-MergeCellMetrics/stdout",
                     "memory": "3.759765625 GB",
-                    "start_time": "2021-02-09T06:35:51.515Z",
-                    "stop_time": "2021-02-09T06:40:55.258Z",
+                    "start_time": "2021-02-09T06:23:44.094Z",
+                    "stop_time": "2021-02-09T06:29:05.479Z",
                     "task_name": "MergeCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -22884,11 +19846,11 @@
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@@ -22896,11 +19858,11 @@
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@@ -22908,11 +19870,11 @@
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@@ -22920,11 +19882,11 @@
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@@ -22932,11 +19894,11 @@
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@@ -22944,11 +19906,11 @@
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@@ -22956,23 +19918,23 @@
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@@ -22980,11 +19942,11 @@
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                     "memory": "15.625 GB",
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-                    "stop_time": "2021-02-09T06:34:16.273Z",
+                    "start_time": "2021-02-09T06:10:19.264Z",
+                    "stop_time": "2021-02-09T06:21:47.491Z",
                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -22992,11 +19954,11 @@
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                     "memory": "36.5234375 GB",
-                    "start_time": "2021-02-08T19:23:54.033Z",
-                    "stop_time": "2021-02-09T02:07:31.260Z",
+                    "start_time": "2021-02-08T21:15:00.746Z",
+                    "stop_time": "2021-02-09T01:23:56.476Z",
                     "task_name": "StarAlign",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -23004,11 +19966,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/f3b53d83-7ee7-42db-b2d5-05a792204872/call-TagGenes/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/f3b53d83-7ee7-42db-b2d5-05a792204872/call-TagGenes/shard-0/stdout",
                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T02:07:32.914Z",
-                    "stop_time": "2021-02-09T03:41:46.263Z",
+                    "start_time": "2021-02-09T01:23:57.834Z",
+                    "stop_time": "2021-02-09T01:53:41.475Z",
                     "task_name": "TagGenes",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -23016,36 +19978,36 @@
                     "cpus": 1,
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                     "docker_image": "ubuntu:18.04",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/f3b53d83-7ee7-42db-b2d5-05a792204872/call-checkOptimusInput/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/f3b53d83-7ee7-42db-b2d5-05a792204872/call-checkOptimusInput/stdout",
                     "memory": "1 GB",
-                    "start_time": "2021-02-08T17:21:06.287Z",
-                    "stop_time": "2021-02-08T17:21:14.390Z",
+                    "start_time": "2021-02-08T21:12:28.751Z",
+                    "stop_time": "2021-02-08T21:15:02.836Z",
                     "task_name": "checkOptimusInput",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 }
             ],
-            "timestamp_start_utc": "2021-02-08T21:12:19.643Z",
-            "timestamp_stop_utc": "2021-02-09T07:52:21.285Z",
+            "timestamp_start_utc": "2021-02-08T21:12:25.667Z",
+            "timestamp_stop_utc": "2021-02-09T07:58:01.394Z",
             "type": {
                 "text": "analysis"
             }
         },
-        "analysis_process_31.json": {
+        "analysis_process_38.json": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
                 {
                     "parameter_name": "r1_fastq",
-                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_058ef571-0842-4255-a4b2-290c6b20be84']"
+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_eadaa69d-0f6a-4c24-a21d-136da13c117e']"
                 },
                 {
                     "parameter_name": "r2_fastq",
-                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_64e4b5f0-ef82-4314-acc5-01a695238d31']"
+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_2335283c-4206-44f5-9e4b-0d20fa2ae808']"
                 },
                 {
                     "parameter_name": "i1_fastq",
-                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_f114568a-30a8-4041-9dfc-eace4ecfdcf0']"
+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_e79f0bde-37ec-425c-a804-8134646898e8']"
                 },
                 {
                     "parameter_name": "whitelist",
@@ -23053,7 +20015,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "5d687d7c-8d96-4203-ad8e-d0668828ad37"
+                    "parameter_value": "0dd65ce8-29ba-4341-9a93-eb2ca1f06c72"
                 },
                 {
                     "parameter_name": "tar_star_reference",
@@ -23073,10 +20035,10 @@
                 }
             ],
             "process_core": {
-                "process_id": "d3c42b32-d484-458c-ad66-e7e9e7889ee9"
+                "process_id": "fbbd6c03-df0d-44dd-b383-c1efb83abb2e"
             },
             "provenance": {
-                "document_id": "d3c42b32-d484-458c-ad66-e7e9e7889ee9",
+                "document_id": "fbbd6c03-df0d-44dd-b383-c1efb83abb2e",
                 "submission_date": "2021-02-09T01:30:00.000000Z"
             },
             "reference_files": [
@@ -23088,35 +20050,35 @@
                     "cpus": 1,
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-CalculateCellMetrics/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-CalculateCellMetrics/shard-0/stdout",
                     "memory": "43.9453125 GB",
-                    "start_time": "2021-02-09T04:29:33.267Z",
-                    "stop_time": "2021-02-09T05:00:07.257Z",
+                    "start_time": "2021-02-09T07:22:54.760Z",
+                    "stop_time": "2021-02-09T07:43:59.312Z",
                     "task_name": "CalculateCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
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-                    "disk_size": "local-disk 5 HDD",
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-                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/d3c42b32-d484-458c-ad66-e7e9e7889ee9/call-CalculateGeneMetrics/shard-0/stderr",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-CalculateGeneMetrics/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-CalculateGeneMetrics/shard-0/stdout",
                     "memory": "29.296875 GB",
-                    "start_time": "2021-02-09T04:43:48.427Z",
-                    "stop_time": "2021-02-09T05:39:46.262Z",
+                    "start_time": "2021-02-09T07:25:24.870Z",
+                    "stop_time": "2021-02-09T07:38:44.315Z",
                     "task_name": "CalculateGeneMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
                     "cpus": 2,
-                    "disk_size": "local-disk 9 HDD",
+                    "disk_size": "local-disk 8 HDD",
                     "docker_image": "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-CellSortBam/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-CellSortBam/shard-0/stdout",
                     "memory": "97.65625 GB",
-                    "start_time": "2021-02-09T04:08:53.796Z",
-                    "stop_time": "2021-02-09T04:29:31.261Z",
+                    "start_time": "2021-02-09T06:57:54.919Z",
+                    "stop_time": "2021-02-09T07:22:53.314Z",
                     "task_name": "CellSortBam",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -23124,11 +20086,11 @@
                     "cpus": 1,
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                     "docker_image": "quay.io/humancellatlas/secondary-analysis-umitools:0.0.1",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-CorrectUMItools/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-CorrectUMItools/shard-0/stdout",
                     "memory": "15.625 GB",
-                    "start_time": "2021-02-09T03:46:56.776Z",
-                    "stop_time": "2021-02-09T04:08:52.256Z",
+                    "start_time": "2021-02-09T06:26:09.499Z",
+                    "stop_time": "2021-02-09T06:57:53.319Z",
                     "task_name": "CorrectUMItools",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -23136,11 +20098,11 @@
                     "cpus": 1,
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                     "docker_image": "quay.io/humancellatlas/secondary-analysis-sctools:v0.3.11",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-CreateSparseCountMatrix/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-CreateSparseCountMatrix/shard-0/stdout",
                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T04:27:05.325Z",
-                    "stop_time": "2021-02-09T05:40:04.260Z",
+                    "start_time": "2021-02-09T07:20:37.069Z",
+                    "stop_time": "2021-02-09T07:29:59.311Z",
                     "task_name": "CreateSparseCountMatrix",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -23148,23 +20110,23 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-FastqProcessing/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-FastqProcessing/stdout",
                     "memory": "39.0625 GB",
-                    "start_time": "2021-02-08T21:11:21.932Z",
-                    "stop_time": "2021-02-08T19:07:20.969Z",
+                    "start_time": "2021-02-08T21:11:24.439Z",
+                    "stop_time": "2021-02-08T21:11:25.752Z",
                     "task_name": "FastqProcessing",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
                 {
                     "cpus": 2,
-                    "disk_size": "local-disk 5 HDD",
+                    "disk_size": "local-disk 4 HDD",
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-GeneSortBam/shard-0/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-GeneSortBam/shard-0/stdout",
                     "memory": "97.65625 GB",
-                    "start_time": "2021-02-09T04:08:53.796Z",
-                    "stop_time": "2021-02-09T04:43:46.432Z",
+                    "start_time": "2021-02-09T06:57:54.919Z",
+                    "stop_time": "2021-02-09T07:25:23.317Z",
                     "task_name": "GeneSortBam",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -23172,11 +20134,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-MergeCellMetrics/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-MergeCellMetrics/stdout",
                     "memory": "3.759765625 GB",
-                    "start_time": "2021-02-09T06:44:49.056Z",
-                    "stop_time": "2021-02-09T06:49:34.253Z",
+                    "start_time": "2021-02-09T07:48:16.879Z",
+                    "stop_time": "2021-02-09T07:54:08.307Z",
                     "task_name": "MergeCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -23184,11 +20146,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-MergeCountFiles/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-MergeCountFiles/stdout",
                     "memory": "8.056640625 GB",
-                    "start_time": "2021-02-09T06:28:27.747Z",
-                    "stop_time": "2021-02-09T06:33:01.268Z",
+                    "start_time": "2021-02-09T07:36:41.229Z",
+                    "stop_time": "2021-02-09T07:42:05.315Z",
                     "task_name": "MergeCountFiles",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -23196,11 +20158,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-MergeGeneMetrics/stderr",
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                     "memory": "3.759765625 GB",
-                    "start_time": "2021-02-09T06:39:33.885Z",
-                    "stop_time": "2021-02-09T07:07:52.250Z",
+                    "start_time": "2021-02-09T07:40:56.250Z",
+                    "stop_time": "2021-02-09T08:08:35.310Z",
                     "task_name": "MergeGeneMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -23208,11 +20170,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-MergeSorted/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fbbd6c03-df0d-44dd-b383-c1efb83abb2e/call-MergeSorted/stdout",
                     "memory": "17.724609375 GB",
-                    "start_time": "2021-02-09T06:16:51.956Z",
-                    "stop_time": "2021-02-09T08:00:31.249Z",
+                    "start_time": "2021-02-09T07:20:31.969Z",
+                    "stop_time": "2021-02-09T09:30:44.306Z",
                     "task_name": "MergeSorted",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -23220,11 +20182,11 @@
                     "cpus": 1,
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                     "docker_image": "quay.io/humancellatlas/modify-gtf:0.1.0",
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@@ -23280,11 +20242,11 @@
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@@ -23292,11 +20254,11 @@
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@@ -23304,11 +20266,11 @@
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@@ -23316,36 +20278,36 @@
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+                    "start_time": "2021-02-08T21:11:24.405Z",
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                     "task_name": "checkOptimusInput",
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-            "timestamp_start_utc": "2021-02-08T21:11:18.774Z",
-            "timestamp_stop_utc": "2021-02-09T08:00:32.894Z",
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+            "timestamp_stop_utc": "2021-02-09T09:30:45.478Z",
             "type": {
                 "text": "analysis"
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         },
-        "analysis_process_32.json": {
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             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
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                 {
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@@ -23353,7 +20315,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "7229676a-4449-4a2f-ac97-284eb599841c"
+                    "parameter_value": "bc583c0e-4336-43d4-a7da-dc7e1f72b50b"
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                 {
                     "parameter_name": "tar_star_reference",
@@ -23373,10 +20335,10 @@
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             "process_core": {
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+                "process_id": "fd0cff96-93f2-4eb4-88f2-991f60542f46"
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             "provenance": {
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                 "submission_date": "2021-02-09T01:30:00.000000Z"
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@@ -23388,11 +20350,11 @@
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                     "memory": "43.9453125 GB",
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-                    "stop_time": "2021-02-09T06:20:14.315Z",
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                     "task_name": "CalculateCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -23400,11 +20362,11 @@
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@@ -23424,11 +20386,11 @@
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@@ -23436,11 +20398,11 @@
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@@ -23448,11 +20410,11 @@
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@@ -23460,11 +20422,11 @@
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@@ -23472,11 +20434,11 @@
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@@ -23484,11 +20446,11 @@
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@@ -23508,11 +20470,11 @@
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@@ -23520,11 +20482,11 @@
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-                    "stop_time": "2021-02-08T21:11:24.815Z",
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+                    "stop_time": "2021-02-08T21:11:29.837Z",
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@@ -23532,11 +20494,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fd0cff96-93f2-4eb4-88f2-991f60542f46/call-OptimusLoomGeneration/stderr",
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-                    "stop_time": "2021-02-09T09:05:29.305Z",
+                    "start_time": "2021-02-09T08:23:39.509Z",
+                    "stop_time": "2021-02-09T08:47:38.309Z",
                     "task_name": "OptimusLoomGeneration",
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@@ -23544,11 +20506,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fd0cff96-93f2-4eb4-88f2-991f60542f46/call-PreCountSort/shard-0/stderr",
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-                    "start_time": "2021-02-09T02:09:22.291Z",
-                    "stop_time": "2021-02-09T03:38:05.346Z",
+                    "start_time": "2021-02-09T05:27:40.060Z",
+                    "stop_time": "2021-02-09T06:02:44.327Z",
                     "task_name": "PreCountSort",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -23556,23 +20518,23 @@
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@@ -23580,11 +20542,11 @@
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@@ -23592,11 +20554,11 @@
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@@ -23604,11 +20566,11 @@
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@@ -23616,36 +20578,36 @@
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                     "memory": "1 GB",
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-                    "stop_time": "2021-02-08T21:11:42.541Z",
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                     "task_name": "checkOptimusInput",
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             ],
-            "timestamp_start_utc": "2021-02-08T21:11:17.160Z",
-            "timestamp_stop_utc": "2021-02-09T09:34:52.318Z",
+            "timestamp_start_utc": "2021-02-08T21:11:17.167Z",
+            "timestamp_stop_utc": "2021-02-09T09:39:21.588Z",
             "type": {
                 "text": "analysis"
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         },
-        "analysis_process_33.json": {
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             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
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+                    "parameter_value": "['drs://jade-terra.datarepo-prod.broadinstitute.org/v1_ec40aa9f-43aa-4839-98e3-6362c96a0bee_b0801ff8-a5c5-4be3-92b9-f125bf3d15a7']"
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                 {
                     "parameter_name": "whitelist",
@@ -23653,7 +20615,7 @@
                 },
                 {
                     "parameter_name": "input_id",
-                    "parameter_value": "1d5a282b-b4b5-41dc-ab46-862476a87c18"
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                 {
                     "parameter_name": "tar_star_reference",
@@ -23673,10 +20635,10 @@
                 }
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             "process_core": {
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                 "submission_date": "2021-02-09T01:30:00.000000Z"
             },
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@@ -23686,49 +20648,49 @@
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                     "task_name": "CorrectUMItools",
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@@ -23736,35 +20698,35 @@
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+                    "start_time": "2021-02-09T04:58:25.068Z",
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                     "task_name": "GeneSortBam",
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@@ -23772,11 +20734,11 @@
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                     "task_name": "MergeCellMetrics",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -23784,11 +20746,11 @@
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                     "task_name": "MergeCountFiles",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -23796,11 +20758,11 @@
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                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -23808,11 +20770,11 @@
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                     "task_name": "MergeSorted",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -23820,11 +20782,11 @@
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-                    "stop_time": "2021-02-08T21:11:28.921Z",
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                     "task_name": "ModifyGtf",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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@@ -23832,47 +20794,47 @@
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                     "memory": "18 GB",
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+                    "start_time": "2021-02-09T08:09:46.189Z",
+                    "stop_time": "2021-02-09T08:35:59.307Z",
                     "task_name": "OptimusLoomGeneration",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
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                 {
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-                    "stop_time": "2021-02-09T06:14:05.315Z",
+                    "start_time": "2021-02-08T23:48:01.749Z",
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                     "task_name": "PreUMISort",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -23880,11 +20842,11 @@
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+                    "log_err": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fe261b23-efd5-445b-8dd4-46e47231ccff/call-RunEmptyDrops/stderr",
+                    "log_out": "gs://fc-31f4efbd-841c-4ea7-b1ca-65567bdd34db/917332c6-9613-43de-8d7c-79787c03d548/Optimus/fe261b23-efd5-445b-8dd4-46e47231ccff/call-RunEmptyDrops/stdout",
                     "memory": "15.625 GB",
-                    "start_time": "2021-02-09T07:37:25.090Z",
-                    "stop_time": "2021-02-09T07:47:44.307Z",
+                    "start_time": "2021-02-09T07:37:09.789Z",
+                    "stop_time": "2021-02-09T07:48:38.311Z",
                     "task_name": "RunEmptyDrops",
                     "zone": "us-central1-b,us-central1-c,us-central1-f"
                 },
@@ -23892,11 +20854,11 @@
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@@ -26074,22 +23609,22 @@
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@@ -26100,23 +23635,77 @@
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@@ -26126,24 +23715,24 @@
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@@ -26153,24 +23742,24 @@
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@@ -26182,22 +23771,22 @@
             },
             "read_index": "read2",
             "insdc_run_accessions": [
-                "ERR3585525"
+                "ERR3585519"
             ],
-            "library_prep_id": "F08-LIV-3p-CD45pos_1",
+            "library_prep_id": "F13-LIV-3p-CD45neg",
             "provenance": {
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-                "submission_date": "2020-08-13T10:24:33.420Z",
-                "update_date": "2020-08-13T11:13:06.966Z",
+                "document_id": "dfe9cbbb-cf19-4e2d-bd3c-70e0d9235f67",
+                "submission_date": "2020-08-13T10:24:33.109Z",
+                "update_date": "2020-08-13T11:34:01.190Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
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         },
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             "schema_type": "file",
             "file_core": {
-                "file_name": "FCAImmP7198434_S1_L001_I1_001.fastq.gz",
+                "file_name": "FCAImmP7179363_S1_L001_R2_001.fastq.gz",
                 "format": "fastq.gz",
                 "content_description": [
                     {
@@ -26207,24 +23796,24 @@
                     }
                 ]
             },
-            "read_index": "index1",
+            "read_index": "read2",
             "insdc_run_accessions": [
-                "ERR3585509"
+                "ERR3585507"
             ],
-            "library_prep_id": "F07-LIV-3p-live",
+            "library_prep_id": "F14-LIV-3p-CD45pos",
             "provenance": {
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-                "submission_date": "2020-08-13T10:24:32.564Z",
-                "update_date": "2020-08-13T10:39:14.148Z",
+                "document_id": "e512685e-d15e-4b12-9f7f-e871da115586",
+                "submission_date": "2020-08-13T10:24:32.515Z",
+                "update_date": "2020-08-13T11:37:49.131Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
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             "schema_type": "file",
             "file_core": {
-                "file_name": "FCAImmP7198630_S1_L001_I1_001.fastq.gz",
+                "file_name": "FCAImmP7579223_S1_L001_R2_001.fastq.gz",
                 "format": "fastq.gz",
                 "content_description": [
                     {
@@ -26234,24 +23823,24 @@
                     }
                 ]
             },
-            "read_index": "index1",
+            "read_index": "read2",
             "insdc_run_accessions": [
-                "ERR3585512"
+                "ERR3585569"
             ],
-            "library_prep_id": "F10-LIV-3p-CD45pos",
+            "library_prep_id": "F11-LIV-3p-CD45neg_2",
             "provenance": {
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-                "submission_date": "2020-08-13T10:24:32.673Z",
-                "update_date": "2020-08-13T10:42:35.843Z",
+                "document_id": "e779b50e-a892-4a0c-af02-2dd400956018",
+                "submission_date": "2020-08-13T10:24:35.477Z",
+                "update_date": "2020-08-13T11:22:43.573Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
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         },
-        "sequence_file_8.json": {
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             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
-                "file_name": "4834STDY7002882_S1_L001_I1_001.fastq.gz",
+                "file_name": "FCAImmP7316892_S1_L001_R1_001.fastq.gz",
                 "format": "fastq.gz",
                 "content_description": [
                     {
@@ -26261,24 +23850,24 @@
                     }
                 ]
             },
-            "read_index": "index1",
+            "read_index": "read1",
             "insdc_run_accessions": [
-                "ERR3585499"
+                "ERR3585528"
             ],
-            "library_prep_id": "F06-LIV-3p-live",
+            "library_prep_id": "F08-LIV-3p-CD45neg_1",
             "provenance": {
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-                "submission_date": "2020-08-13T10:24:32.196Z",
-                "update_date": "2020-08-13T10:37:40.733Z",
+                "document_id": "e79faefc-5135-4e43-a64d-8db7472d3f2e",
+                "submission_date": "2020-08-13T10:24:33.537Z",
+                "update_date": "2020-08-13T10:52:20.471Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_9.json": {
+        "sequence_file_110.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
-                "file_name": "4834STDY7002877_S1_L001_I1_001.fastq.gz",
+                "file_name": "FCAImmP7352194_S1_L001_R2_001.fastq.gz",
                 "format": "fastq.gz",
                 "content_description": [
                     {
@@ -26288,24 +23877,24 @@
                     }
                 ]
             },
-            "read_index": "index1",
+            "read_index": "read2",
             "insdc_run_accessions": [
-                "ERR3585494"
+                "ERR3585541"
             ],
-            "library_prep_id": "F04-LIV-3p-CD45pos",
+            "library_prep_id": "F05-LIV-3p-CD45neg_1",
             "provenance": {
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-                "submission_date": "2020-08-13T10:24:32.019Z",
-                "update_date": "2020-08-13T10:38:39.835Z",
+                "document_id": "e97d853f-aaf2-4b69-8300-f9aac8111c39",
+                "submission_date": "2020-08-13T10:24:34.199Z",
+                "update_date": "2020-08-13T12:05:20.548Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_10.json": {
+        "sequence_file_111.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
-                "file_name": "FCAImmP7555847_S1_L001_R1_001.fastq.gz",
+                "file_name": "4834STDY7038750_S1_L001_R1_001.fastq.gz",
                 "format": "fastq.gz",
                 "content_description": [
                     {
@@ -26317,22 +23906,22 @@
             },
             "read_index": "read1",
             "insdc_run_accessions": [
-                "ERR3585563"
+                "ERR3585503"
             ],
-            "library_prep_id": "F15-LIV-3p-CD45neg",
+            "library_prep_id": "F06-LIV-3p-CD45pos",
             "provenance": {
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-                "submission_date": "2020-08-13T10:24:35.172Z",
-                "update_date": "2020-08-13T11:16:13.175Z",
+                "document_id": "ea99b549-cd95-445b-a796-a4ccd992491d",
+                "submission_date": "2020-08-13T10:24:32.351Z",
+                "update_date": "2020-08-13T11:43:26.209Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_11.json": {
+        "sequence_file_112.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
-                "file_name": "FCAImmP7179364_S1_L001_R2_001.fastq.gz",
+                "file_name": "FCAImmP7277553_S1_L001_I1_001.fastq.gz",
                 "format": "fastq.gz",
                 "content_description": [
                     {
@@ -26342,24 +23931,24 @@
                     }
                 ]
             },
-            "read_index": "read2",
+            "read_index": "index1",
             "insdc_run_accessions": [
-                "ERR3585508"
+                "ERR3585517"
             ],
-            "library_prep_id": "F14-LIV-3p-CD45neg",
+            "library_prep_id": "F16-LIV-3p-CD45neg",
             "provenance": {
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-                "submission_date": "2020-08-13T10:24:32.552Z",
-                "update_date": "2020-08-13T11:31:22.828Z",
+                "document_id": "ed8bc174-30cc-4fa4-9e48-0543b825b1e4",
+                "submission_date": "2020-08-13T10:24:32.870Z",
+                "update_date": "2020-08-13T10:48:28.010Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_12.json": {
+        "sequence_file_113.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
-                "file_name": "FCAImmP7352193_S1_L001_R1_001.fastq.gz",
+                "file_name": "FCAImmP7316894_S1_L001_R1_001.fastq.gz",
                 "format": "fastq.gz",
                 "content_description": [
                     {
@@ -26371,49 +23960,49 @@
             },
             "read_index": "read1",
             "insdc_run_accessions": [
-                "ERR3585540"
+                "ERR3585530"
             ],
-            "library_prep_id": "F05-LIV-3p-CD45pos_2",
+            "library_prep_id": "F02-LIV-3p-CD45pos",
             "provenance": {
-                "document_id": "22d5f584-ff73-4a10-8377-387983b72a87",
-                "submission_date": "2020-08-13T10:24:34.149Z",
-                "update_date": "2020-08-13T10:59:32.332Z",
+                "document_id": "ee9ad501-69c5-49df-89d2-32ea89591634",
+                "submission_date": "2020-08-13T10:24:33.616Z",
+                "update_date": "2020-08-13T10:59:05.921Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_13.json": {
+        "sequence_file_114.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
-                "file_name": "FCAImmP7198629_S1_L001_R2_001.fastq.gz",
+                "file_name": "4834STDY7002877_S1_L001_R2_001.fastq.gz",
                 "format": "fastq.gz",
                 "content_description": [
                     {
                         "text": "single cell RNA sequencing file",
                         "ontology": "data:3495",
-                        "ontology_label": "DNA sequence"
+                        "ontology_label": "Cellular Genetics"
                     }
                 ]
             },
             "read_index": "read2",
             "insdc_run_accessions": [
-                "ERR3585511"
+                "ERR3585494"
             ],
-            "library_prep_id": "F07-LIV-3p-CD45neg",
+            "library_prep_id": "F04-LIV-3p-CD45pos",
             "provenance": {
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-                "submission_date": "2020-08-13T10:24:32.661Z",
-                "update_date": "2020-08-13T11:38:08.593Z",
+                "document_id": "f17d1da2-2965-4732-a94a-6cd2a58fc873",
+                "submission_date": "2020-08-13T10:24:32.044Z",
+                "update_date": "2020-08-13T12:20:35.251Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_14.json": {
+        "sequence_file_115.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
-                "file_name": "4834STDY7038751_S1_L001_R1_001.fastq.gz",
+                "file_name": "FCAImmP7316895_S1_L001_R1_001.fastq.gz",
                 "format": "fastq.gz",
                 "content_description": [
                     {
@@ -26425,22 +24014,22 @@
             },
             "read_index": "read1",
             "insdc_run_accessions": [
-                "ERR3585504"
+                "ERR3585531"
             ],
-            "library_prep_id": "F06-LIV-3p-CD45neg",
+            "library_prep_id": "F02-LIV-3p-CD45neg",
             "provenance": {
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-                "submission_date": "2020-08-13T10:24:32.387Z",
-                "update_date": "2020-08-13T11:41:32.304Z",
+                "document_id": "f683fadf-dd8c-4cfe-ae8b-34e3af5b74a1",
+                "submission_date": "2020-08-13T10:24:33.652Z",
+                "update_date": "2020-08-13T10:58:14.123Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_15.json": {
+        "sequence_file_116.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
-                "file_name": "FCAImmP7579223_S1_L001_I1_001.fastq.gz",
+                "file_name": "FCAImmP7462238_S1_L001_I1_001.fastq.gz",
                 "format": "fastq.gz",
                 "content_description": [
                     {
@@ -26452,22 +24041,22 @@
             },
             "read_index": "index1",
             "insdc_run_accessions": [
-                "ERR3585569"
+                "ERR3585545"
             ],
-            "library_prep_id": "F11-LIV-3p-CD45neg_2",
+            "library_prep_id": "F03-LIV-3p-CD45pos_2",
             "provenance": {
-                "document_id": "24c3ce12-e4f9-4299-a005-320d602716ce",
-                "submission_date": "2020-08-13T10:24:35.400Z",
-                "update_date": "2020-08-13T10:59:45.133Z",
+                "document_id": "f895f666-e3ed-4a7e-a7f5-42586a6244ea",
+                "submission_date": "2020-08-13T10:24:34.328Z",
+                "update_date": "2020-08-13T10:50:43.824Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_16.json": {
+        "sequence_file_117.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
-                "file_name": "FCAImmP7352194_S1_L001_I1_001.fastq.gz",
+                "file_name": "FCAImmP7316892_S1_L001_R2_001.fastq.gz",
                 "format": "fastq.gz",
                 "content_description": [
                     {
@@ -26477,24 +24066,24 @@
                     }
                 ]
             },
-            "read_index": "index1",
+            "read_index": "read2",
             "insdc_run_accessions": [
-                "ERR3585541"
+                "ERR3585528"
             ],
-            "library_prep_id": "F05-LIV-3p-CD45neg_1",
+            "library_prep_id": "F08-LIV-3p-CD45neg_1",
             "provenance": {
-                "document_id": "26131c11-6186-4b1a-b37d-fb12515622bf",
-                "submission_date": "2020-08-13T10:24:34.175Z",
-                "update_date": "2020-08-13T10:50:36.362Z",
+                "document_id": "fa78c4ab-4057-45b1-8266-af045ae28535",
+                "submission_date": "2020-08-13T10:24:33.552Z",
+                "update_date": "2020-08-13T11:49:22.980Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_17.json": {
+        "sequence_file_118.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
-                "file_name": "FCAImmP7316894_S1_L001_R2_001.fastq.gz",
+                "file_name": "FCAImmP7462237_S1_L001_I1_001.fastq.gz",
                 "format": "fastq.gz",
                 "content_description": [
                     {
@@ -26504,24 +24093,24 @@
                     }
                 ]
             },
-            "read_index": "read2",
+            "read_index": "index1",
             "insdc_run_accessions": [
-                "ERR3585530"
+                "ERR3585544"
             ],
-            "library_prep_id": "F02-LIV-3p-CD45pos",
+            "library_prep_id": "F03-LIV-3p-CD45pos_1",
             "provenance": {
-                "document_id": "28f5f863-26d9-4ca8-abb3-705d369250e7",
-                "submission_date": "2020-08-13T10:24:33.628Z",
-                "update_date": "2020-08-13T11:47:12.375Z",
+                "document_id": "fd0752c7-210b-4acd-a7ef-df7ffcdfbd3d",
+                "submission_date": "2020-08-13T10:24:34.290Z",
+                "update_date": "2020-08-13T10:50:37.439Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_18.json": {
+        "sequence_file_119.json": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
-                "file_name": "FCAImmP7198631_S1_L001_R2_001.fastq.gz",
+                "file_name": "FCAImmP7198629_S1_L001_I1_001.fastq.gz",
                 "format": "fastq.gz",
                 "content_description": [
                     {
@@ -26531,2891 +24120,2319 @@
                     }
                 ]
             },
-            "read_index": "read2",
-            "insdc_run_accessions": [
-                "ERR3585513"
-            ],
-            "library_prep_id": "F10-LIV-3p-CD45neg",
+            "read_index": "index1",
+            "insdc_run_accessions": [
+                "ERR3585511"
+            ],
+            "library_prep_id": "F07-LIV-3p-CD45neg",
+            "provenance": {
+                "document_id": "ffba13e2-0937-49b3-961a-2ce3055ad5c6",
+                "submission_date": "2020-08-13T10:24:32.637Z",
+                "update_date": "2020-08-13T10:41:37.764Z",
+                "schema_major_version": 9,
+                "schema_minor_version": 2
+            }
+        },
+        "sequencing_protocol_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "gex_10x_sequencing",
+                "protocol_name": "10x nucleic acid sequencing protocol",
+                "protocol_description": "The libraries from eight loaded channels from each fetal sample were multiplexed together and sequenced on an Illumina HiSeq 4000. The libraries were distributed over eight lanes per flow cell and sequenced using the following parameters: Read1: 26 cycles, i7: 8 cycles, i5: 0 cycles; Read2: 98 cycles to generate 75bp paired end reads."
+            },
+            "instrument_manufacturer_model": {
+                "text": "Illumina HiSeq 4000",
+                "ontology": "EFO:0008563",
+                "ontology_label": "Illumina HiSeq 4000"
+            },
+            "paired_end": false,
+            "method": {
+                "text": "single cell RNA sequencing",
+                "ontology": "EFO:0008440",
+                "ontology_label": "tag based single cell RNA sequencing"
+            },
+            "provenance": {
+                "document_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a",
+                "submission_date": "2020-08-13T10:24:31.936Z",
+                "update_date": "2020-08-13T10:24:38.042Z",
+                "schema_major_version": 10,
+                "schema_minor_version": 1
+            }
+        },
+        "dissociation_protocol_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "haniffa_enzymatic_dissociation",
+                "protocol_name": "Haniffa Lab Enzymatic Dissociation",
+                "protocol_description": "Tissue was digested with 1.6mg/mL collagenase type IV (Worthington) in RPMI (Sigma-Aldrich) supplemented with 10%(v/v) heat-inactivated fetal bovine serum (Gibco), 100U/mL penicillin (Sigma-Aldrich), 0.1mg/mL streptomycin (Sigma-Aldrich), and 2mM L-Glutamine (Sigma-Aldrich) for 30 minutes at 37\u00b0C with intermittent shaking. Digested tissue was passed through a 100\u03bcm filter, and cells collected by centrifugation (500g for 5 minutes at 4\u00b0C). Cells were treated with 1X RBC lysis buffer (eBioscience) for 5 minutes at room temperature and washed once with flow buffer (PBS containing 5%(v/v) FBS and 2mM EDTA) prior to counting."
+            },
+            "method": {
+                "text": "enzymatic dissociation",
+                "ontology": "EFO:0009128",
+                "ontology_label": "enzymatic dissociation"
+            },
+            "provenance": {
+                "document_id": "8881df7f-15da-48a9-8934-a2d65188543e",
+                "submission_date": "2020-08-13T10:24:31.911Z",
+                "update_date": "2020-08-13T10:24:38.803Z",
+                "schema_major_version": 6,
+                "schema_minor_version": 2
+            }
+        },
+        "enrichment_protocol_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "CD45_pos",
+                "protocol_name": "CD45 positive enrichment",
+                "protocol_description": "Antibody panels were designed to allow enrichment of cell fractions for sequencing and cell types validation. Antibodies used for FACS isolation are listed in Supplementary Table 1. An antibody cocktail was prepared fresh by adding 3\u03bcL of each antibody in 50\u03bcL Brilliant Stain Buffer (BD) per tissue. Cells (\u226410x106) were resuspended in 50-100\u03bcL flow buffer and an equal volume of antibody mix was added to cells from each tissue. Cells were stained for 30 minutes on ice, washed with flow buffer and resuspended at 10x106cells/mL. DAPI (Sigma-Aldrich) was added to a final concentration of 3\u03bcM immediately prior to sorting. Flow sorting was performed on a BD FACSAriaTM Fusion instrument using DIVAv8, and data analysed using FlowJoV10.4.1. Cells were gated to remove dead cells and doublets, and then isolated for scRNA-seq analysis (10x or Smart-seq2). For 10x, cells were sorted into chilled FACS tubes coated with FBS and prefilled with 500\u03bcL sterile PBS. For Smart-seq2, single cells were index-sorted into 96-well lo-bind plates (Eppendorf) containing 10\u03bcL lysis buffer (TCL (Qiagen) + 1% (v/v) B-mercaptoethanol) per well. B cells were also investigated by flow cytometry as per Roy et. al.,77."
+            },
+            "method": {
+                "text": "FACs sort",
+                "ontology": "EFO:0009108",
+                "ontology_label": "fluorescence-activated cell sorting"
+            },
+            "markers": "CD45+ HLA-DR+",
             "provenance": {
-                "document_id": "2b40b918-2632-4a06-9746-6f542d884b90",
-                "submission_date": "2020-08-13T10:24:32.734Z",
-                "update_date": "2020-08-13T11:32:35.520Z",
-                "schema_major_version": 9,
-                "schema_minor_version": 2
+                "document_id": "003cb4a8-9871-488f-9042-820504991f17",
+                "submission_date": "2020-08-13T10:24:31.885Z",
+                "update_date": "2020-08-13T10:24:37.977Z",
+                "schema_major_version": 3,
+                "schema_minor_version": 1
             }
         },
-        "sequence_file_19.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
-            "schema_type": "file",
-            "file_core": {
-                "file_name": "4834STDY7038751_S1_L001_I1_001.fastq.gz",
-                "format": "fastq.gz",
-                "content_description": [
-                    {
-                        "text": "single cell RNA sequencing file",
-                        "ontology": "data:3495",
-                        "ontology_label": "DNA sequence"
-                    }
-                ]
+        "enrichment_protocol_1.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "live_cell",
+                "protocol_name": "dead cell removal",
+                "protocol_description": "Cells were gated to remove dead cells and doublets"
             },
-            "read_index": "index1",
-            "insdc_run_accessions": [
-                "ERR3585504"
-            ],
-            "library_prep_id": "F06-LIV-3p-CD45neg",
+            "method": {
+                "text": "dead cell removal",
+                "ontology": "EFO:0009108",
+                "ontology_label": "fluorescence-activated cell sorting"
+            },
+            "markers": "DAPI",
             "provenance": {
-                "document_id": "30286c6d-ca78-4108-aff5-6809618656dc",
-                "submission_date": "2020-08-13T10:24:32.375Z",
-                "update_date": "2020-08-13T10:42:36.486Z",
-                "schema_major_version": 9,
-                "schema_minor_version": 2
+                "document_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea",
+                "submission_date": "2020-08-13T10:24:31.902Z",
+                "update_date": "2020-08-13T10:24:37.891Z",
+                "schema_major_version": 3,
+                "schema_minor_version": 1
             }
         },
-        "sequence_file_20.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
-            "schema_type": "file",
-            "file_core": {
-                "file_name": "FCAImmP7316891_S1_L001_R2_001.fastq.gz",
-                "format": "fastq.gz",
-                "content_description": [
-                    {
-                        "text": "single cell RNA sequencing file",
-                        "ontology": "data:3495",
-                        "ontology_label": "DNA sequence"
-                    }
-                ]
+        "enrichment_protocol_2.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "CD45_neg",
+                "protocol_name": "CD45 negative enrichment",
+                "protocol_description": "Antibody panels were designed to allow enrichment of cell fractions for sequencing and cell types validation. Antibodies used for FACS isolation are listed in Supplementary Table 1. An antibody cocktail was prepared fresh by adding 3\u03bcL of each antibody in 50\u03bcL Brilliant Stain Buffer (BD) per tissue. Cells (\u226410x106) were resuspended in 50-100\u03bcL flow buffer and an equal volume of antibody mix was added to cells from each tissue. Cells were stained for 30 minutes on ice, washed with flow buffer and resuspended at 10x106cells/mL. DAPI (Sigma-Aldrich) was added to a final concentration of 3\u03bcM immediately prior to sorting. Flow sorting was performed on a BD FACSAriaTM Fusion instrument using DIVAv8, and data analysed using FlowJoV10.4.1. Cells were gated to remove dead cells and doublets, and then isolated for scRNA-seq analysis (10x or Smart-seq2). For 10x, cells were sorted into chilled FACS tubes coated with FBS and prefilled with 500\u03bcL sterile PBS. For Smart-seq2, single cells were index-sorted into 96-well lo-bind plates (Eppendorf) containing 10\u03bcL lysis buffer (TCL (Qiagen) + 1% (v/v) B-mercaptoethanol) per well. B cells were also investigated by flow cytometry as per Roy et. al.,77."
             },
-            "read_index": "read2",
-            "insdc_run_accessions": [
-                "ERR3585527"
-            ],
-            "library_prep_id": "F08-LIV-3p-CD45pos_3",
+            "method": {
+                "text": "FACs sort",
+                "ontology": "EFO:0009108",
+                "ontology_label": "fluorescence-activated cell sorting"
+            },
+            "markers": "CD45- HLA-DR-",
             "provenance": {
-                "document_id": "32714f4f-1a04-4fc3-bdd9-2ae6473fe544",
-                "submission_date": "2020-08-13T10:24:33.513Z",
-                "update_date": "2020-08-13T11:52:21.084Z",
+                "document_id": "f1903d0b-1cb2-4208-bc20-a37ad8612452",
+                "submission_date": "2020-08-13T10:24:31.894Z",
+                "update_date": "2020-08-13T10:24:39.224Z",
+                "schema_major_version": 3,
+                "schema_minor_version": 1
+            }
+        },
+        "collection_protocol_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
+            "schema_type": "protocol",
+            "protocol_core": {
+                "protocol_id": "hdbr_collection",
+                "protocol_name": "HDBR collection",
+                "protocol_description": "Tissue was transferred to a sterile 10mm2 tissue culture dish and cut into <1mm3 segments before being transferred to a 50mL conical tube. Tissue was digested with 1.6mg/mL collagenase type IV (Worthington) in RPMI (Sigma- Aldrich) supplemented with 10%(v/v) heat-inactivated fetal bovine serum (Gibco), 100U/mL penicillin (Sigma-Aldrich), 0.1mg/mL streptomycin (Sigma-Aldrich), and 2mM L-Glutamine (Sigma-Aldrich) for 30 minutes at 37\u00b0C with intermittent shaking. Digested tissue was passed through a 100\u03bcm filter, and cells collected by centrifugation (500g for 5 minutes at 4\u00b0C). Cells were treated with 1X RBC lysis buffer (eBioscience) for 5 minutes at room temperature and washed once with flow buffer (PBS containing 5%(v/v) FBS and 2mM EDTA) prior to counting."
+            },
+            "method": {
+                "text": "collecting specimen from organ postmortem",
+                "ontology": "EFO:0009627",
+                "ontology_label": "collecting specimen from organ postmortem"
+            },
+            "provenance": {
+                "document_id": "266cf33e-5540-42cd-84de-757340908d42",
+                "submission_date": "2020-08-13T10:24:31.877Z",
+                "update_date": "2020-08-13T10:24:38.996Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
         },
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-                "file_name": "FCAImmP7198631_S1_L001_I1_001.fastq.gz",
-                "format": "fastq.gz",
-                "content_description": [
-                    {
-                        "text": "single cell RNA sequencing file",
-                        "ontology": "data:3495",
-                        "ontology_label": "DNA sequence"
-                    }
+        "specimen_from_organism_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F05-LIV",
+                "biomaterial_name": "F05-LIV",
+                "biomaterial_description": "Liver sample from F05, F34 in internal tracking",
+                "ncbi_taxon_id": [
+                    9606
                 ]
             },
-            "read_index": "index1",
-            "insdc_run_accessions": [
-                "ERR3585513"
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
+                }
             ],
-            "library_prep_id": "F10-LIV-3p-CD45neg",
+            "organ": {
+                "text": "Liver",
+                "ontology": "UBERON:0002107",
+                "ontology_label": "liver"
+            },
             "provenance": {
-                "document_id": "32a5b3e4-4f2f-4fb1-aeff-7fb01035eb8d",
-                "submission_date": "2020-08-13T10:24:32.709Z",
-                "update_date": "2020-08-13T10:45:47.623Z",
-                "schema_major_version": 9,
-                "schema_minor_version": 2
-            }
+                "document_id": "0d27ca8e-5325-4e47-9807-8afd92e9bf89",
+                "submission_date": "2020-08-13T10:24:30.913Z",
+                "update_date": "2020-08-13T10:24:45.671Z",
+                "schema_major_version": 10,
+                "schema_minor_version": 4
+            },
+            "diseases": [
+                {
+                    "text": "normal",
+                    "ontology_label": "normal",
+                    "ontology": "PATO:0000461"
+                }
+            ]
         },
-        "sequence_file_22.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
-            "schema_type": "file",
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-                "format": "fastq.gz",
-                "content_description": [
-                    {
-                        "text": "single cell RNA sequencing file",
-                        "ontology": "data:3495",
-                        "ontology_label": "Cellular Genetics"
-                    }
+        "specimen_from_organism_1.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F11-LIV",
+                "biomaterial_name": "F11-LIV",
+                "biomaterial_description": "Liver sample from F11, F45 in internal tracking",
+                "ncbi_taxon_id": [
+                    9606
                 ]
             },
-            "read_index": "read1",
-            "insdc_run_accessions": [
-                "ERR3585494"
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
+                }
             ],
-            "library_prep_id": "F04-LIV-3p-CD45pos",
+            "organ": {
+                "text": "Liver",
+                "ontology": "UBERON:0002107",
+                "ontology_label": "liver"
+            },
             "provenance": {
-                "document_id": "336b106c-f5f3-4d35-b583-05fc33ee910f",
-                "submission_date": "2020-08-13T10:24:32.031Z",
-                "update_date": "2020-08-13T11:09:07.268Z",
-                "schema_major_version": 9,
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-            }
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+                "submission_date": "2020-08-13T10:24:31.037Z",
+                "update_date": "2020-08-13T10:24:48.049Z",
+                "schema_major_version": 10,
+                "schema_minor_version": 4
+            },
+            "diseases": [
+                {
+                    "text": "normal",
+                    "ontology_label": "normal",
+                    "ontology": "PATO:0000461"
+                }
+            ]
         },
-        "sequence_file_23.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
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-                "content_description": [
-                    {
-                        "text": "single cell RNA sequencing file",
-                        "ontology": "data:3495",
-                        "ontology_label": "DNA sequence"
-                    }
+        "specimen_from_organism_2.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F12-LIV",
+                "biomaterial_name": "F12-LIV",
+                "biomaterial_description": "Liver sample from F12, F38 in internal tracking",
+                "ncbi_taxon_id": [
+                    9606
                 ]
             },
-            "read_index": "index1",
-            "insdc_run_accessions": [
-                "ERR3585519"
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
+                }
             ],
-            "library_prep_id": "F13-LIV-3p-CD45neg",
+            "organ": {
+                "text": "Liver",
+                "ontology": "UBERON:0002107",
+                "ontology_label": "liver"
+            },
             "provenance": {
-                "document_id": "384733f9-328f-4b3f-b201-9489ae09f5de",
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-                "update_date": "2020-08-13T10:52:42.153Z",
-                "schema_major_version": 9,
-                "schema_minor_version": 2
-            }
+                "document_id": "31899978-a518-4d78-b85a-f62bca7ed723",
+                "submission_date": "2020-08-13T10:24:31.046Z",
+                "update_date": "2020-08-13T10:24:48.247Z",
+                "schema_major_version": 10,
+                "schema_minor_version": 4
+            },
+            "diseases": [
+                {
+                    "text": "normal",
+                    "ontology_label": "normal",
+                    "ontology": "PATO:0000461"
+                }
+            ]
         },
-        "sequence_file_24.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
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-                "content_description": [
-                    {
-                        "text": "single cell RNA sequencing file",
-                        "ontology": "data:3495",
-                        "ontology_label": "DNA sequence"
-                    }
+        "specimen_from_organism_3.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F10-LIV",
+                "biomaterial_name": "F10-LIV",
+                "biomaterial_description": "Liver sample from F10, F23 in internal tracking",
+                "ncbi_taxon_id": [
+                    9606
                 ]
             },
-            "read_index": "index1",
-            "insdc_run_accessions": [
-                "ERR3585566"
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
+                }
             ],
-            "library_prep_id": "F11-LIV-3p-CD45pos_1",
+            "organ": {
+                "text": "Liver",
+                "ontology": "UBERON:0002107",
+                "ontology_label": "liver"
+            },
             "provenance": {
-                "document_id": "38b67b47-7ef3-4e9e-88e1-3a8376769eb0",
-                "submission_date": "2020-08-13T10:24:35.268Z",
-                "update_date": "2020-08-13T11:00:05.681Z",
-                "schema_major_version": 9,
-                "schema_minor_version": 2
-            }
+                "document_id": "54bfca9c-a1f8-4632-a0cb-5f7b5edf48d6",
+                "submission_date": "2020-08-13T10:24:31.028Z",
+                "update_date": "2020-08-13T10:24:47.734Z",
+                "schema_major_version": 10,
+                "schema_minor_version": 4
+            },
+            "diseases": [
+                {
+                    "text": "normal",
+                    "ontology_label": "normal",
+                    "ontology": "PATO:0000461"
+                }
+            ]
         },
-        "sequence_file_25.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
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-                "format": "fastq.gz",
-                "content_description": [
-                    {
-                        "text": "single cell RNA sequencing file",
-                        "ontology": "data:3495",
-                        "ontology_label": "DNA sequence"
-                    }
+        "specimen_from_organism_4.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F02-LIV",
+                "biomaterial_name": "F02-LIV",
+                "biomaterial_description": "Liver sample from F02, F32 in internal tracking",
+                "ncbi_taxon_id": [
+                    9606
                 ]
             },
-            "read_index": "read1",
-            "insdc_run_accessions": [
-                "ERR3585519"
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
+                }
             ],
-            "library_prep_id": "F13-LIV-3p-CD45neg",
+            "organ": {
+                "text": "Liver",
+                "ontology": "UBERON:0002107",
+                "ontology_label": "liver"
+            },
             "provenance": {
-                "document_id": "39c59048-bac9-4b5b-935b-75b150931f41",
-                "submission_date": "2020-08-13T10:24:33.086Z",
-                "update_date": "2020-08-13T11:00:30.339Z",
-                "schema_major_version": 9,
-                "schema_minor_version": 2
-            }
+                "document_id": "619887a0-67fb-4e24-be95-409f9b3e8474",
+                "submission_date": "2020-08-13T10:24:30.811Z",
+                "update_date": "2020-08-13T10:24:44.837Z",
+                "schema_major_version": 10,
+                "schema_minor_version": 4
+            },
+            "diseases": [
+                {
+                    "text": "normal",
+                    "ontology_label": "normal",
+                    "ontology": "PATO:0000461"
+                }
+            ]
         },
-        "sequence_file_26.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
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-                "format": "fastq.gz",
-                "content_description": [
-                    {
-                        "text": "single cell RNA sequencing file",
-                        "ontology": "data:3495",
-                        "ontology_label": "DNA sequence"
-                    }
+        "specimen_from_organism_5.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F04-LIV",
+                "biomaterial_name": "F04-LIV",
+                "biomaterial_description": "Liver sample from F04, F16 in internal tracking",
+                "ncbi_taxon_id": [
+                    9606
                 ]
             },
-            "read_index": "index1",
-            "insdc_run_accessions": [
-                "ERR3585540"
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
+                }
             ],
-            "library_prep_id": "F05-LIV-3p-CD45pos_2",
+            "organ": {
+                "text": "Liver",
+                "ontology": "UBERON:0002107",
+                "ontology_label": "liver"
+            },
             "provenance": {
-                "document_id": "3c6b5196-4dd9-4c23-a9d1-c1341d889ecf",
-                "submission_date": "2020-08-13T10:24:34.137Z",
-                "update_date": "2020-08-13T10:50:36.239Z",
-                "schema_major_version": 9,
-                "schema_minor_version": 2
-            }
+                "document_id": "69576784-ca06-4ccb-bab7-d6e8353a8036",
+                "submission_date": "2020-08-13T10:24:30.896Z",
+                "update_date": "2020-08-13T10:24:45.260Z",
+                "schema_major_version": 10,
+                "schema_minor_version": 4
+            },
+            "diseases": [
+                {
+                    "text": "normal",
+                    "ontology_label": "normal",
+                    "ontology": "PATO:0000461"
+                }
+            ]
         },
-        "sequence_file_27.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
-            "schema_type": "file",
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-                "content_description": [
-                    {
-                        "text": "single cell RNA sequencing file",
-                        "ontology": "data:3495",
-                        "ontology_label": "DNA sequence"
-                    }
+        "specimen_from_organism_6.json": {
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+                "document_id": "f4183399-0e70-466e-8915-8e4481f9b7d1",
+                "submission_date": "2020-08-13T10:24:42.954Z",
+                "update_date": "2020-08-13T10:25:13.344Z",
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
         },
-        "sequencing_protocol_0.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
-            "schema_type": "protocol",
-            "protocol_core": {
-                "protocol_id": "gex_10x_sequencing",
-                "protocol_name": "10x nucleic acid sequencing protocol",
-                "protocol_description": "The libraries from eight loaded channels from each fetal sample were multiplexed together and sequenced on an Illumina HiSeq 4000. The libraries were distributed over eight lanes per flow cell and sequenced using the following parameters: Read1: 26 cycles, i7: 8 cycles, i5: 0 cycles; Read2: 98 cycles to generate 75bp paired end reads."
-            },
-            "instrument_manufacturer_model": {
-                "text": "Illumina HiSeq 4000",
-                "ontology": "EFO:0008563",
-                "ontology_label": "Illumina HiSeq 4000"
+        "process_92.json": {
+            "insdc_experiment": {
+                "insdc_experiment_accession": "ERX3581451"
             },
-            "paired_end": false,
-            "method": {
-                "text": "single cell RNA sequencing",
-                "ontology": "EFO:0008440",
-                "ontology_label": "tag based single cell RNA sequencing"
+            "process_core": {
+                "process_id": "process_id_73"
             },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/9.2.0/process",
             "provenance": {
-                "document_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a",
-                "submission_date": "2020-08-13T10:24:31.936Z",
-                "update_date": "2020-08-13T10:24:38.042Z",
-                "schema_major_version": 10,
-                "schema_minor_version": 1
+                "document_id": "f4a448a7-bc5a-4014-ab1f-0d1a8cd4e47c",
+                "submission_date": "2020-08-13T10:24:40.436Z",
+                "update_date": "2020-08-13T10:25:01.813Z",
+                "schema_major_version": 9,
+                "schema_minor_version": 2
             }
         },
-        "dissociation_protocol_0.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
-            "schema_type": "protocol",
-            "protocol_core": {
-                "protocol_id": "haniffa_enzymatic_dissociation",
-                "protocol_name": "Haniffa Lab Enzymatic Dissociation",
-                "protocol_description": "Tissue was digested with 1.6mg/mL collagenase type IV (Worthington) in RPMI (Sigma-Aldrich) supplemented with 10%(v/v) heat-inactivated fetal bovine serum (Gibco), 100U/mL penicillin (Sigma-Aldrich), 0.1mg/mL streptomycin (Sigma-Aldrich), and 2mM L-Glutamine (Sigma-Aldrich) for 30 minutes at 37\u00b0C with intermittent shaking. Digested tissue was passed through a 100\u03bcm filter, and cells collected by centrifugation (500g for 5 minutes at 4\u00b0C). Cells were treated with 1X RBC lysis buffer (eBioscience) for 5 minutes at room temperature and washed once with flow buffer (PBS containing 5%(v/v) FBS and 2mM EDTA) prior to counting."
+        "process_93.json": {
+            "insdc_experiment": {
+                "insdc_experiment_accession": "ERX3581511"
             },
-            "method": {
-                "text": "enzymatic dissociation",
-                "ontology": "EFO:0009128",
-                "ontology_label": "enzymatic dissociation"
+            "process_core": {
+                "process_id": "process_id_91"
             },
+            "schema_type": "process",
+            "describedBy": "https://schema.humancellatlas.org/type/process/9.2.0/process",
             "provenance": {
-                "document_id": "8881df7f-15da-48a9-8934-a2d65188543e",
-                "submission_date": "2020-08-13T10:24:31.911Z",
-                "update_date": "2020-08-13T10:24:38.803Z",
-                "schema_major_version": 6,
+                "document_id": "f70a20e6-ad33-424e-b385-bb9a19be000e",
+                "submission_date": "2020-08-13T10:24:41.616Z",
+                "update_date": "2020-08-13T10:25:02.813Z",
+                "schema_major_version": 9,
                 "schema_minor_version": 2
             }
         },
-        "enrichment_protocol_0.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
-            "schema_type": "protocol",
-            "protocol_core": {
-                "protocol_id": "CD45_pos",
-                "protocol_name": "CD45 positive enrichment",
-                "protocol_description": "Antibody panels were designed to allow enrichment of cell fractions for sequencing and cell types validation. Antibodies used for FACS isolation are listed in Supplementary Table 1. An antibody cocktail was prepared fresh by adding 3\u03bcL of each antibody in 50\u03bcL Brilliant Stain Buffer (BD) per tissue. Cells (\u226410x106) were resuspended in 50-100\u03bcL flow buffer and an equal volume of antibody mix was added to cells from each tissue. Cells were stained for 30 minutes on ice, washed with flow buffer and resuspended at 10x106cells/mL. DAPI (Sigma-Aldrich) was added to a final concentration of 3\u03bcM immediately prior to sorting. Flow sorting was performed on a BD FACSAriaTM Fusion instrument using DIVAv8, and data analysed using FlowJoV10.4.1. Cells were gated to remove dead cells and doublets, and then isolated for scRNA-seq analysis (10x or Smart-seq2). For 10x, cells were sorted into chilled FACS tubes coated with FBS and prefilled with 500\u03bcL sterile PBS. For Smart-seq2, single cells were index-sorted into 96-well lo-bind plates (Eppendorf) containing 10\u03bcL lysis buffer (TCL (Qiagen) + 1% (v/v) B-mercaptoethanol) per well. B cells were also investigated by flow cytometry as per Roy et. al.,77."
-            },
-            "method": {
-                "text": "FACs sort",
-                "ontology": "EFO:0009108",
-                "ontology_label": "fluorescence-activated cell sorting"
+        "cell_suspension_0.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F08-LIV-3p-CD45pos_2",
+                "ncbi_taxon_id": [
+                    9606
+                ],
+                "biosamples_accession": "SAMEA6060678"
             },
-            "markers": "CD45+ HLA-DR+",
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
+                }
+            ],
+            "estimated_cell_count": 3526,
             "provenance": {
-                "document_id": "003cb4a8-9871-488f-9042-820504991f17",
-                "submission_date": "2020-08-13T10:24:31.885Z",
-                "update_date": "2020-08-13T10:24:37.977Z",
-                "schema_major_version": 3,
-                "schema_minor_version": 1
+                "document_id": "02f33fc2-eb2f-4c78-a7f5-002a1747e71f",
+                "submission_date": "2020-08-13T10:24:31.566Z",
+                "update_date": "2020-08-13T10:24:52.923Z",
+                "schema_major_version": 13,
+                "schema_minor_version": 3
             }
         },
-        "enrichment_protocol_1.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
-            "schema_type": "protocol",
-            "protocol_core": {
-                "protocol_id": "live_cell",
-                "protocol_name": "dead cell removal",
-                "protocol_description": "Cells were gated to remove dead cells and doublets"
-            },
-            "method": {
-                "text": "dead cell removal",
-                "ontology": "EFO:0009108",
-                "ontology_label": "fluorescence-activated cell sorting"
+        "cell_suspension_1.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F14-LIV-3p-CD45pos",
+                "ncbi_taxon_id": [
+                    9606
+                ],
+                "biosamples_accession": "SAMEA6060659"
             },
-            "markers": "DAPI",
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
+                }
+            ],
+            "estimated_cell_count": 2607,
             "provenance": {
-                "document_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea",
-                "submission_date": "2020-08-13T10:24:31.902Z",
-                "update_date": "2020-08-13T10:24:37.891Z",
-                "schema_major_version": 3,
-                "schema_minor_version": 1
+                "document_id": "17782e68-694a-42df-9411-9fd875b95cc7",
+                "submission_date": "2020-08-13T10:24:31.793Z",
+                "update_date": "2020-08-13T10:24:54.923Z",
+                "schema_major_version": 13,
+                "schema_minor_version": 3
             }
         },
-        "enrichment_protocol_2.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
-            "schema_type": "protocol",
-            "protocol_core": {
-                "protocol_id": "CD45_neg",
-                "protocol_name": "CD45 negative enrichment",
-                "protocol_description": "Antibody panels were designed to allow enrichment of cell fractions for sequencing and cell types validation. Antibodies used for FACS isolation are listed in Supplementary Table 1. An antibody cocktail was prepared fresh by adding 3\u03bcL of each antibody in 50\u03bcL Brilliant Stain Buffer (BD) per tissue. Cells (\u226410x106) were resuspended in 50-100\u03bcL flow buffer and an equal volume of antibody mix was added to cells from each tissue. Cells were stained for 30 minutes on ice, washed with flow buffer and resuspended at 10x106cells/mL. DAPI (Sigma-Aldrich) was added to a final concentration of 3\u03bcM immediately prior to sorting. Flow sorting was performed on a BD FACSAriaTM Fusion instrument using DIVAv8, and data analysed using FlowJoV10.4.1. Cells were gated to remove dead cells and doublets, and then isolated for scRNA-seq analysis (10x or Smart-seq2). For 10x, cells were sorted into chilled FACS tubes coated with FBS and prefilled with 500\u03bcL sterile PBS. For Smart-seq2, single cells were index-sorted into 96-well lo-bind plates (Eppendorf) containing 10\u03bcL lysis buffer (TCL (Qiagen) + 1% (v/v) B-mercaptoethanol) per well. B cells were also investigated by flow cytometry as per Roy et. al.,77."
+        "cell_suspension_2.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F15-LIV-3p-CD45pos",
+                "ncbi_taxon_id": [
+                    9606
+                ],
+                "biosamples_accession": "SAMEA6060714"
             },
-            "method": {
-                "text": "FACs sort",
-                "ontology": "EFO:0009108",
-                "ontology_label": "fluorescence-activated cell sorting"
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
+                }
+            ],
+            "estimated_cell_count": 3191,
+            "provenance": {
+                "document_id": "1853e602-4743-4179-863b-fb686a6a7a9a",
+                "submission_date": "2020-08-13T10:24:31.810Z",
+                "update_date": "2020-08-13T10:24:55.090Z",
+                "schema_major_version": 13,
+                "schema_minor_version": 3
+            }
+        },
+        "cell_suspension_3.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F07-LIV-3p-live",
+                "ncbi_taxon_id": [
+                    9606
+                ],
+                "biosamples_accession": "SAMEA6060661"
             },
-            "markers": "CD45- HLA-DR-",
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
+                }
+            ],
+            "estimated_cell_count": 4073,
             "provenance": {
-                "document_id": "f1903d0b-1cb2-4208-bc20-a37ad8612452",
-                "submission_date": "2020-08-13T10:24:31.894Z",
-                "update_date": "2020-08-13T10:24:39.224Z",
-                "schema_major_version": 3,
-                "schema_minor_version": 1
+                "document_id": "19b7eb13-fef6-46a4-abb9-44a310e441b5",
+                "submission_date": "2020-08-13T10:24:31.538Z",
+                "update_date": "2020-08-13T10:24:52.756Z",
+                "schema_major_version": 13,
+                "schema_minor_version": 3
             }
         },
-        "collection_protocol_0.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
-            "schema_type": "protocol",
-            "protocol_core": {
-                "protocol_id": "hdbr_collection",
-                "protocol_name": "HDBR collection",
-                "protocol_description": "Tissue was transferred to a sterile 10mm2 tissue culture dish and cut into <1mm3 segments before being transferred to a 50mL conical tube. Tissue was digested with 1.6mg/mL collagenase type IV (Worthington) in RPMI (Sigma- Aldrich) supplemented with 10%(v/v) heat-inactivated fetal bovine serum (Gibco), 100U/mL penicillin (Sigma-Aldrich), 0.1mg/mL streptomycin (Sigma-Aldrich), and 2mM L-Glutamine (Sigma-Aldrich) for 30 minutes at 37\u00b0C with intermittent shaking. Digested tissue was passed through a 100\u03bcm filter, and cells collected by centrifugation (500g for 5 minutes at 4\u00b0C). Cells were treated with 1X RBC lysis buffer (eBioscience) for 5 minutes at room temperature and washed once with flow buffer (PBS containing 5%(v/v) FBS and 2mM EDTA) prior to counting."
+        "cell_suspension_4.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F11-LIV-3p-CD45pos_1",
+                "ncbi_taxon_id": [
+                    9606
+                ],
+                "biosamples_accession": "SAMEA6060718"
             },
-            "method": {
-                "text": "collecting specimen from organ postmortem",
-                "ontology": "EFO:0009627",
-                "ontology_label": "collecting specimen from organ postmortem"
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
+                }
+            ],
+            "estimated_cell_count": 2050,
+            "provenance": {
+                "document_id": "1b8c4fa4-24d0-42b5-99e1-8c04eba5d8c3",
+                "submission_date": "2020-08-13T10:24:31.669Z",
+                "update_date": "2020-08-13T10:24:53.892Z",
+                "schema_major_version": 13,
+                "schema_minor_version": 3
+            }
+        },
+        "cell_suspension_5.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F13-LIV-3p-CD45neg",
+                "ncbi_taxon_id": [
+                    9606
+                ],
+                "biosamples_accession": "SAMEA6060671"
             },
+            "genus_species": [
+                {
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
+                }
+            ],
+            "estimated_cell_count": 4373,
             "provenance": {
-                "document_id": "266cf33e-5540-42cd-84de-757340908d42",
-                "submission_date": "2020-08-13T10:24:31.877Z",
-                "update_date": "2020-08-13T10:24:38.996Z",
-                "schema_major_version": 9,
-                "schema_minor_version": 2
+                "document_id": "1fe49331-d165-4443-a82b-612309cb9567",
+                "submission_date": "2020-08-13T10:24:31.785Z",
+                "update_date": "2020-08-13T10:24:54.852Z",
+                "schema_major_version": 13,
+                "schema_minor_version": 3
             }
         },
-        "specimen_from_organism_0.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
+        "cell_suspension_6.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
-                "biomaterial_id": "F05-LIV",
-                "biomaterial_name": "F05-LIV",
-                "biomaterial_description": "Liver sample from F05, F34 in internal tracking",
+                "biomaterial_id": "F16-LIV-3p-CD45pos",
                 "ncbi_taxon_id": [
                     9606
-                ]
+                ],
+                "biosamples_accession": "SAMEA6060668"
             },
             "genus_species": [
                 {
@@ -29424,36 +26441,50 @@
                     "ontology_label": "Homo sapiens"
                 }
             ],
-            "organ": {
-                "text": "Liver",
-                "ontology": "UBERON:0002107",
-                "ontology_label": "liver"
-            },
+            "estimated_cell_count": 1909,
             "provenance": {
-                "document_id": "0d27ca8e-5325-4e47-9807-8afd92e9bf89",
-                "submission_date": "2020-08-13T10:24:30.913Z",
-                "update_date": "2020-08-13T10:24:45.671Z",
-                "schema_major_version": 10,
-                "schema_minor_version": 4
+                "document_id": "204dfd1c-ea7a-494b-a151-f1bcd586ddfb",
+                "submission_date": "2020-08-13T10:24:31.844Z",
+                "update_date": "2020-08-13T10:24:55.399Z",
+                "schema_major_version": 13,
+                "schema_minor_version": 3
+            }
+        },
+        "cell_suspension_7.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F14-LIV-3p-CD45neg",
+                "ncbi_taxon_id": [
+                    9606
+                ],
+                "biosamples_accession": "SAMEA6060660"
             },
-            "diseases": [
+            "genus_species": [
                 {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
                 }
-            ]
+            ],
+            "estimated_cell_count": 4050,
+            "provenance": {
+                "document_id": "27749341-b419-4dca-9175-a6a9025116a9",
+                "submission_date": "2020-08-13T10:24:31.801Z",
+                "update_date": "2020-08-13T10:24:55.014Z",
+                "schema_major_version": 13,
+                "schema_minor_version": 3
+            }
         },
-        "specimen_from_organism_1.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
+        "cell_suspension_8.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
-                "biomaterial_id": "F11-LIV",
-                "biomaterial_name": "F11-LIV",
-                "biomaterial_description": "Liver sample from F11, F45 in internal tracking",
+                "biomaterial_id": "F15-LIV-3p-CD45neg",
                 "ncbi_taxon_id": [
                     9606
-                ]
+                ],
+                "biosamples_accession": "SAMEA6060715"
             },
             "genus_species": [
                 {
@@ -29462,36 +26493,50 @@
                     "ontology_label": "Homo sapiens"
                 }
             ],
-            "organ": {
-                "text": "Liver",
-                "ontology": "UBERON:0002107",
-                "ontology_label": "liver"
-            },
+            "estimated_cell_count": 3713,
             "provenance": {
-                "document_id": "1edb7ccc-0cb3-41c4-a193-181542bce479",
-                "submission_date": "2020-08-13T10:24:31.037Z",
-                "update_date": "2020-08-13T10:24:48.049Z",
-                "schema_major_version": 10,
-                "schema_minor_version": 4
+                "document_id": "2b532bac-4ebb-47db-b5e2-37b8da2b5f6c",
+                "submission_date": "2020-08-13T10:24:31.835Z",
+                "update_date": "2020-08-13T10:24:55.330Z",
+                "schema_major_version": 13,
+                "schema_minor_version": 3
+            }
+        },
+        "cell_suspension_9.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
+            "schema_type": "biomaterial",
+            "biomaterial_core": {
+                "biomaterial_id": "F05-LIV-3p-CD45neg_2",
+                "ncbi_taxon_id": [
+                    9606
+                ],
+                "biosamples_accession": "SAMEA6060694"
             },
-            "diseases": [
+            "genus_species": [
                 {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
                 }
-            ]
+            ],
+            "estimated_cell_count": 3296,
+            "provenance": {
+                "document_id": "469016a2-3bea-4244-8bae-835c499c8ac0",
+                "submission_date": "2020-08-13T10:24:31.350Z",
+                "update_date": "2020-08-13T10:24:51.602Z",
+                "schema_major_version": 13,
+                "schema_minor_version": 3
+            }
         },
-        "specimen_from_organism_2.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
+        "cell_suspension_10.json": {
+            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
-                "biomaterial_id": "F12-LIV",
-                "biomaterial_name": "F12-LIV",
-                "biomaterial_description": "Liver sample from F12, F38 in internal tracking",
+                "biomaterial_id": "F07-LIV-3p-CD45pos",
                 "ncbi_taxon_id": [
                     9606
-                ]
+                ],
+                "biosamples_accession": "SAMEA6060662"
             },
             "genus_species": [
                 {
@@ -29500,36 +26545,50 @@
                     "ontology_label": "Homo sapiens"
                 }
             ],
-            "organ": {
-                "text": "Liver",
-                "ontology": "UBERON:0002107",
-                "ontology_label": "liver"
-            },
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-                "update_date": "2020-08-13T10:24:48.247Z",
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+                "submission_date": "2020-08-13T10:24:31.516Z",
+                "update_date": "2020-08-13T10:24:52.586Z",
+                "schema_major_version": 13,
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+            "biomaterial_core": {
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+                "ncbi_taxon_id": [
+                    9606
+                ],
+                "biosamples_accession": "SAMEA6060665"
             },
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                 {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
                 }
-            ]
+            ],
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+            "provenance": {
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+                "submission_date": "2020-08-13T10:24:31.660Z",
+                "update_date": "2020-08-13T10:24:53.810Z",
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-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
+        "cell_suspension_12.json": {
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             "biomaterial_core": {
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-                "biomaterial_name": "F10-LIV",
-                "biomaterial_description": "Liver sample from F10, F23 in internal tracking",
+                "biomaterial_id": "F05-LIV-3p-CD45pos_1",
                 "ncbi_taxon_id": [
                     9606
-                ]
+                ],
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             },
             "genus_species": [
                 {
@@ -29538,36 +26597,50 @@
                     "ontology_label": "Homo sapiens"
                 }
             ],
-            "organ": {
-                "text": "Liver",
-                "ontology": "UBERON:0002107",
-                "ontology_label": "liver"
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+                "update_date": "2020-08-13T10:24:51.261Z",
+                "schema_major_version": 13,
+                "schema_minor_version": 3
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+            "schema_type": "biomaterial",
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+                "ncbi_taxon_id": [
+                    9606
+                ],
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             },
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                 {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
+                    "text": "Homo sapiens",
+                    "ontology": "NCBITaxon:9606",
+                    "ontology_label": "Homo sapiens"
                 }
-            ]
+            ],
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+            "provenance": {
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+                "submission_date": "2020-08-13T10:24:31.408Z",
+                "update_date": "2020-08-13T10:24:51.990Z",
+                "schema_major_version": 13,
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-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
+        "cell_suspension_14.json": {
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             "schema_type": "biomaterial",
             "biomaterial_core": {
-                "biomaterial_id": "F02-LIV",
-                "biomaterial_name": "F02-LIV",
-                "biomaterial_description": "Liver sample from F02, F32 in internal tracking",
+                "biomaterial_id": "F10-LIV-3p-CD45pos",
                 "ncbi_taxon_id": [
                     9606
-                ]
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             },
             "genus_species": [
                 {
@@ -29576,36 +26649,24 @@
                     "ontology_label": "Homo sapiens"
                 }
             ],
-            "organ": {
-                "text": "Liver",
-                "ontology": "UBERON:0002107",
-                "ontology_label": "liver"
-            },
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-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
+                "document_id": "5ee0a825-8c35-4fe5-ab67-454c6bfd949b",
+                "submission_date": "2020-08-13T10:24:31.652Z",
+                "update_date": "2020-08-13T10:24:53.734Z",
+                "schema_major_version": 13,
+                "schema_minor_version": 3
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-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
+        "cell_suspension_15.json": {
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             "schema_type": "biomaterial",
             "biomaterial_core": {
-                "biomaterial_id": "F04-LIV",
-                "biomaterial_name": "F04-LIV",
-                "biomaterial_description": "Liver sample from F04, F16 in internal tracking",
+                "biomaterial_id": "F02-LIV-3p-CD45neg",
                 "ncbi_taxon_id": [
                     9606
-                ]
+                ],
+                "biosamples_accession": "SAMEA6060683"
             },
             "genus_species": [
                 {
@@ -29614,36 +26675,24 @@
                     "ontology_label": "Homo sapiens"
                 }
             ],
-            "organ": {
-                "text": "Liver",
-                "ontology": "UBERON:0002107",
-                "ontology_label": "liver"
-            },
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             "provenance": {
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-            },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
+                "document_id": "5fc661b9-440a-4b6f-b2f9-f847043debec",
+                "submission_date": "2020-08-13T10:24:31.143Z",
+                "update_date": "2020-08-13T10:24:49.691Z",
+                "schema_major_version": 13,
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-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
+        "cell_suspension_16.json": {
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             "schema_type": "biomaterial",
             "biomaterial_core": {
-                "biomaterial_id": "F06-LIV",
-                "biomaterial_name": "F06-LIV",
-                "biomaterial_description": "Liver sample from F06, F17 in internal tracking",
+                "biomaterial_id": "F12-LIV-3p-CD45pos_2",
                 "ncbi_taxon_id": [
                     9606
-                ]
+                ],
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             },
             "genus_species": [
                 {
@@ -29652,36 +26701,24 @@
                     "ontology_label": "Homo sapiens"
                 }
             ],
-            "organ": {
-                "text": "Liver",
-                "ontology": "UBERON:0002107",
-                "ontology_label": "liver"
-            },
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             "provenance": {
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-            "diseases": [
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-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
+                "document_id": "6194245b-1ce5-495e-8e85-d859b3fcce66",
+                "submission_date": "2020-08-13T10:24:31.731Z",
+                "update_date": "2020-08-13T10:24:54.413Z",
+                "schema_major_version": 13,
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+        "cell_suspension_17.json": {
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             "schema_type": "biomaterial",
             "biomaterial_core": {
-                "biomaterial_id": "F08-LIV",
-                "biomaterial_name": "F08-LIV",
-                "biomaterial_description": "Liver sample from F08, F33 in internal tracking",
+                "biomaterial_id": "F05-LIV-3p-CD45pos_2",
                 "ncbi_taxon_id": [
                     9606
-                ]
+                ],
+                "biosamples_accession": "SAMEA6060692"
             },
             "genus_species": [
                 {
@@ -29690,36 +26727,24 @@
                     "ontology_label": "Homo sapiens"
                 }
             ],
-            "organ": {
-                "text": "Liver",
-                "ontology": "UBERON:0002107",
-                "ontology_label": "liver"
-            },
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-            },
-            "diseases": [
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-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
+                "document_id": "64713d72-8e8f-4350-a3ba-e1981c872100",
+                "submission_date": "2020-08-13T10:24:31.320Z",
+                "update_date": "2020-08-13T10:24:51.331Z",
+                "schema_major_version": 13,
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         },
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+        "cell_suspension_18.json": {
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             "schema_type": "biomaterial",
             "biomaterial_core": {
-                "biomaterial_id": "F15-LIV",
-                "biomaterial_name": "F15-LIV",
-                "biomaterial_description": "Liver sample from F15, F41 in internal tracking",
+                "biomaterial_id": "F04-LIV-3p-CD45pos",
                 "ncbi_taxon_id": [
                     9606
-                ]
+                ],
+                "biosamples_accession": "SAMEA6060646"
             },
             "genus_species": [
                 {
@@ -29728,36 +26753,24 @@
                     "ontology_label": "Homo sapiens"
                 }
             ],
-            "organ": {
-                "text": "Liver",
-                "ontology": "UBERON:0002107",
-                "ontology_label": "liver"
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             "provenance": {
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-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
+                "document_id": "6b34fa3f-1878-48ec-84c2-e2d8877903c4",
+                "submission_date": "2020-08-13T10:24:31.258Z",
+                "update_date": "2020-08-13T10:24:50.783Z",
+                "schema_major_version": 13,
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+        "cell_suspension_19.json": {
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             "schema_type": "biomaterial",
             "biomaterial_core": {
-                "biomaterial_id": "F03-LIV",
-                "biomaterial_name": "F03-LIV",
-                "biomaterial_description": "Liver sample from F03, F35 in internal tracking",
+                "biomaterial_id": "F13-LIV-3p-CD45pos",
                 "ncbi_taxon_id": [
                     9606
-                ]
+                ],
+                "biosamples_accession": "SAMEA6060670"
             },
             "genus_species": [
                 {
@@ -29766,36 +26779,24 @@
                     "ontology_label": "Homo sapiens"
                 }
             ],
-            "organ": {
-                "text": "Liver",
-                "ontology": "UBERON:0002107",
-                "ontology_label": "liver"
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             "provenance": {
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-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
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+                "document_id": "700af591-d469-4a3d-a908-cff116f28242",
+                "submission_date": "2020-08-13T10:24:31.769Z",
+                "update_date": "2020-08-13T10:24:54.706Z",
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             "schema_type": "biomaterial",
             "biomaterial_core": {
-                "biomaterial_id": "F07-LIV",
-                "biomaterial_name": "F07-LIV",
-                "biomaterial_description": "Liver sample from F07, F22 in internal tracking",
+                "biomaterial_id": "F06-LIV-3p-CD45pos",
                 "ncbi_taxon_id": [
                     9606
-                ]
+                ],
+                "biosamples_accession": "SAMEA6060655"
             },
             "genus_species": [
                 {
@@ -29804,36 +26805,24 @@
                     "ontology_label": "Homo sapiens"
                 }
             ],
-            "organ": {
-                "text": "Liver",
-                "ontology": "UBERON:0002107",
-                "ontology_label": "liver"
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             "provenance": {
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-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
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+                "document_id": "7318a24c-7abf-445d-b4d2-2c5acc01e715",
+                "submission_date": "2020-08-13T10:24:31.393Z",
+                "update_date": "2020-08-13T10:24:51.897Z",
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             "schema_type": "biomaterial",
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-                "biomaterial_id": "F14-LIV",
-                "biomaterial_name": "F14-LIV",
-                "biomaterial_description": "Liver sample from F14, F21 in internal tracking",
+            "biomaterial_core": {
+                "biomaterial_id": "F08-LIV-3p-CD45pos_1",
                 "ncbi_taxon_id": [
                     9606
-                ]
+                ],
+                "biosamples_accession": "SAMEA6060677"
             },
             "genus_species": [
                 {
@@ -29842,36 +26831,24 @@
                     "ontology_label": "Homo sapiens"
                 }
             ],
-            "organ": {
-                "text": "Liver",
-                "ontology": "UBERON:0002107",
-                "ontology_label": "liver"
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             "provenance": {
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-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
+                "document_id": "732d6ffa-1d89-4476-ad10-5ce9d83a78ad",
+                "submission_date": "2020-08-13T10:24:31.550Z",
+                "update_date": "2020-08-13T10:24:52.835Z",
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+        "cell_suspension_22.json": {
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             "schema_type": "biomaterial",
             "biomaterial_core": {
-                "biomaterial_id": "F16-LIV",
-                "biomaterial_name": "F16-LIV",
-                "biomaterial_description": "Liver sample from F16, F29 in internal tracking",
+                "biomaterial_id": "F08-LIV-3p-CD45neg_1",
                 "ncbi_taxon_id": [
                     9606
-                ]
+                ],
+                "biosamples_accession": "SAMEA6060680"
             },
             "genus_species": [
                 {
@@ -29880,36 +26857,24 @@
                     "ontology_label": "Homo sapiens"
                 }
             ],
-            "organ": {
-                "text": "Liver",
-                "ontology": "UBERON:0002107",
-                "ontology_label": "liver"
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-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
+                "document_id": "74d1b609-5477-4ec3-840e-fa721ffa580f",
+                "submission_date": "2020-08-13T10:24:31.585Z",
+                "update_date": "2020-08-13T10:24:53.116Z",
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+        "cell_suspension_23.json": {
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                 {
@@ -29918,3135 +26883,6170 @@
                     "ontology_label": "Homo sapiens"
                 }
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+                    },
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+                        "input_id": "8f63d864-87e5-40f3-8f68-936640010c7d"
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+                    }
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+                    },
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+                    }
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+                        "output_type": "cell_suspension",
+                        "output_id": "6194245b-1ce5-495e-8e85-d859b3fcce66"
+                    }
+                ],
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+                    }
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+                        "input_id": "7c2c2ced-a0e3-4df7-ae1d-890218465626"
+                    }
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+                    },
+                    {
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+                        "input_id": "0d27ca8e-5325-4e47-9807-8afd92e9bf89"
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+                ],
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+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "7c2c2ced-a0e3-4df7-ae1d-890218465626"
+                    }
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+                    },
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+                        "input_id": "e8fbe9c1-ab25-4300-a40d-65d0e8f627e0"
+                    }
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+                        "output_type": "specimen_from_organism",
+                        "output_id": "0d27ca8e-5325-4e47-9807-8afd92e9bf89"
+                    }
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+                        "input_type": "cell_suspension",
+                        "input_id": "19b7eb13-fef6-46a4-abb9-44a310e441b5"
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+                        "output_type": "sequence_file",
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+                    },
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+                        "input_id": "b8912f33-12a7-4bf8-9f25-e91fbc77517c"
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+                        "output_type": "cell_suspension",
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+                    }
+                ],
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+                        "input_type": "donor_organism",
+                        "input_id": "dd19fdc7-35a9-432f-9a97-670637433eda"
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+                        "output_type": "specimen_from_organism",
+                        "output_id": "b8912f33-12a7-4bf8-9f25-e91fbc77517c"
+                    }
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+                        "input_type": "cell_suspension",
+                        "input_id": "17782e68-694a-42df-9411-9fd875b95cc7"
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+                        "input_type": "specimen_from_organism",
+                        "input_id": "bed46309-3752-4115-a307-8c20d93dce55"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "17782e68-694a-42df-9411-9fd875b95cc7"
+                    }
+                ],
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+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
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-                "ncbi_taxon_id": [
-                    9606
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+                    }
                 ],
-                "biosamples_accession": "SAMEA6060678"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "bed46309-3752-4115-a307-8c20d93dce55"
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+                ],
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-                    9606
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+                "link_type": "process_link",
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+                        "output_type": "analysis_file"
+                    },
+                    {
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-                    9606
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                 ],
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+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "7318a24c-7abf-445d-b4d2-2c5acc01e715"
+                    }
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+                    },
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-                    9606
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+                    }
                 ],
-                "biosamples_accession": "SAMEA6060662"
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+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "6b94e023-9280-45df-ac3d-5a258e19bf29"
+                    }
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             },
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-                    9606
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                 ],
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+                    },
+                    {
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+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
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+                        "protocol_type": "sequencing_protocol",
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-                    "text": "Homo sapiens",
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-            "biomaterial_core": {
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-                    9606
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+                        "input_id": "31899978-a518-4d78-b85a-f62bca7ed723"
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+                ],
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+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "ae38fa93-e50c-4033-a1e9-ac404ede7380"
+                    }
+                ],
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+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
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+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
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                 ],
-                "biosamples_accession": "SAMEA6060691"
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+                        "output_id": "31899978-a518-4d78-b85a-f62bca7ed723"
+                    }
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-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
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-                "document_id": "4dae1604-6e74-4306-ae82-2da7ca2efd77",
-                "submission_date": "2020-08-13T10:24:31.312Z",
-                "update_date": "2020-08-13T10:24:51.261Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_13.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F06-LIV-3p-CD45neg",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "37925a3b-3bce-4876-bb29-745922b2c972",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "8d7b1004-5265-40cd-8912-336d71e0f296"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060656"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "24c3ce12-e4f9-4299-a005-320d602716ce"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "daa5945d-5d1f-4586-9c85-e3fa5af8bfb5"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "e779b50e-a892-4a0c-af02-2dd400956018"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 639,
-            "provenance": {
-                "document_id": "4fd506bc-5824-4a7b-a44a-8d02532c5277",
-                "submission_date": "2020-08-13T10:24:31.408Z",
-                "update_date": "2020-08-13T10:24:51.990Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_14.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F10-LIV-3p-CD45pos",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "f70a20e6-ad33-424e-b385-bb9a19be000e",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "1edb7ccc-0cb3-41c4-a193-181542bce479"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060664"
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "8d7b1004-5265-40cd-8912-336d71e0f296"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "f1903d0b-1cb2-4208-bc20-a37ad8612452"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 2653,
-            "provenance": {
-                "document_id": "5ee0a825-8c35-4fe5-ab67-454c6bfd949b",
-                "submission_date": "2020-08-13T10:24:31.652Z",
-                "update_date": "2020-08-13T10:24:53.734Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_15.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F02-LIV-3p-CD45neg",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "f027f9ff-0d24-49e2-b71d-18543a4631f2",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "9417041b-2952-41d5-b0d8-b42694f4fd4a"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060683"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "1edb7ccc-0cb3-41c4-a193-181542bce479"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 3335,
-            "provenance": {
-                "document_id": "5fc661b9-440a-4b6f-b2f9-f847043debec",
-                "submission_date": "2020-08-13T10:24:31.143Z",
-                "update_date": "2020-08-13T10:24:49.691Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_16.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F12-LIV-3p-CD45pos_2",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "0ceed66e-513f-450f-89e9-3206f4485cdf",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "469016a2-3bea-4244-8bae-835c499c8ac0"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060710"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "82c6f8e4-79f9-48b7-aab5-35853db742a4"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "49a158d2-9786-4f54-bac9-67244497c9c9"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "d5744e7d-7ab9-4d86-8a3a-bfc9e96946fc"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 2070,
-            "provenance": {
-                "document_id": "6194245b-1ce5-495e-8e85-d859b3fcce66",
-                "submission_date": "2020-08-13T10:24:31.731Z",
-                "update_date": "2020-08-13T10:24:54.413Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_17.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F05-LIV-3p-CD45pos_2",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "9210ccdd-107f-4ef3-9a2d-f9c573788f43",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "0d27ca8e-5325-4e47-9807-8afd92e9bf89"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060692"
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "469016a2-3bea-4244-8bae-835c499c8ac0"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "f1903d0b-1cb2-4208-bc20-a37ad8612452"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
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-            "provenance": {
-                "document_id": "64713d72-8e8f-4350-a3ba-e1981c872100",
-                "submission_date": "2020-08-13T10:24:31.320Z",
-                "update_date": "2020-08-13T10:24:51.331Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_18.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F04-LIV-3p-CD45pos",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "136b438c-b819-4da2-8cc1-d6cace9c716c",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "e8fbe9c1-ab25-4300-a40d-65d0e8f627e0"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060646"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "0d27ca8e-5325-4e47-9807-8afd92e9bf89"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 98,
-            "provenance": {
-                "document_id": "6b34fa3f-1878-48ec-84c2-e2d8877903c4",
-                "submission_date": "2020-08-13T10:24:31.258Z",
-                "update_date": "2020-08-13T10:24:50.783Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_19.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F13-LIV-3p-CD45pos",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "inputs": [
+                    {
+                        "input_id": "8fee28bf-4f9b-4d62-814b-ea97119048ee",
+                        "input_type": "sequence_file"
+                    },
+                    {
+                        "input_id": "32714f4f-1a04-4fc3-bdd9-2ae6473fe544",
+                        "input_type": "sequence_file"
+                    },
+                    {
+                        "input_id": "9d578de9-08fb-47f8-9bc4-77e9577965e7",
+                        "input_type": "sequence_file"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060670"
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "9baa3062-0022-53e2-a3df-14df08c4c66c",
+                        "output_type": "analysis_file"
+                    },
+                    {
+                        "output_id": "d41aa539-54ba-5f2e-bfd6-4c9905ee38a1",
+                        "output_type": "analysis_file"
+                    }
+                ],
+                "process_id": "fbbd6c03-df0d-44dd-b383-c1efb83abb2e",
+                "process_type": "analysis_process",
+                "protocols": [
+                    {
+                        "protocol_id": "289ec28b-ce11-5be8-89ab-92fbceb874a0",
+                        "protocol_type": "analysis_protocol"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 5357,
-            "provenance": {
-                "document_id": "700af591-d469-4a3d-a908-cff116f28242",
-                "submission_date": "2020-08-13T10:24:31.769Z",
-                "update_date": "2020-08-13T10:24:54.706Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_20.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F06-LIV-3p-CD45pos",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "e23d96b7-a271-403e-a29e-b2bdb1949070",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "ef50dd96-a305-4edd-84e7-aae93377c488"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060655"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "f895f666-e3ed-4a7e-a7f5-42586a6244ea"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "c0e0476d-b0c5-434b-9c33-92e52900341d"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "4e7c6725-5d49-4ed6-9a5f-b7d0eaf75469"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 208,
-            "provenance": {
-                "document_id": "7318a24c-7abf-445d-b4d2-2c5acc01e715",
-                "submission_date": "2020-08-13T10:24:31.393Z",
-                "update_date": "2020-08-13T10:24:51.897Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_21.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F08-LIV-3p-CD45pos_1",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "43c13443-4e03-42b3-a32f-d048c8ea465e",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "ae073235-e422-4c3a-8bf4-9892d6e769b3"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060677"
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "ef50dd96-a305-4edd-84e7-aae93377c488"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "003cb4a8-9871-488f-9042-820504991f17"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 3526,
-            "provenance": {
-                "document_id": "732d6ffa-1d89-4476-ad10-5ce9d83a78ad",
-                "submission_date": "2020-08-13T10:24:31.550Z",
-                "update_date": "2020-08-13T10:24:52.835Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_22.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F08-LIV-3p-CD45neg_1",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "57c18bb9-bb99-48dc-bf49-70e3e558deeb",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "8f63d864-87e5-40f3-8f68-936640010c7d"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060680"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "ae073235-e422-4c3a-8bf4-9892d6e769b3"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 3174,
-            "provenance": {
-                "document_id": "74d1b609-5477-4ec3-840e-fa721ffa580f",
-                "submission_date": "2020-08-13T10:24:31.585Z",
-                "update_date": "2020-08-13T10:24:53.116Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_23.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F05-LIV-3p-CD45neg_1",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "22ccc95d-d789-4398-a790-83f86bb420d8",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "91a5af73-4a8a-4285-bcbb-42344e18745f"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060693"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "ffba13e2-0937-49b3-961a-2ce3055ad5c6"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "71c8dfa2-0a8c-4ae0-8161-933454f56420"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "232c6da0-b86b-4995-8da1-a428211af836"
+                    }
+                ],
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+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
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-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
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-                "update_date": "2020-08-13T10:24:51.520Z",
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-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F06-LIV-3p-live",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "5c745dc7-ece2-4df5-96b3-bca92b832c73",
+                "process_type": "process",
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+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "b8912f33-12a7-4bf8-9f25-e91fbc77517c"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060651"
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "91a5af73-4a8a-4285-bcbb-42344e18745f"
+                    }
+                ],
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+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "f1903d0b-1cb2-4208-bc20-a37ad8612452"
+                    }
+                ]
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-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
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-                "update_date": "2020-08-13T10:24:52.064Z",
-                "schema_major_version": 13,
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-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F16-LIV-3p-CD45neg",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "5fbb11aa-074b-42ad-bb8c-13d80c3b2490",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "dd19fdc7-35a9-432f-9a97-670637433eda"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060669"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "b8912f33-12a7-4bf8-9f25-e91fbc77517c"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
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-                "submission_date": "2020-08-13T10:24:31.853Z",
-                "update_date": "2020-08-13T10:24:55.469Z",
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-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F11-LIV-3p-CD45neg_2",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "inputs": [
+                    {
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+                        "input_type": "sequence_file"
+                    },
+                    {
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+                        "input_type": "sequence_file"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "11712f1f-d3c5-54b4-9ab3-cd12b8eb15b7",
+                        "output_type": "analysis_file"
+                    },
+                    {
+                        "output_id": "33055074-248b-57fe-99fd-b5deab653ac0",
+                        "output_type": "analysis_file"
+                    }
                 ],
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+                "process_id": "e607b72f-3024-4d7e-8292-19d2d53a3a95",
+                "process_type": "analysis_process",
+                "protocols": [
+                    {
+                        "protocol_id": "289ec28b-ce11-5be8-89ab-92fbceb874a0",
+                        "protocol_type": "analysis_protocol"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
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-                "submission_date": "2020-08-13T10:24:31.711Z",
-                "update_date": "2020-08-13T10:24:54.261Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
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-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F11-LIV-3p-CD45pos_2",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "b1883730-3304-48c1-904b-eb90ab226168",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "02f33fc2-eb2f-4c78-a7f5-002a1747e71f"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060720"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "7efd8179-7a9a-4ef1-b199-46f94581cb1a"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "455c6c50-9424-4dac-b67c-1be48276d5b5"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "c27ebc26-f0b4-4f42-8b10-061fb04f77bd"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
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-                "submission_date": "2020-08-13T10:24:31.677Z",
-                "update_date": "2020-08-13T10:24:53.968Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_28.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F07-LIV-3p-CD45neg",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "71aef8a5-add1-46ce-b5e9-c172a52414a2",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "75b6d713-08dc-4eff-9347-95c9519a34cd"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060663"
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "02f33fc2-eb2f-4c78-a7f5-002a1747e71f"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "003cb4a8-9871-488f-9042-820504991f17"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
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-                "submission_date": "2020-08-13T10:24:31.527Z",
-                "update_date": "2020-08-13T10:24:52.669Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
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-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F08-LIV-3p-CD45pos_3",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "204a3bb9-d52f-407e-a3ed-f051a40dd7c3",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "ae71343b-df16-49a3-829d-a6e61afdc079"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060679"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "75b6d713-08dc-4eff-9347-95c9519a34cd"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
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-                "submission_date": "2020-08-13T10:24:31.575Z",
-                "update_date": "2020-08-13T10:24:53.030Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
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-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F03-LIV-3p-CD45pos_1",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "c301901f-95cd-4a3e-a4df-761fa21e92af",
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+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "700af591-d469-4a3d-a908-cff116f28242"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060696"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "9403a717-07d2-4510-9f19-77d41747c188"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "611d7372-2d5d-4b93-9cb8-b6d689b0f905"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "9a4277c3-806b-4906-a777-613f01a51003"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
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-                "submission_date": "2020-08-13T10:24:31.188Z",
-                "update_date": "2020-08-13T10:24:50.189Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
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-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F03-LIV-3p-CD45neg",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "d7f083b3-1e02-4838-a7a2-a52bc7bcb1bb",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "fbed02e6-1547-469c-b96f-45c61111af53"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060698"
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "700af591-d469-4a3d-a908-cff116f28242"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "003cb4a8-9871-488f-9042-820504991f17"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
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-                "submission_date": "2020-08-13T10:24:31.205Z",
-                "update_date": "2020-08-13T10:24:50.328Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
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-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F12-LIV-3p-CD45neg_2",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "a0cf7b57-f8ac-4591-bfe5-a9a2b7416057",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "1b5a4bc7-5a90-4782-a657-536a8b533156"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060712"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "fbed02e6-1547-469c-b96f-45c61111af53"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
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-                "submission_date": "2020-08-13T10:24:31.761Z",
-                "update_date": "2020-08-13T10:24:54.633Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
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-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F11-LIV-3p-CD45neg_1",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "inputs": [
+                    {
+                        "input_id": "1a17a213-3a73-4af8-a105-6e5b3d056263",
+                        "input_type": "sequence_file"
+                    },
+                    {
+                        "input_id": "4bd54cd4-ca70-4566-a2bf-9fecb4dfbc34",
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+                    },
+                    {
+                        "input_id": "05345715-8f9f-44fe-8f28-f75552b17d5d",
+                        "input_type": "sequence_file"
+                    }
+                ],
+                "link_type": "process_link",
+                "outputs": [
+                    {
+                        "output_id": "69cc1f24-8be9-58aa-af3e-99c13507216e",
+                        "output_type": "analysis_file"
+                    },
+                    {
+                        "output_id": "00dbea45-4e4d-5220-985e-afd8dcfce0b5",
+                        "output_type": "analysis_file"
+                    }
+                ],
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+                "process_type": "analysis_process",
+                "protocols": [
+                    {
+                        "protocol_id": "289ec28b-ce11-5be8-89ab-92fbceb874a0",
+                        "protocol_type": "analysis_protocol"
+                    }
+                ]
+            },
+            {
+                "link_type": "process_link",
+                "process_id": "b7914794-f8a7-4fba-bb5b-10536eac7d8b",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "5fc661b9-440a-4b6f-b2f9-f847043debec"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060719"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "41a13523-c45b-4546-8273-9321d9a2c250"
+                    },
+                    {
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+                        "output_id": "82fc4ead-bf34-4834-91ed-cb6ec1717baa"
+                    }
+                ],
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+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 2137,
-            "provenance": {
-                "document_id": "b5e9df12-e333-4754-a01b-c83c4b8f644a",
-                "submission_date": "2020-08-13T10:24:31.702Z",
-                "update_date": "2020-08-13T10:24:54.185Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_34.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F12-LIV-3p-CD45neg_1",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "69ccee6f-c88d-4443-88a0-e46ed47bf2a1",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "619887a0-67fb-4e24-be95-409f9b3e8474"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060711"
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "5fc661b9-440a-4b6f-b2f9-f847043debec"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "f1903d0b-1cb2-4208-bc20-a37ad8612452"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 2640,
-            "provenance": {
-                "document_id": "c57bdaec-21df-479e-857e-ddb6f5f78f95",
-                "submission_date": "2020-08-13T10:24:31.749Z",
-                "update_date": "2020-08-13T10:24:54.560Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_35.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F04-LIV-3p-CD45neg",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "c0c71843-6831-4e91-90cf-cb31d4a4b277",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "d0baedfe-0556-4c2b-a1a0-d1e28ef07bb5"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060647"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "619887a0-67fb-4e24-be95-409f9b3e8474"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 1037,
-            "provenance": {
-                "document_id": "c8d8c14f-4e5e-4911-a386-391fd1153969",
-                "submission_date": "2020-08-13T10:24:31.267Z",
-                "update_date": "2020-08-13T10:24:50.861Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_36.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F12-LIV-3p-CD45pos_1",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "f26c4715-5488-4d7f-ae0e-1c965128fbb1",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "74d1b609-5477-4ec3-840e-fa721ffa580f"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060709"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "9c6fffe5-0f64-4325-8e2f-8be4fa5417b9"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "e79faefc-5135-4e43-a64d-8db7472d3f2e"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "fa78c4ab-4057-45b1-8266-af045ae28535"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 2070,
-            "provenance": {
-                "document_id": "d4b2569d-4f63-41c0-9a11-97068ee3ae68",
-                "submission_date": "2020-08-13T10:24:31.722Z",
-                "update_date": "2020-08-13T10:24:54.333Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_37.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F08-LIV-3p-CD45neg_2",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "e9eb59a6-8324-47c7-8d54-4517587c6802",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "75b6d713-08dc-4eff-9347-95c9519a34cd"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060681"
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "74d1b609-5477-4ec3-840e-fa721ffa580f"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "f1903d0b-1cb2-4208-bc20-a37ad8612452"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 3174,
-            "provenance": {
-                "document_id": "d94541a9-1505-4a33-8ff5-fcb2b19b0d92",
-                "submission_date": "2020-08-13T10:24:31.594Z",
-                "update_date": "2020-08-13T10:24:53.194Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_38.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F03-LIV-3p-CD45pos_2",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "204a3bb9-d52f-407e-a3ed-f051a40dd7c3",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "ae71343b-df16-49a3-829d-a6e61afdc079"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060697"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "75b6d713-08dc-4eff-9347-95c9519a34cd"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 2852,
-            "provenance": {
-                "document_id": "ef50dd96-a305-4edd-84e7-aae93377c488",
-                "submission_date": "2020-08-13T10:24:31.197Z",
-                "update_date": "2020-08-13T10:24:50.258Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "cell_suspension_39.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F02-LIV-3p-CD45pos",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "42b114bb-27ee-4415-b046-7ee5581adc27",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "64713d72-8e8f-4350-a3ba-e1981c872100"
+                    }
                 ],
-                "biosamples_accession": "SAMEA6060682"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "3c6b5196-4dd9-4c23-a9d1-c1341d889ecf"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "22d5f584-ff73-4a10-8377-387983b72a87"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "601bacd5-c250-4dd3-a83d-c9f31a1b0dd8"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "estimated_cell_count": 3418,
-            "provenance": {
-                "document_id": "ffe830d9-c586-47d1-9bb4-33baed6dcdc7",
-                "submission_date": "2020-08-13T10:24:31.133Z",
-                "update_date": "2020-08-13T10:24:49.619Z",
-                "schema_major_version": 13,
-                "schema_minor_version": 3
-            }
-        },
-        "donor_organism_0.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F13",
-                "biomaterial_name": "F30",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F30 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "5a0999a5-9945-4d18-8f0a-7ed5a6b1f27b",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "0d27ca8e-5325-4e47-9807-8afd92e9bf89"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "64713d72-8e8f-4350-a3ba-e1981c872100"
+                    }
                 ],
-                "genotype": "rsa(13,15,16,18,21,22)x2 (X,Y)x1",
-                "HDBR_accession": "13944"
-            },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "male",
-            "is_living": "no",
-            "development_stage": {
-                "text": "15pcw",
-                "ontology": "HsapDv:0000052",
-                "ontology_label": "15th week post-fertilization human stage"
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "003cb4a8-9871-488f-9042-820504991f17"
+                    }
+                ]
             },
-            "gestational_age": "17",
-            "provenance": {
-                "document_id": "1b5a4bc7-5a90-4782-a657-536a8b533156",
-                "submission_date": "2020-08-13T10:24:30.757Z",
-                "update_date": "2020-08-13T10:24:44.552Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "136b438c-b819-4da2-8cc1-d6cace9c716c",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "e8fbe9c1-ab25-4300-a40d-65d0e8f627e0"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "0d27ca8e-5325-4e47-9807-8afd92e9bf89"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        },
-        "donor_organism_1.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F14",
-                "biomaterial_name": "F21",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F21 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "7f0f3ad8-9052-4003-ac7d-4e2e509b85f5",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "4c32ae0b-8338-4906-90ef-06e1e4fd7577"
+                    }
                 ],
-                "genotype": "46, XY",
-                "HDBR_accession": "13890"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "32a5b3e4-4f2f-4fb1-aeff-7fb01035eb8d"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "807e13ad-b807-44b5-92c8-9057b858968f"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "2b40b918-2632-4a06-9746-6f542d884b90"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "male",
-            "is_living": "no",
-            "development_stage": {
-                "text": "16pcw",
-                "ontology": "HsapDv:0000053",
-                "ontology_label": "16th week post-fertilization human stage"
+            {
+                "link_type": "process_link",
+                "process_id": "8d4c4056-6a9b-4c33-907c-66f4351fe7c1",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "54bfca9c-a1f8-4632-a0cb-5f7b5edf48d6"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "4c32ae0b-8338-4906-90ef-06e1e4fd7577"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "f1903d0b-1cb2-4208-bc20-a37ad8612452"
+                    }
+                ]
             },
-            "gestational_age": "18",
-            "provenance": {
-                "document_id": "39046bdd-483c-44ad-9b50-dea608d34255",
-                "submission_date": "2020-08-13T10:24:30.765Z",
-                "update_date": "2020-08-13T10:24:44.580Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "16d53d3e-88ef-444a-aaec-e7947fc3e779",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "eed4d335-880b-4735-9d04-cdbf706e3d44"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "54bfca9c-a1f8-4632-a0cb-5f7b5edf48d6"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        },
-        "donor_organism_2.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F04",
-                "biomaterial_name": "F16",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F16 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "7fa6adde-000d-4360-9f45-2b5da4721f70",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "1b8c4fa4-24d0-42b5-99e1-8c04eba5d8c3"
+                    }
                 ],
-                "genotype": "46, XY",
-                "HDBR_accession": "13678"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "38b67b47-7ef3-4e9e-88e1-3a8376769eb0"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "0b9d7ae0-f6af-40e5-898d-7b2afc48c4b1"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "4b06739c-d81c-45cd-825f-cc5145f15065"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "male",
-            "is_living": "no",
-            "development_stage": {
-                "text": "L8pcw",
-                "ontology": "HsapDv:0000015",
-                "ontology_label": "organogenesis stage"
+            {
+                "link_type": "process_link",
+                "process_id": "b92aadd5-3603-4e12-a92d-22e1f9757361",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "1edb7ccc-0cb3-41c4-a193-181542bce479"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "1b8c4fa4-24d0-42b5-99e1-8c04eba5d8c3"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "003cb4a8-9871-488f-9042-820504991f17"
+                    }
+                ]
             },
-            "gestational_age": "10",
-            "provenance": {
-                "document_id": "5baa7164-60f5-4b28-8bad-e9a0563cac70",
-                "submission_date": "2020-08-13T10:24:30.656Z",
-                "update_date": "2020-08-13T10:24:44.208Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "f027f9ff-0d24-49e2-b71d-18543a4631f2",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "9417041b-2952-41d5-b0d8-b42694f4fd4a"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "1edb7ccc-0cb3-41c4-a193-181542bce479"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        },
-        "donor_organism_3.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F12",
-                "biomaterial_name": "F38",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F38 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "232174af-3ebf-4b3b-97fd-35547950c4c8",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "c8d8c14f-4e5e-4911-a386-391fd1153969"
+                    }
                 ],
-                "genotype": "rsa(13,15,16,18,21,22)x2(X,Y)x1",
-                "HDBR_accession": "14146"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "0619dd26-7a22-4fc9-ac35-7a381a502e6f"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "a3bef94d-a68f-43d4-8cb8-58977b20f849"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "c30c31d2-ccfb-4651-8b78-a25a23ab4e95"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "male",
-            "is_living": "no",
-            "development_stage": {
-                "text": "13pcw",
-                "ontology": "HsapDv:0000050",
-                "ontology_label": "13th week post-fertilization human stage"
+            {
+                "link_type": "process_link",
+                "process_id": "f3e0b538-bf64-417d-8746-52d5ad9311be",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "69576784-ca06-4ccb-bab7-d6e8353a8036"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "c8d8c14f-4e5e-4911-a386-391fd1153969"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "f1903d0b-1cb2-4208-bc20-a37ad8612452"
+                    }
+                ]
             },
-            "gestational_age": "15",
-            "provenance": {
-                "document_id": "793d9bf6-00cb-49e6-acc2-2cc724036645",
-                "submission_date": "2020-08-13T10:24:30.748Z",
-                "update_date": "2020-08-13T10:24:44.524Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "a2653332-1aab-49d6-8da8-b5c5fe004e70",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "5baa7164-60f5-4b28-8bad-e9a0563cac70"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "69576784-ca06-4ccb-bab7-d6e8353a8036"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        },
-        "donor_organism_4.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F06",
-                "biomaterial_name": "F17",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F17 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "a0e661e2-dac9-4004-9605-8307c15f831d",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "732d6ffa-1d89-4476-ad10-5ce9d83a78ad"
+                    }
                 ],
-                "genotype": "46, XX",
-                "HDBR_accession": "13687"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "d3c05176-1d0b-4ce1-b005-0af8c35129cd"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "835ec088-c1a5-4b0c-897c-22bc92950587"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "0f15fb43-c791-4113-a721-a9e3767e8f6d"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "female",
-            "is_living": "no",
-            "development_stage": {
-                "text": "9pcw",
-                "ontology": "HsapDv:0000046",
-                "ontology_label": "9th week post-fertilization human stage"
+            {
+                "link_type": "process_link",
+                "process_id": "61a4052c-bbc0-4666-9747-ed6b4c706ac6",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "75b6d713-08dc-4eff-9347-95c9519a34cd"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "732d6ffa-1d89-4476-ad10-5ce9d83a78ad"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "003cb4a8-9871-488f-9042-820504991f17"
+                    }
+                ]
             },
-            "gestational_age": "11",
-            "provenance": {
-                "document_id": "85dc3748-6751-482b-b7cd-c1e08f7df5c0",
-                "submission_date": "2020-08-13T10:24:30.684Z",
-                "update_date": "2020-08-13T10:24:44.299Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "204a3bb9-d52f-407e-a3ed-f051a40dd7c3",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "ae71343b-df16-49a3-829d-a6e61afdc079"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "75b6d713-08dc-4eff-9347-95c9519a34cd"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        },
-        "donor_organism_5.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F03",
-                "biomaterial_name": "F35",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F35 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "73bd1209-cfb5-420f-bd97-574ed9c7cd0e",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "d4b2569d-4f63-41c0-9a11-97068ee3ae68"
+                    }
                 ],
-                "genotype": "not available",
-                "HDBR_accession": "14087"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "da490be5-56d8-4510-a3c9-c256666fbe4d"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "ba276a56-3bdf-42ff-93f4-2920c3a288f9"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "be3cffb9-150a-4a1e-8f4b-a0afde4eea5a"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "female",
-            "is_living": "no",
-            "development_stage": {
-                "text": "CS23",
-                "ontology": "HsapDv:0000030",
-                "ontology_label": "Carnegie stage 23"
+            {
+                "link_type": "process_link",
+                "process_id": "aa76f640-744e-4c50-92af-33c7f54fc7ee",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "31899978-a518-4d78-b85a-f62bca7ed723"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "d4b2569d-4f63-41c0-9a11-97068ee3ae68"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "003cb4a8-9871-488f-9042-820504991f17"
+                    }
+                ]
             },
-            "gestational_age": "9",
-            "provenance": {
-                "document_id": "8f63d864-87e5-40f3-8f68-936640010c7d",
-                "submission_date": "2020-08-13T10:24:30.639Z",
-                "update_date": "2020-08-13T10:24:44.155Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "68b20827-e2b9-4d02-ac17-32ebf7aaf49c",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "793d9bf6-00cb-49e6-acc2-2cc724036645"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "31899978-a518-4d78-b85a-f62bca7ed723"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        },
-        "donor_organism_6.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F11",
-                "biomaterial_name": "F45",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F45 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "bc5ba4f6-a3f1-4156-830f-11228df251bc",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "90ab9fe3-3847-4477-bff8-66db44610c92"
+                    }
                 ],
-                "genotype": "rsa(13,15,16,18,21,22,X)x2",
-                "HDBR_accession": "14215"
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "71e9623c-1cfa-4efe-9448-f4014da727dc"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "96cbabdb-30b4-4c71-9250-bb7efcd9ee1e"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "44c70c3c-6fe7-4186-9aa5-b2cb1ea3b9d8"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "female",
-            "is_living": "no",
-            "development_stage": {
-                "text": "12pcw",
-                "ontology": "HsapDv:0000049",
-                "ontology_label": "12th week post-fertilization human stage"
+            {
+                "link_type": "process_link",
+                "process_id": "a753faac-75d8-442d-a44d-b0320ba88fe0",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "1edb7ccc-0cb3-41c4-a193-181542bce479"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "90ab9fe3-3847-4477-bff8-66db44610c92"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "003cb4a8-9871-488f-9042-820504991f17"
+                    }
+                ]
             },
-            "gestational_age": "14",
-            "provenance": {
-                "document_id": "9417041b-2952-41d5-b0d8-b42694f4fd4a",
-                "submission_date": "2020-08-13T10:24:30.739Z",
-                "update_date": "2020-08-13T10:24:44.494Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "f027f9ff-0d24-49e2-b71d-18543a4631f2",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "9417041b-2952-41d5-b0d8-b42694f4fd4a"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "1edb7ccc-0cb3-41c4-a193-181542bce479"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        },
-        "donor_organism_7.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F08",
-                "biomaterial_name": "F33",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F33 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "b49fb5d4-6f31-4b7d-827e-bc09ed30a167",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "1fe49331-d165-4443-a82b-612309cb9567"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "384733f9-328f-4b3f-b201-9489ae09f5de"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "39c59048-bac9-4b5b-935b-75b150931f41"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "dfe9cbbb-cf19-4e2d-bd3c-70e0d9235f67"
+                    }
                 ],
-                "genotype": "rsa(13,15,16,18,21,22)x2 (X,X)x1",
-                "HDBR_accession": "14011"
-            },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "female",
-            "is_living": "no",
-            "development_stage": {
-                "text": "9pcw",
-                "ontology": "HsapDv:0000046",
-                "ontology_label": "9th week post-fertilization human stage"
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "gestational_age": "11",
-            "provenance": {
-                "document_id": "ae71343b-df16-49a3-829d-a6e61afdc079",
-                "submission_date": "2020-08-13T10:24:30.711Z",
-                "update_date": "2020-08-13T10:24:44.369Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "282fda83-f6d8-4d5b-b47a-14d13d5206fe",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "fbed02e6-1547-469c-b96f-45c61111af53"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "1fe49331-d165-4443-a82b-612309cb9567"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "f1903d0b-1cb2-4208-bc20-a37ad8612452"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        },
-        "donor_organism_8.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F16",
-                "biomaterial_name": "F29",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F29 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "a0cf7b57-f8ac-4591-bfe5-a9a2b7416057",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "1b5a4bc7-5a90-4782-a657-536a8b533156"
+                    }
                 ],
-                "genotype": "rsa(13,15,16,18,21,22)x2 (X,X)x1",
-                "HDBR_accession": "13935"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "fbed02e6-1547-469c-b96f-45c61111af53"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "female",
-            "is_living": "no",
-            "development_stage": {
-                "text": "17pcw",
-                "ontology": "HsapDv:0000054",
-                "ontology_label": "17th week post-fertilization human stage"
+            {
+                "link_type": "process_link",
+                "process_id": "951a8ffc-69c5-4f7c-8ee8-39b76171f630",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "85e09b5b-24a8-4eea-9b0a-8ca17f9db79d"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "ed8bc174-30cc-4fa4-9e48-0543b825b1e4"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "785275c2-08e7-486f-bed5-850993b704d3"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "75017000-be20-4f58-91ea-abaf63344959"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "gestational_age": "19",
-            "provenance": {
-                "document_id": "ba005942-3abb-4988-90a4-57747fb05b8b",
-                "submission_date": "2020-08-13T10:24:30.782Z",
-                "update_date": "2020-08-13T10:24:44.626Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "72abfd0e-51d3-4b13-8495-bfaab2f1096b",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "dba60b5a-af86-4fde-8cfc-49b008f5adad"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "85e09b5b-24a8-4eea-9b0a-8ca17f9db79d"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "f1903d0b-1cb2-4208-bc20-a37ad8612452"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        },
-        "donor_organism_9.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F02",
-                "biomaterial_name": "F32",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F32 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "ea7b5ae7-acdc-4d67-8665-c8a0b52da561",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "ba005942-3abb-4988-90a4-57747fb05b8b"
+                    }
                 ],
-                "genotype": "rsa(13,15,16,18,21,22,X)x2",
-                "HDBR_accession": "13994"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "dba60b5a-af86-4fde-8cfc-49b008f5adad"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "female",
-            "is_living": "no",
-            "development_stage": {
-                "text": "CS23",
-                "ontology": "HsapDv:0000030",
-                "ontology_label": "Carnegie stage 23"
+            {
+                "link_type": "process_link",
+                "process_id": "2d0d630a-58dd-42f7-bd7e-579ebec98d48",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "4dae1604-6e74-4306-ae82-2da7ca2efd77"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "b61e4f40-1742-4bbb-a20d-78a934c5f8de"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "81204476-377f-4bf9-b5de-27f8b14d47c5"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "c79e49e1-62b2-41c4-a3eb-96bbe01a2ed4"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "gestational_age": "9",
-            "provenance": {
-                "document_id": "d0baedfe-0556-4c2b-a1a0-d1e28ef07bb5",
-                "submission_date": "2020-08-13T10:24:30.629Z",
-                "update_date": "2020-08-13T10:24:44.081Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "87fa5eb0-98d2-40ae-8bb1-445d0d2d0c11",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "0d27ca8e-5325-4e47-9807-8afd92e9bf89"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "4dae1604-6e74-4306-ae82-2da7ca2efd77"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "003cb4a8-9871-488f-9042-820504991f17"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        },
-        "donor_organism_10.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F07",
-                "biomaterial_name": "F22",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F22 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "136b438c-b819-4da2-8cc1-d6cace9c716c",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "e8fbe9c1-ab25-4300-a40d-65d0e8f627e0"
+                    }
                 ],
-                "genotype": "46, XX",
-                "HDBR_accession": "13899"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "0d27ca8e-5325-4e47-9807-8afd92e9bf89"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "female",
-            "is_living": "no",
-            "development_stage": {
-                "text": "10pcw",
-                "ontology": "HsapDv:0000047",
-                "ontology_label": "10th week post-fertilization human stage"
+            {
+                "link_type": "process_link",
+                "process_id": "62a131e1-c415-460e-bc5b-75cca5d3323b",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "470877fd-03da-40a6-9508-330b580cf728"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "7ae24487-8546-422c-ad9b-bfa36bdd6ba4"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "b4d16fe2-eeac-4a26-9cc3-17414b87f3b1"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "9c25532b-bbac-408a-8b3b-4d7f565f11b9"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "gestational_age": "12",
-            "provenance": {
-                "document_id": "dd19fdc7-35a9-432f-9a97-670637433eda",
-                "submission_date": "2020-08-13T10:24:30.696Z",
-                "update_date": "2020-08-13T10:24:44.321Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "b2b1e2e5-b9f9-4a5f-91c5-ea7cda58cffe",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "b8912f33-12a7-4bf8-9f25-e91fbc77517c"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "470877fd-03da-40a6-9508-330b580cf728"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "003cb4a8-9871-488f-9042-820504991f17"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        },
-        "donor_organism_11.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F05",
-                "biomaterial_name": "F34",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F34 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "5fbb11aa-074b-42ad-bb8c-13d80c3b2490",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "dd19fdc7-35a9-432f-9a97-670637433eda"
+                    }
                 ],
-                "genotype": "rsa(13,15,16,18,21,22,X)x2",
-                "HDBR_accession": "14023"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "b8912f33-12a7-4bf8-9f25-e91fbc77517c"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "female",
-            "is_living": "no",
-            "development_stage": {
-                "text": "CS23",
-                "ontology": "HsapDv:0000030",
-                "ontology_label": "Carnegie stage 23"
+            {
+                "link_type": "process_link",
+                "process_id": "9bb08d39-3957-4ff7-a20d-cc45a1cb38ab",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "4fd506bc-5824-4a7b-a44a-8d02532c5277"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "30286c6d-ca78-4108-aff5-6809618656dc"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "23a28752-d0c7-4a3c-8548-acc8ddc26af4"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "d1bbc8a6-9320-4527-bca3-2dbb172bea38"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "gestational_age": "10",
-            "provenance": {
-                "document_id": "e8fbe9c1-ab25-4300-a40d-65d0e8f627e0",
-                "submission_date": "2020-08-13T10:24:30.672Z",
-                "update_date": "2020-08-13T10:24:44.246Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "96d2674c-2f8f-4495-b95f-a6be448ba8fb",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "6b94e023-9280-45df-ac3d-5a258e19bf29"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "4fd506bc-5824-4a7b-a44a-8d02532c5277"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "f1903d0b-1cb2-4208-bc20-a37ad8612452"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        },
-        "donor_organism_12.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F10",
-                "biomaterial_name": "F23",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F23 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "9f686a8c-9b49-4b37-9c5e-a6017b4aaf0e",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "85dc3748-6751-482b-b7cd-c1e08f7df5c0"
+                    }
                 ],
-                "genotype": "46, XY",
-                "HDBR_accession": "13900"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "6b94e023-9280-45df-ac3d-5a258e19bf29"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "male",
-            "is_living": "no",
-            "development_stage": {
-                "text": "11pcw",
-                "ontology": "HsapDv:0000048",
-                "ontology_label": "11th week post-fertilization human stage"
+            {
+                "link_type": "process_link",
+                "process_id": "0dd65ce8-29ba-4341-9a93-eb2ca1f06c72",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "a69fcb4d-a7ec-4101-9e5a-1959bc3265ae"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "9d578de9-08fb-47f8-9bc4-77e9577965e7"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "8fee28bf-4f9b-4d62-814b-ea97119048ee"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "32714f4f-1a04-4fc3-bdd9-2ae6473fe544"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "gestational_age": "13",
-            "provenance": {
-                "document_id": "eed4d335-880b-4735-9d04-cdbf706e3d44",
-                "submission_date": "2020-08-13T10:24:30.730Z",
-                "update_date": "2020-08-13T10:24:44.459Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "796e5529-dd1a-4579-a469-a770eaa2216f",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "75b6d713-08dc-4eff-9347-95c9519a34cd"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "a69fcb4d-a7ec-4101-9e5a-1959bc3265ae"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "003cb4a8-9871-488f-9042-820504991f17"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        },
-        "donor_organism_13.json": {
-            "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
-            "schema_type": "biomaterial",
-            "biomaterial_core": {
-                "biomaterial_id": "F15",
-                "biomaterial_name": "F41",
-                "biomaterial_description": "prenatal donor from HDBR tracked with internal code F41 in internal tracking",
-                "ncbi_taxon_id": [
-                    9606
+            {
+                "link_type": "process_link",
+                "process_id": "204a3bb9-d52f-407e-a3ed-f051a40dd7c3",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "ae71343b-df16-49a3-829d-a6e61afdc079"
+                    }
                 ],
-                "genotype": "rsa(13,15,16,18,21,22,X)x2",
-                "HDBR_accession": "14167"
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "75b6d713-08dc-4eff-9347-95c9519a34cd"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
             },
-            "genus_species": [
-                {
-                    "text": "Homo Sapiens",
-                    "ontology": "NCBITaxon:9606",
-                    "ontology_label": "Homo sapiens"
-                }
-            ],
-            "sex": "female",
-            "is_living": "no",
-            "development_stage": {
-                "text": "16pcw",
-                "ontology": "HsapDv:0000053",
-                "ontology_label": "16th week post-fertilization human stage"
+            {
+                "link_type": "process_link",
+                "process_id": "536ba4f7-6694-4a31-8df1-0e6668ed10da",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "cell_suspension",
+                        "input_id": "2b532bac-4ebb-47db-b5e2-37b8da2b5f6c"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "05345715-8f9f-44fe-8f28-f75552b17d5d"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "1a17a213-3a73-4af8-a105-6e5b3d056263"
+                    },
+                    {
+                        "output_type": "sequence_file",
+                        "output_id": "4bd54cd4-ca70-4566-a2bf-9fecb4dfbc34"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "565d6b74-caae-44f1-a1fc-a0b29a1f24f1"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "4adcb95e-8d5d-41dd-8299-8a7b686e8e4a"
+                    }
+                ]
             },
-            "gestational_age": "18",
-            "provenance": {
-                "document_id": "f2ed99b4-a68d-4d54-8c65-9534ad5931b5",
-                "submission_date": "2020-08-13T10:24:30.774Z",
-                "update_date": "2020-08-13T10:24:44.602Z",
-                "schema_major_version": 15,
-                "schema_minor_version": 5
+            {
+                "link_type": "process_link",
+                "process_id": "aeaa76b1-161d-4d9f-a520-d30e87d9c1d9",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "specimen_from_organism",
+                        "input_id": "94259313-d341-4b1f-b9cc-48a760d81c19"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "cell_suspension",
+                        "output_id": "2b532bac-4ebb-47db-b5e2-37b8da2b5f6c"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "8881df7f-15da-48a9-8934-a2d65188543e"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "ad3e2c96-e515-431a-a1fa-fc7b57cff8ea"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "f1903d0b-1cb2-4208-bc20-a37ad8612452"
+                    }
+                ]
             },
-            "diseases": [
-                {
-                    "text": "normal",
-                    "ontology_label": "normal",
-                    "ontology": "PATO:0000461"
-                }
-            ]
-        }
+            {
+                "link_type": "process_link",
+                "process_id": "2415ecb9-08af-4ecc-868b-69ba70a43c81",
+                "process_type": "process",
+                "inputs": [
+                    {
+                        "input_type": "donor_organism",
+                        "input_id": "f2ed99b4-a68d-4d54-8c65-9534ad5931b5"
+                    }
+                ],
+                "outputs": [
+                    {
+                        "output_type": "specimen_from_organism",
+                        "output_id": "94259313-d341-4b1f-b9cc-48a760d81c19"
+                    }
+                ],
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "266cf33e-5540-42cd-84de-757340908d42"
+                    }
+                ]
+            }
+        ]
     }
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
index 2cd51a806..6c56e7d7c 100644
--- a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
+++ b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
@@ -935,73 +935,73 @@
                 "schema_major_version": 9,
                 "schema_minor_version": 2
             }
-        },
-        "links.json": {
-            "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
-            "schema_type": "link_bundle",
-            "schema_version": "1.1.5",
-            "links": [
-                {
-                    "process": "74fa0d9c-438f-42b7-94c7-7dd63ab67c12",
-                    "inputs": [
-                        "0432e9a5-604f-4cb7-8571-014eb5fd8ba2"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "4015da8b-18d8-4f3c-b2b0-54f0b77ae80a",
-                        "fa17159e-52ec-4a88-80cf-a3be5e2e9988"
-                    ],
-                    "output_type": "file",
-                    "protocols": [
-                        {
-                            "protocol_type": "library_preparation_protocol",
-                            "protocol_id": "76a9a285-f79c-4754-bd26-310b80965b8f"
-                        },
-                        {
-                            "protocol_type": "sequencing_protocol",
-                            "protocol_id": "63afce7b-829a-491d-a6ed-ab27bf3b4fbc"
-                        }
-                    ]
-                },
-                {
-                    "process": "c6598ea5-a7d0-4898-a640-66eb7aba33a4",
-                    "inputs": [
-                        "caadf4b5-f5e4-4416-9f04-9c1f902cc601"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "0432e9a5-604f-4cb7-8571-014eb5fd8ba2"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "dissociation_protocol",
-                            "protocol_id": "78b86ffb-3c85-4b24-81ae-af54815bf222"
-                        },
-                        {
-                            "protocol_type": "enrichment_protocol",
-                            "protocol_id": "8ec628d3-91d2-46f3-82aa-67c2b831160d"
-                        }
-                    ]
-                },
-                {
-                    "process": "c7070951-ec8a-492f-a7be-354b5670c056",
-                    "inputs": [
-                        "e66ac278-96b3-4713-9c5f-5c70b1efb6e3"
-                    ],
-                    "input_type": "biomaterial",
-                    "outputs": [
-                        "caadf4b5-f5e4-4416-9f04-9c1f902cc601"
-                    ],
-                    "output_type": "biomaterial",
-                    "protocols": [
-                        {
-                            "protocol_type": "collection_protocol",
-                            "protocol_id": "a7257865-6a66-472c-bdd1-6314c8a7d4b0"
-                        }
-                    ]
-                }
-            ]
         }
+    },
+    "links": {
+        "describedBy": "https://schema.humancellatlas.org/system/1.1.5/links",
+        "schema_type": "link_bundle",
+        "schema_version": "1.1.5",
+        "links": [
+            {
+                "process": "74fa0d9c-438f-42b7-94c7-7dd63ab67c12",
+                "inputs": [
+                    "0432e9a5-604f-4cb7-8571-014eb5fd8ba2"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "4015da8b-18d8-4f3c-b2b0-54f0b77ae80a",
+                    "fa17159e-52ec-4a88-80cf-a3be5e2e9988"
+                ],
+                "output_type": "file",
+                "protocols": [
+                    {
+                        "protocol_type": "library_preparation_protocol",
+                        "protocol_id": "76a9a285-f79c-4754-bd26-310b80965b8f"
+                    },
+                    {
+                        "protocol_type": "sequencing_protocol",
+                        "protocol_id": "63afce7b-829a-491d-a6ed-ab27bf3b4fbc"
+                    }
+                ]
+            },
+            {
+                "process": "c6598ea5-a7d0-4898-a640-66eb7aba33a4",
+                "inputs": [
+                    "caadf4b5-f5e4-4416-9f04-9c1f902cc601"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "0432e9a5-604f-4cb7-8571-014eb5fd8ba2"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "dissociation_protocol",
+                        "protocol_id": "78b86ffb-3c85-4b24-81ae-af54815bf222"
+                    },
+                    {
+                        "protocol_type": "enrichment_protocol",
+                        "protocol_id": "8ec628d3-91d2-46f3-82aa-67c2b831160d"
+                    }
+                ]
+            },
+            {
+                "process": "c7070951-ec8a-492f-a7be-354b5670c056",
+                "inputs": [
+                    "e66ac278-96b3-4713-9c5f-5c70b1efb6e3"
+                ],
+                "input_type": "biomaterial",
+                "outputs": [
+                    "caadf4b5-f5e4-4416-9f04-9c1f902cc601"
+                ],
+                "output_type": "biomaterial",
+                "protocols": [
+                    {
+                        "protocol_type": "collection_protocol",
+                        "protocol_id": "a7257865-6a66-472c-bdd1-6314c8a7d4b0"
+                    }
+                ]
+            }
+        ]
     }
 }
\ No newline at end of file
diff --git a/test/indexer/test_indexer.py b/test/indexer/test_indexer.py
index 229bc5cb7..b2d5bc6af 100644
--- a/test/indexer/test_indexer.py
+++ b/test/indexer/test_indexer.py
@@ -243,15 +243,12 @@ def test_indexing(self):
                                     entity_id = ReplicaCoordinates.from_hit(hit).entity.entity_id
                                     replicas.append(entity_id)
                                     if entity_id == bundle.uuid:
-                                        expected = bundle.metadata_files['links.json']
+                                        expected = bundle.links
                                     else:
                                         expected = one(
                                             m
                                             for m in bundle.metadata_files.values()
-                                            if (
-                                                m['schema_type'] != 'link_bundle'
-                                                and m['provenance']['document_id'] == entity_id
-                                            )
+                                            if m['provenance']['document_id'] == entity_id
                                         )
                                     # Replica contents should match the entity
                                     # metadata as supplied by the repository
@@ -292,7 +289,8 @@ def test_deletion(self):
                 bundle = self._load_canned_bundle(bundle_fqid)
                 bundle = DSSBundle(fqid=bundle_fqid,
                                    manifest=bundle.manifest,
-                                   metadata_files=bundle.metadata_files)
+                                   metadata_files=bundle.metadata_files,
+                                   links=bundle.links)
                 self.index_service.create_indices(self.catalog)
                 try:
                     self._index_bundle(bundle)
@@ -602,6 +600,7 @@ def _walkthrough(v):
                 assert False, f'Cannot handle values of type {type(v)}'
 
         bundle.metadata_files = _walkthrough(bundle.metadata_files)
+        bundle.links = _walkthrough(bundle.links)
         return old_file_uuid
 
     def _num_docs_by_index(self, hits) -> Mapping[tuple[str, DocumentType], int]:
@@ -1465,7 +1464,7 @@ def mocked_mget(self, body, _source_includes):
         for bundle_fqid in bundles:
             bundle = self._load_canned_bundle(bundle_fqid)
             for doc in bundle.metadata_files.values():
-                if doc.get('content', {}).get('schema_type') == 'file':
+                if doc['content']['schema_type'] == 'file':
                     file_document_ids.add(doc['hca_ingest']['document_id'])
         self.assertEqual(file_document_ids, file_uuids)
 
diff --git a/test/indexer/test_tdr.py b/test/indexer/test_tdr.py
index 175a49e18..d109a3623 100644
--- a/test/indexer/test_tdr.py
+++ b/test/indexer/test_tdr.py
@@ -357,6 +357,7 @@ def _test_fetch_bundle(self,
         # Manifest and metadata should both be sorted by entity UUID
         self.assertEqual(test_bundle.manifest, emulated_bundle.manifest)
         self.assertEqual(test_bundle.metadata_files, emulated_bundle.metadata_files)
+        self.assertEqual(test_bundle.links, emulated_bundle.links)
 
 
 class TestTDRSourceList(AzulUnitTestCase):
diff --git a/test/integration_test.py b/test/integration_test.py
index 6f421705b..6729ca4f8 100644
--- a/test/integration_test.py
+++ b/test/integration_test.py
@@ -1931,13 +1931,15 @@ def _test_catalog(self, catalog: config.Catalog):
 
             metadata_plugin_name = catalog.plugins['metadata'].name
             if metadata_plugin_name == 'hca':
-                self.assertEqual({'manifest', 'metadata'}, bundle_json.keys())
-                manifest, metadata = bundle_json['manifest'], bundle_json['metadata']
+                self.assertEqual({'manifest', 'metadata', 'links'}, bundle_json.keys())
+                manifest = bundle_json['manifest']
+                metadata = bundle_json['metadata']
+                links = bundle_json['links']
                 self.assertIsInstance(manifest, list)
                 self.assertIsInstance(metadata, dict)
+                self.assertIsInstance(links, dict)
                 manifest_files = sorted(e['name'] for e in manifest if e['indexed'])
                 metadata_files = sorted(metadata.keys())
-                metadata_files.remove('links.json')
                 self.assertListEqual(manifest_files, metadata_files)
             elif metadata_plugin_name == 'anvil':
                 self.assertEqual({'entities', 'links'}, bundle_json.keys())
diff --git a/test/service/test_manifest.py b/test/service/test_manifest.py
index 0bd177bfb..8f69e21f0 100644
--- a/test/service/test_manifest.py
+++ b/test/service/test_manifest.py
@@ -371,11 +371,13 @@ def _shared_file_bundle(self, bundle):
             'ontology': 'UBERON:0002048',
             'ontology_label': 'lung'
         }
+        links = self._replace_uuids(bundle.links, old_to_new)
         assert isinstance(manifest, list)
         return DSSBundle(fqid=self.bundle_fqid(uuid=old_to_new[bundle.uuid],
                                                version=bundle.version),
                          manifest=cast(MutableJSONs, manifest),
-                         metadata_files=metadata_files)
+                         metadata_files=metadata_files,
+                         links=links)
 
     def _replace_uuids(self,
                        object_: JSON,
@@ -401,7 +403,7 @@ def _add_ageless_donor(self, bundle):
         donor_id = '0895599c-f57d-4843-963e-11eab29f883b'
         duplicate_donor['provenance']['document_id'] = donor_id
         bundle.metadata_files['donor_organism_1.json'] = duplicate_donor
-        donor_link = one(ln for ln in bundle.metadata_files['links.json']['links']
+        donor_link = one(ln for ln in bundle.links['links']
                          if one(ln['inputs'])['input_type'] == 'donor_organism')
         new_donor_reference = {
             'input_id': donor_id,
@@ -567,11 +569,13 @@ def test_compact_manifest(self):
         }
         # This is an older bundle so there are no supplementary file links.
         # The existing links reference entities that weren't copied to the mock bundle.
-        metadata_files['links.json']['links'].clear()
+        links = bundle.links
+        links['links'].clear()
         self._index_bundle(DSSBundle(fqid=self.bundle_fqid(uuid='b81656cf-231b-47a3-9317-10f1e501a05c',
                                                            version='2000-01-01T01:00:00.000000Z'),
                                      manifest=manifest,
-                                     metadata_files=metadata_files))
+                                     metadata_files=metadata_files,
+                                     links=links))
 
         filters = {
             'fileId': {
@@ -1330,21 +1334,25 @@ def test_manifest_content_disposition_header(self):
                         self.assertEqual(expected_cd, actual_cd)
 
     def test_verbatim_jsonl_manifest(self):
-        expected = [
-            {
-                'type': replica_type,
-                'value': bundle.metadata_files[key],
-            }
-            for bundle in map(self._load_canned_bundle, self.bundles())
+        expected = []
+        for bundle in self.bundles():
+            bundle = self._load_canned_bundle(bundle)
+            expected.append({
+                'type': 'links',
+                'value': bundle.links
+            })
             for replica_type, key in [
-                ('links', 'links.json'),
                 ('cell_suspension', 'cell_suspension_0.json'),
                 ('project', 'project_0.json'),
                 ('sequence_file', 'sequence_file_0.json'),
                 ('sequence_file', 'sequence_file_1.json'),
                 ('specimen_from_organism', 'specimen_from_organism_0.json')
-            ]
-        ]
+            ]:
+                expected.append({
+                    'type': replica_type,
+                    'value': bundle.metadata_files[key],
+                })
+
         response = self._get_manifest(ManifestFormat.verbatim_jsonl, {})
         self.assertEqual(200, response.status_code)
         self._assert_jsonl(expected, response)

From 0e8d7f9ea779ed9de4f0994d2dd18d8ae09cc964 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Wed, 7 Aug 2024 17:37:45 -0700
Subject: [PATCH 12/20] Refactor `TDRHCABundle._parse_drs_uri`

---
 src/azul/plugins/repository/tdr_hca/__init__.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py
index 203f85040..2c0a6c2fe 100644
--- a/src/azul/plugins/repository/tdr_hca/__init__.py
+++ b/src/azul/plugins/repository/tdr_hca/__init__.py
@@ -245,11 +245,6 @@ def _add_manifest_entry(self,
                             is_stitched: bool,
                             checksums: Optional[Checksums] = None,
                             drs_uri: Optional[str] = None) -> None:
-        # These requirements prevent mismatches in the DRS domain, and ensure
-        # that changes to the column syntax don't go undetected.
-        if drs_uri is not None:
-            parsed = RegularDRSURI.parse(drs_uri)
-            require(parsed.uri.netloc == config.tdr_service_url.netloc)
         self.manifest.append({
             'name': name,
             'uuid': uuid,
@@ -288,6 +283,10 @@ def _parse_drs_uri(self,
                     external_drs_uri = None
                 return external_drs_uri
         else:
+            # This requirement prevent mismatches in the DRS domain, and ensures
+            # that changes to the column syntax don't go undetected.
+            parsed = RegularDRSURI.parse(file_id)
+            require(parsed.uri.netloc == config.tdr_service_url.netloc)
             return file_id
 
 

From 49d8db5bc14b70c6d4bd39dbf9939551b796176c Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Fri, 9 Aug 2024 16:54:43 -0700
Subject: [PATCH 13/20] Refactor `TDRHCABundle.add_entity`

---
 .../plugins/repository/tdr_hca/__init__.py    | 31 +++++++++----------
 1 file changed, 15 insertions(+), 16 deletions(-)

diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py
index 2c0a6c2fe..df8720fe7 100644
--- a/src/azul/plugins/repository/tdr_hca/__init__.py
+++ b/src/azul/plugins/repository/tdr_hca/__init__.py
@@ -185,21 +185,20 @@ def canning_qualifier(cls) -> str:
     def add_entity(self,
                    *,
                    entity_key: str,
-                   entity_type: EntityType,
-                   entity_row: BigQueryRow,
+                   entity: EntityReference,
+                   row: BigQueryRow,
                    is_stitched: bool
                    ) -> None:
-        entity_id = entity_row[entity_type + '_id']
         self._add_manifest_entry(name=entity_key,
-                                 uuid=entity_id,
-                                 version=TDRPlugin.format_version(entity_row['version']),
-                                 size=entity_row['content_size'],
+                                 uuid=entity.entity_id,
+                                 version=TDRPlugin.format_version(row['version']),
+                                 size=row['content_size'],
                                  content_type='application/json',
-                                 dcp_type=f'"metadata/{entity_row["schema_type"]}"',
+                                 dcp_type=f'"metadata/{row["schema_type"]}"',
                                  is_stitched=is_stitched)
-        if entity_type.endswith('_file'):
-            descriptor = json.loads(entity_row['descriptor'])
-            self._add_manifest_entry(name=entity_row['file_name'],
+        if entity.entity_type.endswith('_file'):
+            descriptor = json.loads(row['descriptor'])
+            self._add_manifest_entry(name=row['file_name'],
                                      uuid=descriptor['file_id'],
                                      version=descriptor['file_version'],
                                      size=descriptor['size'],
@@ -207,8 +206,8 @@ def add_entity(self,
                                      dcp_type='data',
                                      is_stitched=is_stitched,
                                      checksums=Checksums.from_json(descriptor),
-                                     drs_uri=self._parse_drs_uri(entity_row['file_id'], descriptor))
-        content = entity_row['content']
+                                     drs_uri=self._parse_drs_uri(row['file_id'], descriptor))
+        content = row['content']
         self.metadata_files[entity_key] = (json.loads(content)
                                            if isinstance(content, str)
                                            else content)
@@ -360,11 +359,11 @@ def _emulate_bundle(self, bundle_fqid: TDRBundleFQID) -> TDRHCABundle:
                     pk_column = entity_type + '_id'
                     rows.sort(key=itemgetter(pk_column))
                     for i, row in enumerate(rows):
-                        is_stitched = EntityReference(entity_id=row[pk_column],
-                                                      entity_type=entity_type) not in root_entities
+                        entity = EntityReference(entity_id=row[pk_column], entity_type=entity_type)
+                        is_stitched = entity not in root_entities
                         bundle.add_entity(entity_key=f'{entity_type}_{i}.json',
-                                          entity_type=entity_type,
-                                          entity_row=row,
+                                          entity=entity,
+                                          row=row,
                                           is_stitched=is_stitched)
                 else:
                     log.error('TDR worker failed to retrieve entities of type %r',

From 0069fdd641045d84ebd33539dc8a5660a995e843 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Wed, 7 Aug 2024 21:42:11 -0700
Subject: [PATCH 14/20] [p] Extract `is_stitched` from manifest entries
 (partial #6299)

---
 attic/scripts/recan_bundle_tdr.py             |    1 -
 src/azul/plugins/metadata/hca/__init__.py     |    3 +-
 src/azul/plugins/metadata/hca/bundle.py       |   10 +-
 .../plugins/metadata/hca/indexer/transform.py |    6 +-
 .../plugins/repository/tdr_hca/__init__.py    |    8 +-
 src/humancellatlas/data/metadata/api.py       |   36 +-
 ...3-5e9d-52cd-b32d-af88edccabfa.dss.hca.json |  180 +-
 ...5-71e2-48ca-a87b-e256938c6a98.dss.hca.json |  104 +-
 ...3-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json | 1517 ++++++++---------
 ...c-6778-423d-8fe9-869e2a515d35.dss.hca.json |   20 +-
 ...8-01a0-464a-9599-7375fda3353d.dss.hca.json |    3 +-
 ...8-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json |    4 +-
 ...8-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json |  106 +-
 ...0-eaba-531d-ba9e-db80164d65ef.dss.hca.json |    3 +-
 ...4-fa14-5c6f-a474-a742540108a3.dss.hca.json |    3 +-
 ...5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json |   20 +-
 ...c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json |    3 +-
 ...8-658e-4c51-9de4-a768322f84c5.dss.hca.json |   18 +-
 ...3-93e1-56b4-b857-59497f5d942d.dss.hca.json |    3 +-
 ...a-940e-49b1-9bcc-25699a55b295.dss.hca.json |    3 +-
 ...f-61a7-4504-a57c-fc70f38d5b13.dss.hca.json |    3 +-
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json |    3 +-
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json |    3 +-
 ...5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json |   53 +-
 ...a-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json |    3 +-
 ...e-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json |   21 +-
 ...8-adab-59a9-b6c4-3a61242cc972.dss.hca.json |    3 +-
 ...e-7554-4b5d-96a2-7df127a7640b.dss.hca.json |    3 +-
 ...4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json |    3 +-
 ...0.2020-12-10T10:30:00.000000Z.dss.hca.json |  764 +++++----
 ...1-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json |    3 +-
 ...f-8346-5420-b7e4-b486f99451a8.dss.hca.json |   46 +-
 ...e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json |   21 +-
 ...1-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json |   11 +-
 ...f-4c01-48d5-a79f-1c5439659da3.dss.hca.json |    3 +-
 ...3-1885-545f-9381-0dab1edf6074.dss.hca.json |    3 +-
 ...e-9a5d-4e3d-ada2-0414b666b880.dss.hca.json |    3 +-
 ...2-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json |    3 +-
 ...3-f0ac-417a-8a29-221c77debde8.dss.hca.json |    3 +-
 ...6-ced8-448a-8e45-1fc7846d8995.dss.hca.json |    3 +-
 ...d.2018-11-02T11:33:44.698028Z.dss.hca.json |    3 +-
 ...d.2018-11-04T11:33:44.698028Z.dss.hca.json |    3 +-
 ...9-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json |    3 +-
 ...8-7eaa-45f4-8077-5a3fb4204953.dss.hca.json |    3 +-
 ...e-9b7b-4800-8977-fe7c94e131df.dss.hca.json |    3 +-
 ...9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json |    3 +-
 ...4-dc9f-439e-af29-f8eb75b0729d.dss.hca.json |    3 +-
 ...4-9a58-4763-9e66-59894efbdaa8.dss.hca.json |    3 +-
 ...d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json |    3 +-
 ...f-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json |    3 +-
 ...1-4766-4210-966c-f9ee25d19190.dss.hca.json |    3 +-
 ...a-2b51-4419-9cde-34df44c6458a.dss.hca.json |    3 +-
 ...e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json |    3 +-
 ...4-6b80-4eed-97c9-4984de81a47c.dss.hca.json |    3 +-
 ...7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json |    3 +-
 ...b-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json |    3 +-
 ...7-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json | 1229 +++++++------
 ...f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json |    3 +-
 test/indexer/test_tdr.py                      |    2 +-
 test/integration_test.py                      |   12 +-
 60 files changed, 2050 insertions(+), 2253 deletions(-)

diff --git a/attic/scripts/recan_bundle_tdr.py b/attic/scripts/recan_bundle_tdr.py
index 372504a2c..55428237e 100644
--- a/attic/scripts/recan_bundle_tdr.py
+++ b/attic/scripts/recan_bundle_tdr.py
@@ -177,7 +177,6 @@ def dss_bundle_to_tdr(bundle: Bundle, source: TDRSourceRef) -> TDRHCABundle:
     links_entry = None
     for entry in manifest:
         entry['version'] = convert_version(entry['version'])
-        entry['is_stitched'] = False
         if entry['name'] == 'links.json':
             links_entry = entry
         if entry['indexed']:
diff --git a/src/azul/plugins/metadata/hca/__init__.py b/src/azul/plugins/metadata/hca/__init__.py
index 49c6ee3d1..f1698b1cb 100644
--- a/src/azul/plugins/metadata/hca/__init__.py
+++ b/src/azul/plugins/metadata/hca/__init__.py
@@ -81,7 +81,8 @@ def transformers(self,
                                 version=bundle.version,
                                 manifest=bundle.manifest,
                                 metadata_files=bundle.metadata_files,
-                                links_json=bundle.links)
+                                links_json=bundle.links,
+                                stitched_entity_ids=bundle.stitched)
 
         def transformers():
             for transformer_cls in self.transformer_types():
diff --git a/src/azul/plugins/metadata/hca/bundle.py b/src/azul/plugins/metadata/hca/bundle.py
index 44e648d50..d1d08ef5d 100644
--- a/src/azul/plugins/metadata/hca/bundle.py
+++ b/src/azul/plugins/metadata/hca/bundle.py
@@ -41,6 +41,7 @@ class HCABundle(Bundle[BUNDLE_FQID], ABC):
     """
     metadata_files: MutableJSON
     links: MutableJSON
+    stitched: set[str] = attrs.field(factory=set)
 
     def reject_joiner(self, catalog: CatalogName):
         self._reject_joiner(self.manifest)
@@ -52,6 +53,7 @@ def to_json(self) -> MutableJSON:
             'manifest': self.manifest,
             'metadata': self.metadata_files,
             'links': self.links,
+            'stitched': sorted(self.stitched)
         }
 
     @classmethod
@@ -59,7 +61,13 @@ def from_json(cls, fqid: BUNDLE_FQID, json_: JSON) -> 'Bundle':
         manifest = json_['manifest']
         metadata = json_['metadata']
         links = json_['links']
+        stitched = json_['stitched']
         assert isinstance(manifest, list), manifest
         assert isinstance(metadata, dict), metadata
         assert isinstance(links, dict), links
-        return cls(fqid=fqid, manifest=manifest, metadata_files=metadata, links=links)
+        assert isinstance(stitched, list), stitched
+        return cls(fqid=fqid,
+                   manifest=manifest,
+                   metadata_files=metadata,
+                   links=links,
+                   stitched=set(stitched))
diff --git a/src/azul/plugins/metadata/hca/indexer/transform.py b/src/azul/plugins/metadata/hca/indexer/transform.py
index 0ca2ccd61..7c833b742 100644
--- a/src/azul/plugins/metadata/hca/indexer/transform.py
+++ b/src/azul/plugins/metadata/hca/indexer/transform.py
@@ -1428,7 +1428,7 @@ def entity_type(cls) -> str:
         return 'files'
 
     def _entities(self) -> Iterable[api.File]:
-        return api.not_stitched(self.api_bundle.files.values())
+        return self.api_bundle.not_stitched(self.api_bundle.files)
 
     def _transform(self, files: Iterable[api.File]) -> Iterable[Contribution]:
         zarr_stores: Mapping[str, list[api.File]] = self.group_zarrs(files)
@@ -1586,7 +1586,7 @@ def inner_entity_types(cls) -> frozenset[str]:
 
     def _entities(self) -> Iterable[Sample]:
         samples: dict[str, Sample] = dict()
-        for file in api.not_stitched(self.api_bundle.files.values()):
+        for file in self.api_bundle.not_stitched(self.api_bundle.files):
             self._find_ancestor_samples(file, samples)
         return samples.values()
 
@@ -1643,7 +1643,7 @@ def _singleton_entity(self) -> DatedEntity:
         raise NotImplementedError
 
     def _dated_entities(self) -> Iterable[DatedEntity]:
-        return api.not_stitched(self.api_bundle.entities.values())
+        return self.api_bundle.not_stitched(self.api_bundle.entities)
 
     def estimate(self, partition: BundlePartition) -> int:
         return int(partition.contains(self._singleton_id))
diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py
index df8720fe7..f326c7b58 100644
--- a/src/azul/plugins/repository/tdr_hca/__init__.py
+++ b/src/azul/plugins/repository/tdr_hca/__init__.py
@@ -189,13 +189,14 @@ def add_entity(self,
                    row: BigQueryRow,
                    is_stitched: bool
                    ) -> None:
+        if is_stitched:
+            self.stitched.add(entity.entity_id)
         self._add_manifest_entry(name=entity_key,
                                  uuid=entity.entity_id,
                                  version=TDRPlugin.format_version(row['version']),
                                  size=row['content_size'],
                                  content_type='application/json',
-                                 dcp_type=f'"metadata/{row["schema_type"]}"',
-                                 is_stitched=is_stitched)
+                                 dcp_type=f'"metadata/{row["schema_type"]}"')
         if entity.entity_type.endswith('_file'):
             descriptor = json.loads(row['descriptor'])
             self._add_manifest_entry(name=row['file_name'],
@@ -204,7 +205,6 @@ def add_entity(self,
                                      size=descriptor['size'],
                                      content_type=descriptor['content_type'],
                                      dcp_type='data',
-                                     is_stitched=is_stitched,
                                      checksums=Checksums.from_json(descriptor),
                                      drs_uri=self._parse_drs_uri(row['file_id'], descriptor))
         content = row['content']
@@ -241,7 +241,6 @@ def _add_manifest_entry(self,
                             size: int,
                             content_type: str,
                             dcp_type: str,
-                            is_stitched: bool,
                             checksums: Optional[Checksums] = None,
                             drs_uri: Optional[str] = None) -> None:
         self.manifest.append({
@@ -250,7 +249,6 @@ def _add_manifest_entry(self,
             'version': version,
             'content-type': f'{content_type}; dcp-type={dcp_type}',
             'size': size,
-            'is_stitched': is_stitched,
             **(
                 {
                     'indexed': True,
diff --git a/src/humancellatlas/data/metadata/api.py b/src/humancellatlas/data/metadata/api.py
index 63b7cec50..e4752f40f 100644
--- a/src/humancellatlas/data/metadata/api.py
+++ b/src/humancellatlas/data/metadata/api.py
@@ -18,8 +18,8 @@
     chain,
 )
 from typing import (
+    Collection,
     Iterable,
-    Iterator,
     Mapping,
     MutableMapping,
     TypeVar,
@@ -75,7 +75,6 @@ class ManifestEntry:
     # FIXME: Change Bundle.version and ManifestEntry.version from string to datetime
     #        https://github.com/DataBiosphere/hca-metadata-api/issues/48
     version: str
-    is_stitched: bool = field(init=False)
 
     def __init__(self, json: MutableJSON):
         # '/' was once forbidden in file paths and was encoded with '!'. Now
@@ -85,7 +84,6 @@ def __init__(self, json: MutableJSON):
         self.json = json
         self.content_type = json['content-type']
         self.uuid = UUID4(json['uuid'])
-        self.is_stitched = json.get('is_stitched', False)
         for f in fields(self):
             if f.init:
                 value = json.get(f.name)
@@ -104,13 +102,6 @@ class Entity:
     submission_date: datetime
     update_date: datetime | None
 
-    @property
-    def is_stitched(self):
-        if self.metadata_manifest_entry is None:
-            return False
-        else:
-            return self.metadata_manifest_entry.is_stitched
-
     @classmethod
     def from_json(cls,
                   json: JSON,
@@ -168,20 +159,6 @@ def accept(self, visitor: 'EntityVisitor') -> None:
 E = TypeVar('E', bound=Entity)
 
 
-# noinspection PyPep8Naming
-@dataclass(frozen=True)
-class not_stitched(Iterable[E]):
-    """
-    An iterable of the entities in the argument iterable that are not stitched.
-    This is an iterable, so it can be consumed repeatedly.
-    """
-
-    entities: Iterable[E]
-
-    def __iter__(self) -> Iterator[E]:
-        return (e for e in self.entities if not e.is_stitched)
-
-
 class TypeLookupError(Exception):
 
     def __init__(self, described_by: str) -> None:
@@ -999,10 +976,12 @@ def __init__(self,
                  version: str,
                  manifest: MutableJSONs,
                  metadata_files: Mapping[str, JSON],
-                 links_json: JSON):
+                 links_json: JSON,
+                 stitched_entity_ids: Collection[str] = ()):
         self.uuid = UUID4(uuid)
         self.version = version
         self.manifest = {m.name: m for m in map(ManifestEntry, manifest)}
+        self.stitched = frozenset(map(UUID4, stitched_entity_ids))
 
         json_by_core_cls: MutableMapping[type[E], list[tuple[JSON, ManifestEntry]]] = defaultdict(list)
         for file_name, json in metadata_files.items():
@@ -1096,6 +1075,13 @@ def visit(entity: Entity) -> Mapping[UUID4, L]:
 
         return recurse(self.root_entities().values())
 
+    def not_stitched(self, entities: Mapping[UUID, E]) -> list[E]:
+        return [
+            entity
+            for uuid, entity in entities.items()
+            if uuid not in self.stitched
+        ]
+
     @cached_property
     def leaf_cell_suspensions(self) -> Mapping[UUID4, CellSuspension]:
         return self.leaf_entities(CellSuspension)
diff --git a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
index 747dabfc9..504a1f5f5 100644
--- a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
+++ b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
@@ -6,7 +6,6 @@
             "version": "2019-09-13T09:16:27.260339Z",
             "content-type": "application/gzip; dcp-type=data",
             "size": 847438091,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_b9549f9f-d892-4093-93fd-197d02ec7c97",
             "crc32c": "0292db90",
@@ -20,7 +19,6 @@
             "version": "2019-09-13T09:16:28.234453Z",
             "content-type": "application/gzip; dcp-type=data",
             "size": 3115598454,
-            "is_stitched": true,
             "indexed": false,
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@@ -34,7 +32,6 @@
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@@ -45,7 +42,6 @@
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@@ -56,7 +52,6 @@
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@@ -67,7 +62,6 @@
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@@ -78,7 +72,6 @@
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@@ -92,7 +85,6 @@
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@@ -103,7 +95,6 @@
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@@ -114,7 +105,6 @@
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@@ -137,7 +126,6 @@
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@@ -148,7 +136,6 @@
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@@ -170,7 +156,6 @@
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@@ -206,7 +189,6 @@
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@@ -217,7 +199,6 @@
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@@ -228,7 +209,6 @@
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@@ -239,7 +219,6 @@
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@@ -250,7 +229,6 @@
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@@ -261,7 +239,6 @@
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@@ -275,7 +252,6 @@
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@@ -298,7 +273,6 @@
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@@ -309,7 +283,6 @@
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@@ -359,7 +329,6 @@
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@@ -370,7 +339,6 @@
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@@ -500,7 +458,6 @@
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@@ -511,7 +468,6 @@
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@@ -522,7 +478,6 @@
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@@ -555,7 +508,6 @@
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@@ -578,7 +529,6 @@
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@@ -592,7 +542,6 @@
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@@ -603,7 +552,6 @@
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@@ -614,7 +562,6 @@
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@@ -637,7 +583,6 @@
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@@ -648,7 +593,6 @@
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@@ -682,7 +624,6 @@
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@@ -718,7 +657,6 @@
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@@ -741,7 +678,6 @@
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@@ -752,7 +688,6 @@
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@@ -763,7 +698,6 @@
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             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -774,7 +708,6 @@
             "version": "2019-09-13T09:16:26.425735Z",
             "content-type": "application/gzip; dcp-type=data",
             "size": 1071829396,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_5c7817ba-9ebe-4ee4-adf4-7e377576c709",
             "crc32c": "de18d088",
@@ -788,7 +721,6 @@
             "version": "2019-09-13T08:54:12.962000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 608,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -799,7 +731,6 @@
             "version": "2019-09-13T08:37:53.838000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 583,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -810,7 +741,6 @@
             "version": "2019-09-13T08:37:57.252000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 301,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -821,7 +751,6 @@
             "version": "2019-09-13T08:37:53.853000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 847,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -832,7 +761,6 @@
             "version": "2020-02-03T10:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 327,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -843,7 +771,6 @@
             "version": "2019-09-13T09:16:27.945734Z",
             "content-type": "application/gzip; dcp-type=data",
             "size": 20962104505,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_2b407a11-dc22-4313-a523-f0cd6387bd13",
             "crc32c": "b844e997",
@@ -857,7 +784,6 @@
             "version": "2019-09-13T08:37:53.832000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 668,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -868,7 +794,6 @@
             "version": "2020-02-03T10:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 417,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -879,7 +804,6 @@
             "version": "2021-02-11T23:11:45.000000Z",
             "content-type": "application/vnd.loom; dcp-type=data",
             "size": 255471211,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_b4cdcc6c-15ea-4f43-a872-0d2fc7db6fd8",
             "crc32c": "d1b06ce5",
@@ -891,7 +815,6 @@
             "version": "2021-02-03T21:08:27.000000Z",
             "content-type": "application/vnd.loom; dcp-type=data",
             "size": 972969186,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_f76e3d66-f748-4d82-b345-69e7ef60b1ab",
             "crc32c": "567bee09",
@@ -903,7 +826,6 @@
             "version": "2020-02-03T10:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 522,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -914,7 +836,6 @@
             "version": "2019-09-13T09:16:27.063168Z",
             "content-type": "application/gzip; dcp-type=data",
             "size": 5915975880,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_7da1904a-5076-46fd-b95e-2366a907d789",
             "crc32c": "1c00b5b2",
@@ -928,7 +849,6 @@
             "version": "2020-02-03T10:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 417,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -939,7 +859,6 @@
             "version": "2019-09-13T09:16:27.300840Z",
             "content-type": "application/gzip; dcp-type=data",
             "size": 20619721127,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_a18a7953-48aa-4e6b-810b-caf5767095c7",
             "crc32c": "a5db114b",
@@ -953,7 +872,6 @@
             "version": "2019-09-13T08:53:22.108000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 603,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -964,7 +882,6 @@
             "version": "2019-09-13T08:37:57.269000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 301,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -975,7 +892,6 @@
             "version": "2019-09-13T09:07:14.915000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 608,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -986,7 +902,6 @@
             "version": "2019-09-13T08:37:53.864000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 569,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -997,7 +912,6 @@
             "version": "2019-09-13T08:37:53.864000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 838,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -1008,7 +922,6 @@
             "version": "2020-02-03T10:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 417,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -1019,7 +932,6 @@
             "version": "2019-09-13T08:49:05.856000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 608,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -1030,7 +942,6 @@
             "version": "2019-09-13T08:37:53.809000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 970,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -1041,7 +952,6 @@
             "version": "2020-02-03T10:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 462,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -4892,5 +4802,93 @@
                 ]
             }
         ]
-    }
+    },
+
+    "stitched": [
+        "07b45ad4-7797-4c16-bfae-493fb41d6600",
+        "09eb8fc6-9e27-4f08-87c5-bfccf918ee12",
+        "0aabed05-6a89-4141-9384-828a33581419",
+        "1016adeb-cdc3-47d6-a89e-771c763dd2e7",
+        "1116b396-448e-4dd1-b9c9-78357c511e15",
+        "15f64718-69cf-462c-9704-e8a1f54c27c8",
+        "1985c53a-b78f-4d9e-9563-dffed8207efd",
+        "1d3e48d7-d80f-4b99-85bd-04ff393288e7",
+        "1dda6a28-cbaa-4506-be47-fa117e8f463c",
+        "20329887-aab3-55fb-ba2c-e3eb27a20f6d",
+        "2509f42a-0328-4e33-8d21-79d37560d846",
+        "252b008d-8b5a-450c-a17c-4e779a17ff26",
+        "25999eea-6f12-40a8-aecf-d1524c7cf564",
+        "262f55a3-d03d-49ae-8080-1a6208fddb4f",
+        "27622c20-c017-4a98-b62c-76035758bc09",
+        "289ec28b-ce11-5be8-89ab-92fbceb874a0",
+        "2f8a07c2-4a6b-47ac-a304-0dead66eee9e",
+        "30040306-be5c-48f9-b221-e666e279ab5b",
+        "3030903f-4a4b-4b30-ab93-3b10183181e0",
+        "33682180-6cdf-4d0c-9fe0-e1c029ac13b2",
+        "366c7a41-3b80-4c7d-af4b-20248e69425f",
+        "39255288-6791-45b0-ac7e-b3ef4c981a3b",
+        "39ae3998-72a4-41ba-b00f-526bfecb8ca2",
+        "3ac6d370-c10b-54a2-a1ed-52f661aae1d7",
+        "3ad5d964-6c2c-4adc-badb-9100ceada68c",
+        "3d7a4690-8760-491c-98f9-9a1aea3f79b5",
+        "3e2b02f8-5b3b-4ab2-8ef4-7ae8a856854e",
+        "3e3505f9-4f47-402f-bfb8-960af07f91da",
+        "3f615b1d-d507-4912-82c5-9cb575cd19c1",
+        "4054b722-a585-4e90-8d74-a02fb4d98202",
+        "427c0a62-9baf-42ab-a3a3-f48d10544280",
+        "43598186-06cd-5f4b-95d9-fecb0a35d3ab",
+        "48a0c58c-ea67-4014-8752-6339de02b70e",
+        "4b611790-d17b-5938-86c4-695480abb4ef",
+        "4c866eb3-7470-5ee8-91b9-942246f19fde",
+        "5140b603-8cc1-4566-9043-e68145efbbd6",
+        "52149e21-dcd2-4288-a5eb-e526c3dcf745",
+        "5a11ed4f-41d1-53b4-9e62-3c0bbd04b4b0",
+        "5ceca6a5-2bc0-4b38-908b-01d4fec71d9f",
+        "640e64f1-6ada-5d12-a772-fe4ed4eeecea",
+        "66b7152c-8e94-412b-b0e4-f8fbf554df5a",
+        "6bd884d2-fccf-4227-8efc-184751527dfb",
+        "6d52232d-dc77-4070-bdb1-9bb0ee59d309",
+        "70ff6783-333f-5c1b-8208-3b495df95620",
+        "759bad57-b725-5346-b3ff-9fb80b27cfe7",
+        "76502973-5eb8-40b1-a0dc-17c4f772edaa",
+        "76fc7a86-572e-5e00-ac87-b55d81a8515d",
+        "799f314f-7c6c-4981-be36-8e1310bf38e6",
+        "79f589cb-32a2-4ba6-a091-7c5d820d02df",
+        "7a96a0c2-e22a-57ad-ac46-4c2433a63d94",
+        "820c396e-248b-5b4e-91b9-d7801cd9725f",
+        "8b81f0c2-3b57-4072-8a10-c169fece543e",
+        "932000d6-c63b-40f0-bdd5-469fa4db8be2",
+        "98ab4428-d66a-57b7-a802-83fdec68d744",
+        "98c88684-6469-4bb3-90aa-57a4ea101244",
+        "9b4ae2d9-d681-4f08-b111-6f1878145b35",
+        "9d720856-425d-404f-bb5b-51c225e92dd6",
+        "9f8f5212-0749-460b-9a46-2949dea45d52",
+        "a166be3d-6e84-4058-a1bd-edf90cf3ee88",
+        "a301dcb4-6a8f-5ef8-af7e-6a9fe44058e8",
+        "a5e37780-0b71-4610-8a7c-26142dedfcec",
+        "a7915c55-1d80-5724-9c81-6dd0a9130361",
+        "a7b21a25-e76e-420d-8892-538062bfefbf",
+        "ad220152-0eb4-4f85-a03e-c7e81ea3f167",
+        "ad5fed6e-b0e1-40a0-82e8-0cfc2eca0786",
+        "b01b2e61-3ebd-48cc-b071-f2e8cb42ff7c",
+        "b1b6ea44-e0b7-425a-9faa-51ecff56783e",
+        "b360251f-7550-4c08-b576-781858554ea1",
+        "b8049daa-7458-47bf-8ec2-3f5c56d2cb34",
+        "b949e4b6-c3fb-58b4-865b-40cb3ef2b6c6",
+        "b9ab7f46-071a-48cf-bc7f-fdb9c8dd0c22",
+        "ba595d79-aa43-4e3a-ad10-89f92ef4f22f",
+        "bc111cd3-bf54-57ce-8af1-88f5997a0a9d",
+        "bdd02a5f-2007-56f9-abeb-8c2c5c99a08e",
+        "d65c128c-3bb7-4da3-8d56-b60007cf8d15",
+        "d90280cc-a294-57de-b350-5234a5278c19",
+        "d94b88bc-3507-4644-a221-1c99861895e2",
+        "e0efcd8d-8433-4b40-9eee-11dafb699a5a",
+        "e511e7ff-e67c-4eb3-b0db-13aecefb5486",
+        "e92c42c7-f238-44ea-b147-e199b768d450",
+        "eb32bfc6-e7be-4093-8959-b8bf27f2404f",
+        "edc72947-b776-4150-8bfe-b7331acfa66f",
+        "f51568e8-b84c-504b-82f0-3ad5975d4bcb",
+        "f6407a7a-eecc-4735-a96a-b8bb634118e4",
+        "fa99959f-faa2-4d69-a092-48333e59f5f3"
+    ]
 }
\ No newline at end of file
diff --git a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
index c431a7e9a..c40636930 100644
--- a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
+++ b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
@@ -6,7 +6,6 @@
             "version": "2021-06-28T14:21:17.533000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 629,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -17,7 +16,6 @@
             "version": "2021-06-28T14:21:17.953000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 482,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -28,7 +26,6 @@
             "version": "2021-06-28T14:21:16.902000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 944,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -39,7 +36,6 @@
             "version": "2021-06-28T14:21:18.700000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 411,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -50,7 +46,6 @@
             "version": "2021-06-28T14:21:17.506000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 2833603821,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_5b9faa43-71d3-4421-9147-c35c5a1020d6",
             "crc32c": "99e502af",
@@ -64,7 +59,6 @@
             "version": "2021-06-28T14:21:17.989000Z",
             "content-type": "application/octet-stream; dcp-type=data; dcp-type=data",
             "size": 264733,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_06900980-e0f1-4600-8fb4-b091fbbeca82",
             "crc32c": "a161ac05",
@@ -78,7 +72,6 @@
             "version": "2021-06-28T14:21:17.521000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 629,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -89,7 +82,6 @@
             "version": "2021-06-28T14:21:17.337000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 834,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -100,7 +92,6 @@
             "version": "2021-06-28T14:21:17.614000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 617,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -111,7 +102,6 @@
             "version": "2021-06-28T14:21:17.481000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 4088255061,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_632ab1c1-1e1e-4475-b8b0-4684c9204e45",
             "crc32c": "ce40df66",
@@ -125,7 +115,6 @@
             "version": "2021-06-28T14:21:17.582000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 2868503392,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_8beb3758-3c01-4925-b455-46fa31a78641",
             "crc32c": "b05bd34e",
@@ -139,7 +128,6 @@
             "version": "2021-06-28T14:21:18.054000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 351,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -150,7 +138,6 @@
             "version": "2021-06-28T14:21:18.018000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 351,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -161,7 +148,6 @@
             "version": "2021-06-28T14:21:18.691000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 411,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -172,7 +158,6 @@
             "version": "2021-06-28T14:21:17.456000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 1856426785,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_928b877a-0d23-4661-a577-85dc213cea43",
             "crc32c": "0b7968e1",
@@ -186,7 +171,6 @@
             "version": "2021-06-28T14:21:17.965000Z",
             "content-type": "application/octet-stream; dcp-type=data; dcp-type=data",
             "size": 184842,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_b7f242d4-8641-4765-9f8d-c1b8ceaa1e8e",
             "crc32c": "b8c266c7",
@@ -200,7 +184,6 @@
             "version": "2021-06-28T14:21:17.637000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 617,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -211,7 +194,6 @@
             "version": "2021-06-28T14:21:17.977000Z",
             "content-type": "application/octet-stream; dcp-type=data; dcp-type=data",
             "size": 193841,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_b7503d91-124b-4275-a220-5a3e023e1217",
             "crc32c": "5ebb84c6",
@@ -225,7 +207,6 @@
             "version": "2021-06-28T14:21:18.634000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 352,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -236,7 +217,6 @@
             "version": "2021-06-28T14:21:17.929000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 549,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -247,7 +227,6 @@
             "version": "2021-06-28T14:21:17.953000Z",
             "content-type": "application/octet-stream; dcp-type=data; dcp-type=data",
             "size": 57834,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_70dd09f2-b511-4ba0-b9a9-c29f9970bddb",
             "crc32c": "f345df0c",
@@ -261,7 +240,6 @@
             "version": "2021-06-28T14:21:16.987000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 916,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -272,7 +250,6 @@
             "version": "2021-06-28T14:21:17.626000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 1022583763,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_1cd03a77-2af0-4507-a0c9-0edc2579c71f",
             "crc32c": "2e806c02",
@@ -286,7 +263,6 @@
             "version": "2021-06-28T14:21:16.920000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 916,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -297,7 +273,6 @@
             "version": "2021-06-28T14:21:16.928000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 916,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -308,7 +283,6 @@
             "version": "2021-06-28T14:21:16.911000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 916,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -319,7 +293,6 @@
             "version": "2021-06-28T14:21:17.557000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 4203835842,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_13506603-a2be-4cc7-bd11-4711bb0b7d7d",
             "crc32c": "e6f8d11a",
@@ -333,7 +306,6 @@
             "version": "2021-06-28T14:21:17.614000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 700197355,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_15d3e34d-828d-40d3-867a-1204fc662dad",
             "crc32c": "d0e55a31",
@@ -347,7 +319,6 @@
             "version": "2021-06-28T14:21:17.398000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1410,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -358,7 +329,6 @@
             "version": "2021-06-28T14:21:17.426000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 885,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -369,7 +339,6 @@
             "version": "2021-06-28T14:21:17.941000Z",
             "content-type": "application/octet-stream; dcp-type=data; dcp-type=data",
             "size": 547824,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_82d416d0-30c5-455f-a219-b0c98956acd8",
             "crc32c": "cb0ebb55",
@@ -383,7 +352,6 @@
             "version": "2021-06-28T14:21:17.456000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 629,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -394,7 +362,6 @@
             "version": "2021-06-28T14:21:17.941000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 509,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -405,7 +372,6 @@
             "version": "2021-06-28T14:21:17.533000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 1908869082,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_f257507e-5911-4421-ab82-37ee6f10da74",
             "crc32c": "6611c40b",
@@ -419,7 +385,6 @@
             "version": "2021-06-28T14:21:18.027000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 351,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -430,7 +395,6 @@
             "version": "2021-06-28T14:21:17.998000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 351,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -441,7 +405,6 @@
             "version": "2021-06-28T14:21:17.493000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 629,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -452,7 +415,6 @@
             "version": "2021-06-28T14:21:18.008000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 351,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -463,7 +425,6 @@
             "version": "2021-06-28T14:21:17.521000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 4272849055,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_9e70df3e-e8ee-4f80-a7ab-203a2dd88aa0",
             "crc32c": "2468ae75",
@@ -477,7 +438,6 @@
             "version": "2021-06-28T14:21:17.435000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1270,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -488,7 +448,6 @@
             "version": "2021-06-28T14:21:17.929000Z",
             "content-type": "application/octet-stream; dcp-type=data; dcp-type=data",
             "size": 87863503,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_2966f26e-7628-415b-9348-8878d982a676",
             "crc32c": "55189345",
@@ -502,7 +461,6 @@
             "version": "2021-06-28T14:21:17.469000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 629,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -513,7 +471,6 @@
             "version": "2021-06-28T14:21:17.626000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 617,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -524,7 +481,6 @@
             "version": "2021-06-28T14:21:18.070000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 351,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -535,7 +491,6 @@
             "version": "2021-06-28T14:21:16.972000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 916,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -546,7 +501,6 @@
             "version": "2021-06-28T14:21:17.599000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 4325523016,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_91e61cc0-f5ee-4fa7-b77d-1526fe370117",
             "crc32c": "f848708b",
@@ -560,7 +514,6 @@
             "version": "2021-06-28T14:21:17.469000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 2711169529,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_da6a4e63-7d13-4cdd-8fc7-3d1e5c39ca8d",
             "crc32c": "b80517a8",
@@ -574,7 +527,6 @@
             "version": "2021-06-28T14:21:18.035000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 351,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -585,7 +537,6 @@
             "version": "2021-06-28T14:21:17.557000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 629,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -596,7 +547,6 @@
             "version": "2021-06-28T14:21:17.355000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 732,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -607,7 +557,6 @@
             "version": "2021-06-28T14:21:17.965000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 504,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -618,7 +567,6 @@
             "version": "2021-06-28T14:21:17.637000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 1541984087,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_af994530-3921-487c-94cc-acbaff660b0a",
             "crc32c": "576c4860",
@@ -632,7 +580,6 @@
             "version": "2021-06-28T14:21:16.961000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 916,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -643,7 +590,6 @@
             "version": "2021-06-28T14:21:16.940000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 916,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -654,7 +600,6 @@
             "version": "2021-06-28T14:21:17.481000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 629,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -665,7 +610,6 @@
             "version": "2021-06-28T14:21:18.045000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 351,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -676,7 +620,6 @@
             "version": "2021-06-28T14:21:16.893000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 952,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -687,7 +630,6 @@
             "version": "2021-06-28T14:21:17.409000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1412,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -698,7 +640,6 @@
             "version": "2021-06-28T14:21:17.989000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 486,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -709,7 +650,6 @@
             "version": "2021-06-28T14:21:17.506000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 629,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -720,7 +660,6 @@
             "version": "2021-06-28T14:21:17.977000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 490,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -731,7 +670,6 @@
             "version": "2021-06-28T14:21:17.382000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1197,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -742,7 +680,6 @@
             "version": "2021-06-28T14:21:17.493000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 1940279193,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_67f2c31b-0e63-4bd2-9e3c-92c006f95717",
             "crc32c": "a50e0bbc",
@@ -756,7 +693,6 @@
             "version": "2021-06-28T14:21:17.569000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 1964146384,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_e01c4a62-ecd9-4a8d-9178-c3602160d045",
             "crc32c": "925cac87",
@@ -770,7 +706,6 @@
             "version": "2021-06-28T14:21:17.582000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 629,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -781,7 +716,6 @@
             "version": "2021-06-28T14:21:18.755000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 343,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -792,7 +726,6 @@
             "version": "2021-06-28T14:21:17.282000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 728,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -803,7 +736,6 @@
             "version": "2021-06-22T08:36:39.408000Z",
             "content-type": "application/json; dcp-type=\"metadata/project\"",
             "size": 5999,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -814,7 +746,6 @@
             "version": "2021-06-28T14:21:17.569000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 629,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -825,7 +756,6 @@
             "version": "2021-06-28T14:21:17.006000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 916,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -836,7 +766,6 @@
             "version": "2021-06-28T14:21:17.599000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 629,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -847,7 +776,6 @@
             "version": "2021-06-28T14:21:17.545000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 629,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -858,7 +786,6 @@
             "version": "2021-06-28T14:21:17.545000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 2787792522,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_08755a99-c8f0-420a-9d21-4dca10b40ba5_0a3b3a90-9b36-4030-821e-7e50c1f833d9",
             "crc32c": "71b46fde",
@@ -3691,5 +3618,34 @@
                 ]
             }
         ]
-    }
+    },
+
+    "stitched": [
+        "000d1e4b-4c1f-40de-8fd6-8a3d1a26e1d2",
+        "035ded30-cc0f-4e93-b675-8496f7146a27",
+        "06d54587-f54b-490c-8d29-3d84025e3b14",
+        "16c2629e-f042-4eef-a40e-3643dacf9926",
+        "1a2e6680-19be-406a-852f-51eda87d7e42",
+        "39fdb0ae-9a00-4829-a581-e7cb59798f02",
+        "3cd05b67-22cf-4bea-988a-7a1fb8104fa9",
+        "64eeaef0-b669-4637-9333-466c78643c09",
+        "6a72730a-1485-48f4-9b26-adc87380ad9b",
+        "6b94ce38-27b9-460e-ab1b-bceb18275c71",
+        "7113cb1e-7289-4fe2-ba15-bbe0620bd808",
+        "7c1802b3-0be5-4202-b14e-141974ca7fb3",
+        "87e562e3-cb28-4239-bdf6-5c562d35963a",
+        "9610cb70-57c1-466d-b9c9-faa22aa7b917",
+        "9c473261-cbb8-462f-ae4a-778a3ae8c566",
+        "9fa34db2-7968-4749-a83f-91ec2b12982d",
+        "a97f4858-0f13-405a-8b28-98ee5f997999",
+        "bca273dd-1758-4439-b7e0-745755dcffa0",
+        "c87f6dbf-1062-4e72-a19d-db779f1d3e66",
+        "d3965eac-1d56-4809-bf64-8291c9bbdf2f",
+        "d5925eb4-5192-4bc0-83e4-5c6d847118ef",
+        "d86c34c4-0aeb-4f50-a53e-5a0983c906b7",
+        "dc5b2d96-ba74-4bd0-bcf0-747548e1c6d7",
+        "eacaacbb-f514-49bb-bfbf-ccb123c5bf2e",
+        "ee52ecd1-68c0-48dd-82c2-6d3e45869b38",
+        "fd13fc62-8767-45d7-aa48-8a140f9a5005"
+    ]
 }
\ No newline at end of file
diff --git a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
index 3fead213a..73a3e138f 100644
--- a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
+++ b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
@@ -6,7 +6,6 @@
             "version": "2021-05-10T23:24:56.599000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 1399015453,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_a0c5b82e-0a50-469c-a3e9-a99d24b75abe",
             "crc32c": "9483ee43",
@@ -20,7 +19,6 @@
             "version": "2021-05-10T23:24:57.256000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 885462729,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_14c0d71c-bf57-4261-846c-0b656ab50896",
             "crc32c": "acca3bca",
@@ -34,7 +32,6 @@
             "version": "2021-05-10T23:24:55.848000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 2606100857,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_74dac87d-312a-44a5-ad01-8629fff394aa",
             "crc32c": "c8b99ec9",
@@ -48,7 +45,6 @@
             "version": "2021-05-10T23:24:56.488000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 613,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -59,7 +55,6 @@
             "version": "2021-05-10T23:24:59.557000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 805287802,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_f4cdaaf4-e41d-402b-8974-d1be58dfe0b1",
             "crc32c": "07caf594",
@@ -73,7 +68,6 @@
             "version": "2021-05-10T23:24:59.120000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 2531485579,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_0341ee2d-395d-4397-8f2f-4735417958d6",
             "crc32c": "c27a96d1",
@@ -87,7 +81,6 @@
             "version": "2021-05-10T23:25:00.590000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 615,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -98,7 +91,6 @@
             "version": "2021-05-10T23:24:58.005000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 612,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -109,7 +101,6 @@
             "version": "2021-05-10T23:24:58.932000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 611,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -120,7 +111,6 @@
             "version": "2021-05-10T23:24:56.019000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 520184625,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_e952d2a9-b409-4e4c-becc-7916f53514f3",
             "crc32c": "2f72380e",
@@ -134,7 +124,6 @@
             "version": "2021-05-10T23:24:55.864000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 334402592,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_1b776641-33ba-43b8-a306-012d75c3e113",
             "crc32c": "14ab6d09",
@@ -148,7 +137,6 @@
             "version": "2021-05-10T23:24:56.725000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 306146480,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_37919f15-34b1-4ba8-9f93-44083f801720",
             "crc32c": "3b9d25a3",
@@ -162,7 +150,6 @@
             "version": "2021-05-10T23:24:59.644000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 612,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -173,7 +160,6 @@
             "version": "2021-05-10T23:24:54.910000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 990,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -184,7 +170,6 @@
             "version": "2021-05-10T23:25:12.412000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 412,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -195,7 +180,6 @@
             "version": "2021-05-10T23:24:56.774000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 611,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -206,7 +190,6 @@
             "version": "2021-05-10T23:24:58.209000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 429897750,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_58329552-c7a7-4fbc-82e7-baeb98b8a3da",
             "crc32c": "3a46f1cf",
@@ -220,7 +203,6 @@
             "version": "2021-05-10T23:24:58.895000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 132046032,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_d5ceed15-cf4c-44a7-86dd-4baf882152aa",
             "crc32c": "c18682e1",
@@ -234,7 +216,6 @@
             "version": "2021-05-10T23:25:05.832000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 612,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -245,7 +226,6 @@
             "version": "2021-05-10T23:24:59.488000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 297397325,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_382f6f5c-5944-4738-b338-ac0ea389b458",
             "crc32c": "9898acae",
@@ -259,7 +239,6 @@
             "version": "2021-05-10T23:24:57.328000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 300595882,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_40f16128-7fb1-48f3-98de-a2aa191f110e",
             "crc32c": "4b659dfb",
@@ -273,7 +252,6 @@
             "version": "2021-05-10T23:24:57.823000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 612,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -284,7 +262,6 @@
             "version": "2021-05-10T23:25:00.232000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 615,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -295,7 +272,6 @@
             "version": "2021-05-10T23:24:55.652000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 1118040836,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_20ee57a6-930b-435a-b126-379b1a051e6d",
             "crc32c": "e795d8bc",
@@ -309,7 +285,6 @@
             "version": "2021-05-10T23:24:59.945000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 2160782487,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_98365f97-c1e7-4242-b6e4-bc1103869889",
             "crc32c": "6ac94e8d",
@@ -323,7 +298,6 @@
             "version": "2021-05-10T23:24:55.328000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 2454,
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             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -334,7 +308,6 @@
             "version": "2021-05-10T23:25:12.039000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 352,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -345,7 +318,6 @@
             "version": "2021-05-10T23:24:56.550000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 604854646,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_4198c4d0-1696-4ec4-8333-1b2c6f13f1bc",
             "crc32c": "aa162e31",
@@ -359,7 +331,6 @@
             "version": "2021-05-10T23:25:12.151000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
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             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -370,7 +341,6 @@
             "version": "2021-05-10T23:24:57.569000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
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             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -381,7 +351,6 @@
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             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_c8437b86-5c16-4baf-a4e5-74b76907b3c3",
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@@ -395,7 +364,6 @@
             "version": "2021-05-10T23:24:59.957000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
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             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -406,7 +374,6 @@
             "version": "2021-05-10T23:24:57.193000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
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             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -417,7 +384,6 @@
             "version": "2021-05-10T23:24:57.341000Z",
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             "crc32c": "5a80e0c8",
@@ -431,7 +397,6 @@
             "version": "2021-05-10T23:24:57.806000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
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             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -442,7 +407,6 @@
             "version": "2021-05-10T23:24:58.005000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
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             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_fb8aa41e-6226-4d61-b7fa-d4c0c44b74f2",
             "crc32c": "8f86f908",
@@ -456,7 +420,6 @@
             "version": "2021-05-10T23:24:57.453000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
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             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_14387732-8ee0-4f48-80de-d7ef71898029",
             "crc32c": "a0f3c2d8",
@@ -470,7 +433,6 @@
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             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_a32acfed-cdd1-47f9-bcde-3a7ce2a6c707",
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@@ -484,7 +446,6 @@
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@@ -495,7 +456,6 @@
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@@ -506,7 +466,6 @@
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@@ -517,7 +476,6 @@
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@@ -531,7 +489,6 @@
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@@ -545,7 +502,6 @@
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@@ -556,7 +512,6 @@
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@@ -570,7 +525,6 @@
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@@ -581,7 +535,6 @@
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@@ -592,7 +545,6 @@
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@@ -603,7 +555,6 @@
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@@ -617,7 +568,6 @@
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@@ -631,7 +581,6 @@
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@@ -642,7 +591,6 @@
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@@ -656,7 +604,6 @@
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@@ -667,7 +614,6 @@
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@@ -678,7 +624,6 @@
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@@ -689,7 +634,6 @@
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@@ -700,7 +644,6 @@
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@@ -781,7 +719,6 @@
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@@ -806,7 +742,6 @@
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@@ -917,7 +844,6 @@
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@@ -1106,7 +1018,6 @@
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@@ -1153,7 +1061,6 @@
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@@ -1175,7 +1081,6 @@
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@@ -1239,7 +1140,6 @@
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@@ -1367,7 +1258,6 @@
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@@ -3436,7 +3161,6 @@
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@@ -3450,7 +3174,6 @@
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@@ -3464,7 +3187,6 @@
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@@ -3475,7 +3197,6 @@
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@@ -3489,7 +3210,6 @@
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@@ -3503,7 +3223,6 @@
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@@ -3517,7 +3236,6 @@
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@@ -3531,7 +3249,6 @@
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@@ -3545,7 +3262,6 @@
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@@ -3556,7 +3272,6 @@
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@@ -3567,7 +3282,6 @@
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@@ -3578,7 +3292,6 @@
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@@ -3592,7 +3305,6 @@
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@@ -3603,7 +3315,6 @@
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@@ -3617,7 +3328,6 @@
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@@ -3628,7 +3338,6 @@
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@@ -3639,7 +3348,6 @@
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@@ -3653,7 +3361,6 @@
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@@ -3664,7 +3371,6 @@
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@@ -3678,7 +3384,6 @@
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@@ -3689,7 +3394,6 @@
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@@ -3700,7 +3404,6 @@
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@@ -3711,7 +3414,6 @@
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@@ -3725,7 +3427,6 @@
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@@ -3736,7 +3437,6 @@
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@@ -3761,7 +3460,6 @@
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@@ -3775,7 +3473,6 @@
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@@ -3789,7 +3486,6 @@
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@@ -3800,7 +3496,6 @@
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@@ -3814,7 +3509,6 @@
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@@ -3825,7 +3519,6 @@
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@@ -3836,7 +3529,6 @@
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@@ -3850,7 +3542,6 @@
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@@ -3861,7 +3552,6 @@
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@@ -3872,7 +3562,6 @@
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@@ -3883,7 +3572,6 @@
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@@ -3894,7 +3582,6 @@
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@@ -3905,7 +3592,6 @@
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@@ -3916,7 +3602,6 @@
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@@ -3927,7 +3612,6 @@
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@@ -3938,7 +3622,6 @@
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@@ -3949,7 +3632,6 @@
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@@ -3960,7 +3642,6 @@
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@@ -3971,7 +3652,6 @@
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@@ -3985,7 +3665,6 @@
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@@ -3996,7 +3675,6 @@
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@@ -4010,7 +3688,6 @@
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@@ -4021,7 +3698,6 @@
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@@ -4046,7 +3721,6 @@
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@@ -4057,7 +3731,6 @@
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@@ -4068,7 +3741,6 @@
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@@ -4079,7 +3751,6 @@
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@@ -4090,7 +3761,6 @@
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@@ -4104,7 +3774,6 @@
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@@ -4118,7 +3787,6 @@
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@@ -4129,7 +3797,6 @@
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@@ -5325,7 +4896,6 @@
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@@ -5519,7 +5074,6 @@
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@@ -5533,7 +5087,6 @@
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@@ -5544,7 +5097,6 @@
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@@ -5558,7 +5110,6 @@
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@@ -5572,7 +5123,6 @@
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@@ -5583,7 +5133,6 @@
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@@ -5594,7 +5143,6 @@
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@@ -5608,7 +5156,6 @@
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@@ -5622,7 +5169,6 @@
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@@ -5633,7 +5179,6 @@
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@@ -5658,7 +5202,6 @@
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@@ -5669,7 +5212,6 @@
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@@ -5683,7 +5225,6 @@
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@@ -5694,7 +5235,6 @@
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@@ -5719,7 +5258,6 @@
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@@ -5730,7 +5268,6 @@
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@@ -5741,7 +5278,6 @@
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@@ -5755,7 +5291,6 @@
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@@ -5769,7 +5304,6 @@
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@@ -5872,7 +5399,6 @@
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@@ -5897,7 +5422,6 @@
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@@ -5911,7 +5435,6 @@
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@@ -5925,7 +5448,6 @@
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@@ -5936,7 +5458,6 @@
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@@ -5947,7 +5468,6 @@
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@@ -5958,7 +5478,6 @@
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@@ -6022,7 +5537,6 @@
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@@ -6069,7 +5580,6 @@
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@@ -6097,7 +5606,6 @@
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@@ -6150,7 +5655,6 @@
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@@ -6267,7 +5763,6 @@
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@@ -6444,7 +5925,6 @@
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@@ -6858,7 +6306,6 @@
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@@ -6897,7 +6342,6 @@
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@@ -7036,7 +6470,6 @@
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@@ -7427,7 +6829,6 @@
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@@ -8304,7 +7635,6 @@
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@@ -8315,7 +7645,6 @@
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@@ -8326,7 +7655,6 @@
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@@ -8340,7 +7668,6 @@
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@@ -9017,7 +8290,6 @@
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@@ -9039,7 +8310,6 @@
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@@ -9095,7 +8362,6 @@
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@@ -9106,7 +8372,6 @@
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@@ -9120,7 +8385,6 @@
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@@ -9159,7 +8421,6 @@
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@@ -9173,7 +8434,6 @@
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@@ -9184,7 +8444,6 @@
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@@ -9223,7 +8480,6 @@
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@@ -9234,7 +8490,6 @@
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@@ -9270,7 +8523,6 @@
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@@ -9295,7 +8546,6 @@
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@@ -9320,7 +8569,6 @@
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@@ -9331,7 +8579,6 @@
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@@ -9342,7 +8589,6 @@
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@@ -9353,7 +8599,6 @@
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@@ -9367,7 +8612,6 @@
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@@ -9381,7 +8625,6 @@
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@@ -9392,7 +8635,6 @@
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@@ -9403,7 +8645,6 @@
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@@ -9414,7 +8655,6 @@
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@@ -9425,7 +8665,6 @@
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@@ -9439,7 +8678,6 @@
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@@ -9464,7 +8701,6 @@
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@@ -9475,7 +8711,6 @@
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@@ -9489,7 +8724,6 @@
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@@ -9503,7 +8737,6 @@
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@@ -9517,7 +8750,6 @@
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@@ -9528,7 +8760,6 @@
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@@ -9539,7 +8770,6 @@
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@@ -9550,7 +8780,6 @@
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@@ -9561,7 +8790,6 @@
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@@ -9572,7 +8800,6 @@
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@@ -9600,7 +8826,6 @@
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@@ -9611,7 +8836,6 @@
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@@ -9622,7 +8846,6 @@
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@@ -9633,7 +8856,6 @@
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@@ -9647,7 +8869,6 @@
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@@ -9658,7 +8879,6 @@
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@@ -9669,7 +8889,6 @@
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@@ -9680,7 +8899,6 @@
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             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 1826231331,
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             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_e71dd85f-91b9-434a-b7da-e3bf3bd45b1e",
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@@ -9694,7 +8912,6 @@
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             "content-type": "application/json; dcp-type=\"metadata/file\"",
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@@ -9705,7 +8922,6 @@
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             "content-type": "application/json; dcp-type=\"metadata/file\"",
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@@ -9716,7 +8932,6 @@
             "version": "2021-05-10T23:25:12.382000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
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@@ -9727,7 +8942,6 @@
             "version": "2021-05-10T23:25:06.490000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
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-            "is_stitched": true,
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             "crc32c": "",
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@@ -9738,7 +8952,6 @@
             "version": "2021-05-10T23:24:56.235000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
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             "crc32c": "",
             "sha256": ""
@@ -9749,7 +8962,6 @@
             "version": "2021-05-10T23:24:55.554000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 2656158282,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_c575780d-6457-4f09-b208-68eb382f72b1",
             "crc32c": "7650b91b",
@@ -9763,7 +8975,6 @@
             "version": "2021-05-10T23:24:56.379000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 611,
-            "is_stitched": true,
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             "crc32c": "",
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@@ -9774,7 +8985,6 @@
             "version": "2021-05-10T23:24:59.401000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 612,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -39331,5 +38541,730 @@
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-    }
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+        "e163d226-febb-4ecf-80db-8e60680be2ab",
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+        "e1bf51d5-e656-49de-9b55-8ad814870da7",
+        "e1c334fa-b493-4892-a48b-3fe594e98b30",
+        "e2112f19-f48b-4f9b-acca-53c0e966baff",
+        "e28d2a66-f506-4a4d-b2c6-823e4e8124d6",
+        "e2d181be-9c2f-4b06-a1ca-68965b5abd5b",
+        "e381aa0d-c2ce-4fe4-9acd-030d9023fcb6",
+        "e41aceeb-21ab-420d-a393-244aac597625",
+        "e4468469-2eab-48b1-9c5f-b72eeee2da3a",
+        "e48fabae-c5df-4906-96b8-a45c77e48af0",
+        "e4cfd5be-adcb-4ddd-b263-659ab56591b3",
+        "e4d3b43a-a03c-40d4-bf8a-bc0719d773e2",
+        "e4d6ced4-50a3-402a-bbbc-ae329cd3689d",
+        "e4e308fd-c449-4aad-b61a-43c595e3da00",
+        "e57453f7-04f8-445a-9b64-24c5b82d95c4",
+        "e5bba055-1268-4e04-99ea-71660fd31c08",
+        "e5d2cef3-3902-418c-b905-001052979a54",
+        "e61740c1-0e70-4d25-a912-32617d2e71fa",
+        "e61fff58-84e1-41cf-86f2-7d5c120b17d5",
+        "e6565b7b-b195-4554-bf60-4b80f2c6dd13",
+        "e6aa2bc0-9650-4ba6-89fc-033a7a95f796",
+        "e6b33ccb-99f6-4c02-aa69-e7b581832d04",
+        "e6f5097f-6e88-4703-91a3-1f8af0a04ca2",
+        "e72b1bd6-2847-408b-9ae6-66f187d293e4",
+        "e744fafb-3c4b-47c3-91db-db8bb8751279",
+        "e8081e5b-30a8-4ed7-88df-07c9e81688c6",
+        "e882d829-b80b-4699-b909-269337998882",
+        "e91bb61d-e965-46e5-b6b3-53e3593de931",
+        "e9b50275-4ebe-43fe-b3de-1fe3ab930a23",
+        "e9def19b-3967-47e7-a2dd-1bc5f9297959",
+        "e9f719d5-786b-439e-bdb5-1a0434d1e815",
+        "ea1d2072-66cc-4e8d-8547-7197973e43a7",
+        "ea9a283e-ec06-432a-8bf3-40133f8f9cfc",
+        "eb10f476-5ffe-4954-b2e9-8a6a768fe46c",
+        "ebbc0d72-0743-41b8-88f6-736c36bd6499",
+        "ebc98059-556f-4a51-b1d3-e5afb40fe80e",
+        "eccad683-4c2d-4d7f-a141-1effb429fef7",
+        "ecfb5b99-5606-483c-817b-fbcce96ee9be",
+        "ed3df4c8-d006-4edc-b5fb-65af588b5984",
+        "ed4c7767-277c-4d39-89cf-6144161985d2",
+        "ed884cca-c961-40d2-bc8b-b358ea4fb780",
+        "edbe53c5-208b-436d-b283-1aa4ee94800c",
+        "ee28d3e7-02df-46a0-a3ba-f55ad747b214",
+        "ee36a1ac-7426-4253-81b8-715f37a2ba69",
+        "eff0eba9-ed02-43c2-9861-d34edfaf9f30",
+        "f00513d4-c39b-4607-b43e-51bc36293e3d",
+        "f1b0bc3c-0856-4493-95af-6b5ec42d09cc",
+        "f1ba59ae-f42b-403b-a777-69ced3930293",
+        "f26b81f5-8f36-4998-90c0-0f30ea866f41",
+        "f28f5241-9275-48ef-9779-0356be81a14f",
+        "f296caba-7bdc-47d1-a7ef-b39e358d0e3e",
+        "f29dfd6b-dcb8-4c50-ba95-58c2be9c7a16",
+        "f366ef43-bfe1-4649-9d08-3eef088ff99a",
+        "f3aeccbe-aa7c-46a4-8eba-34c6b90c85a9",
+        "f3e5a38a-c62b-4100-9fcc-18ffbe346be5",
+        "f4b0febc-2a23-436f-916c-2ddb328dddd4",
+        "f5274b10-d3ea-44c9-9f27-9af574dea10c",
+        "f55166a1-c4f0-4fda-ac9f-164489040ee5",
+        "f57edc37-d012-4382-8d4b-0e250cafa81d",
+        "f5ada827-68c0-4af6-88c6-7e9256b663ff",
+        "f5fae200-b633-4ade-8871-94cf47475c67",
+        "f61ff371-7c67-45cc-af18-e94ed874baba",
+        "f648cc69-80e7-46a1-8575-aae76b30367c",
+        "f6bd08a6-5630-460c-a1bc-e13a3340f7bc",
+        "f70ce593-fe86-4bef-9e0b-c68a09a12ccc",
+        "f77883e0-6609-4bda-b446-331adbd9d357",
+        "f78279da-e39f-463b-a1a9-02d4f99f85a5",
+        "f7a68998-a02b-4d1c-8768-0abb9e9ae35a",
+        "f7e7009f-d6e8-4fc9-92db-921d32531262",
+        "f8153a7e-c5fe-43b9-bb7a-90ea3d059772",
+        "f859d1ff-df51-4548-b8a4-9eca26bf7454",
+        "f8988fe1-225c-40b4-933d-9dacb8b4728f",
+        "f89c0972-79b4-4338-b37c-7bbfdc121f60",
+        "f9951b26-b6cf-40f1-9a78-37cb8f130b19",
+        "f9db3e23-91ca-487f-a3ec-11ffa8b8f939",
+        "f9eef16f-b9cc-43bb-b9f3-bf0948766e7e",
+        "fa17dd22-2d46-44dd-bf29-7ba21c575a6c",
+        "fb59546f-ca17-40ae-b0b8-ca16c1b94de9",
+        "fb71e3ae-31d9-4ce1-8d14-25955525b515",
+        "fb771836-467f-4897-a755-a17ab281a385",
+        "fbec3e01-aaf4-41a3-b667-1f0268571d10",
+        "fc1541f1-27bb-4cd1-be90-2b04c29a902e",
+        "fd0547d5-7f16-46e4-8948-45c82f923f69",
+        "fd3a8466-6eaf-4251-be4a-f46f85403719",
+        "fd5331f0-025b-4370-94bf-a2a2d1812704",
+        "fd563e44-5e1a-4dfc-bfbd-42ef32c62d69",
+        "fd7e7e85-7747-42c3-bc6b-0e4718202d63",
+        "fdb8e413-a62a-4c6c-9890-3945c0f19ce8",
+        "fdd026f9-0ab6-49ef-88f9-4a5d61d12188",
+        "fe2c65ca-06af-4760-9df8-086a81611a31",
+        "fe586661-4878-4882-a38f-0b6321df5c99",
+        "fea581ad-b8a8-47d1-a4bb-e18f0753bf13",
+        "fea7ae13-ad77-4b59-9922-14f748263eac",
+        "fecea080-2c71-42f2-a2cd-3dbd89e04c80",
+        "fed19e4a-e9e5-4d4c-9c5f-0c6f333b40ce",
+        "fed6f8f3-2c61-4361-8160-2c5a13db83d4",
+        "fed76aa9-d126-4747-b53e-b357fbbaed47",
+        "fedc286a-9bbc-4db0-8bf5-b3f0b69fb559",
+        "ff19abb9-e4d9-4fc4-ad5e-1fbafcbdedf2",
+        "ffb352c5-f9e2-497c-940c-7cb5dd0eaa5e",
+        "ffb64e6b-8924-4adf-ae8f-e55b4dd019dd",
+        "fff15476-7228-42be-be8a-bd6b02ee9f81"
+    ]
 }
\ No newline at end of file
diff --git a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
index 19613f43d..bdf5655d1 100644
--- a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
+++ b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
@@ -6,7 +6,6 @@
             "version": "2021-03-18T11:38:47.812000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1628,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -17,7 +16,6 @@
             "version": "2021-03-18T11:38:49.863000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 412,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -28,7 +26,6 @@
             "version": "2021-04-22T15:50:01.103000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 851,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -39,7 +36,6 @@
             "version": "2021-03-18T11:38:49.142000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 415,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -50,7 +46,6 @@
             "version": "2021-01-21T12:00:11.354000Z",
             "content-type": "application/json; dcp-type=\"metadata/project\"",
             "size": 3832,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -61,7 +56,6 @@
             "version": "2021-03-18T11:38:48.652000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 11636297998,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_8ab15f7b-ec0f-433a-b6fb-28cbe0fb8dc3_cc8da2bc-eeed-4c04-b069-764c0ec9f7f6",
             "crc32c": "d04bf2d8",
@@ -75,7 +69,6 @@
             "version": "2021-03-18T11:38:48.639000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 4535175932,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_8ab15f7b-ec0f-433a-b6fb-28cbe0fb8dc3_1e60afef-6c94-4eb9-84f2-ff59398ca9da",
             "crc32c": "5fa7dd50",
@@ -89,7 +82,6 @@
             "version": "2021-03-18T11:38:47.910000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 821,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -100,7 +92,6 @@
             "version": "2021-03-18T11:38:48.652000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 538,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -111,7 +102,6 @@
             "version": "2021-03-18T11:38:47.844000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 793,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -122,7 +112,6 @@
             "version": "2021-03-18T11:38:49.499000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 352,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -133,7 +122,6 @@
             "version": "2021-03-18T11:38:48.639000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 538,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -144,7 +132,6 @@
             "version": "2021-03-18T11:38:47.755000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 845,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -155,7 +142,6 @@
             "version": "2021-03-18T11:38:47.884000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1095,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -166,7 +152,6 @@
             "version": "2021-03-18T11:38:47.207000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 1047,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -177,7 +162,6 @@
             "version": "2021-03-18T11:38:47.509000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 836,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -188,7 +172,6 @@
             "version": "2021-03-18T11:38:47.863000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 710,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -779,5 +762,6 @@
         "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links",
         "schema_version": "2.1.1",
         "schema_type": "links"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json b/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
index fd0370015..7a4c949ff 100644
--- a/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
+++ b/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
@@ -878,5 +878,6 @@
         "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
         "schema_version": "1.0.0",
         "schema_type": "link_bundle"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
index 395685928..7f8f9aee6 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
@@ -1358,5 +1358,7 @@
                 ]
             }
         ]
-    }
+    },
+
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
index feca4bb2a..2411d9a0d 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
@@ -9,7 +9,6 @@
             "version": "2019-09-24T09:35:06.958773Z",
             "crc32c": "",
             "sha256": "",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_1d239f78-f3e6-5dfb-aeb0-f50d8d97b51c"
         },
         {
@@ -20,8 +19,7 @@
             "size": 1036,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "IDC9_L001_I1.fastq.gz",
@@ -34,7 +32,6 @@
             "sha1": "82599ed6a9e0beb47fd5bd87e718959dbbecb0bd",
             "sha256": "5a51c7ea8ce08cafb06d279041bd65f0759ab24bb6d2c25f2ca488d017cd2bc6",
             "s3_etag": "4cc2f68ce54b988081c14118adc480c4-7",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_c82292d3-61d1-5785-b8dc-24b9365df5bd"
         },
         {
@@ -45,8 +42,7 @@
             "size": 4304,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "sequence_file_0.json",
@@ -56,8 +52,7 @@
             "size": 645,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "process_0.json",
@@ -67,8 +62,7 @@
             "size": 388,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "c343a47d-683f-571d-99c4-1331841b4e63_file_name.fmt",
@@ -79,7 +73,6 @@
             "version": "2019-09-24T09:35:06.958773Z",
             "crc32c": "",
             "sha256": "",
-            "is_stitched": false,
             "drs_uri": null
         },
         {
@@ -93,7 +86,6 @@
             "sha1": "8e36f67ce2f1ac6771a42c6b7b6053786d39c356",
             "sha256": "439112aa9aebd86f7e6a0c2206e005c8824994105aad3844090d765397931ed2",
             "s3_etag": "c9c70827a7c5d23bb150105a14112af9-20",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_385feda5-d1e3-5a51-8e55-f4f491a4e7bf"
         },
         {
@@ -107,7 +99,6 @@
             "sha1": "73ce5b30e5c71e0ed538d67cf13e2bd638a86243",
             "sha256": "6d84bb5bcfec87db8480a01e0c65f44f7caf1af8668010cb825ef8114de130e7",
             "s3_etag": "06705170a39d451d000c0143135fc5c3-64",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_83e89c54-4fc6-58b0-800c-3788539c41e7"
         },
         {
@@ -118,8 +109,7 @@
             "indexed": true,
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "sequence_file_1.json",
@@ -129,8 +119,7 @@
             "size": 645,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "sequence_file_2.json",
@@ -140,8 +129,7 @@
             "size": 645,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "IDC9_L002_R1.fastq.gz",
@@ -154,7 +142,6 @@
             "sha1": "b46f3cda41226009ad7b0caeefd76cccb4f7b7bc",
             "sha256": "125e5c181744e2dacf0b156d4c0b82ce771701947b26ca738689edddfc3af97e",
             "s3_etag": "31985ad7f32b053fa97f05216c6e805e-20",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_dba31e1c-1b9c-56ae-af74-16b00b8144d2"
         },
         {
@@ -165,8 +152,7 @@
             "size": 931,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "donor_organism_0.json",
@@ -176,8 +162,7 @@
             "size": 1041,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "enrichment_protocol_0.json",
@@ -187,8 +172,7 @@
             "size": 815,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "sequence_file_3.json",
@@ -198,8 +182,7 @@
             "size": 645,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "sequence_file_4.json",
@@ -209,8 +192,7 @@
             "size": 645,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "sequence_file_5.json",
@@ -220,8 +202,7 @@
             "size": 645,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "process_1.json",
@@ -231,8 +212,7 @@
             "size": 368,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "supplementary_file_1.json",
@@ -242,8 +222,7 @@
             "indexed": true,
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "507d2814-1688-54e7-b73e-2f831aa34368_file_name.fmt",
@@ -254,7 +233,6 @@
             "version": "2019-09-24T09:35:06.958773Z",
             "crc32c": "",
             "sha256": "",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_9d6f268f-f484-5381-9095-f0998fa0c961"
         },
         {
@@ -265,8 +243,7 @@
             "size": 645,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "sequence_file_7.json",
@@ -276,8 +253,7 @@
             "size": 645,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "sequence_file_8.json",
@@ -287,8 +263,7 @@
             "size": 645,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "cell_line_0.json",
@@ -298,8 +273,7 @@
             "size": 1207,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "collection_protocol_0.json",
@@ -309,8 +283,7 @@
             "size": 1256,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "IDC9_L003_R1.fastq.gz",
@@ -323,7 +296,6 @@
             "sha1": "a2493797f5cd1a2e644a08a0a81bc329c78ab950",
             "sha256": "55bd588c98a7caa2089271d79b6e0838ea8036726a7e56619786d4a23afa53c9",
             "s3_etag": "fc818501a59964e076aff1bc7f7068c6-20",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_a5e4e698-1d4c-5a5d-8d7c-5c84ea0f30d8"
         },
         {
@@ -334,8 +306,7 @@
             "size": 781,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "sequence_file_9.json",
@@ -345,8 +316,7 @@
             "size": 645,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "sequence_file_10.json",
@@ -356,8 +326,7 @@
             "size": 645,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "IDC9_L004_R2.fastq.gz",
@@ -370,7 +339,6 @@
             "sha1": "9ee5c924eb8cce21b2544b92cea7df0ac84e6e2f",
             "sha256": "4c9b22cfd3eb141a30a43fd52ce576b586279ca021444ff191c460a26cf1e4cc",
             "s3_etag": "c92e5374ac0a53b228d4c1511c2d2842-63",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_065dad63-3e05-5738-8ba5-9925d5d73d5e"
         },
         {
@@ -381,8 +349,7 @@
             "indexed": true,
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "IDC9_L001_R1.fastq.gz",
@@ -395,7 +362,6 @@
             "sha1": "4cf46e3cc2f8bc7fb019920ef0ff88c8d4541ef2",
             "sha256": "c2910761bfe2eb3ec958d653bc518988a8ecc081628a07d11f3308e25fb8f05d",
             "s3_etag": "046326b00d6cc7485eba093190ee7610-20",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_93ce1f3e-a963-5463-948f-44751a37f48d"
         },
         {
@@ -409,7 +375,6 @@
             "sha1": "b851d8660a9dc81813f6d31d75e7b248241b575f",
             "sha256": "3813e23040c8e6a26a43fd1f164b2ec1d118e8f52b9d4510640f990d8e969dd8",
             "s3_etag": "3188a7180ba75349ca223905e3f589c1-64",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_e6c1d2ce-d6ad-500e-8682-626a555992ab"
         },
         {
@@ -420,8 +385,7 @@
             "size": 368,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "specimen_from_organism_0.json",
@@ -431,8 +395,7 @@
             "size": 946,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "IDC9_L003_I1.fastq.gz",
@@ -445,7 +408,6 @@
             "sha1": "7e0667acc57bba6e57022d6e9e31dfa86f401ac1",
             "sha256": "17456db03c93cef439a31b1a43f3165db4f27a1dc93dbc76263beb5d002a0530",
             "s3_etag": "d7046367bee15cd004af8f9882874042-7",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_bb455f5a-a70f-5155-85a0-46f475856e9f"
         },
         {
@@ -456,8 +418,7 @@
             "size": 368,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "sequence_file_11.json",
@@ -467,8 +428,7 @@
             "size": 645,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "IDC9_L002_R2.fastq.gz",
@@ -481,7 +441,6 @@
             "sha1": "5d0217eedef4e8b60f0730de08c845b50890a2f9",
             "sha256": "e65d5d070584e7b08847fac0be1f89b7760ee9b301df792a66e5698d7d76d7f5",
             "s3_etag": "29da5762d5a55b9ecbd14c8663039f11-62",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_f140bd59-16c2-5082-aaf6-1c929e7063c6"
         },
         {
@@ -492,8 +451,7 @@
             "size": 702,
             "indexed": true,
             "crc32c": "",
-            "sha256": "",
-            "is_stitched": false
+            "sha256": ""
         },
         {
             "name": "IDC9_L002_I1.fastq.gz",
@@ -506,7 +464,6 @@
             "sha1": "9a51a048fa73b59aa84f2a6b300bf3c57fb70346",
             "sha256": "45ada227726e92de0638c50f4c2ac20ff3e2250f1138b436112d91d20fed19a3",
             "s3_etag": "4077676da51c8b6eff706b1ebf43114c-7",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_b644bacb-5e69-5f73-baaf-f32178b0d0fd"
         },
         {
@@ -520,7 +477,6 @@
             "sha1": "9a726b1fcd446ad3777e5537d4ee809fa393b8b5",
             "sha256": "8af97d885b995e7239a409f490e915f4754e7d1902f4a620f464995a422fb61f",
             "s3_etag": "20497e6cbc5f671fa94cf69bf0febdad-7",
-            "is_stitched": false,
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_a694f8a4-424d-56db-9329-d449667416ea"
         }
     ],
@@ -1560,5 +1516,7 @@
                 ]
             }
         ]
-    }
+    },
+
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json b/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
index 42b024d94..8ce0c37f3 100644
--- a/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
+++ b/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
@@ -767,5 +767,6 @@
         ],
         "schema_type": "links",
         "schema_version": "3.1.0"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json b/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
index 308cd36dd..4018030db 100644
--- a/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
+++ b/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
@@ -614,5 +614,6 @@
         ],
         "schema_type": "links",
         "schema_version": "3.1.0"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
index 1bc9e5dda..f8ae11f25 100644
--- a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
+++ b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
@@ -6,7 +6,6 @@
             "version": "2021-03-18T11:38:49.524000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 352,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -17,7 +16,6 @@
             "version": "2021-03-18T11:38:48.691000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 538,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -28,18 +26,17 @@
             "version": "2021-01-21T12:00:11.354000Z",
             "content-type": "application/json; dcp-type=\"metadata/project\"",
             "size": 3832,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
         },
         {
+
             "name": "process_1.json",
             "uuid": "1fd499c5-f397-4bff-9af0-eb42c37d5fbe",
             "version": "2021-03-18T11:38:49.884000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 412,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -50,7 +47,6 @@
             "version": "2021-03-18T11:38:48.691000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 15984291821,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_8ab15f7b-ec0f-433a-b6fb-28cbe0fb8dc3_470ac083-a0ce-4494-9acc-45f1be4282ed",
             "crc32c": "922d645b",
@@ -64,7 +60,6 @@
             "version": "2021-03-18T11:38:47.910000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 821,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -75,7 +70,6 @@
             "version": "2021-03-18T11:38:48.731000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 414,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -86,7 +80,6 @@
             "version": "2021-03-18T11:38:47.196000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 965,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -97,7 +90,6 @@
             "version": "2021-03-18T11:38:48.705000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 538,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -108,7 +100,6 @@
             "version": "2021-03-18T11:38:47.792000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 884,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -119,7 +110,6 @@
             "version": "2021-03-18T11:38:47.172000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 1119,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -130,7 +120,6 @@
             "version": "2021-03-18T11:38:47.874000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1232,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -141,7 +130,6 @@
             "version": "2021-03-18T11:38:48.705000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 5572888190,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_8ab15f7b-ec0f-433a-b6fb-28cbe0fb8dc3_4fb1d1c9-ec68-490f-9e1d-9f764f4a3e13",
             "crc32c": "2535659f",
@@ -155,7 +143,6 @@
             "version": "2021-03-18T11:38:47.779000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 651,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -166,7 +153,6 @@
             "version": "2021-03-18T11:38:47.822000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1236,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -177,7 +163,6 @@
             "version": "2021-03-18T11:38:47.853000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 923,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -756,5 +741,6 @@
         "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links",
         "schema_version": "2.1.1",
         "schema_type": "links"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json b/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
index ad30a46e3..10d2338e7 100644
--- a/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
+++ b/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
@@ -12796,5 +12796,6 @@
         "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
         "schema_version": "1.0.0",
         "schema_type": "link_bundle"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
index ef0488229..4cb6e918f 100644
--- a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
+++ b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
@@ -6,7 +6,6 @@
             "version": "2021-09-21T17:27:23.898000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 353,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -17,7 +16,6 @@
             "version": "2021-09-21T17:27:13.154000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 506,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -28,7 +26,6 @@
             "version": "2021-09-21T17:26:50.176000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 963,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -39,7 +36,6 @@
             "version": "2021-09-21T17:26:49.830000Z",
             "content-type": "application/json; dcp-type=\"metadata/project\"",
             "size": 4672,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -50,7 +46,6 @@
             "version": "2021-09-21T17:26:50.745000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1461,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -61,7 +56,6 @@
             "version": "2021-09-21T17:26:50.716000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1391,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -72,7 +66,6 @@
             "version": "2021-09-21T17:27:13.278000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 351,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -83,7 +76,6 @@
             "version": "2021-09-21T17:36:41.225000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 1180,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -94,7 +86,6 @@
             "version": "2021-09-21T17:26:50.487000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 945,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -105,7 +96,6 @@
             "version": "2021-09-21T17:26:50.735000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 738,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -116,7 +106,6 @@
             "version": "2021-09-21T17:27:13.953000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 416,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -127,7 +116,6 @@
             "version": "2021-09-21T17:26:50.755000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1003,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -138,7 +126,6 @@
             "version": "2021-09-21T17:26:50.725000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1057,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -149,7 +136,6 @@
             "version": "2021-09-21T17:26:50.764000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1348,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -160,7 +146,6 @@
             "version": "2021-09-21T17:27:13.154000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 33226060,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_e2464476-c0b4-4a92-a5fe-96094905825c_8bd7e274-de04-48de-8adc-32ea86d528f8",
             "crc32c": "8af9f820",
@@ -804,5 +789,6 @@
         "describedBy": "https://schema.humancellatlas.org/system/3.0.0/links",
         "schema_version": "3.0.0",
         "schema_type": "links"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json b/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
index 9cf666e5a..651581ca8 100644
--- a/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
+++ b/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
@@ -563,5 +563,6 @@
         ],
         "schema_type": "links",
         "schema_version": "3.1.0"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
index 12762e864..83d2ed630 100644
--- a/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
+++ b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
@@ -1583,5 +1583,6 @@
                 ]
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
index 9aa314dea..5459e5d70 100644
--- a/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
+++ b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
@@ -2386,5 +2386,6 @@
                 "protocols": []
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index 4e5006c45..653d6ce95 100644
--- a/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
+++ b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
@@ -3110,5 +3110,6 @@
                 "protocols": []
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index 8586061d3..c4507901f 100644
--- a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
+++ b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
@@ -3110,5 +3110,6 @@
                 "protocols": []
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
index 2c9aa4a67..3676cbfc0 100644
--- a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
+++ b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
@@ -6,7 +6,6 @@
             "version": "2019-05-14T11:01:09.564000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 403,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -17,7 +16,6 @@
             "version": "2020-08-10T21:24:26.174274Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 547,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -28,7 +26,6 @@
             "version": "2019-10-03T10:54:38.894000Z",
             "content-type": "application/json; dcp-type=\"metadata/project\"",
             "size": 4304,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -39,7 +36,6 @@
             "version": "2019-05-14T12:06:23.503000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 628,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -50,7 +46,6 @@
             "version": "2021-04-09T18:59:13.000000Z",
             "content-type": "application/octet-stream; dcp-type=data",
             "size": 1335488,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_tdr.lan/v1_446f8fa3-4244-42ba-b0a1-00e16b426cf4_6783e9b7-f3f3-4e4f-845f-0f3cc9743c91",
             "crc32c": "776f1ec2",
@@ -62,7 +57,6 @@
             "version": "2019-05-14T11:29:52.575000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 1267,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -73,7 +67,6 @@
             "version": "2019-05-14T12:29:57.858000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 317,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -84,7 +77,6 @@
             "version": "2019-05-14T11:06:42.648000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 794,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -95,7 +87,6 @@
             "version": "2019-05-14T11:59:17.317000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 617,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -106,7 +97,6 @@
             "version": "2019-05-16T06:24:31.517373Z",
             "content-type": "application/pdf; dcp-type=data",
             "size": 32748,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_tdr.lan/v1_446f8fa3-4244-42ba-b0a1-00e16b426cf4_f2c46f89-130f-4972-8014-74129e7a0ac5",
             "crc32c": "847325b6",
@@ -120,7 +110,6 @@
             "version": "2019-05-14T12:20:34.464000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 318,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -131,7 +120,6 @@
             "version": "2020-08-10T21:24:26.174274Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 350,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -142,7 +130,6 @@
             "version": "2020-08-10T21:24:26.174274Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 2123,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -153,7 +140,6 @@
             "version": "2019-05-14T12:18:53.532000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 382,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -164,7 +150,6 @@
             "version": "2019-05-14T11:01:09.596000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 403,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -175,7 +160,6 @@
             "version": "2020-08-10T21:24:26.174274Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 354,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -186,7 +170,6 @@
             "version": "2019-05-16T06:24:31.828599Z",
             "content-type": "application/pdf; dcp-type=data",
             "size": 61134,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_tdr.lan/v1_446f8fa3-4244-42ba-b0a1-00e16b426cf4_f80622ef-aba2-460a-adcf-d2017bb54284",
             "crc32c": "3658ec51",
@@ -200,7 +183,6 @@
             "version": "2019-05-14T12:26:53.666000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 315,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -211,7 +193,6 @@
             "version": "2021-04-09T18:59:14.000000Z",
             "content-type": "application/octet-stream; dcp-type=data",
             "size": 1683777,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_tdr.lan/v1_446f8fa3-4244-42ba-b0a1-00e16b426cf4_3e8ae9cf-cb0c-40db-adf9-29289d2bceed",
             "crc32c": "663a65bd",
@@ -223,7 +204,6 @@
             "version": "2019-05-16T06:24:31.672118Z",
             "content-type": "application/pdf; dcp-type=data",
             "size": 29230,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_tdr.lan/v1_446f8fa3-4244-42ba-b0a1-00e16b426cf4_4f8be791-addf-4633-991f-fdeda3bac8c8",
             "crc32c": "b9364bfa",
@@ -237,7 +217,6 @@
             "version": "2019-05-14T11:06:42.695000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 574,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -248,7 +227,6 @@
             "version": "2019-05-14T11:01:15.816000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 407,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -259,7 +237,6 @@
             "version": "2019-05-16T02:50:21.018890Z",
             "content-type": "application/gzip; dcp-type=data",
             "size": 718443,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_tdr.lan/v1_446f8fa3-4244-42ba-b0a1-00e16b426cf4_0800619e-5da7-4a4d-a082-3953ddc3e7fa",
             "crc32c": "b679ed09",
@@ -273,7 +250,6 @@
             "version": "2019-05-14T11:06:42.648000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 758,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -284,7 +260,6 @@
             "version": "2019-05-14T12:13:41.926000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 382,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -295,7 +270,6 @@
             "version": "2019-05-16T02:50:21.322397Z",
             "content-type": "application/gzip; dcp-type=data",
             "size": 761919,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_tdr.lan/v1_446f8fa3-4244-42ba-b0a1-00e16b426cf4_dc202bb3-425a-405f-99bd-75ac07a33131",
             "crc32c": "0127ea62",
@@ -309,7 +283,6 @@
             "version": "2019-05-14T11:06:42.781000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 590,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -1044,5 +1017,29 @@
                 ]
             }
         ]
-    }
+    },
+    "stitched": [
+        "01a1d04b-05d0-4904-b627-68b0dc02bc17",
+        "201ae4d0-c7c6-4777-947f-18f5268884b6",
+        "3211ef8f-a60c-4892-ae55-91d6752dcd75",
+        "33e31f6f-fe78-45bd-ae57-10d2d14253cf",
+        "5b503dcb-dca6-4e4f-988b-f7100c030dc5",
+        "5d82b884-7db4-47fa-9ccd-03054065c509",
+        "6578c322-7060-4c82-8469-9e54100e6b44",
+        "6f5ddf2c-382d-4c0a-a506-3a5286067c83",
+        "7a015307-6db9-541f-aaae-db9fdb41000f",
+        "8f8b9587-237f-4995-9461-c96eac53d615",
+        "a06cb5d5-2675-4d64-aeb8-79e0103715f3",
+        "bf92ef4a-c422-44fb-bfc1-c2f86528b86b",
+        "c0d18b81-0b54-4a11-864b-cd3f43b7e7bf",
+        "c8e93df7-2623-5e86-890a-aca3e925795e",
+        "cd8e02d1-d0f9-4094-9a31-329931df60dc",
+        "dd7f3d64-4b79-48f0-9d8c-4324594fe820",
+        "e738a267-87fc-4070-abc7-b3be6442c6d0",
+        "ebf2947d-76d2-405b-a559-68c6ebb1b2d5",
+        "eca2ab79-ad61-411f-815a-4f6d936d992b",
+        "ee7404a4-c183-4a75-8bd1-34b5fc140e81",
+        "f4132e3a-c468-4ca3-ad7b-b97b61054151",
+        "fcba26aa-658c-4120-ab31-cc5a5a00f759"
+    ]
 }
\ No newline at end of file
diff --git a/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json b/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json
index 6c391784d..cb038433c 100644
--- a/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json
+++ b/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json
@@ -12796,5 +12796,6 @@
         "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
         "schema_version": "1.0.0",
         "schema_type": "link_bundle"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json b/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
index 10a3d0b1a..a74884da3 100644
--- a/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
+++ b/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
@@ -6,7 +6,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 656,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -17,19 +16,18 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/zip; dcp-type=data",
             "size": 15535233,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_47bc2618-c6e0-4352-8350-bd5ccf7748f5",
             "crc32c": "5bf9776f",
             "sha256": "053074e25a96a463c081e38bcd02662ba1536dd0cb71411bd111b8a2086a03e1"
         },
         {
+
             "name": "supplementary_file_1.json",
             "uuid": "5b465aad-0981-5152-b468-e615e20f5884",
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 656,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -40,7 +38,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/zip; dcp-type=data",
             "size": 7570475,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_3d334510-824b-4a28-8205-03fb50744c01",
             "crc32c": "c8c42fc3",
@@ -52,7 +49,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 656,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -63,7 +59,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/zip; dcp-type=data",
             "size": 38722784,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_7337ebf7-0428-4a49-bb8d-755b88aa6e8c",
             "crc32c": "82ee1217",
@@ -75,7 +70,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 656,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -86,7 +80,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/zip; dcp-type=data",
             "size": 118250749,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_456d748a-6823-4225-871f-acf42c9624ea",
             "crc32c": "15b69eed",
@@ -98,7 +91,6 @@
             "version": "2019-09-13T08:37:53.825000Z",
             "content-type": "application/json; dcp-type=\"metadata/project\"",
             "size": 11767,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -109,7 +101,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 656,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -120,7 +111,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/zip; dcp-type=data",
             "size": 69813802,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_8c9a8805-d265-4767-8294-76f269dd18c8",
             "crc32c": "4f3d0c47",
@@ -132,7 +122,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 651,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -143,7 +132,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/octet-stream; dcp-type=data",
             "size": 2300969,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_8167c570-ced0-42cd-b7cf-3a18accec2d9",
             "crc32c": "42fcdb28",
@@ -155,7 +143,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 656,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -166,7 +153,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/zip; dcp-type=data",
             "size": 187835236,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_bd2f1c8c-91bf-479a-9cc4-2776a5b19260",
             "crc32c": "0209e859",
@@ -178,7 +164,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 656,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -189,7 +174,6 @@
             "version": "2021-02-10T16:56:40.419579Z",
             "content-type": "application/zip; dcp-type=data",
             "size": 17985905,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_e36038df-51fd-4939-b65a-1241b00e98e2",
             "crc32c": "a21bdb72",
@@ -849,5 +833,6 @@
                 ]
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json b/test/indexer/data/4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json
index 805546939..0ed08faae 100644
--- a/test/indexer/data/4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json
+++ b/test/indexer/data/4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json
@@ -727,5 +727,6 @@
         ],
         "schema_type": "links",
         "schema_version": "3.1.0"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json b/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json
index b5359ad6e..097d41d96 100644
--- a/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json
+++ b/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json
@@ -580,5 +580,6 @@
         "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
         "schema_version": "1.0.0",
         "schema_type": "link_bundle"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
index bb0cb58b2..fc7618848 100644
--- a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
+++ b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
@@ -2138,5 +2138,6 @@
                 "protocols": []
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
index 26154b0f7..8b4844b98 100644
--- a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
+++ b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
@@ -6,7 +6,6 @@
             "version": "2019-10-22T17:46:02.113000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 704,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -17,7 +16,6 @@
             "version": "2020-02-03T10:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 327,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -28,7 +26,6 @@
             "version": "2019-10-22T17:46:06.177000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 320,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -39,7 +36,6 @@
             "version": "2019-10-22T17:46:04.919000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 302,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -50,7 +46,6 @@
             "version": "2019-10-22T17:46:01.981000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 1110,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -61,7 +56,6 @@
             "version": "2019-10-22T17:46:02.097000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 938,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -72,7 +66,6 @@
             "version": "2019-10-22T19:46:28.778000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 446,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -83,7 +76,6 @@
             "version": "2019-10-23T14:49:35.991570Z",
             "content-type": "application/gzip; dcp-type=data",
             "size": 7934794716,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_b4e4823f-5d20-46dd-afa2-853f0f7e51ab_7d899eb7-411e-4a83-ac78-d4f656f06916",
             "crc32c": "661e7ca7",
@@ -97,7 +89,6 @@
             "version": "2019-10-23T14:49:36.039396Z",
             "content-type": "application/gzip; dcp-type=data",
             "size": 34998841412,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_b4e4823f-5d20-46dd-afa2-853f0f7e51ab_fa1c9793-47ae-43c9-8297-39fd1a19e074",
             "crc32c": "3b1ce216",
@@ -111,7 +102,6 @@
             "version": "2019-10-22T17:46:06.486000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 320,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -122,7 +112,6 @@
             "version": "2019-10-22T17:46:02.644000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 301,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -133,7 +122,6 @@
             "version": "2020-02-03T10:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 14716,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -144,7 +132,6 @@
             "version": "2019-10-22T17:46:06.278000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 320,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -155,7 +142,6 @@
             "version": "2019-10-22T19:55:25.167000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 382,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -166,7 +152,6 @@
             "version": "2021-02-04T15:19:30.000000Z",
             "content-type": "application/octet-stream; dcp-type=data",
             "size": 69727417013,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_b4e4823f-5d20-46dd-afa2-853f0f7e51ab_49096abc-210a-455f-9e40-48f030c2077c",
             "crc32c": "1747a06c",
@@ -178,7 +163,6 @@
             "version": "2019-10-22T17:46:02.024000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 773,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -189,7 +173,6 @@
             "version": "2019-10-22T17:46:04.924000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 302,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -200,7 +183,6 @@
             "version": "2021-02-04T15:10:36.000000Z",
             "content-type": "application/octet-stream; dcp-type=data",
             "size": 16753121529,
-            "is_stitched": true,
             "indexed": false,
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@@ -260,7 +238,6 @@
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@@ -977,7 +894,6 @@
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@@ -1032,7 +944,6 @@
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@@ -1133,7 +1036,6 @@
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@@ -1158,7 +1059,6 @@
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@@ -1169,7 +1069,6 @@
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@@ -1346,7 +1231,6 @@
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@@ -1414,7 +1293,6 @@
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@@ -1439,7 +1316,6 @@
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@@ -1450,7 +1326,6 @@
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@@ -1461,7 +1336,6 @@
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@@ -1472,7 +1346,6 @@
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@@ -1483,7 +1356,6 @@
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@@ -1494,7 +1366,6 @@
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@@ -1505,7 +1376,6 @@
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@@ -1516,7 +1386,6 @@
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@@ -1527,7 +1396,6 @@
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@@ -1541,7 +1409,6 @@
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@@ -1555,7 +1422,6 @@
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@@ -1566,7 +1432,6 @@
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@@ -1580,7 +1445,6 @@
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@@ -1591,7 +1455,6 @@
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@@ -1614,7 +1476,6 @@
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@@ -1625,7 +1486,6 @@
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@@ -1636,7 +1496,6 @@
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@@ -1647,7 +1506,6 @@
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@@ -1658,7 +1516,6 @@
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@@ -2250,7 +2059,6 @@
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@@ -2261,7 +2069,6 @@
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@@ -2320,7 +2123,6 @@
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@@ -2807,7 +2567,6 @@
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@@ -2832,7 +2590,6 @@
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@@ -2868,7 +2623,6 @@
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@@ -2925,7 +2675,6 @@
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@@ -2959,7 +2706,6 @@
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@@ -2981,7 +2726,6 @@
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@@ -2992,7 +2736,6 @@
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@@ -3003,7 +2746,6 @@
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@@ -3053,7 +2792,6 @@
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@@ -3064,7 +2802,6 @@
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@@ -3075,7 +2812,6 @@
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@@ -3112,7 +2846,6 @@
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@@ -3472,7 +3175,6 @@
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@@ -3508,7 +3208,6 @@
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@@ -3519,7 +3218,6 @@
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@@ -3530,7 +3228,6 @@
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@@ -3567,7 +3262,6 @@
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@@ -3578,7 +3272,6 @@
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@@ -3617,7 +3308,6 @@
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@@ -3628,7 +3318,6 @@
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@@ -3639,7 +3328,6 @@
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@@ -3650,7 +3338,6 @@
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@@ -3664,7 +3351,6 @@
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@@ -3689,7 +3374,6 @@
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@@ -3700,7 +3384,6 @@
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@@ -3711,7 +3394,6 @@
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@@ -3722,7 +3404,6 @@
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@@ -3733,7 +3414,6 @@
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@@ -3744,7 +3424,6 @@
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@@ -3783,7 +3460,6 @@
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@@ -3794,7 +3470,6 @@
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@@ -3834,7 +3507,6 @@
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@@ -4027,7 +3683,6 @@
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@@ -4085,7 +3736,6 @@
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@@ -4122,7 +3770,6 @@
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@@ -4335,7 +3965,6 @@
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@@ -4347,7 +3976,6 @@
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@@ -4361,7 +3989,6 @@
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@@ -4375,7 +4002,6 @@
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@@ -4386,7 +4012,6 @@
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@@ -4400,7 +4025,6 @@
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@@ -4414,7 +4038,6 @@
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@@ -4425,7 +4048,6 @@
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@@ -4439,7 +4061,6 @@
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@@ -4453,7 +4074,6 @@
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@@ -4467,7 +4087,6 @@
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@@ -19896,5 +19515,384 @@
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+        "c72eb744-4971-4525-802c-d898349b392a",
+        "c79356b3-d639-4026-8865-73a20225efd4",
+        "c8758f13-7e9b-464a-bada-b41b8b9e925f",
+        "c89d294a-1921-46fa-9392-b714af40c97c",
+        "c8b8eac3-92be-5a6c-94ac-e554face58a8",
+        "c98d14ec-8761-45f7-8e86-e63c188bd97f",
+        "c99659fc-134b-4290-aae6-0bd6adbe3f0a",
+        "c9c4fc85-aaf7-4fa3-9ab1-2d0b0a886f62",
+        "ca6b8d6b-6d19-4ff0-b487-c13cdf801a60",
+        "ca707466-c643-54d0-a251-d4314081608b",
+        "ca78a1a9-375c-4aa8-bfdc-822279d0eca3",
+        "caee5d2b-466f-5762-a565-8fa4a520faba",
+        "caf7fc00-38ab-4af5-beda-c70c1fb4448e",
+        "cb189806-adb0-42d2-b519-b9e48a23bc94",
+        "cb6662a8-c395-4f75-b6fa-87c186917ed2",
+        "cb7a8922-0b74-42f5-9346-f80ebbaddb57",
+        "cbc88af9-e283-49fa-8c4d-7931a266d2fb",
+        "cc5a78a1-539f-4dec-80b6-62f35dcafd89",
+        "cc671147-98a3-4e96-ae78-7f6b637271d6",
+        "cc811606-6aff-421b-ac56-b26adbfe67f4",
+        "cca2842a-813b-4f29-a8d5-98ebdb6d1b4c",
+        "d18bbb45-9103-421a-b0cf-a40e2821ff5b",
+        "d1f0becb-7640-4861-aee5-0578cd987194",
+        "d3ea1255-7208-4952-be7f-7372d2dc9466",
+        "d8577b2c-16a2-484f-9269-9196d7cca451",
+        "d8c08782-6f69-4314-947c-1afe6928cbce",
+        "d96cdcd2-d832-470d-96d8-db8f92075703",
+        "da200c32-cfbd-435f-8786-2cf542b87367",
+        "db9fbac5-641e-4dad-af15-a7afa407654b",
+        "dc31f31d-ab56-4025-9834-99be638a2d50",
+        "dc4b7fff-0876-4f92-96cc-167efc91b516",
+        "dc6cba3b-5de7-5405-80ba-ba0d16f9285f",
+        "dce25965-6000-496a-b884-fa4dc0491a4d",
+        "dd3dccbb-4bc8-5384-8693-96b82fe5f685",
+        "dd584f8a-9127-4d00-b251-a3042b2528f4",
+        "ddc00ab2-17ea-4b61-8f75-29e26d82551c",
+        "ddd10ecc-f7b7-4370-82cf-14e30987b751",
+        "de1febb4-49dd-4a8a-b9c0-7ea493dd2d5a",
+        "de4c5a98-eea2-4790-92fe-dd0adc5c05b2",
+        "de9d1258-715d-47f9-8480-5695c198f6cc",
+        "dec92f6d-8aa9-48e5-9c8d-5d0c2cfb7749",
+        "df5af5d4-56e1-517b-8f47-7bf4888c853a",
+        "df9eea5a-6dea-55bc-9257-35cd9e7c58cc",
+        "dfad809b-a282-5bb4-9d71-0a5bf3da0417",
+        "e0556c96-db70-426b-a44d-63da9c722734",
+        "e28e68a3-3042-45f6-a714-ba8622a4b34e",
+        "e3777b07-1706-4434-a523-1335f0b96b30",
+        "e5b37a2a-d819-4961-8fa5-f47ce08532a9",
+        "e68843c2-df7c-4607-b98f-84b39b31963c",
+        "e6e30d90-6a3f-4b47-9d7b-6a66989271da",
+        "e768a12c-327e-4d27-85e0-347d95921452",
+        "e957cc11-3b0d-41ab-9f4e-3bb45688fd8e",
+        "e9af9182-ea0a-4942-9ae5-e2fc36272da6",
+        "ec1af218-9b00-4366-8890-5cebf580f225",
+        "ed31fe54-3acf-4fdd-9877-3f241b6480a6",
+        "ee2bfb40-7aa4-4c78-b78a-91aa69c7dc6e",
+        "ee6f108e-efd4-4eb3-8e51-76fcef37455b",
+        "ef880b39-ded0-529f-8b50-44961b8f852e",
+        "eff119a8-5bdb-473d-8479-27b3aa0926bc",
+        "f11f27c5-f4b0-4d20-9c8f-d1af764c7c0a",
+        "f1aecf03-b60d-483c-a09f-69223cc1ad0e",
+        "f2393819-bde7-5d77-a1ef-ea58d87e5232",
+        "f2f0f2f6-21bb-4672-8cbe-6143c5586b69",
+        "f37a0dec-b7ba-4b34-8e51-732fb5ac7213",
+        "f3b306f2-3627-4fbe-b4d0-9968ee934452",
+        "f44d6b65-0866-47d5-bfb2-8173b1b6a2b3",
+        "f47bb6a8-a753-4d40-8254-28fee9d03c1b",
+        "f5d590c5-b307-4b99-af98-8ddba1e2a266",
+        "f6809490-ac47-5fe5-af87-1923c320164e",
+        "f6cf748f-03ac-411c-8e52-d5a5c606e673",
+        "f870bf7e-2cb7-44b2-a299-f4e06da4453c",
+        "f9703a2c-b024-4917-a6b0-981b38cfb784",
+        "f9b8be35-2641-5f85-af13-c0390b7bfe23",
+        "f9bf5721-5ee8-5837-8eb9-da3810cf04f1",
+        "fb5fdf8f-f79f-479a-a662-2f3bed88e960",
+        "fbcc2483-8a75-50ec-8cb6-8148a5087dce",
+        "fd1a13ab-4a77-4f7c-964b-7e07722581c1",
+        "fe320cac-6005-46ab-a023-1c7157f5d426",
+        "fe71fe4a-0903-42e0-9a65-d985abd943ca",
+        "fe86eb27-196d-48be-a58b-840d7add69ec",
+        "feb85664-ff85-4b95-9198-036360f87cc9",
+        "febe54b0-6388-5024-a971-fa88862a4e62",
+        "fede9b23-84cc-4d8e-97e3-9bd3fa3f4b19",
+        "ff6b12b6-7733-476d-a081-32904abff547",
+        "ffa809d2-47c7-45c6-b221-7c9d2478caa6",
+        "ffac7235-fb12-4e0d-ac86-c608d45f43c3"
+    ]
 }
\ No newline at end of file
diff --git a/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json b/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
index b4aee82a8..81c367be0 100644
--- a/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
+++ b/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
@@ -731,5 +731,6 @@
         ],
         "schema_type": "links",
         "schema_version": "3.1.0"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
index f93a841a6..711aaa080 100644
--- a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
+++ b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
@@ -6,7 +6,6 @@
             "version": "2019-09-13T08:37:57.269000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 302,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -17,7 +16,6 @@
             "version": "2019-09-13T09:16:23.710869Z",
             "content-type": "application/gzip; dcp-type=data",
             "size": 1110577684,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_cd7ace86-c1f9-4c36-8ba0-078520babe83",
             "crc32c": "3f0921bb",
@@ -31,7 +29,6 @@
             "version": "2019-09-13T08:37:53.822000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 758,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -42,7 +39,6 @@
             "version": "2021-02-26T16:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 401,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -53,7 +49,6 @@
             "version": "2019-09-13T08:43:56.724000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 608,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -64,7 +59,6 @@
             "version": "2019-09-13T08:37:53.821000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 894,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -75,7 +69,6 @@
             "version": "2019-09-13T08:54:00.067000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 608,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -86,7 +79,6 @@
             "version": "2020-02-03T10:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 14716,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -97,7 +89,6 @@
             "version": "2019-09-13T09:16:24.192766Z",
             "content-type": "application/gzip; dcp-type=data",
             "size": 9820193406,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_7b607ae7-1136-41f7-937e-ea2c3015a949",
             "crc32c": "3c380752",
@@ -111,7 +102,6 @@
             "version": "2021-02-03T21:08:31.000000Z",
             "content-type": "application/vnd.loom; dcp-type=data",
             "size": 1016626791,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_55cb0c0b-e617-491a-b055-a7cd1a438c96",
             "crc32c": "9d1f0a8c",
@@ -123,7 +113,6 @@
             "version": "2021-02-03T20:52:27.000000Z",
             "content-type": "application/octet-stream; dcp-type=data",
             "size": 13010167180,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_4bc6a861-4ecb-4758-ba27-8326821d6be5",
             "crc32c": "2ad80e5f",
@@ -135,7 +124,6 @@
             "version": "2019-09-13T09:16:23.982952Z",
             "content-type": "application/gzip; dcp-type=data",
             "size": 2950925436,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_96e58cce-a961-48c5-b4fd-84f4e994e10a",
             "crc32c": "068824ae",
@@ -144,12 +132,12 @@
             "s3_etag": "be870140031523af537bbb3861fff77e-44"
         },
         {
+
             "name": "project_0.json",
             "uuid": "8185730f-4113-40d3-9cc3-929271784c2b",
             "version": "2019-09-13T08:37:53.825000Z",
             "content-type": "application/json; dcp-type=\"metadata/project\"",
             "size": 11767,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -160,7 +148,6 @@
             "version": "2019-09-13T08:37:53.868000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 569,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -171,7 +158,6 @@
             "version": "2019-09-13T08:57:01.788000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 608,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -182,7 +168,6 @@
             "version": "2019-09-13T08:37:53.815000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 915,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -193,7 +178,6 @@
             "version": "2019-09-13T08:37:57.174000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 301,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -204,7 +188,6 @@
             "version": "2019-09-13T08:37:57.252000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 301,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -215,7 +198,6 @@
             "version": "2019-09-13T08:37:53.853000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 847,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -226,7 +208,6 @@
             "version": "2020-02-03T10:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 327,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -237,7 +218,6 @@
             "version": "2019-09-13T08:37:53.832000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 668,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -248,7 +228,6 @@
             "version": "2020-02-03T10:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 417,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -259,7 +238,6 @@
             "version": "2019-09-13T08:37:53.864000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 838,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -270,7 +248,6 @@
             "version": "2019-09-13T08:37:53.809000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 970,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -1522,5 +1499,24 @@
                 ]
             }
         ]
-    }
+    },
+    "stitched": [
+        "1116b396-448e-4dd1-b9c9-78357c511e15",
+        "1985c53a-b78f-4d9e-9563-dffed8207efd",
+        "2509f42a-0328-4e33-8d21-79d37560d846",
+        "30040306-be5c-48f9-b221-e666e279ab5b",
+        "3030903f-4a4b-4b30-ab93-3b10183181e0",
+        "39255288-6791-45b0-ac7e-b3ef4c981a3b",
+        "5140b603-8cc1-4566-9043-e68145efbbd6",
+        "79f589cb-32a2-4ba6-a091-7c5d820d02df",
+        "932000d6-c63b-40f0-bdd5-469fa4db8be2",
+        "9f8f5212-0749-460b-9a46-2949dea45d52",
+        "a166be3d-6e84-4058-a1bd-edf90cf3ee88",
+        "a5e37780-0b71-4610-8a7c-26142dedfcec",
+        "b360251f-7550-4c08-b576-781858554ea1",
+        "b8049daa-7458-47bf-8ec2-3f5c56d2cb34",
+        "ba595d79-aa43-4e3a-ad10-89f92ef4f22f",
+        "edc72947-b776-4150-8bfe-b7331acfa66f",
+        "fa99959f-faa2-4d69-a092-48333e59f5f3"
+    ]
 }
\ No newline at end of file
diff --git a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
index 22ea45006..fd7ce1a28 100644
--- a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
+++ b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
@@ -6,7 +6,6 @@
             "version": "2021-03-12T22:38:42.790000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 93750142,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_e2464476-c0b4-4a92-a5fe-96094905825c_6d790286-6350-4c5c-b59d-4928d0aba9c2",
             "crc32c": "2176c107",
@@ -20,7 +19,6 @@
             "version": "2021-06-16T11:07:31.803000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 1143,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -31,7 +29,6 @@
             "version": "2021-09-30T17:37:33.058000Z",
             "content-type": "application/json; dcp-type=\"metadata/project\"",
             "size": 3756,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -42,7 +39,6 @@
             "version": "2021-03-12T22:30:59.855000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 795,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -53,7 +49,6 @@
             "version": "2021-03-12T22:30:47.194000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 971,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -64,7 +59,6 @@
             "version": "2021-03-12T22:30:59.983000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1587,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -75,7 +69,6 @@
             "version": "2021-03-12T22:40:56.568000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 354,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -86,7 +79,6 @@
             "version": "2021-03-12T22:31:00.073000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 904,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -97,7 +89,6 @@
             "version": "2021-03-12T22:28:36.842000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 1099,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -108,7 +99,6 @@
             "version": "2021-03-12T22:30:59.796000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1124,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -119,7 +109,6 @@
             "version": "2021-03-12T22:38:42.790000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 587,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -130,7 +119,6 @@
             "version": "2021-03-12T22:38:42.802000Z",
             "content-type": "binary/octet-stream; dcp-type=data; dcp-type=data",
             "size": 101854552,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_e2464476-c0b4-4a92-a5fe-96094905825c_57e4e9ad-2bdf-49aa-9576-aa6a851534f8",
             "crc32c": "2fd3d7c6",
@@ -139,12 +127,12 @@
             "s3_etag": "4a55ee383287a1b4f0aa4e756178c73f-2"
         },
         {
+
             "name": "process_1.json",
             "uuid": "80baee6e-00a5-4fdc-bfe3-d339ff8a7178",
             "version": "2021-03-12T22:43:32.330000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 351,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -155,7 +143,6 @@
             "version": "2021-03-12T22:30:59.829000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 716,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -166,7 +153,6 @@
             "version": "2021-03-12T22:31:00.063000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1156,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -177,7 +163,6 @@
             "version": "2021-03-12T22:38:42.802000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 587,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -188,7 +173,6 @@
             "version": "2021-03-12T22:38:42.888000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 351,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -835,5 +819,6 @@
         "describedBy": "https://schema.humancellatlas.org/system/2.1.1/links",
         "schema_version": "2.1.1",
         "schema_type": "links"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
index 558da1965..b7fb2ac93 100644
--- a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
+++ b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
@@ -6,7 +6,6 @@
             "version": "2020-12-03T10:39:17.144517Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 671,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -17,7 +16,6 @@
             "version": "2020-12-03T10:39:17.144517Z",
             "content-type": "application/zip; dcp-type=data",
             "size": 76742835,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_c3c588a8-be3f-467f-a244-da614be6889a_ad683500-3756-4a85-aba8-05a9165aac90",
             "crc32c": "97a7a932",
@@ -29,7 +27,6 @@
             "version": "2020-12-03T10:39:17.144517Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 671,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -40,7 +37,6 @@
             "version": "2020-12-03T10:39:17.144517Z",
             "content-type": "application/zip; dcp-type=data",
             "size": 124022765,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_c3c588a8-be3f-467f-a244-da614be6889a_df2476d4-ed12-4891-92cc-7384c32be978",
             "crc32c": "7de6e00e",
@@ -52,18 +48,17 @@
             "version": "2019-09-13T08:37:53.825000Z",
             "content-type": "application/json; dcp-type=\"metadata/project\"",
             "size": 11767,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
         },
         {
+
             "name": "supplementary_file_2.json",
             "uuid": "8d2ba1c1-bc9f-5c2a-a74d-fe5e09bdfb18",
             "version": "2020-12-03T10:39:17.144517Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 669,
-            "is_stitched": false,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -74,7 +69,6 @@
             "version": "2020-12-03T10:39:17.144517Z",
             "content-type": "application/vnd.loom; dcp-type=data",
             "size": 154980798,
-            "is_stitched": false,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_c3c588a8-be3f-467f-a244-da614be6889a_0b9a12c6-95df-487b-87ce-84e278e66789",
             "crc32c": "d675b7ea",
@@ -599,5 +593,6 @@
                 ]
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json b/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
index ed5b8ff49..41ea4d045 100644
--- a/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
+++ b/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
@@ -678,5 +678,6 @@
         "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
         "schema_version": "1.0.0",
         "schema_type": "link_bundle"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json b/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
index df8102870..8f26b1b31 100644
--- a/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
+++ b/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
@@ -706,5 +706,6 @@
         ],
         "schema_type": "links",
         "schema_version": "3.1.0"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
index 13f42e0e2..1a3f56c0c 100644
--- a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
+++ b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
@@ -1697,5 +1697,6 @@
                 ]
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
index 610482401..c8e3d57e3 100644
--- a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
+++ b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
@@ -11966,5 +11966,6 @@
                 ]
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
index 82b13a528..bdec17aa3 100644
--- a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
+++ b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
@@ -926,5 +926,6 @@
                 ]
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json b/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
index b197d3ad9..28347ab78 100644
--- a/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
+++ b/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
@@ -580,5 +580,6 @@
         "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
         "schema_version": "1.0.0",
         "schema_type": "link_bundle"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
index 7988bc571..fa7da5135 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
@@ -587,5 +587,6 @@
                 "protocols": []
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
index 1bf0a58dc..c2778bb99 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
@@ -587,5 +587,6 @@
                 "protocols": []
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json b/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
index 5c4c24ec6..3ba38f5c5 100644
--- a/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
+++ b/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
@@ -12796,5 +12796,6 @@
         "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
         "schema_version": "1.0.0",
         "schema_type": "link_bundle"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json b/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
index a494c951c..ba60102af 100644
--- a/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
+++ b/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
@@ -627,5 +627,6 @@
         "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
         "schema_version": "1.0.0",
         "schema_type": "link_bundle"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
index b29f6b7b8..cb8aed169 100644
--- a/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
+++ b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
@@ -690,5 +690,6 @@
                 "protocols": []
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json b/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
index 0ac584027..24f48db53 100644
--- a/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
+++ b/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
@@ -12409,5 +12409,6 @@
         "describedBy": "https://schema.humancellatlas.org/bundle/1.0.0/links",
         "schema_version": "1.0.0",
         "schema_type": "link_bundle"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
index 0b5d0344b..11c229559 100644
--- a/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
+++ b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
@@ -763,5 +763,6 @@
                 ]
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
index cd2ef9a55..5ad13428b 100644
--- a/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
+++ b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
@@ -42432,5 +42432,6 @@
                 ]
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
index ddb6fed8b..e4e69c1de 100644
--- a/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
+++ b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
@@ -2167,5 +2167,6 @@
                 "protocols": []
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json b/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
index 0c4e3609b..b9bf43801 100644
--- a/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
+++ b/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
@@ -779,5 +779,6 @@
         ],
         "schema_type": "links",
         "schema_version": "3.1.0"
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
index d632a9c69..e71b4214b 100644
--- a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
+++ b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
@@ -3110,5 +3110,6 @@
                 "protocols": []
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
index b269b25d5..ef78a318b 100644
--- a/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
+++ b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
@@ -812,5 +812,6 @@
                 "protocols": []
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
index 10c5888fd..643a84c16 100644
--- a/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
+++ b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
@@ -2386,5 +2386,6 @@
                 "protocols": []
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
index 31e7ea289..ee0385e96 100644
--- a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
+++ b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
@@ -11892,5 +11892,6 @@
                 ]
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
index caff9c466..9563b6f1e 100644
--- a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
+++ b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
@@ -810,5 +810,6 @@
                 "protocols": []
             }
         ]
-    }
+    },
+    "stitched": []
 }
diff --git a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
index 90063e3b0..9caadc848 100644
--- a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
+++ b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
@@ -1611,5 +1611,6 @@
                 ]
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
index da70bd714..1654e0ae7 100644
--- a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
+++ b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
@@ -6,7 +6,6 @@
             "version": "2020-08-13T10:24:31.885000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
             "size": 1801,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -17,7 +16,6 @@
             "version": "2021-02-09T01:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 327,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -28,7 +26,6 @@
             "version": "2020-08-13T10:24:32.490000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 614,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -39,7 +36,6 @@
             "version": "2020-08-13T10:24:33.604000Z",
             "content-type": "application/gzip; dcp-type=data; dcp-type=data",
             "size": 2552809421,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_ab47b7b4-2df9-47b4-bbb4-57d69a382a87",
             "crc32c": "3426d4b4",
@@ -53,7 +49,6 @@
             "version": "2021-02-09T01:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 14716,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -64,7 +59,6 @@
             "version": "2020-08-13T10:24:31.566000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
             "size": 576,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -75,7 +69,6 @@
             "version": "2020-08-13T10:24:39.091000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 415,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -86,7 +79,6 @@
             "version": "2020-08-13T10:24:34.163000Z",
             "content-type": "application/gzip; dcp-type=data; dcp-type=data",
             "size": 29797316111,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_b56c571e-d974-47a7-941b-b44a53124dc2",
             "crc32c": "27ce82ad",
@@ -100,7 +92,6 @@
             "version": "2020-08-13T10:24:35.160000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 614,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -111,7 +102,6 @@
             "version": "2020-08-13T10:24:32.576000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 610,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -122,7 +112,6 @@
             "version": "2020-08-13T10:24:32.055000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 615,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -133,7 +122,6 @@
             "version": "2021-02-09T01:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 417,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -144,7 +132,6 @@
             "version": "2021-02-09T01:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 417,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -155,7 +142,6 @@
             "version": "2021-02-09T01:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 417,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -166,7 +152,6 @@
             "version": "2020-08-13T10:24:33.458000Z",
             "content-type": "application/gzip; dcp-type=data; dcp-type=data",
             "size": 7988836041,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_37204ac6-191f-47ba-b3c7-3d927d9e522b",
             "crc32c": "24a02c8f",
@@ -180,7 +165,6 @@
             "version": "2021-02-09T01:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
             "size": 417,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -191,7 +175,6 @@
             "version": "2020-08-13T10:24:41.908000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 354,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -202,7 +185,6 @@
             "version": "2021-02-09T01:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 14716,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
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@@ -213,7 +195,6 @@
             "version": "2021-02-09T01:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
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             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -224,7 +205,6 @@
             "version": "2021-02-09T10:00:00.000000Z",
             "content-type": "application/octet-stream; dcp-type=data",
             "size": 61104038030,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_8fa0492a-20cc-44cb-b62d-98cb1b1cb02a",
             "crc32c": "f9e695e2",
@@ -236,7 +216,6 @@
             "version": "2021-02-09T08:34:58.000000Z",
             "content-type": "application/vnd.loom; dcp-type=data",
             "size": 1705801482,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_e9b071f2-1584-428b-9e3c-9a5943905a7d",
             "crc32c": "792b4a5d",
@@ -248,7 +227,6 @@
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             "content-type": "application/json; dcp-type=\"metadata/file\"",
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-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -259,7 +237,6 @@
             "version": "2020-08-13T10:24:35.916000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
             "size": 352,
-            "is_stitched": true,
             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -270,7 +247,6 @@
             "version": "2020-08-13T10:24:34.100000Z",
             "content-type": "application/gzip; dcp-type=data; dcp-type=data",
             "size": 2603387356,
-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_c97495cc-41f5-4662-af51-77846111717a",
             "crc32c": "dcc11ef6",
@@ -284,7 +260,6 @@
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             "content-type": "application/vnd.loom; dcp-type=data",
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-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_8b6e01b6-7e12-4b8f-9f16-97a1dd354215",
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@@ -296,7 +271,6 @@
             "version": "2021-02-09T01:30:00.000000Z",
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             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -307,7 +281,6 @@
             "version": "2020-08-13T10:24:42.459000Z",
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             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -318,7 +291,6 @@
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             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
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             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -329,7 +301,6 @@
             "version": "2021-02-09T01:30:00.000000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
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@@ -340,7 +311,6 @@
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             "content-type": "application/json; dcp-type=\"metadata/process\"",
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             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -351,7 +321,6 @@
             "version": "2020-08-13T10:24:32.650000Z",
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             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_78ce92be-f82c-41dd-827c-d5cef8a348f4",
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@@ -365,7 +334,6 @@
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             "content-type": "application/octet-stream; dcp-type=data",
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-            "is_stitched": true,
             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_76492cfb-8b1b-4c35-b6b1-557d42f5d60c",
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@@ -377,7 +345,6 @@
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             "indexed": true,
             "crc32c": "",
             "sha256": ""
@@ -388,7 +355,6 @@
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             "indexed": true,
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@@ -399,7 +365,6 @@
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@@ -410,7 +375,6 @@
             "version": "2020-08-13T10:24:32.673000Z",
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@@ -421,7 +385,6 @@
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             "indexed": false,
             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_959f3d74-1e15-4ca8-9acc-4e0ae60ba748",
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@@ -433,7 +396,6 @@
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             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_746bffff-170c-441b-a24f-08b86f5a5d20",
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@@ -447,7 +409,6 @@
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@@ -458,7 +419,6 @@
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             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_4d25fa13-4b11-4c21-957c-e4ba8b261610",
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@@ -472,7 +432,6 @@
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@@ -483,7 +442,6 @@
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@@ -494,7 +452,6 @@
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@@ -505,7 +462,6 @@
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@@ -517,7 +473,6 @@
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@@ -531,7 +486,6 @@
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@@ -542,7 +496,6 @@
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@@ -554,7 +507,6 @@
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             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_2335283c-4206-44f5-9e4b-0d20fa2ae808",
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@@ -568,7 +520,6 @@
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@@ -579,7 +530,6 @@
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@@ -590,7 +540,6 @@
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@@ -601,7 +550,6 @@
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@@ -613,7 +561,6 @@
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@@ -624,7 +571,6 @@
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             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_6bb86ff7-8f4a-4a06-bd75-57137cfd935d",
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@@ -636,7 +582,6 @@
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@@ -647,7 +592,6 @@
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@@ -658,7 +602,6 @@
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             "drs_uri": "drs://mock_drs_domain.lan/v1_6f1987da-5cbf-492c-b930-fd24891099a8_fc7ae751-2405-4c9c-8a49-777eb1f6f1d4",
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@@ -672,7 +615,6 @@
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@@ -683,7 +625,6 @@
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@@ -694,7 +635,6 @@
             "version": "2020-08-13T10:24:35.172000Z",
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@@ -705,7 +645,6 @@
             "version": "2021-02-09T01:30:00.000000Z",
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@@ -716,7 +655,6 @@
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@@ -1160,7 +1061,6 @@
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@@ -1343,7 +1228,6 @@
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@@ -1369,7 +1252,6 @@
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@@ -1380,7 +1262,6 @@
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@@ -1391,7 +1272,6 @@
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@@ -1402,7 +1282,6 @@
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@@ -1435,7 +1312,6 @@
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@@ -1446,7 +1322,6 @@
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@@ -1480,7 +1353,6 @@
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@@ -1491,7 +1363,6 @@
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@@ -1530,7 +1399,6 @@
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@@ -1541,7 +1409,6 @@
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@@ -1552,7 +1419,6 @@
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@@ -1575,7 +1440,6 @@
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@@ -1586,7 +1450,6 @@
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@@ -1597,7 +1460,6 @@
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@@ -1611,7 +1473,6 @@
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@@ -1622,7 +1483,6 @@
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@@ -1634,7 +1494,6 @@
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@@ -1645,7 +1504,6 @@
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@@ -1657,7 +1515,6 @@
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@@ -1668,7 +1525,6 @@
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@@ -1693,7 +1548,6 @@
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@@ -1704,7 +1558,6 @@
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@@ -1729,7 +1581,6 @@
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@@ -1834,7 +1677,6 @@
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@@ -1845,7 +1687,6 @@
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@@ -1882,7 +1721,6 @@
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@@ -1904,7 +1741,6 @@
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@@ -1915,7 +1751,6 @@
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@@ -1940,7 +1774,6 @@
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@@ -1963,7 +1795,6 @@
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@@ -1998,7 +1827,6 @@
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@@ -2009,7 +1837,6 @@
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@@ -2020,7 +1847,6 @@
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@@ -2032,7 +1858,6 @@
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@@ -2043,7 +1868,6 @@
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@@ -2054,7 +1878,6 @@
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@@ -2090,7 +1911,6 @@
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@@ -2101,7 +1921,6 @@
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@@ -2126,7 +1944,6 @@
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@@ -2137,7 +1954,6 @@
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@@ -2176,7 +1990,6 @@
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@@ -2187,7 +2000,6 @@
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@@ -2201,7 +2013,6 @@
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@@ -2215,7 +2026,6 @@
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@@ -2238,7 +2047,6 @@
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@@ -2249,7 +2057,6 @@
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@@ -2260,7 +2067,6 @@
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@@ -2271,7 +2077,6 @@
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@@ -2282,7 +2087,6 @@
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@@ -2296,7 +2100,6 @@
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@@ -2310,7 +2113,6 @@
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@@ -2324,7 +2126,6 @@
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@@ -2335,7 +2136,6 @@
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@@ -2346,7 +2146,6 @@
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@@ -2357,7 +2156,6 @@
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@@ -2368,7 +2166,6 @@
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@@ -2382,7 +2179,6 @@
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@@ -2393,7 +2189,6 @@
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@@ -2404,7 +2199,6 @@
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@@ -2418,7 +2212,6 @@
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@@ -2444,7 +2236,6 @@
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@@ -2467,7 +2257,6 @@
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@@ -2481,7 +2270,6 @@
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@@ -2506,7 +2293,6 @@
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@@ -2517,7 +2303,6 @@
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@@ -2540,7 +2324,6 @@
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@@ -2551,7 +2334,6 @@
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@@ -2577,7 +2358,6 @@
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@@ -2588,7 +2368,6 @@
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@@ -2599,7 +2378,6 @@
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@@ -2610,7 +2388,6 @@
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@@ -2621,7 +2398,6 @@
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@@ -2632,7 +2408,6 @@
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@@ -2655,7 +2429,6 @@
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@@ -2666,7 +2439,6 @@
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@@ -2677,7 +2449,6 @@
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@@ -2688,7 +2459,6 @@
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@@ -2699,7 +2469,6 @@
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@@ -2710,7 +2479,6 @@
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@@ -2721,7 +2489,6 @@
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@@ -2732,7 +2499,6 @@
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@@ -2757,7 +2522,6 @@
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@@ -2791,7 +2553,6 @@
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@@ -2805,7 +2566,6 @@
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@@ -2819,7 +2579,6 @@
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@@ -2831,7 +2590,6 @@
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@@ -2845,7 +2603,6 @@
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@@ -2856,7 +2613,6 @@
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@@ -2867,7 +2623,6 @@
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@@ -2878,7 +2633,6 @@
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@@ -2925,7 +2676,6 @@
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@@ -2947,7 +2696,6 @@
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@@ -2981,7 +2727,6 @@
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@@ -2992,7 +2737,6 @@
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@@ -3026,7 +2768,6 @@
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@@ -3066,7 +2805,6 @@
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@@ -3077,7 +2815,6 @@
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@@ -3244,7 +2968,6 @@
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@@ -3293,7 +3013,6 @@
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@@ -3304,7 +3023,6 @@
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@@ -3315,7 +3033,6 @@
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@@ -3326,7 +3043,6 @@
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@@ -3337,7 +3053,6 @@
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@@ -3384,7 +3096,6 @@
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@@ -3395,7 +3106,6 @@
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@@ -3406,7 +3116,6 @@
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@@ -3417,7 +3126,6 @@
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@@ -3429,7 +3137,6 @@
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@@ -3443,7 +3150,6 @@
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@@ -3455,7 +3161,6 @@
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@@ -3467,7 +3172,6 @@
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@@ -3478,7 +3182,6 @@
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@@ -3492,7 +3195,6 @@
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@@ -3506,7 +3208,6 @@
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@@ -3517,7 +3218,6 @@
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@@ -3528,7 +3228,6 @@
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@@ -3540,7 +3239,6 @@
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@@ -3551,7 +3249,6 @@
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@@ -3562,7 +3259,6 @@
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@@ -3573,7 +3269,6 @@
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@@ -3665,7 +3353,6 @@
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@@ -3746,7 +3427,6 @@
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@@ -3757,7 +3437,6 @@
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@@ -3892,7 +3560,6 @@
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@@ -4006,7 +3664,6 @@
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@@ -4042,7 +3697,6 @@
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@@ -4056,7 +3710,6 @@
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@@ -4081,7 +3733,6 @@
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@@ -4103,7 +3753,6 @@
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@@ -4114,7 +3763,6 @@
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@@ -4125,7 +3773,6 @@
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@@ -4136,7 +3783,6 @@
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@@ -4197,7 +3839,6 @@
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@@ -4208,7 +3849,6 @@
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@@ -4219,7 +3859,6 @@
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@@ -4230,7 +3869,6 @@
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@@ -4306,7 +3939,6 @@
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@@ -4354,7 +3983,6 @@
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@@ -4413,7 +4037,6 @@
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@@ -4446,7 +4067,6 @@
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@@ -4468,7 +4087,6 @@
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@@ -4479,7 +4097,6 @@
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@@ -4490,7 +4107,6 @@
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@@ -4501,7 +4117,6 @@
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@@ -4538,7 +4151,6 @@
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@@ -4582,7 +4191,6 @@
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@@ -4593,7 +4201,6 @@
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@@ -4604,7 +4211,6 @@
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@@ -4653,7 +4256,6 @@
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@@ -4664,7 +4266,6 @@
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@@ -4675,7 +4276,6 @@
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@@ -4700,7 +4299,6 @@
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@@ -4711,7 +4309,6 @@
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@@ -4722,7 +4319,6 @@
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@@ -4733,7 +4329,6 @@
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@@ -4744,7 +4339,6 @@
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@@ -4755,7 +4349,6 @@
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@@ -4766,7 +4359,6 @@
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@@ -4806,7 +4396,6 @@
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@@ -4817,7 +4406,6 @@
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@@ -4842,7 +4429,6 @@
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@@ -4853,7 +4439,6 @@
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@@ -4864,7 +4449,6 @@
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@@ -4875,7 +4459,6 @@
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@@ -4886,7 +4469,6 @@
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@@ -4897,7 +4479,6 @@
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@@ -4908,7 +4489,6 @@
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@@ -4919,7 +4499,6 @@
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@@ -4931,7 +4510,6 @@
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@@ -4967,7 +4543,6 @@
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@@ -4978,7 +4553,6 @@
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@@ -4989,7 +4563,6 @@
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@@ -5003,7 +4576,6 @@
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@@ -5014,7 +4586,6 @@
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@@ -5025,7 +4596,6 @@
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@@ -5581,7 +5104,6 @@
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@@ -5618,7 +5138,6 @@
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@@ -5704,7 +5217,6 @@
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@@ -5741,7 +5251,6 @@
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@@ -5824,7 +5327,6 @@
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@@ -5838,7 +5340,6 @@
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@@ -5860,7 +5360,6 @@
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@@ -5918,7 +5413,6 @@
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@@ -5979,7 +5469,6 @@
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@@ -5990,7 +5479,6 @@
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@@ -6015,7 +5502,6 @@
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@@ -6029,7 +5515,6 @@
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@@ -6184,7 +5657,6 @@
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@@ -6195,7 +5667,6 @@
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@@ -6209,7 +5680,6 @@
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@@ -6220,7 +5690,6 @@
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@@ -6232,7 +5701,6 @@
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@@ -6254,7 +5721,6 @@
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@@ -6265,7 +5731,6 @@
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@@ -6276,7 +5741,6 @@
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@@ -6287,7 +5751,6 @@
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@@ -6298,7 +5761,6 @@
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@@ -6309,7 +5771,6 @@
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@@ -6321,7 +5782,6 @@
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@@ -6333,7 +5793,6 @@
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@@ -6366,7 +5823,6 @@
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@@ -6377,7 +5833,6 @@
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@@ -6402,7 +5856,6 @@
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@@ -6416,7 +5869,6 @@
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@@ -6427,7 +5879,6 @@
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@@ -6441,7 +5892,6 @@
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@@ -6453,7 +5903,6 @@
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@@ -6511,7 +5956,6 @@
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@@ -6522,7 +5966,6 @@
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@@ -6533,7 +5976,6 @@
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@@ -6584,7 +6023,6 @@
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@@ -6595,7 +6033,6 @@
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@@ -6606,7 +6043,6 @@
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@@ -6640,7 +6074,6 @@
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@@ -6665,7 +6097,6 @@
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@@ -6676,7 +6107,6 @@
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@@ -7023,7 +6424,6 @@
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@@ -7110,7 +6504,6 @@
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@@ -7168,7 +6557,6 @@
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@@ -7179,7 +6567,6 @@
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@@ -7190,7 +6577,6 @@
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+        "dbe02baf-4c99-4784-bf03-2ebeeef70288",
+        "dbe117fc-c5ee-4347-bb8a-1a3fb9c89895",
+        "dc9ec562-3a71-5e42-b486-4f846ff7fcc0",
+        "dcaba295-f646-562f-8752-6f6fa634bc4f",
+        "dd19fdc7-35a9-432f-9a97-670637433eda",
+        "de694c96-1135-4d40-a44c-88ca899d164c",
+        "ded9b30e-12df-4998-846a-7cef685e4bd6",
+        "df1913aa-439c-587d-8192-5e2e66bc5262",
+        "dfd63958-121b-54a8-9b8b-707f3e28d3da",
+        "dfe9cbbb-cf19-4e2d-bd3c-70e0d9235f67",
+        "e0b0252f-8351-5ce3-a804-632a1cd78d28",
+        "e1b9ecf6-6fd8-4bc1-a28d-e9c9850055af",
+        "e23d96b7-a271-403e-a29e-b2bdb1949070",
+        "e29a9b1c-1ea6-4774-876f-765c7ac65d02",
+        "e3735012-e613-5a77-b38e-68fb27f9fdd7",
+        "e48d6415-0b7b-4e06-9c7b-861f33c1f1c7",
+        "e512685e-d15e-4b12-9f7f-e871da115586",
+        "e512c10b-854a-4c57-8c56-c84c84875664",
+        "e54680ad-0ebf-50cd-bf66-8d7b888af34c",
+        "e5ca2d0e-2fd8-4a89-88af-ad54c5f36290",
+        "e607b72f-3024-4d7e-8292-19d2d53a3a95",
+        "e6604cbc-c882-5f03-b4d0-807eb969a293",
+        "e6a532d6-bba0-5304-809c-5fc5f8373529",
+        "e779b50e-a892-4a0c-af02-2dd400956018",
+        "e79faefc-5135-4e43-a64d-8db7472d3f2e",
+        "e7b60260-7ae4-4d5a-b1a4-51622467e4b3",
+        "e7bd55f0-f6b6-4bfc-9395-35297fffd7d4",
+        "e7c8ff09-e97d-4b2e-8892-49cabbacb4c2",
+        "e85fcce7-59a6-593d-a52a-d25b47fafbfe",
+        "e8cb5e82-22fa-5e54-984e-3d2e4b91a100",
+        "e8fbe9c1-ab25-4300-a40d-65d0e8f627e0",
+        "e97d853f-aaf2-4b69-8300-f9aac8111c39",
+        "e9de5082-46c8-4b26-83c0-7fd480dcb142",
+        "e9eb59a6-8324-47c7-8d54-4517587c6802",
+        "ea737bae-7b34-4fb1-96a0-c3375446206c",
+        "ea7b5ae7-acdc-4d67-8665-c8a0b52da561",
+        "ea99b549-cd95-445b-a796-a4ccd992491d",
+        "eb8efbdd-147c-5206-b23c-f561d07335f7",
+        "ebde6cd6-26b6-40d6-9fa4-efe43d99ee8f",
+        "ecfd0cb5-5755-5852-b84f-dcaad39a6ddc",
+        "ed8bc174-30cc-4fa4-9e48-0543b825b1e4",
+        "ee40ec89-7cd0-5a9f-9f21-a1a4d69f5a1d",
+        "ee9ad501-69c5-49df-89d2-32ea89591634",
+        "eed4d335-880b-4735-9d04-cdbf706e3d44",
+        "eed7135f-d544-4e23-b8c9-266999b4135f",
+        "ef50dd96-a305-4edd-84e7-aae93377c488",
+        "f027f9ff-0d24-49e2-b71d-18543a4631f2",
+        "f0e53f0b-f5b9-4b5e-a168-de936401dc24",
+        "f17d1da2-2965-4732-a94a-6cd2a58fc873",
+        "f1903d0b-1cb2-4208-bc20-a37ad8612452",
+        "f1a64a47-3ed4-4570-99d7-ea6194826b07",
+        "f1f25c56-1cd7-44e4-8e58-7adafd43529c",
+        "f264de1c-35b3-5f4e-8d6f-f3a11bd30e93",
+        "f26c4715-5488-4d7f-ae0e-1c965128fbb1",
+        "f2b68b09-0776-5913-a34a-0944942c2b87",
+        "f2ed99b4-a68d-4d54-8c65-9534ad5931b5",
+        "f2fa48aa-5197-40a8-9c2a-c75c5c5f7264",
+        "f333416d-7f9e-4e54-9fbb-2ee29d55aed9",
+        "f3b53d83-7ee7-42db-b2d5-05a792204872",
+        "f3e0b538-bf64-417d-8746-52d5ad9311be",
+        "f4183399-0e70-466e-8915-8e4481f9b7d1",
+        "f4a448a7-bc5a-4014-ab1f-0d1a8cd4e47c",
+        "f683fadf-dd8c-4cfe-ae8b-34e3af5b74a1",
+        "f706178d-1afd-4bbb-bb69-12645ec038a6",
+        "f70a20e6-ad33-424e-b385-bb9a19be000e",
+        "f895f666-e3ed-4a7e-a7f5-42586a6244ea",
+        "f8dcbc35-bb0b-4bd4-ae8d-9be72b39dc16",
+        "f9173d91-b535-40f1-9937-2d0f00f4432f",
+        "f97aef9d-20fe-4872-88d1-9b44f174a16c",
+        "fa5185cb-e48d-5ab8-90b8-5499c3a725b6",
+        "fa78c4ab-4057-45b1-8266-af045ae28535",
+        "fbbd6c03-df0d-44dd-b383-c1efb83abb2e",
+        "fbed02e6-1547-469c-b96f-45c61111af53",
+        "fd0752c7-210b-4acd-a7ef-df7ffcdfbd3d",
+        "fd0cff96-93f2-4eb4-88f2-991f60542f46",
+        "fd5a2b33-eebc-41e3-b880-a39736a47a7c",
+        "fda0ea89-2300-59ed-9125-784883c5e211",
+        "fe261b23-efd5-445b-8dd4-46e47231ccff",
+        "fe4686b9-acd3-5237-acf1-1bd9cc0c19c5",
+        "ff3b3d1c-2ba9-50a9-9ca7-0558012cbe7d",
+        "ffba13e2-0937-49b3-961a-2ce3055ad5c6",
+        "ffe830d9-c586-47d1-9bb4-33baed6dcdc7"
+    ]
 }
\ No newline at end of file
diff --git a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
index 6c56e7d7c..8451d28e2 100644
--- a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
+++ b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
@@ -1003,5 +1003,6 @@
                 ]
             }
         ]
-    }
+    },
+    "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/test_tdr.py b/test/indexer/test_tdr.py
index d109a3623..cb1450eff 100644
--- a/test/indexer/test_tdr.py
+++ b/test/indexer/test_tdr.py
@@ -336,7 +336,7 @@ def test_subgraph_stitching(self):
         bundle = self._load_canned_bundle(SourcedBundleFQID(source=self.source,
                                                             uuid=downstream_uuid,
                                                             version='2020-08-10T21:24:26.174274Z'))
-        assert any(e['is_stitched'] for e in bundle.manifest)
+        assert len(bundle.stitched) > 0
         with self.assertLogs(plugin_log, level=logging.DEBUG) as cm:
             self._test_fetch_bundle(bundle, load_tables=True)
         record = one(r for r in cm.records if 'Stitched 2 bundle(s): ' in r.message)
diff --git a/test/integration_test.py b/test/integration_test.py
index 6729ca4f8..3d4970621 100644
--- a/test/integration_test.py
+++ b/test/integration_test.py
@@ -1931,16 +1931,26 @@ def _test_catalog(self, catalog: config.Catalog):
 
             metadata_plugin_name = catalog.plugins['metadata'].name
             if metadata_plugin_name == 'hca':
-                self.assertEqual({'manifest', 'metadata', 'links'}, bundle_json.keys())
+                self.assertEqual({'manifest',
+                                  'metadata',
+                                  'links',
+                                  'stitched'}, bundle_json.keys())
                 manifest = bundle_json['manifest']
                 metadata = bundle_json['metadata']
                 links = bundle_json['links']
+                stitched = bundle_json['stitched']
                 self.assertIsInstance(manifest, list)
                 self.assertIsInstance(metadata, dict)
                 self.assertIsInstance(links, dict)
+                self.assertIsInstance(stitched, list)
                 manifest_files = sorted(e['name'] for e in manifest if e['indexed'])
                 metadata_files = sorted(metadata.keys())
                 self.assertListEqual(manifest_files, metadata_files)
+                metadata_ids = {
+                    entry['provenance']['document_id']
+                    for entry in metadata.values()
+                }
+                self.assertIsSubset(set(stitched), metadata_ids)
             elif metadata_plugin_name == 'anvil':
                 self.assertEqual({'entities', 'links'}, bundle_json.keys())
                 entities, links = bundle_json['entities'], bundle_json['links']

From 171535da78bf752a36b31b86c5b23a2dfe4aae6b Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Wed, 7 Aug 2024 21:42:56 -0700
Subject: [PATCH 15/20] Remove manifest entries from `api.Entity`

---
 src/humancellatlas/data/metadata/api.py | 154 +++++++-----------------
 1 file changed, 45 insertions(+), 109 deletions(-)

diff --git a/src/humancellatlas/data/metadata/api.py b/src/humancellatlas/data/metadata/api.py
index e4752f40f..41fa40cb6 100644
--- a/src/humancellatlas/data/metadata/api.py
+++ b/src/humancellatlas/data/metadata/api.py
@@ -98,14 +98,12 @@ class Entity:
     json: JSON = field(repr=False)
     document_id: UUID4
     submitter_id: str | None
-    metadata_manifest_entry: ManifestEntry | None
     submission_date: datetime
     update_date: datetime | None
 
     @classmethod
     def from_json(cls,
                   json: JSON,
-                  metadata_manifest_entry: ManifestEntry | None,
                   **kwargs):
         content = json.get('content', json)
         described_by = content['describedBy']
@@ -114,22 +112,15 @@ def from_json(cls,
             sub_cls = entity_types[schema_name]
         except KeyError:
             raise TypeLookupError(described_by)
-        return sub_cls(json, metadata_manifest_entry, **kwargs)
+        return sub_cls(json, **kwargs)
 
     def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
+                 json: JSON
                  ) -> None:
         super().__init__()
         self.json = json
-        self.metadata_manifest_entry = metadata_manifest_entry
         provenance = json.get('hca_ingest') or json['provenance']
         self.document_id = UUID4(provenance['document_id'])
-        # Some older DCP/1 bundles use different UUIDs in the manifest and
-        # metadata.
-        if False:
-            if self.metadata_manifest_entry is not None:
-                assert self.document_id == self.metadata_manifest_entry.uuid
         self.submitter_id = provenance.get('submitter_id')
         submission_date = lookup(provenance, 'submission_date', 'submissionDate')
         self.submission_date = self._datetime(submission_date)
@@ -182,10 +173,9 @@ def _connect_to(self, other: Entity, forward: bool) -> None:
         raise NotImplementedError()
 
     def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
+                 json: JSON
                  ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+        super().__init__(json)
         self.children = {}
         self.parents = {}
 
@@ -299,11 +289,8 @@ class Project(Entity):
     estimated_cell_count: int | None
     bionetworks: OrderedSet[Bionetwork]
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+    def __init__(self, json: JSON) -> None:
+        super().__init__(json)
         content = json.get('content', json)
         core = content['project_core']
         self.project_short_name = lookup(core, 'project_short_name', 'project_shortname')
@@ -375,11 +362,8 @@ class Biomaterial(LinkedEntity):
     from_processes: MutableMapping[UUID4, 'Process'] = field(repr=False)
     to_processes: MutableMapping[UUID4, 'Process']
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+    def __init__(self, json: JSON) -> None:
+        super().__init__(json)
         content = json.get('content', json)
         self.biomaterial_id = content['biomaterial_core']['biomaterial_id']
         self.ncbi_taxon_id = content['biomaterial_core']['ncbi_taxon_id']
@@ -406,11 +390,8 @@ class DonorOrganism(Biomaterial):
     sex: str
     development_stage: str | None
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+    def __init__(self, json: JSON) -> None:
+        super().__init__(json)
         content = json.get('content', json)
         self.genus_species = {ontology_label(gs) for gs in content['genus_species']}
         self.diseases = {ontology_label(d) for d in lookup(content, 'diseases', 'disease', default=[]) if d}
@@ -447,11 +428,8 @@ class SpecimenFromOrganism(Biomaterial):
     organ: str | None
     organ_parts: set[str]
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+    def __init__(self, json: JSON) -> None:
+        super().__init__(json)
         content = json.get('content', json)
         preservation_storage = content.get('preservation_storage')
         self.storage_method = preservation_storage.get('storage_method') if preservation_storage else None
@@ -483,11 +461,8 @@ def organ_part(self):
 class ImagedSpecimen(Biomaterial):
     slice_thickness: float | int
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+    def __init__(self, json: JSON) -> None:
+        super().__init__(json)
         self.slice_thickness = json['slice_thickness']
 
 
@@ -496,11 +471,8 @@ class CellSuspension(Biomaterial):
     estimated_cell_count: int | None
     selected_cell_types: set[str]
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+    def __init__(self, json: JSON) -> None:
+        super().__init__(json)
         content = json.get('content', json)
         self.estimated_cell_count = lookup(content, 'estimated_cell_count', 'total_estimated_cells', default=None)
         self.selected_cell_types = {ontology_label(sct) for sct in
@@ -524,11 +496,8 @@ class CellLine(Biomaterial):
     type: str
     model_organ: str | None
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+    def __init__(self, json: JSON) -> None:
+        super().__init__(json)
         content = json.get('content', json)
         self.type = lookup(content, 'type', 'cell_line_type')
         self.model_organ = ontology_label(content.get('model_organ'), default=None)
@@ -545,11 +514,8 @@ class Organoid(Biomaterial):
     model_organ: str
     model_organ_part: str | None
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+    def __init__(self, json: JSON) -> None:
+        super().__init__(json)
         content = json.get('content', json)
         self.model_organ = ontology_label(lookup(content, 'model_organ', 'model_for_organ'), default=None)
         self.model_organ_part = ontology_label(content.get('model_organ_part'), default=None)
@@ -565,11 +531,8 @@ class Process(LinkedEntity):
     output_files: MutableMapping[UUID4, 'File']
     protocols: MutableMapping[UUID4, 'Protocol']
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+    def __init__(self, json: JSON) -> None:
+        super().__init__(json)
         content = json.get('content', json)
         process_core = content['process_core']
         self.process_id = process_core['process_id']
@@ -607,35 +570,26 @@ class AnalysisProcess(Process):
 @dataclass(init=False)
 class DissociationProcess(Process):
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
+    def __init__(self, json: JSON) -> None:
         warnings.warn(f"{type(self)} is deprecated", DeprecationWarning)
-        super().__init__(json, metadata_manifest_entry)
+        super().__init__(json)
 
 
 @dataclass(init=False)
 class EnrichmentProcess(Process):
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
+    def __init__(self, json: JSON) -> None:
         warnings.warn(f"{type(self)} is deprecated", DeprecationWarning)
-        super().__init__(json, metadata_manifest_entry)
+        super().__init__(json)
 
 
 @dataclass(init=False)
 class LibraryPreparationProcess(Process):
     library_construction_approach: str
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
+    def __init__(self, json: JSON) -> None:
         warnings.warn(f"{type(self)} is deprecated", DeprecationWarning)
-        super().__init__(json, metadata_manifest_entry)
+        super().__init__(json)
         content = json.get('content', json)
         self.library_construction_approach = content['library_construction_approach']
 
@@ -644,12 +598,9 @@ def __init__(self,
 class SequencingProcess(Process):
     instrument_manufacturer_model: str
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
+    def __init__(self, json: JSON) -> None:
         warnings.warn(f"{type(self)} is deprecated", DeprecationWarning)
-        super().__init__(json, metadata_manifest_entry)
+        super().__init__(json)
         content = json.get('content', json)
         self.instrument_manufacturer_model = ontology_label(content['instrument_manufacturer_model'])
 
@@ -672,11 +623,8 @@ class Protocol(LinkedEntity):
     protocol_id: str
     protocol_name: str | None
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+    def __init__(self, json: JSON) -> None:
+        super().__init__(json)
         content = json.get('content', json)
         protocol_core = content['protocol_core']
         self.protocol_id = protocol_core['protocol_id']
@@ -694,11 +642,8 @@ class LibraryPreparationProtocol(Protocol):
     library_construction_method: str
     nucleic_acid_source: str | None
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+    def __init__(self, json: JSON) -> None:
+        super().__init__(json)
         content = json.get('content', json)
         temp = lookup(content, 'library_construction_method', 'library_construction_approach')
         self.library_construction_method = ontology_label(temp) if isinstance(temp, dict) else temp
@@ -716,11 +661,8 @@ class SequencingProtocol(Protocol):
     instrument_manufacturer_model: str
     paired_end: bool | None
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+    def __init__(self, json: JSON) -> None:
+        super().__init__(json)
         content = json.get('content', json)
         self.instrument_manufacturer_model = ontology_label(content.get('instrument_manufacturer_model'), default=None)
         self.paired_end = lookup(content, 'paired_end', 'paired_ends', default=None)
@@ -770,11 +712,8 @@ class TreatmentProtocol(Protocol):
 class ImagingProtocol(Protocol):
     probe: list[ImagingProbe]  # A list so all the ImagingProbe objects can be tallied when indexed
 
-    def __init__(self,
-                 json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None
-                 ) -> None:
-        super().__init__(json, metadata_manifest_entry)
+    def __init__(self, json: JSON) -> None:
+        super().__init__(json)
         content = json.get('content', json)
         self.probe = [
             ImagingProbe.from_json(probe)
@@ -804,9 +743,8 @@ class File(LinkedEntity):
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry: ManifestEntry | None,
                  manifest: Mapping[str, ManifestEntry]):
-        super().__init__(json, metadata_manifest_entry)
+        super().__init__(json)
         content = json.get('content', json)
         # '/' was once forbidden in file paths and was encoded with '!'. Now
         # '/' is allowed and we force it in the metadata so that backwards
@@ -847,9 +785,8 @@ class SequenceFile(File):
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry,
                  manifest: Mapping[str, ManifestEntry]):
-        super().__init__(json, metadata_manifest_entry, manifest)
+        super().__init__(json, manifest)
         content = json.get('content', json)
         self.read_index = content['read_index']
         self.lane_index = content.get('lane_index')
@@ -866,9 +803,8 @@ class AnalysisFile(File):
 
     def __init__(self,
                  json: JSON,
-                 metadata_manifest_entry,
                  manifest: Mapping[str, ManifestEntry]):
-        super().__init__(json, metadata_manifest_entry, manifest)
+        super().__init__(json, manifest)
         content = json.get('content', json)
         self.matrix_cell_count = content.get('matrix_cell_count')
 
@@ -983,22 +919,22 @@ def __init__(self,
         self.manifest = {m.name: m for m in map(ManifestEntry, manifest)}
         self.stitched = frozenset(map(UUID4, stitched_entity_ids))
 
-        json_by_core_cls: MutableMapping[type[E], list[tuple[JSON, ManifestEntry]]] = defaultdict(list)
+        json_by_core_cls: MutableMapping[type[E], list[JSON]] = defaultdict(list)
         for file_name, json in metadata_files.items():
             assert file_name.endswith('.json')
             schema_name, _, suffix = file_name[:-5].rpartition('_')
             if schema_name and suffix.isdigit():
                 entity_cls = entity_types[schema_name]
                 core_cls = core_types[entity_cls]
-                json_by_core_cls[core_cls].append((json, self.manifest.get(file_name)))
+                json_by_core_cls[core_cls].append(json)
 
         def from_json_vx(core_cls: type[E],
                          **kwargs
                          ) -> MutableMapping[UUID4, E]:
             json_entities = json_by_core_cls[core_cls]
             entities = (
-                core_cls.from_json(entity, manifest_entry, **kwargs)
-                for entity, manifest_entry in json_entities
+                core_cls.from_json(entity, **kwargs)
+                for entity in json_entities
             )
             return {entity.document_id: entity for entity in entities}
 

From 5a90e006f1b2acde2983f91480ca6d437c2bb359 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Fri, 9 Aug 2024 15:39:02 -0700
Subject: [PATCH 16/20] Rename attribute and derived variables

---
 src/azul/plugins/metadata/hca/__init__.py     |  2 +-
 src/azul/plugins/metadata/hca/bundle.py       |  8 +--
 .../plugins/repository/canned/__init__.py     |  2 +-
 src/azul/plugins/repository/dss/__init__.py   |  2 +-
 .../plugins/repository/tdr_hca/__init__.py    |  8 +--
 src/humancellatlas/data/metadata/api.py       |  4 +-
 test/hca_metadata_api/test.py                 | 66 +++++++++----------
 test/indexer/test_indexer.py                  | 20 +++---
 test/indexer/test_tdr.py                      |  2 +-
 test/service/test_manifest.py                 | 18 ++---
 test/service/test_response.py                 |  2 +-
 11 files changed, 67 insertions(+), 67 deletions(-)

diff --git a/src/azul/plugins/metadata/hca/__init__.py b/src/azul/plugins/metadata/hca/__init__.py
index f1698b1cb..2edcd38ba 100644
--- a/src/azul/plugins/metadata/hca/__init__.py
+++ b/src/azul/plugins/metadata/hca/__init__.py
@@ -80,7 +80,7 @@ def transformers(self,
         api_bundle = api.Bundle(uuid=bundle.uuid,
                                 version=bundle.version,
                                 manifest=bundle.manifest,
-                                metadata_files=bundle.metadata_files,
+                                metadata=bundle.metadata,
                                 links_json=bundle.links,
                                 stitched_entity_ids=bundle.stitched)
 
diff --git a/src/azul/plugins/metadata/hca/bundle.py b/src/azul/plugins/metadata/hca/bundle.py
index d1d08ef5d..6af8e81fd 100644
--- a/src/azul/plugins/metadata/hca/bundle.py
+++ b/src/azul/plugins/metadata/hca/bundle.py
@@ -39,19 +39,19 @@ class HCABundle(Bundle[BUNDLE_FQID], ABC):
         'version': '2019-05-16T162155.020000Z'
     }
     """
-    metadata_files: MutableJSON
+    metadata: MutableJSON
     links: MutableJSON
     stitched: set[str] = attrs.field(factory=set)
 
     def reject_joiner(self, catalog: CatalogName):
         self._reject_joiner(self.manifest)
-        self._reject_joiner(self.metadata_files)
+        self._reject_joiner(self.metadata)
         self._reject_joiner(self.links)
 
     def to_json(self) -> MutableJSON:
         return {
             'manifest': self.manifest,
-            'metadata': self.metadata_files,
+            'metadata': self.metadata,
             'links': self.links,
             'stitched': sorted(self.stitched)
         }
@@ -68,6 +68,6 @@ def from_json(cls, fqid: BUNDLE_FQID, json_: JSON) -> 'Bundle':
         assert isinstance(stitched, list), stitched
         return cls(fqid=fqid,
                    manifest=manifest,
-                   metadata_files=metadata,
+                   metadata=metadata,
                    links=links,
                    stitched=set(stitched))
diff --git a/src/azul/plugins/repository/canned/__init__.py b/src/azul/plugins/repository/canned/__init__.py
index 965c9ac25..e032646ab 100644
--- a/src/azul/plugins/repository/canned/__init__.py
+++ b/src/azul/plugins/repository/canned/__init__.py
@@ -199,7 +199,7 @@ def fetch_bundle(self, bundle_fqid: CannedBundleFQID) -> CannedBundle:
                                            version=version)
         bundle = CannedBundle(fqid=bundle_fqid,
                               manifest=manifest,
-                              metadata_files=metadata,
+                              metadata=metadata,
                               links=links)
         assert version == bundle.version, (version, bundle)
         log.info('It took %.003fs to download bundle %s.%s',
diff --git a/src/azul/plugins/repository/dss/__init__.py b/src/azul/plugins/repository/dss/__init__.py
index d0863a4b3..f250d46a5 100644
--- a/src/azul/plugins/repository/dss/__init__.py
+++ b/src/azul/plugins/repository/dss/__init__.py
@@ -140,7 +140,7 @@ def list_bundles(self,
     def fetch_bundle(self, bundle_fqid: DSSBundleFQID) -> DSSBundle:
         assert False, 'DSS is EOL'
         # noinspection PyUnreachableCode
-        return DSSBundle(fqid=bundle_fqid, manifest=[], metadata_files={}, links={})
+        return DSSBundle(fqid=bundle_fqid, manifest=[], metadata={}, links={})
 
     def dss_subscription_query(self, prefix: str) -> JSON:
         return {
diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py
index f326c7b58..9b9cc606f 100644
--- a/src/azul/plugins/repository/tdr_hca/__init__.py
+++ b/src/azul/plugins/repository/tdr_hca/__init__.py
@@ -208,9 +208,9 @@ def add_entity(self,
                                      checksums=Checksums.from_json(descriptor),
                                      drs_uri=self._parse_drs_uri(row['file_id'], descriptor))
         content = row['content']
-        self.metadata_files[entity_key] = (json.loads(content)
-                                           if isinstance(content, str)
-                                           else content)
+        self.metadata[entity_key] = (json.loads(content)
+                                     if isinstance(content, str)
+                                     else content)
 
     metadata_columns: ClassVar[set[str]] = {
         'version',
@@ -337,7 +337,7 @@ def _query_unique_sorted(self,
     def _emulate_bundle(self, bundle_fqid: TDRBundleFQID) -> TDRHCABundle:
         bundle = TDRHCABundle(fqid=bundle_fqid,
                               manifest=[],
-                              metadata_files={},
+                              metadata={},
                               links={})
         entities, root_entities, links_jsons = self._stitch_bundles(bundle)
         bundle.links = self._merge_links(links_jsons)
diff --git a/src/humancellatlas/data/metadata/api.py b/src/humancellatlas/data/metadata/api.py
index 41fa40cb6..f24cc6122 100644
--- a/src/humancellatlas/data/metadata/api.py
+++ b/src/humancellatlas/data/metadata/api.py
@@ -911,7 +911,7 @@ def __init__(self,
                  uuid: str,
                  version: str,
                  manifest: MutableJSONs,
-                 metadata_files: Mapping[str, JSON],
+                 metadata: Mapping[str, JSON],
                  links_json: JSON,
                  stitched_entity_ids: Collection[str] = ()):
         self.uuid = UUID4(uuid)
@@ -920,7 +920,7 @@ def __init__(self,
         self.stitched = frozenset(map(UUID4, stitched_entity_ids))
 
         json_by_core_cls: MutableMapping[type[E], list[JSON]] = defaultdict(list)
-        for file_name, json in metadata_files.items():
+        for file_name, json in metadata.items():
             assert file_name.endswith('.json')
             schema_name, _, suffix = file_name[:-5].rpartition('_')
             if schema_name and suffix.isdigit():
diff --git a/test/hca_metadata_api/test.py b/test/hca_metadata_api/test.py
index 2dd4cfbf5..fd4b28e77 100644
--- a/test/hca_metadata_api/test.py
+++ b/test/hca_metadata_api/test.py
@@ -144,12 +144,12 @@ def _test_example_bundle(self, directory, **kwargs):
         uuid = 'b2216048-7eaa-45f4-8077-5a3fb4204953'
         version = '2018-08-03T082009.272868Z'
         canning_directory = os.path.join('examples', directory)
-        manifest, metadata_files, links = self._canned_bundle(canning_directory, uuid, version)
+        manifest, metadata, links = self._canned_bundle(canning_directory, uuid, version)
         self.assertIsNotNone(manifest)
         self._assert_bundle(uuid=uuid,
                             version=version,
                             manifest=manifest,
-                            metadata_files=metadata_files,
+                            metadata=metadata,
                             links=links,
                             **kwargs)
 
@@ -157,7 +157,7 @@ def _canned_bundle_path(self, directory, uuid, version):
         name = f'{uuid}.{version}.json'
         return os.path.join(os.path.dirname(__file__), 'cans', directory, name)
 
-    def _can_bundle(self, directory, uuid, version, manifest, metadata_files, links):  # pragma: no cover
+    def _can_bundle(self, directory, uuid, version, manifest, metadata, links):  # pragma: no cover
         """
         Save a bundle's manifest & metadata files to a local directory
         """
@@ -166,7 +166,7 @@ def _can_bundle(self, directory, uuid, version, manifest, metadata_files, links)
         with atomic_write(path, overwrite=True) as f:
             json.dump({
                 'manifest': manifest,
-                'metadata': metadata_files,
+                'metadata': metadata,
                 'links': links
             }, f)
 
@@ -342,8 +342,8 @@ def test_file_core_bundle(self):
     def test_sequencing_process_paired_end(self):
         uuid = '6b498499-c5b4-452f-9ff9-2318dbb86000'
         version = '2019-01-03T163633.780215Z'
-        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
-        bundle = Bundle(uuid, version, manifest, metadata_files, links)
+        manifest, metadata, links = self._canned_bundle('prod', uuid, version)
+        bundle = Bundle(uuid, version, manifest, metadata, links)
         sequencing_protocols = [p for p in bundle.protocols.values() if isinstance(p, SequencingProtocol)]
         self.assertEqual(len(sequencing_protocols), 1)
         self.assertEqual(sequencing_protocols[0].paired_end, True)
@@ -355,16 +355,16 @@ def _test_bundle(self,
                      **assertion_kwargs
                      ) -> Bundle:
 
-        manifest, metadata_files, links = self._canned_bundle(deployment, uuid, version)
+        manifest, metadata, links = self._canned_bundle(deployment, uuid, version)
 
         return self._assert_bundle(uuid=uuid,
                                    version=version,
                                    manifest=manifest,
-                                   metadata_files=metadata_files,
+                                   metadata=metadata,
                                    links=links,
                                    **assertion_kwargs)
 
-    def _assert_bundle(self, uuid, version, manifest, metadata_files, links,
+    def _assert_bundle(self, uuid, version, manifest, metadata, links,
                        age_range=None,
                        diseases=frozenset({None}),
                        project_roles=frozenset({None}),
@@ -381,7 +381,7 @@ def _assert_bundle(self, uuid, version, manifest, metadata_files, links,
                        slice_thickness=None,
                        ncbi_taxon_ids=None,
                        content_description=None) -> Bundle:
-        bundle = Bundle(uuid, version, manifest, metadata_files, links)
+        bundle = Bundle(uuid, version, manifest, metadata, links)
 
         # Every data file's manifest entry should be referenced by a metadata
         # entity that describes the data file. id() is used to work around the
@@ -517,8 +517,8 @@ def test_canned_staging_area(self):
     def test_analysis_protocol(self):
         uuid = 'ffee7f29-5c38-461a-8771-a68e20ec4a2e'
         version = '2019-02-02T065454.662896Z'
-        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
-        bundle = Bundle(uuid, version, manifest, metadata_files, links)
+        manifest, metadata, links = self._canned_bundle('prod', uuid, version)
+        bundle = Bundle(uuid, version, manifest, metadata, links)
         analysis_protocols = [p for p in bundle.protocols.values() if isinstance(p, AnalysisProtocol)]
         self.assertEqual(len(analysis_protocols), 1)
         self.assertEqual(str(analysis_protocols[0].document_id), 'bb17ee61-193e-4ae1-a014-4f1b1c19b8b7')
@@ -528,8 +528,8 @@ def test_analysis_protocol(self):
     def test_imaging_protocol(self):
         uuid = '94f2ba52-30c8-4de0-a78e-f95a3f8deb9c'
         version = '2019-04-03T103426.471000Z'
-        manifest, metadata_files, links = self._canned_bundle('staging', uuid, version)
-        bundle = Bundle(uuid, version, manifest, metadata_files, links)
+        manifest, metadata, links = self._canned_bundle('staging', uuid, version)
+        bundle = Bundle(uuid, version, manifest, metadata, links)
         imaging_protocol = one(p for p in bundle.protocols.values() if isinstance(p, ImagingProtocol))
         self.assertEqual(len(imaging_protocol.probe), 240)
         assay_types = {probe.assay_type for probe in imaging_protocol.probe}
@@ -538,8 +538,8 @@ def test_imaging_protocol(self):
     def test_cell_line(self):
         uuid = 'ffee3a9b-14de-4dda-980f-c08092b2dabe'
         version = '2019-04-17T175706.867000Z'
-        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
-        bundle = Bundle(uuid, version, manifest, metadata_files, links)
+        manifest, metadata, links = self._canned_bundle('prod', uuid, version)
+        bundle = Bundle(uuid, version, manifest, metadata, links)
         cell_lines = [cl for cl in bundle.biomaterials.values() if isinstance(cl, CellLine)]
         self.assertEqual(len(cell_lines), 1)
         self.assertEqual(str(cell_lines[0].document_id), '961092cd-dcff-4b59-a0d2-ceeef0aece74')
@@ -556,8 +556,8 @@ def test_links_json_v2_0_0(self):
         """
         uuid = 'cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439'
         version = '2019-05-15T222432.561000Z'
-        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
-        bundle = Bundle(uuid, version, manifest, metadata_files, links)
+        manifest, metadata, links = self._canned_bundle('prod', uuid, version)
+        bundle = Bundle(uuid, version, manifest, metadata, links)
         for expected_count, link_type in [(6, 'process_link'), (2, 'supplementary_file_link')]:
             actual_count = sum(1 for link in bundle.links if link.link_type == link_type)
             self.assertEqual(expected_count, actual_count)
@@ -572,10 +572,10 @@ def test_links_json_v2_0_0(self):
     def test_project_fields(self):
         uuid = '68bdc676-c442-4581-923e-319c1c2d9018'
         version = '2018-10-07T130111.835234Z'
-        manifest, metadata_files, links = self._canned_bundle('staging', uuid, version)
+        manifest, metadata, links = self._canned_bundle('staging', uuid, version)
 
         def assert_bundle():
-            bundle = Bundle(uuid, version, manifest, metadata_files, links)
+            bundle = Bundle(uuid, version, manifest, metadata, links)
             project = bundle.projects[UUID('519b58ef-6462-4ed3-8c0d-375b54f53c31')]
             self.assertEqual(len(project.publications), 1)
             publication = project.publications.pop()
@@ -595,9 +595,9 @@ def assert_bundle():
 
         assert_bundle()
 
-        for publication in metadata_files['project_0.json']['publications']:
+        for publication in metadata['project_0.json']['publications']:
             self._rename_keys(publication, title='publication_title', url='publication_url')
-        for contributor in metadata_files['project_0.json']['contributors']:
+        for contributor in metadata['project_0.json']['contributors']:
             if 'project_role' in contributor:
                 contributor['project_role'] = dict(text=contributor['project_role'])
 
@@ -606,10 +606,10 @@ def assert_bundle():
     def test_project_contact(self):
         uuid = '6b498499-c5b4-452f-9ff9-2318dbb86000'
         version = '2019-01-03T163633.780215Z'
-        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
+        manifest, metadata, links = self._canned_bundle('prod', uuid, version)
 
         def assert_bundle():
-            bundle = Bundle(uuid, version, manifest, metadata_files, links)
+            bundle = Bundle(uuid, version, manifest, metadata, links)
             project = bundle.projects[UUID('d96c2451-6e22-441f-a3e6-70fd0878bb1b')]
             self.assertEqual(len(project.contributors), 5)
             expected_names = {
@@ -625,7 +625,7 @@ def assert_bundle():
 
         assert_bundle()
 
-        for contributor in metadata_files['project_0.json']['contributors']:
+        for contributor in metadata['project_0.json']['contributors']:
             self._rename_keys(contributor, name='contact_name')
 
         assert_bundle()
@@ -633,10 +633,10 @@ def assert_bundle():
     def test_file_format(self):
         uuid = '6b498499-c5b4-452f-9ff9-2318dbb86000'
         version = '2019-01-03T163633.780215Z'
-        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
+        manifest, metadata, links = self._canned_bundle('prod', uuid, version)
 
         def assert_bundle():
-            bundle = Bundle(uuid, version, manifest, metadata_files, links)
+            bundle = Bundle(uuid, version, manifest, metadata, links)
             self.assertEqual(len(bundle.files), 6)
             for file in bundle.files.values():
                 if isinstance(file, SequenceFile):
@@ -648,7 +648,7 @@ def assert_bundle():
 
         assert_bundle()
 
-        for file_name, file_content in metadata_files.items():
+        for file_name, file_content in metadata.items():
             if file_name.startswith('sequence_file_') or file_name.startswith('supplementary_file_'):
                 self._rename_keys(file_content['file_core'], format='file_format')
 
@@ -657,10 +657,10 @@ def assert_bundle():
     def test_link_destination_type(self):
         uuid = '6b498499-c5b4-452f-9ff9-2318dbb86000'
         version = '2019-01-03T163633.780215Z'
-        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
+        manifest, metadata, links = self._canned_bundle('prod', uuid, version)
 
         def assert_bundle():
-            bundle = Bundle(uuid, version, manifest, metadata_files, links)
+            bundle = Bundle(uuid, version, manifest, metadata, links)
             destination_types = {link.destination_type for link in bundle.links}
             expected_types = {
                 'library_preparation_protocol',
@@ -701,7 +701,7 @@ def test_missing_mandatory_checksums(self):
                                **case
                            }
                        ],
-                       metadata_files={},
+                       metadata={},
                        links_json={})
             self.assertEqual(cm.exception.args[0], 'Property cannot be absent or None')
             checksums.append(cm.exception.args[1])
@@ -710,7 +710,7 @@ def test_missing_mandatory_checksums(self):
     def test_name_substitution(self):
         uuid = 'ffee7f29-5c38-461a-8771-a68e20ec4a2e'
         version = '2019-02-02T065454.662896Z'
-        manifest, metadata_files, links = self._canned_bundle('prod', uuid, version)
+        manifest, metadata, links = self._canned_bundle('prod', uuid, version)
 
         files_before = [f['name'] for f in manifest]
         with_bang_before = set(f for f in files_before if '!' in f)
@@ -736,7 +736,7 @@ def test_name_substitution(self):
         with_slash_before = set(f for f in files_before if '/' in f)
         self.assertEqual(set(), with_slash_before)
 
-        bundle = Bundle(uuid, version, manifest, metadata_files, links)
+        bundle = Bundle(uuid, version, manifest, metadata, links)
 
         expected_slash_after = set(f1.replace('!', '/') for f1 in with_bang_before)
         entity_json_file_names = set(e.json['file_core']['file_name']
diff --git a/test/indexer/test_indexer.py b/test/indexer/test_indexer.py
index b2d5bc6af..c88649c1a 100644
--- a/test/indexer/test_indexer.py
+++ b/test/indexer/test_indexer.py
@@ -188,7 +188,7 @@ def _assert_hit_counts(self,
     def _write_transforms(cls, bundle: HCABundle) -> Tallies:
         bundle = attr.evolve(bundle,
                              manifest=deepcopy(bundle.manifest),
-                             metadata_files=deepcopy(bundle.metadata_files))
+                             metadata=deepcopy(bundle.metadata))
         transforms = cls.index_service.transform(cls.catalog, bundle, delete=False)
         contributions, replicas = transforms
         cls.index_service.replicate(cls.catalog, replicas)
@@ -247,7 +247,7 @@ def test_indexing(self):
                                     else:
                                         expected = one(
                                             m
-                                            for m in bundle.metadata_files.values()
+                                            for m in bundle.metadata.values()
                                             if m['provenance']['document_id'] == entity_id
                                         )
                                     # Replica contents should match the entity
@@ -289,7 +289,7 @@ def test_deletion(self):
                 bundle = self._load_canned_bundle(bundle_fqid)
                 bundle = DSSBundle(fqid=bundle_fqid,
                                    manifest=bundle.manifest,
-                                   metadata_files=bundle.metadata_files,
+                                   metadata=bundle.metadata,
                                    links=bundle.links)
                 self.index_service.create_indices(self.catalog)
                 try:
@@ -396,7 +396,7 @@ def test_duplicate_notification(self):
         entity = next(e for e in tallies_1.keys() if e.entity_type != 'bundles')
         tallies_1.pop(entity)
 
-        entity_contents = bundle.metadata_files[
+        entity_contents = bundle.metadata[
             one(m for m in bundle.manifest if m['uuid'] == entity.entity_id)['name']
         ]
         coordinates = [
@@ -599,7 +599,7 @@ def _walkthrough(v):
             else:
                 assert False, f'Cannot handle values of type {type(v)}'
 
-        bundle.metadata_files = _walkthrough(bundle.metadata_files)
+        bundle.metadata = _walkthrough(bundle.metadata)
         bundle.links = _walkthrough(bundle.links)
         return old_file_uuid
 
@@ -1463,7 +1463,7 @@ def mocked_mget(self, body, _source_includes):
         self.assertEqual(4, len(file_uuids))
         for bundle_fqid in bundles:
             bundle = self._load_canned_bundle(bundle_fqid)
-            for doc in bundle.metadata_files.values():
+            for doc in bundle.metadata.values():
                 if doc['content']['schema_type'] == 'file':
                     file_document_ids.add(doc['hca_ingest']['document_id'])
         self.assertEqual(file_document_ids, file_uuids)
@@ -1843,8 +1843,8 @@ def assert_cell_suspension(expected: JSON, hits: list[JSON]):
         # We patch the project entity to ensure that the project aggregate gets
         # cell suspensions from both bundles.
         #
-        target_metadata = has_cells_bundle.metadata_files
-        source_metadata = no_cells_bundle.metadata_files
+        target_metadata = has_cells_bundle.metadata
+        source_metadata = no_cells_bundle.metadata
         target_metadata['project_0.json'] = source_metadata['project_0.json']
         self._index_bundle(has_cells_bundle)
         expected = {
@@ -2101,7 +2101,7 @@ def test_downstream_entities(self):
 
         # The bundles that motivated this test case lack `estimated_cell_count`,
         # so we inject it here to avoid nulls in the index.
-        for document in bundle.metadata_files.values():
+        for document in bundle.metadata.values():
             if document['describedBy'].endswith('/cell_suspension'):
                 document['estimated_cell_count'] = expected_cell_count
 
@@ -2171,7 +2171,7 @@ def test_disallow_manifest_column_joiner(self):
         bundle_fqid = self.bundle_fqid(uuid='1b6d8348-d6e9-406a-aa6a-7ee886e52bf9',
                                        version='2019-10-03T10:55:24.911627Z')
         bundle = self._load_canned_bundle(bundle_fqid)
-        project = bundle.metadata_files['project_0.json']
+        project = bundle.metadata['project_0.json']
         contributor = project['contributors'][0]
         assert contributor['institution'] == 'Lund University'
         contributor['institution'] += ' || LabMED'
diff --git a/test/indexer/test_tdr.py b/test/indexer/test_tdr.py
index cb1450eff..62aab9dfe 100644
--- a/test/indexer/test_tdr.py
+++ b/test/indexer/test_tdr.py
@@ -356,7 +356,7 @@ def _test_fetch_bundle(self,
         assert isinstance(emulated_bundle, TDRHCABundle)
         # Manifest and metadata should both be sorted by entity UUID
         self.assertEqual(test_bundle.manifest, emulated_bundle.manifest)
-        self.assertEqual(test_bundle.metadata_files, emulated_bundle.metadata_files)
+        self.assertEqual(test_bundle.metadata, emulated_bundle.metadata)
         self.assertEqual(test_bundle.links, emulated_bundle.links)
 
 
diff --git a/test/service/test_manifest.py b/test/service/test_manifest.py
index 8f69e21f0..c6a1826aa 100644
--- a/test/service/test_manifest.py
+++ b/test/service/test_manifest.py
@@ -364,9 +364,9 @@ def _shared_file_bundle(self, bundle):
             '224d3750-f1f7-5b04-bbce-e23f09eea7d7': '5275e5a0-6043-4ec9-86a1-6c1140cbeede',
         }
         manifest = self._replace_uuids(bundle.manifest, old_to_new)
-        metadata_files = self._replace_uuids(bundle.metadata_files, old_to_new)
+        metadata = self._replace_uuids(bundle.metadata, old_to_new)
         # Change organ to prevent cell_suspensions aggregating together
-        metadata_files['specimen_from_organism_0.json']['organ'] = {
+        metadata['specimen_from_organism_0.json']['organ'] = {
             'text': 'lung',
             'ontology': 'UBERON:0002048',
             'ontology_label': 'lung'
@@ -376,7 +376,7 @@ def _shared_file_bundle(self, bundle):
         return DSSBundle(fqid=self.bundle_fqid(uuid=old_to_new[bundle.uuid],
                                                version=bundle.version),
                          manifest=cast(MutableJSONs, manifest),
-                         metadata_files=metadata_files,
+                         metadata=metadata,
                          links=links)
 
     def _replace_uuids(self,
@@ -397,12 +397,12 @@ def _add_ageless_donor(self, bundle):
         bundle = self._load_canned_bundle(bundle)
         # Since most of the metadata is duplicated (including biomaterial_id)
         # the donor_count will not increase.
-        duplicate_donor = deepcopy(bundle.metadata_files['donor_organism_0.json'])
+        duplicate_donor = deepcopy(bundle.metadata['donor_organism_0.json'])
         del duplicate_donor['organism_age']
         del duplicate_donor['organism_age_unit']
         donor_id = '0895599c-f57d-4843-963e-11eab29f883b'
         duplicate_donor['provenance']['document_id'] = donor_id
-        bundle.metadata_files['donor_organism_1.json'] = duplicate_donor
+        bundle.metadata['donor_organism_1.json'] = duplicate_donor
         donor_link = one(ln for ln in bundle.links['links']
                          if one(ln['inputs'])['input_type'] == 'donor_organism')
         new_donor_reference = {
@@ -562,9 +562,9 @@ def test_compact_manifest(self):
             for entry in bundle.manifest
             if entry['name'] in files_names
         ]
-        metadata_files = {
+        metadata = {
             file_name: copy_json(content)
-            for file_name, content in bundle.metadata_files.items()
+            for file_name, content in bundle.metadata.items()
             if file_name in files_names
         }
         # This is an older bundle so there are no supplementary file links.
@@ -574,7 +574,7 @@ def test_compact_manifest(self):
         self._index_bundle(DSSBundle(fqid=self.bundle_fqid(uuid='b81656cf-231b-47a3-9317-10f1e501a05c',
                                                            version='2000-01-01T01:00:00.000000Z'),
                                      manifest=manifest,
-                                     metadata_files=metadata_files,
+                                     metadata=metadata,
                                      links=links))
 
         filters = {
@@ -1350,7 +1350,7 @@ def test_verbatim_jsonl_manifest(self):
             ]:
                 expected.append({
                     'type': replica_type,
-                    'value': bundle.metadata_files[key],
+                    'value': bundle.metadata[key],
                 })
 
         response = self._get_manifest(ManifestFormat.verbatim_jsonl, {})
diff --git a/test/service/test_response.py b/test/service/test_response.py
index 7606ce6c5..857f5cfdc 100644
--- a/test/service/test_response.py
+++ b/test/service/test_response.py
@@ -1835,7 +1835,7 @@ def test_contributors_order(self):
         # First assert the order of the contributors in the indexed bundle
         bundle = self.indexed_bundles[bundle_uuid]
         assert isinstance(bundle, HCABundle)
-        project = bundle.metadata_files['project_0.json']
+        project = bundle.metadata['project_0.json']
         self.assertEqual(project_id, project['provenance']['document_id'])
         actual = [c['email'] for c in project['contributors']]
         self.assertEqual(expected, actual)

From 133e3cb00834f6436af0947b643d34f656164238 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Fri, 16 Aug 2024 18:50:08 -0700
Subject: [PATCH 17/20] Replace file names with entity references in HCA bundle
 metadata

---
 .../plugins/repository/tdr_hca/__init__.py    |    6 +-
 src/humancellatlas/data/metadata/api.py       |   16 +-
 .../data/metadata/helpers/staging_area.py     |    6 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   22 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   28 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   86 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   22 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   24 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   22 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   36 +-
 ...318dbb86000.2019-01-03T163633.780215Z.json |   86 +-
 ...61d6da02d44.2019-09-20T103932.395795Z.json |   38 +-
 ...a3fb4204953.2018-03-29T142048.835519Z.json |   32 +-
 ...d019d1c9439.2019-05-15T222432.561000Z.json |   20 +-
 ...08092b2dabe.2019-04-17T175706.867000Z.json |   32 +-
 ...68e20ec4a2e.2019-02-02T065454.662896Z.json |  102 +-
 ...19c1c2d9018.2018-10-07T130111.835234Z.json |   28 +-
 ...406a478d5ab.2018-09-05T182535.846470Z.json |   26 +-
 ...95a3f8deb9c.2019-04-03T103426.471000Z.json |  474 ++---
 ...720f33a5dde.2019-03-17T220646.332108Z.json |   30 +-
 test/hca_metadata_api/test.py                 |   21 +-
 ...3-5e9d-52cd-b32d-af88edccabfa.dss.hca.json |  128 +-
 ...5-71e2-48ca-a87b-e256938c6a98.dss.hca.json |  104 +-
 ...3-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json |  854 ++++-----
 ...c-6778-423d-8fe9-869e2a515d35.dss.hca.json |   30 +-
 ...8-01a0-464a-9599-7375fda3353d.dss.hca.json |   42 +-
 ...8-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json |   52 +-
 ...8-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json |   58 +-
 ...0-eaba-531d-ba9e-db80164d65ef.dss.hca.json |   30 +-
 ...4-fa14-5c6f-a474-a742540108a3.dss.hca.json |   24 +-
 ...5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json |   28 +-
 ...c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json |  660 +++----
 ...8-658e-4c51-9de4-a768322f84c5.dss.hca.json |   28 +-
 ...3-93e1-56b4-b857-59497f5d942d.dss.hca.json |   22 +-
 ...a-940e-49b1-9bcc-25699a55b295.dss.hca.json |   60 +-
 ...f-61a7-4504-a57c-fc70f38d5b13.dss.hca.json |   96 +-
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json |  114 +-
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json |  114 +-
 ...5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json |   40 +-
 ...a-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json |  660 +++----
 ...e-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json |   18 +-
 ...8-adab-59a9-b6c4-3a61242cc972.dss.hca.json |   28 +-
 ...e-7554-4b5d-96a2-7df127a7640b.dss.hca.json |   30 +-
 ...4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json |   88 +-
 ...0.2020-12-10T10:30:00.000000Z.dss.hca.json |  522 +++---
 ...1-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json |   28 +-
 ...f-8346-5420-b7e4-b486f99451a8.dss.hca.json |   38 +-
 ...e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json |   30 +-
 ...1-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json |    8 +-
 ...f-4c01-48d5-a79f-1c5439659da3.dss.hca.json |   34 +-
 ...3-1885-545f-9381-0dab1edf6074.dss.hca.json |   28 +-
 ...e-9a5d-4e3d-ada2-0414b666b880.dss.hca.json |   58 +-
 ...2-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json |  474 ++---
 ...3-f0ac-417a-8a29-221c77debde8.dss.hca.json |   28 +-
 ...6-ced8-448a-8e45-1fc7846d8995.dss.hca.json |   30 +-
 ...d.2018-11-02T11:33:44.698028Z.dss.hca.json |   26 +-
 ...d.2018-11-04T11:33:44.698028Z.dss.hca.json |   26 +-
 ...9-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json |  660 +++----
 ...8-7eaa-45f4-8077-5a3fb4204953.dss.hca.json |   32 +-
 ...e-9b7b-4800-8977-fe7c94e131df.dss.hca.json |   30 +-
 ...9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json |  640 +++----
 ...4-dc9f-439e-af29-f8eb75b0729d.dss.hca.json |   30 +-
 ...4-9a58-4763-9e66-59894efbdaa8.dss.hca.json | 1562 ++++++++---------
 ...d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json |   88 +-
 ...f-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json |   30 +-
 ...1-4766-4210-966c-f9ee25d19190.dss.hca.json |  114 +-
 ...a-2b51-4419-9cde-34df44c6458a.dss.hca.json |   36 +-
 ...e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json |   96 +-
 ...4-6b80-4eed-97c9-4984de81a47c.dss.hca.json |  600 +++----
 ...7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json |   36 +-
 ...b-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json |   60 +-
 ...7-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json |  828 ++++-----
 ...f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json |   28 +-
 test/indexer/test_indexer.py                  |   20 +-
 test/integration_test.py                      |    9 +-
 test/service/test_manifest.py                 |   51 +-
 test/service/test_response.py                 |    2 +-
 77 files changed, 5383 insertions(+), 5364 deletions(-)

diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py
index 9b9cc606f..0cb76e5a3 100644
--- a/src/azul/plugins/repository/tdr_hca/__init__.py
+++ b/src/azul/plugins/repository/tdr_hca/__init__.py
@@ -208,9 +208,9 @@ def add_entity(self,
                                      checksums=Checksums.from_json(descriptor),
                                      drs_uri=self._parse_drs_uri(row['file_id'], descriptor))
         content = row['content']
-        self.metadata[entity_key] = (json.loads(content)
-                                     if isinstance(content, str)
-                                     else content)
+        self.metadata[str(entity)] = (json.loads(content)
+                                      if isinstance(content, str)
+                                      else content)
 
     metadata_columns: ClassVar[set[str]] = {
         'version',
diff --git a/src/humancellatlas/data/metadata/api.py b/src/humancellatlas/data/metadata/api.py
index f24cc6122..5aefe26d4 100644
--- a/src/humancellatlas/data/metadata/api.py
+++ b/src/humancellatlas/data/metadata/api.py
@@ -36,6 +36,10 @@
     OrderedSet,
     dict_merge,
 )
+
+from azul.indexer.document import (
+    EntityReference,
+)
 from azul.types import (
     JSON,
     MutableJSON,
@@ -920,13 +924,11 @@ def __init__(self,
         self.stitched = frozenset(map(UUID4, stitched_entity_ids))
 
         json_by_core_cls: MutableMapping[type[E], list[JSON]] = defaultdict(list)
-        for file_name, json in metadata.items():
-            assert file_name.endswith('.json')
-            schema_name, _, suffix = file_name[:-5].rpartition('_')
-            if schema_name and suffix.isdigit():
-                entity_cls = entity_types[schema_name]
-                core_cls = core_types[entity_cls]
-                json_by_core_cls[core_cls].append(json)
+        for key, json in metadata.items():
+            schema_name = EntityReference.parse(key).entity_type
+            entity_cls = entity_types[schema_name]
+            core_cls = core_types[entity_cls]
+            json_by_core_cls[core_cls].append(json)
 
         def from_json_vx(core_cls: type[E],
                          **kwargs
diff --git a/src/humancellatlas/data/metadata/helpers/staging_area.py b/src/humancellatlas/data/metadata/helpers/staging_area.py
index 026d99398..f9a970bc0 100644
--- a/src/humancellatlas/data/metadata/helpers/staging_area.py
+++ b/src/humancellatlas/data/metadata/helpers/staging_area.py
@@ -29,6 +29,9 @@
     reject,
     require,
 )
+from azul.indexer.document import (
+    EntityReference,
+)
 from azul.types import (
     JSON,
     MutableJSON,
@@ -158,7 +161,8 @@ def get_bundle_parts(self, subgraph_id: str) -> tuple[str, MutableJSONs, Mutable
                 json_file_name = f'{entity_type}_{i}.json'
                 metadata_file = self.metadata[entity_id]
                 json_content = metadata_file.content
-                metadata[json_file_name] = json_content
+                key = str(EntityReference(entity_type=entity_type, entity_id=entity_id))
+                metadata[key] = json_content
                 file_manifest = {
                     'content-type': 'application/json;',
                     'crc32c': '0' * 8,
diff --git a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index b43a40d08..0dbe6df85 100644
--- a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -146,7 +146,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/7b53bae2-2424-44c0-9d80-ad72e8bca136": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -174,7 +174,7 @@
                 "update_date": "2018-09-04T12:27:19.625Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/eebf404f-4fbb-41b0-a9c6-81586f729599": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -192,7 +192,7 @@
                 "update_date": "2018-09-04T12:26:56.433Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/628e8b1d-a1ce-4dee-b15a-3fd33290eafe": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -246,7 +246,7 @@
                 "update_date": "2018-09-04T12:27:10.175Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/e4024c4a-dbce-4bda-bed8-21414091e7ce": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/4.3.2/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -281,7 +281,7 @@
                 "update_date": "2018-09-04T12:27:50.909Z"
             }
         },
-        "process_0.json": {
+        "process/98442f49-9afb-491e-8347-f891f39d8d70": {
             "process_core": {
                 "process_id": "process_id_128"
             },
@@ -293,7 +293,7 @@
                 "update_date": "2018-09-04T12:28:00.426Z"
             }
         },
-        "process_1.json": {
+        "process/d691bda4-ed01-48b6-a4ea-65b70f6a3946": {
             "process_core": {
                 "process_id": "process_id_255"
             },
@@ -305,7 +305,7 @@
                 "update_date": "2018-09-04T12:28:06.541Z"
             }
         },
-        "process_2.json": {
+        "process/5aa4645b-2802-4140-9b15-d1008338b1c9": {
             "process_core": {
                 "process_id": "process_id_1"
             },
@@ -317,7 +317,7 @@
                 "update_date": "2018-09-04T12:27:51.508Z"
             }
         },
-        "project_0.json": {
+        "project/617eb7c1-a3bc-4dd3-9a2a-50a77c998e22": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/project/9.0.2/project",
             "schema_type": "project",
             "project_core": {
@@ -461,7 +461,7 @@
                 "update_date": "2018-09-04T12:27:09.930Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/36d7f891-8a43-4ae4-8472-a34dcb2be643": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -478,7 +478,7 @@
                 "update_date": "2018-09-04T12:27:39.827Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/aaa08845-5150-4a4f-9c44-5ea22add1fc3": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -502,7 +502,7 @@
                 "update_date": "2018-09-04T12:27:50.911Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/6228558b-436a-46c9-9cd3-ea9b5c123070": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
diff --git a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 0f8006f7a..c4a5b2b76 100644
--- a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -182,7 +182,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/cc0d9bf0-6ad5-4489-994b-db26ff761c5a": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -217,7 +217,7 @@
                 "update_date": "2018-09-05T09:53:09.415Z"
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/f8d9778f-0f72-4432-a929-1096fd9ca2f4": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/8.2.6/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -236,7 +236,7 @@
                 "update_date": "2018-09-05T09:52:05.472Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/a934e15c-e1ce-423b-b554-9203d4e93f41": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -255,7 +255,7 @@
                 "update_date": "2018-09-05T09:51:59.418Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/25e083e3-d747-4295-86c8-c7ddc4b975be": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -298,7 +298,7 @@
                 "update_date": "2018-09-05T09:50:15.914Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/80921b90-fe8d-45e1-a5e5-4fdb55f9a3fa": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -317,7 +317,7 @@
                 "update_date": "2018-09-05T09:52:05.683Z"
             }
         },
-        "enrichment_protocol_1.json": {
+        "enrichment_protocol/77c71448-fb32-472f-9d44-ea9a42867a41": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
             "schema_type": "protocol",
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@@ -337,7 +337,7 @@
                 "update_date": "2018-09-05T09:51:58.823Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/0ea30fa0-7183-4ffc-a4b8-537c6de32e65": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/4.3.2/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -372,7 +372,7 @@
                 "update_date": "2018-09-05T09:52:00.867Z"
             }
         },
-        "process_0.json": {
+        "process/bcfcb3d7-674a-429f-8bf9-347a0f222db2": {
             "insdc_experiment": {
                 "insdc_experiment": "SRX3364233"
             },
@@ -387,7 +387,7 @@
                 "update_date": "2018-09-05T09:56:34.501Z"
             }
         },
-        "process_1.json": {
+        "process/f8e3c0b7-ed2a-464d-bff4-b80fac2a3849": {
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@@ -399,7 +399,7 @@
                 "update_date": "2018-09-05T09:55:08.938Z"
             }
         },
-        "process_2.json": {
+        "process/4e504efb-a65b-4fe5-97f5-8148f6a8ed4d": {
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                 "process_location": "Sri Lanka",
                 "process_id": "process_id_16"
@@ -412,7 +412,7 @@
                 "update_date": "2018-09-05T09:55:08.214Z"
             }
         },
-        "project_0.json": {
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@@ -497,7 +497,7 @@
                 "update_date": "2018-09-05T09:50:15.608Z"
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         },
-        "sequence_file_0.json": {
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@@ -515,7 +515,7 @@
                 "update_date": "2018-09-05T09:54:36.578Z"
             }
         },
-        "sequencing_protocol_0.json": {
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@@ -538,7 +538,7 @@
                 "update_date": "2018-09-05T09:51:58.194Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/ff63b5d7-e702-40da-bbe9-619e52131b63": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
             "schema_type": "biomaterial",
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diff --git a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 4591e9d13..8684d8653 100644
--- a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
+++ b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
@@ -590,7 +590,7 @@
         }
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@@ -637,7 +637,7 @@
                 "update_date": "2018-09-05T09:25:11.221Z"
             }
         },
-        "cell_line_1.json": {
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             "biomaterial_core": {
@@ -684,7 +684,7 @@
                 "update_date": "2018-09-05T09:25:10.838Z"
             }
         },
-        "cell_line_2.json": {
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@@ -731,7 +731,7 @@
                 "update_date": "2018-09-05T09:25:05.636Z"
             }
         },
-        "cell_line_3.json": {
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             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.2/cell_line",
             "schema_type": "biomaterial",
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@@ -778,7 +778,7 @@
                 "update_date": "2018-09-05T09:25:11.557Z"
             }
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/8fc8b364-98bb-4082-98af-e3fdffcf82b7": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -808,7 +808,7 @@
                 "update_date": "2018-09-05T09:25:12.353Z"
             }
         },
-        "differentiation_protocol_0.json": {
+        "differentiation_protocol/537b3c44-998f-43c2-8146-7e3e2932c30b": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/1.3.0/differentiation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -829,7 +829,7 @@
                 "update_date": "2018-09-05T09:25:11.867Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/58334256-af4f-4754-9455-668fb31bbcff": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -854,7 +854,7 @@
                 "update_date": "2018-09-05T09:25:09.326Z"
             }
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-        "donor_organism_0.json": {
+        "donor_organism/5554b939-a268-4619-9cef-0f09151454fc": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -899,7 +899,7 @@
                 "update_date": "2018-09-05T09:25:09.818Z"
             }
         },
-        "donor_organism_1.json": {
+        "donor_organism/eea3dd19-90e0-45c4-803d-4620d1fab90d": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -944,7 +944,7 @@
                 "update_date": "2018-09-05T09:25:09.806Z"
             }
         },
-        "donor_organism_2.json": {
+        "donor_organism/fbd4c071-58bd-4818-8ddd-2c31ddb60363": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -989,7 +989,7 @@
                 "update_date": "2018-09-05T09:25:09.903Z"
             }
         },
-        "donor_organism_3.json": {
+        "donor_organism/62ee5119-4fa1-4508-95f3-59c7b0fddd34": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1034,7 +1034,7 @@
                 "update_date": "2018-09-05T09:25:09.841Z"
             }
         },
-        "ipsc_induction_protocol_0.json": {
+        "ipsc_induction_protocol/9e3b5ef9-cbb0-43ef-a194-1ce1969cfd62": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/2.0.1/ipsc_induction_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1057,7 +1057,7 @@
                 "update_date": "2018-09-05T09:25:09.069Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/853c2086-1ac4-488e-b3b3-fe7956e74283": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/4.3.2/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1098,7 +1098,7 @@
                 "update_date": "2018-09-05T09:25:09.008Z"
             }
         },
-        "organoid_0.json": {
+        "organoid/e4307721-7d92-4f92-a6f1-6f1d4ecf1835": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.3.6/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1133,7 +1133,7 @@
                 "update_date": "2018-09-05T09:25:10.346Z"
             }
         },
-        "organoid_1.json": {
+        "organoid/dfd95ce4-c5be-4175-9e9a-249b1b09f5d9": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.3.6/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1168,7 +1168,7 @@
                 "update_date": "2018-09-05T09:25:10.134Z"
             }
         },
-        "organoid_2.json": {
+        "organoid/08936dad-6f12-4f43-8bd2-b6863f166a21": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.3.6/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1203,7 +1203,7 @@
                 "update_date": "2018-09-05T09:25:10.146Z"
             }
         },
-        "organoid_3.json": {
+        "organoid/77a87953-5d2d-4e22-9c8b-c012fa8656b9": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.3.6/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1238,7 +1238,7 @@
                 "update_date": "2018-09-05T09:25:10.427Z"
             }
         },
-        "process_0.json": {
+        "process/359f3d8c-e29c-41f1-b058-1854a7d7e79e": {
             "process_core": {
                 "process_id": "process_id_1"
             },
@@ -1250,7 +1250,7 @@
                 "update_date": "2018-09-05T09:25:09.834Z"
             }
         },
-        "process_1.json": {
+        "process/f999e1a4-31fc-4298-b958-8f567511935e": {
             "process_core": {
                 "process_id": "process_id_18"
             },
@@ -1262,7 +1262,7 @@
                 "update_date": "2018-09-05T09:25:12.150Z"
             }
         },
-        "process_10.json": {
+        "process/3ef770a1-1f72-47f2-952e-9fd584e74598": {
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                 "process_id": "process_id_9"
             },
@@ -1274,7 +1274,7 @@
                 "update_date": "2018-09-05T09:25:11.841Z"
             }
         },
-        "process_11.json": {
+        "process/9c2903a9-d93e-41a4-88bf-61647c6990a6": {
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                 "process_id": "process_id_2"
             },
@@ -1286,7 +1286,7 @@
                 "update_date": "2018-09-05T09:25:11.730Z"
             }
         },
-        "process_12.json": {
+        "process/1ff79cfa-57e9-4af1-a754-51bdf36c4414": {
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                 "process_id": "process_id_15"
             },
@@ -1298,7 +1298,7 @@
                 "update_date": "2018-09-05T09:25:12.025Z"
             }
         },
-        "process_13.json": {
+        "process/88ef68b1-0c0b-4594-be46-4bb0bcf2025d": {
             "process_core": {
                 "process_id": "tech_rep_1"
             },
@@ -1310,7 +1310,7 @@
                 "update_date": "2018-09-05T09:25:10.851Z"
             }
         },
-        "process_2.json": {
+        "process/0ec71414-3c56-4347-85a2-a2b66a4a147d": {
             "process_core": {
                 "process_id": "process_id_6"
             },
@@ -1322,7 +1322,7 @@
                 "update_date": "2018-09-05T09:25:11.878Z"
             }
         },
-        "process_3.json": {
+        "process/d3c8ba6e-e552-48cc-ab34-38a95712b3f7": {
             "process_core": {
                 "process_id": "process_id_21"
             },
@@ -1334,7 +1334,7 @@
                 "update_date": "2018-09-05T09:25:12.221Z"
             }
         },
-        "process_4.json": {
+        "process/4e60bff4-9ede-42e2-9152-7f8f445938f5": {
             "process_core": {
                 "process_id": "process_id_8"
             },
@@ -1346,7 +1346,7 @@
                 "update_date": "2018-09-05T09:25:06.559Z"
             }
         },
-        "process_5.json": {
+        "process/6ecf593a-c3d6-42a8-bf4e-a47549e7bb1f": {
             "process_core": {
                 "process_id": "process_id_4"
             },
@@ -1358,7 +1358,7 @@
                 "update_date": "2018-09-05T09:25:11.893Z"
             }
         },
-        "process_6.json": {
+        "process/1c4b3da5-41c3-40bd-b128-4a4a94fb876e": {
             "process_core": {
                 "process_id": "process_id_5"
             },
@@ -1370,7 +1370,7 @@
                 "update_date": "2018-09-05T09:25:11.945Z"
             }
         },
-        "process_7.json": {
+        "process/85e8adfd-f23b-47fb-9617-e51593923405": {
             "process_core": {
                 "process_id": "process_id_3"
             },
@@ -1382,7 +1382,7 @@
                 "update_date": "2018-09-05T09:25:11.959Z"
             }
         },
-        "process_8.json": {
+        "process/df40cef2-60ae-400c-bece-947329b40946": {
             "process_core": {
                 "process_id": "process_id_12"
             },
@@ -1394,7 +1394,7 @@
                 "update_date": "2018-09-05T09:25:12.073Z"
             }
         },
-        "process_9.json": {
+        "process/94b7d3a9-2a09-40d1-ba0e-80e8410b3d55": {
             "process_core": {
                 "process_id": "process_id_7"
             },
@@ -1406,7 +1406,7 @@
                 "update_date": "2018-09-05T09:25:12.053Z"
             }
         },
-        "project_0.json": {
+        "project/88f5dff1-d784-4d9a-9c5d-f309fbe738c8": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/project/9.0.2/project",
             "schema_type": "project",
             "project_core": {
@@ -1467,7 +1467,7 @@
                 "update_date": "2018-09-05T09:25:05.557Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/740b2221-41c6-498d-87de-8b2937a5ebed": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1484,7 +1484,7 @@
                 "update_date": "2018-09-05T09:25:03.221Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/a3f614b3-e6cf-4751-a15d-ff623efea62a": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1501,7 +1501,7 @@
                 "update_date": "2018-09-05T09:25:03.230Z"
             }
         },
-        "sequence_file_2.json": {
+        "sequence_file/56c2a158-e389-40a3-97a7-0f2966a393b8": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1518,7 +1518,7 @@
                 "update_date": "2018-09-05T09:25:03.244Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/0b1dfbd4-1fbe-42a4-9213-b66dac4d4ac0": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1542,7 +1542,7 @@
                 "update_date": "2018-09-05T09:25:09.017Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/54046c37-b50d-41ae-a95f-2db29b1b706b": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1579,7 +1579,7 @@
                 "update_date": "2018-09-05T09:25:10.219Z"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/2b541914-778d-4b24-9680-9d2643cfeff9": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1616,7 +1616,7 @@
                 "update_date": "2018-09-05T09:25:05.620Z"
             }
         },
-        "specimen_from_organism_2.json": {
+        "specimen_from_organism/440a306a-54c6-4193-9b60-ad4423c8a62b": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1653,7 +1653,7 @@
                 "update_date": "2018-09-05T09:25:10.273Z"
             }
         },
-        "specimen_from_organism_3.json": {
+        "specimen_from_organism/4eb07fdb-dcd8-4805-89ad-6068071c80c9": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1690,7 +1690,7 @@
                 "update_date": "2018-09-05T09:25:09.878Z"
             }
         },
-        "supplementary_file_0.json": {
+        "supplementary_file/a0eb3208-97e4-498c-993b-20757231b233": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/1.1.3/supplementary_file",
             "schema_type": "file",
             "file_core": {
@@ -1704,7 +1704,7 @@
                 "update_date": "2018-09-05T09:25:02.972Z"
             }
         },
-        "supplementary_file_1.json": {
+        "supplementary_file/e01ee650-58b3-4f3c-8da8-4483700a1eae": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/1.1.3/supplementary_file",
             "schema_type": "file",
             "file_core": {
@@ -1718,7 +1718,7 @@
                 "update_date": "2018-09-05T09:25:03.001Z"
             }
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-        "supplementary_file_2.json": {
+        "supplementary_file/5ab06a61-c66b-4d3d-9889-ab47371a65b0": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/1.1.3/supplementary_file",
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             "file_core": {
diff --git a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index b9138a275..64ededa29 100644
--- a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -146,7 +146,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/1200f5bf-7d45-4f26-865e-b560797f1808": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
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             "biomaterial_core": {
@@ -177,7 +177,7 @@
                 "update_date": "2018-09-05T12:21:55.818Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/6029a289-861c-4349-9614-4c244103be21": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
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@@ -196,7 +196,7 @@
                 "update_date": "2018-09-05T12:17:49.721Z"
             }
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-        "donor_organism_0.json": {
+        "donor_organism/8bb4258a-90c7-4af6-8a1b-c4ab6c5483e2": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
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@@ -242,7 +242,7 @@
                 "update_date": "2018-09-05T12:14:26.204Z"
             }
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-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/079bc155-71c9-45ab-bd12-cab025890d82": {
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@@ -274,7 +274,7 @@
                 "update_date": "2018-09-05T12:17:48.051Z"
             }
         },
-        "process_0.json": {
+        "process/aa67d2ed-e4ea-4cdf-92ed-7d5e6dc1f6fa": {
             "insdc_experiment": {
                 "insdc_experiment": "ERX1700368"
             },
@@ -289,7 +289,7 @@
                 "update_date": "2018-09-05T12:26:35.419Z"
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-        "process_1.json": {
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@@ -301,7 +301,7 @@
                 "update_date": "2018-09-05T12:25:01.078Z"
             }
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-        "process_2.json": {
+        "process/738243c5-e336-4c55-a8b6-b192b6f98fe7": {
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@@ -313,7 +313,7 @@
                 "update_date": "2018-09-05T12:25:00.908Z"
             }
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-        "project_0.json": {
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@@ -414,7 +414,7 @@
                 "update_date": "2018-09-05T12:14:26.167Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/60471337-a47b-4b9c-95e7-4a19349a5e05": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/6.5.2/sequence_file",
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             "file_core": {
@@ -432,7 +432,7 @@
                 "update_date": "2018-09-05T12:27:42.525Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/3aece946-4be6-4a0c-af23-ac884a87bcbb": {
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             "schema_type": "protocol",
             "protocol_core": {
@@ -456,7 +456,7 @@
                 "update_date": "2018-09-05T12:16:50.390Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/38002d8f-eac5-4ee4-8290-03d323bf780e": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
diff --git a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 149c49ade..09aacf25f 100644
--- a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -158,7 +158,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/1446ca36-ba75-45ea-b6ab-a80641a88812": {
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             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -192,7 +192,7 @@
                 "update_date": "2018-09-04T13:12:52.699Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/7142ed25-3237-4156-b10d-0aa74b2c37b3": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -210,7 +210,7 @@
                 "update_date": "2018-09-04T12:58:01.497Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/b56697f5-d350-4e1d-93b2-72eee68c972e": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -253,7 +253,7 @@
                 "update_date": "2018-09-04T13:08:09.637Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/4a19c599-e429-4eda-9644-3a46c1202c7f": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -271,7 +271,7 @@
                 "update_date": "2018-09-04T12:57:51.962Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/38e07040-6198-4a46-b195-88c0680ef283": {
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@@ -302,7 +302,7 @@
                 "update_date": "2018-09-04T12:55:56.069Z"
             }
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-        "process_0.json": {
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@@ -314,7 +314,7 @@
                 "update_date": "2018-09-04T13:23:54.508Z"
             }
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-        "process_1.json": {
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             },
@@ -326,7 +326,7 @@
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             }
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-        "process_2.json": {
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@@ -338,7 +338,7 @@
                 "update_date": "2018-09-04T13:27:57.677Z"
             }
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-        "project_0.json": {
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@@ -452,7 +452,7 @@
                 "update_date": "2018-09-04T13:08:08.264Z"
             }
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-        "sequence_file_0.json": {
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             "file_core": {
@@ -467,7 +467,7 @@
                 "update_date": "2018-09-04T13:20:33.745Z"
             }
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-        "sequencing_protocol_0.json": {
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@@ -489,7 +489,7 @@
                 "update_date": "2018-09-04T12:57:59.862Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/6dc01fb6-6aba-432e-828e-ae3045914f34": {
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             "schema_type": "biomaterial",
             "biomaterial_core": {
diff --git a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 9bc6d2ee6..3ef7e9534 100644
--- a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -158,7 +158,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/c61125ab-d5e0-4d93-b0a7-2deac1729f65": {
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@@ -182,7 +182,7 @@
                 "update_date": "2018-09-06T14:25:54.342Z"
             }
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-        "donor_organism_0.json": {
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@@ -228,7 +228,7 @@
                 "update_date": "2018-09-06T14:23:05.946Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/34c6db60-ef27-4502-9191-102d1a235adc": {
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             "protocol_core": {
@@ -256,7 +256,7 @@
                 "update_date": "2018-09-06T14:18:35.854Z"
             }
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-        "process_0.json": {
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             },
@@ -268,7 +268,7 @@
                 "update_date": "2018-09-06T14:31:09.024Z"
             }
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-        "process_1.json": {
+        "process/5f868fc6-dc13-4f06-a82e-ff83497d03ee": {
             "process_core": {
                 "process_id": "SRR3562210"
             },
@@ -280,7 +280,7 @@
                 "update_date": "2018-09-06T14:31:54.751Z"
             }
         },
-        "process_2.json": {
+        "process/0aede7bd-0a5d-4dc5-a8e8-2d4ad6d01bfb": {
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             },
@@ -292,7 +292,7 @@
                 "update_date": "2018-09-06T14:31:08.929Z"
             }
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-        "project_0.json": {
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@@ -338,7 +338,7 @@
                 "update_date": "2018-09-06T14:23:05.636Z"
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         },
-        "sequence_file_0.json": {
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             "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -356,7 +356,7 @@
                 "update_date": "2018-09-06T14:29:33.854Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/0494ee09-b1e2-437a-986f-06d5df4a6858": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -374,7 +374,7 @@
                 "update_date": "2018-09-06T14:29:33.843Z"
             }
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-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/319dd8c8-e9d6-40df-bf72-e0423f4f5418": {
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@@ -394,7 +394,7 @@
                 "update_date": "2018-09-06T14:18:35.890Z"
             }
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-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/07282a68-dca4-449e-81b6-7b0da34230df": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
diff --git a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index dc6d04dfa..84f4ad58f 100644
--- a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -326,7 +326,7 @@
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+        "cell_suspension/932dae75-ba79-42a6-915a-c6a67b39835c": {
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@@ -351,7 +351,7 @@
                 "update_date": "2018-09-05T09:15:05.597Z"
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-        "dissociation_protocol_0.json": {
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@@ -369,7 +369,7 @@
                 "update_date": "2018-09-05T09:15:02.163Z"
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@@ -429,7 +429,7 @@
                 "update_date": "2018-09-05T09:15:03.935Z"
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-        "enrichment_protocol_0.json": {
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@@ -448,7 +448,7 @@
                 "update_date": "2018-09-05T09:15:02.160Z"
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-        "library_preparation_protocol_0.json": {
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@@ -484,7 +484,7 @@
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@@ -496,7 +496,7 @@
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@@ -508,7 +508,7 @@
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-        "project_0.json": {
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@@ -656,7 +656,7 @@
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@@ -674,7 +674,7 @@
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@@ -698,7 +698,7 @@
                 "update_date": "2018-09-05T09:15:02.167Z"
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-        "supplementary_file_0.json": {
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@@ -713,7 +713,7 @@
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-        "supplementary_file_1.json": {
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@@ -727,7 +727,7 @@
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@@ -742,7 +742,7 @@
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@@ -757,7 +757,7 @@
                 "update_date": "2018-09-05T09:14:56.827Z"
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@@ -771,7 +771,7 @@
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@@ -784,7 +784,7 @@
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@@ -799,7 +799,7 @@
                 "update_date": "2018-09-05T09:14:56.865Z"
             }
         },
-        "supplementary_file_7.json": {
+        "supplementary_file/f863f044-f904-4bf2-8535-fa45f123f237": {
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diff --git a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
index 783556e2b..790373aac 100644
--- a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
+++ b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
@@ -586,7 +586,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/c2396f83-22e4-4a2d-8cce-a30feb533603": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.6.2/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -618,7 +618,7 @@
                 "update_date": "2019-01-03T12:08:03.256Z"
             }
         },
-        "organoid_0.json": {
+        "organoid/a690df06-cc52-4346-a926-fe5e5b3a7547": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.3.9/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -656,7 +656,7 @@
                 "update_date": "2019-01-03T12:08:02.342Z"
             }
         },
-        "organoid_1.json": {
+        "organoid/f0b636ce-505c-4339-a69c-2305352b6796": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.3.9/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -694,7 +694,7 @@
                 "update_date": "2019-01-03T12:08:02.944Z"
             }
         },
-        "organoid_2.json": {
+        "organoid/46e7ed04-5916-4c10-8a05-fe510eda819a": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.3.9/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -732,7 +732,7 @@
                 "update_date": "2019-01-03T12:08:02.497Z"
             }
         },
-        "organoid_3.json": {
+        "organoid/d49998ff-c873-41fd-bb44-f221f89b8f15": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.3.9/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -770,7 +770,7 @@
                 "update_date": "2019-01-03T12:08:02.781Z"
             }
         },
-        "cell_line_0.json": {
+        "cell_line/a689172e-cae2-4e2c-b1d2-5aeff0a90171": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/9.0.1/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -820,7 +820,7 @@
                 "update_date": "2019-01-03T12:08:03.319Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/597b4050-0778-4a81-b882-e1704ab0b6ad": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/6.3.4/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -862,7 +862,7 @@
                 "update_date": "2019-01-03T12:08:03.189Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/4934d9c3-753b-47bc-b2d5-468ce255a139": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.2.1/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -911,7 +911,7 @@
                 "update_date": "2019-01-03T12:08:02.040Z"
             }
         },
-        "cell_line_1.json": {
+        "cell_line/37833da3-505d-4bb2-916e-26aa8985d183": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/9.0.1/cell_line",
             "schema_type": "biomaterial",
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@@ -961,7 +961,7 @@
                 "update_date": "2019-01-03T12:08:03.268Z"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/1fc181fe-60c6-4b94-85c1-1f227be60658": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/6.3.4/specimen_from_organism",
             "schema_type": "biomaterial",
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@@ -1003,7 +1003,7 @@
                 "update_date": "2019-01-03T12:08:03.087Z"
             }
         },
-        "donor_organism_1.json": {
+        "donor_organism/7c3a6d87-9f43-4de5-b47d-6fa78a897624": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.2.1/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1052,7 +1052,7 @@
                 "update_date": "2019-01-03T12:08:01.492Z"
             }
         },
-        "cell_line_2.json": {
+        "cell_line/d954547d-94bc-401d-bdff-ccd727251c74": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/9.0.1/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1102,7 +1102,7 @@
                 "update_date": "2019-01-03T12:08:03.322Z"
             }
         },
-        "specimen_from_organism_2.json": {
+        "specimen_from_organism/ad702cb9-3b40-4f8f-b9a5-331eeb153d9b": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/6.3.4/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1144,7 +1144,7 @@
                 "update_date": "2019-01-03T12:08:02.789Z"
             }
         },
-        "donor_organism_2.json": {
+        "donor_organism/3322ea3a-30ea-4e6e-b187-18525de4ee3e": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.2.1/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1193,7 +1193,7 @@
                 "update_date": "2019-01-03T12:08:02.270Z"
             }
         },
-        "cell_line_3.json": {
+        "cell_line/95deef55-86e9-42be-9f82-3102b0d89dbe": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/9.0.1/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1243,7 +1243,7 @@
                 "update_date": "2019-01-03T12:08:03.373Z"
             }
         },
-        "specimen_from_organism_3.json": {
+        "specimen_from_organism/2e32e319-53d4-4e69-af0f-c43e2b15a94f": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/6.3.4/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1285,7 +1285,7 @@
                 "update_date": "2019-01-03T12:08:03.124Z"
             }
         },
-        "donor_organism_3.json": {
+        "donor_organism/872169f4-8479-4476-9646-20b3997e1f01": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.2.1/donor_organism",
             "schema_type": "biomaterial",
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@@ -1334,7 +1334,7 @@
                 "update_date": "2019-01-03T12:08:02.262Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/9c49bbf2-cf62-4f94-9b9d-a3da42e2d52a": {
             "describedBy": "https://schema.humancellatlas.org/type/file/7.0.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1351,7 +1351,7 @@
                 "update_date": "2019-01-03T12:16:54.090Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/ac93d656-4aa5-4f6c-b273-dc1d8be1934c": {
             "describedBy": "https://schema.humancellatlas.org/type/file/7.0.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1368,7 +1368,7 @@
                 "update_date": "2019-01-03T12:20:06.160Z"
             }
         },
-        "sequence_file_2.json": {
+        "sequence_file/5989ca50-45b5-4834-bfde-d290a8dfa97e": {
             "describedBy": "https://schema.humancellatlas.org/type/file/7.0.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1385,7 +1385,7 @@
                 "update_date": "2019-01-03T12:28:59.095Z"
             }
         },
-        "supplementary_file_0.json": {
+        "supplementary_file/434fa581-90e3-43cc-8ff5-2596e6e8d366": {
             "describedBy": "https://schema.humancellatlas.org/type/file/1.1.5/supplementary_file",
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@@ -1399,7 +1399,7 @@
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-        "supplementary_file_1.json": {
+        "supplementary_file/f126dd41-0041-46b7-8c63-7da264be6b81": {
             "describedBy": "https://schema.humancellatlas.org/type/file/1.1.5/supplementary_file",
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@@ -1413,7 +1413,7 @@
                 "update_date": "2019-01-03T12:11:14.380Z"
             }
         },
-        "supplementary_file_2.json": {
+        "supplementary_file/f48ebd9a-f3ac-4e02-b698-7146cd396946": {
             "describedBy": "https://schema.humancellatlas.org/type/file/1.1.5/supplementary_file",
             "schema_type": "file",
             "file_core": {
@@ -1427,7 +1427,7 @@
                 "update_date": "2019-01-03T12:11:14.378Z"
             }
         },
-        "project_0.json": {
+        "project/d96c2451-6e22-441f-a3e6-70fd0878bb1b": {
             "describedBy": "https://schema.humancellatlas.org/type/project/9.0.4/project",
             "schema_type": "project",
             "project_core": {
@@ -1488,7 +1488,7 @@
                 "update_date": "2019-01-03T12:07:59.988Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/65ce5281-b07e-4b21-be8d-66ac5dea4d69": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/4.4.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1531,7 +1531,7 @@
                 "update_date": "2019-01-03T12:07:58.774Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/1547584e-d9e4-4519-a72a-91db0d0fec3c": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/9.0.3/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1557,7 +1557,7 @@
                 "update_date": "2019-01-03T12:07:58.338Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/c23de226-536c-403d-a757-f4200cb1777b": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1584,7 +1584,7 @@
                 "update_date": "2019-01-03T12:07:58.689Z"
             }
         },
-        "differentiation_protocol_0.json": {
+        "differentiation_protocol/3ec905f4-5950-4cfa-bd0b-86cc0370fd47": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/1.3.0/differentiation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1608,7 +1608,7 @@
                 "update_date": "2019-01-03T12:07:58.180Z"
             }
         },
-        "ipsc_induction_protocol_0.json": {
+        "ipsc_induction_protocol/97a30135-246f-4c0d-aef8-4e33183d1ff7": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/2.0.1/ipsc_induction_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1631,7 +1631,7 @@
                 "update_date": "2019-01-03T12:07:58.380Z"
             }
         },
-        "process_0.json": {
+        "process/54438211-29fb-4e57-87f4-95412e5d8b15": {
             "process_core": {
                 "process_id": "tech_rep_3"
             },
@@ -1643,7 +1643,7 @@
                 "update_date": "2019-01-03T12:07:59.105Z"
             }
         },
-        "process_1.json": {
+        "process/7d683bc4-6e59-4c7e-bbc8-5dad46fe2684": {
             "process_core": {
                 "process_id": "process_id_22"
             },
@@ -1655,7 +1655,7 @@
                 "update_date": "2019-01-03T12:07:59.380Z"
             }
         },
-        "process_2.json": {
+        "process/d1a9aae1-99dc-4b49-bee3-af685b7f013a": {
             "process_core": {
                 "process_id": "process_id_10"
             },
@@ -1667,7 +1667,7 @@
                 "update_date": "2019-01-03T12:08:00.039Z"
             }
         },
-        "process_3.json": {
+        "process/a02a2a59-cdb4-4261-b220-b0cfebaec5ac": {
             "process_core": {
                 "process_id": "process_id_5"
             },
@@ -1679,7 +1679,7 @@
                 "update_date": "2019-01-03T12:07:58.898Z"
             }
         },
-        "process_4.json": {
+        "process/01e52705-77de-4715-b35f-442aff9312be": {
             "process_core": {
                 "process_id": "process_id_1"
             },
@@ -1691,7 +1691,7 @@
                 "update_date": "2019-01-03T12:07:59.330Z"
             }
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-        "process_5.json": {
+        "process/58a58315-2f03-4a36-9cea-dd306b609ba9": {
             "process_core": {
                 "process_id": "process_id_13"
             },
@@ -1703,7 +1703,7 @@
                 "update_date": "2019-01-03T12:07:59.265Z"
             }
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-        "process_6.json": {
+        "process/56c911d5-6b99-486c-9ce7-141ee41528eb": {
             "process_core": {
                 "process_id": "process_id_6"
             },
@@ -1715,7 +1715,7 @@
                 "update_date": "2019-01-03T12:07:59.791Z"
             }
         },
-        "process_7.json": {
+        "process/23fe1739-6bbe-4a86-be96-bd75f19f8375": {
             "process_core": {
                 "process_id": "process_id_2"
             },
@@ -1727,7 +1727,7 @@
                 "update_date": "2019-01-03T12:07:58.637Z"
             }
         },
-        "process_8.json": {
+        "process/831dc734-9813-4c34-a163-16dd5b75d9a0": {
             "process_core": {
                 "process_id": "process_id_16"
             },
@@ -1739,7 +1739,7 @@
                 "update_date": "2019-01-03T12:07:59.485Z"
             }
         },
-        "process_9.json": {
+        "process/d8f1d436-6bc3-4638-9801-8a9241996d28": {
             "process_core": {
                 "process_id": "process_id_7"
             },
@@ -1751,7 +1751,7 @@
                 "update_date": "2019-01-03T12:07:59.548Z"
             }
         },
-        "process_10.json": {
+        "process/a9a39b30-8243-4d08-8f36-8f2e1275e8d0": {
             "process_core": {
                 "process_id": "process_id_3"
             },
@@ -1763,7 +1763,7 @@
                 "update_date": "2019-01-03T12:07:58.435Z"
             }
         },
-        "process_11.json": {
+        "process/024c9f05-1743-4d66-83b7-134a31cd1c27": {
             "process_core": {
                 "process_id": "process_id_19"
             },
@@ -1775,7 +1775,7 @@
                 "update_date": "2019-01-03T12:07:59.150Z"
             }
         },
-        "process_12.json": {
+        "process/50d53f80-5e54-4cda-97f0-5acb4d686d3e": {
             "process_core": {
                 "process_id": "process_id_8"
             },
@@ -1787,7 +1787,7 @@
                 "update_date": "2019-01-03T12:07:59.502Z"
             }
         },
-        "process_13.json": {
+        "process/baa3a061-534c-4b6e-8c51-a11a8307f537": {
             "process_core": {
                 "process_id": "process_id_4"
             },
diff --git a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
index fa187ba7e..0a1c182fb 100644
--- a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
+++ b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
@@ -314,7 +314,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/eb27c398-f017-4ef1-acc8-3f51af87fe17": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -348,7 +348,7 @@
                 "schema_minor_version": 3
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/0a63e007-09d0-4330-989b-ca248f8b3c3c": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -386,7 +386,7 @@
                 "schema_minor_version": 4
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/fa1bd656-7f7b-4288-84c6-d511232cfe95": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -448,7 +448,7 @@
                 "schema_minor_version": 5
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-        "sequence_file_0.json": {
+        "sequence_file/12484c33-24ec-4293-8f96-4cb1a43a6479": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -473,7 +473,7 @@
                 "schema_minor_version": 2
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-        "sequence_file_1.json": {
+        "sequence_file/f85b458b-b189-4ee7-939a-c905b70ae431": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -497,7 +497,7 @@
                 "schema_minor_version": 2
             }
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-        "sequence_file_2.json": {
+        "sequence_file/18feeb7d-66ca-4ea4-a019-a10e5b762465": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
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             "file_core": {
@@ -522,7 +522,7 @@
                 "schema_minor_version": 2
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-        "supplementary_file_0.json": {
+        "supplementary_file/2e64e936-85ec-49a0-8365-578b5621bcb1": {
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             "schema_type": "file",
             "file_core": {
@@ -539,7 +539,7 @@
                 "schema_minor_version": 2
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-        "supplementary_file_1.json": {
+        "supplementary_file/720e6453-71ff-4742-ba6a-e5a3a5d3cee0": {
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             "schema_type": "file",
             "file_core": {
@@ -556,7 +556,7 @@
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-        "supplementary_file_2.json": {
+        "supplementary_file/09917cf3-76de-4b85-8944-03664cd0d954": {
             "describedBy": "https://schema.humancellatlas.org/type/file/2.2.0/supplementary_file",
             "schema_type": "file",
             "file_core": {
@@ -573,7 +573,7 @@
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-        "supplementary_file_3.json": {
+        "supplementary_file/8fb964a1-fd66-43b6-9d13-57db6bd185f2": {
             "describedBy": "https://schema.humancellatlas.org/type/file/2.2.0/supplementary_file",
             "schema_type": "file",
             "file_core": {
@@ -590,7 +590,7 @@
                 "schema_minor_version": 2
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         },
-        "project_0.json": {
+        "project/9c20a245-f2c0-43ae-82c9-2232ec6b594f": {
             "describedBy": "https://schema.humancellatlas.org/type/project/14.1.0/project",
             "schema_type": "project",
             "project_core": {
@@ -794,7 +794,7 @@
                 "schema_minor_version": 1
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/6ce5a9c7-b4f7-41e5-a182-21e85627feee": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -846,7 +846,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/e01aa420-488b-4189-a8c8-98ada395ee91": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -879,7 +879,7 @@
                 "schema_minor_version": 1
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/a3623f22-83e7-4207-b204-34041abb54e2": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -900,7 +900,7 @@
                 "schema_minor_version": 2
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/76f64d5b-fa01-4efe-ad4a-097d70311581": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -923,7 +923,7 @@
                 "schema_minor_version": 1
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/9a46c161-fb6e-4a4f-8c8d-a91a3c7b99c2": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -945,7 +945,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_0.json": {
+        "process/a29d4d8a-e8bf-4e1a-aacc-eeea8f3b65d2": {
             "start_time": "2019/08/28",
             "process_core": {
                 "process_id": "lib_prep10"
@@ -960,7 +960,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_1.json": {
+        "process/b6e09f03-0ddc-44ff-8cc9-7caf9eb70f57": {
             "process_core": {
                 "process_id": "process_id_19"
             },
@@ -974,7 +974,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_2.json": {
+        "process/b3cddf6f-65ee-4aa8-8682-60f00c55be73": {
             "process_core": {
                 "process_id": "process_id_7"
             },
diff --git a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
index 66bf6d7b8..848545261 100644
--- a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
+++ b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
@@ -86,7 +86,7 @@
         }
     ],
     "metadata": {
-        "project_0.json": {
+        "project/93f6a42f-1790-4af4-b5d1-8c436cb6feae": {
             "content": {
                 "describedBy": "https://schema.humancellatlas.org/type/project/5.1.0/project",
                 "project_core": {
@@ -185,7 +185,7 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/603a818f-dbe7-466a-8241-58b9c1618846": {
             "content": {
                 "genus_species": [
                     {
@@ -216,7 +216,7 @@
                 "document_id": "603a818f-dbe7-466a-8241-58b9c1618846"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/4e41a067-dbb7-439f-b72f-80240ce858f6": {
             "content": {
                 "biomaterial_core": {
                     "has_input_biomaterial": "1139",
@@ -248,7 +248,7 @@
                 "document_id": "4e41a067-dbb7-439f-b72f-80240ce858f6"
             }
         },
-        "donor_organism_2.json": {
+        "donor_organism/bf8492ad-1d45-46aa-9fe9-67058b8c2410": {
             "content": {
                 "is_living": false,
                 "mus_musculus_specific": {
@@ -293,7 +293,7 @@
                 "document_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/d2f32681-9c1a-4dfd-b506-c24327afb8d1": {
             "content": {
                 "file_core": {
                     "file_name": "22011_1#268_1.fastq.gz",
@@ -309,7 +309,7 @@
                 "document_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/aa662c76-d220-49f4-8316-f4af5820d60b": {
             "content": {
                 "file_core": {
                     "file_name": "22011_1#268_2.fastq.gz",
@@ -325,7 +325,7 @@
                 "document_id": "aa662c76-d220-49f4-8316-f4af5820d60b"
             }
         },
-        "dissociation_process_0.json": {
+        "dissociation_process/b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -343,7 +343,7 @@
                 "document_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902"
             }
         },
-        "process_1.json": {
+        "process/f03590d8-4e65-478e-bc67-a8c64d2c93e9": {
             "content": {
                 "process_core": {
                     "process_id": "sampling_process_6"
@@ -358,7 +358,7 @@
                 "document_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9"
             }
         },
-        "enrichment_process_2.json": {
+        "enrichment_process/2f2fb366-249f-49e3-b47d-a0bb39d9bc78": {
             "content": {
                 "enrichment_method": "FACS",
                 "process_core": {
@@ -375,7 +375,7 @@
                 "document_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78"
             }
         },
-        "enrichment_process_3.json": {
+        "enrichment_process/a192f0d7-8e8e-48ae-b80d-3cb18acb3215": {
             "content": {
                 "enrichment_method": "FACS",
                 "process_core": {
@@ -392,7 +392,7 @@
                 "document_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215"
             }
         },
-        "library_preparation_process_4.json": {
+        "library_preparation_process/687065f3-c70f-46c3-8452-a5eead33a1bf": {
             "content": {
                 "input_nucleic_acid_molecule": {
                     "text": "polyA RNA",
@@ -421,7 +421,7 @@
                 "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
             }
         },
-        "sequencing_process_5.json": {
+        "sequencing_process/2580dcf9-3f7d-4421-b962-ab860e10d072": {
             "content": {
                 "paired_ends": true,
                 "instrument_manufacturer_model": {
@@ -446,7 +446,7 @@
                 "document_id": "2580dcf9-3f7d-4421-b962-ab860e10d072"
             }
         },
-        "protocol_0.json": {
+        "protocol/c9a1e203-bddc-45d3-87c4-6010be8e0127": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "Extracting cells from lymph nodes",
@@ -463,7 +463,7 @@
                 "document_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127"
             }
         },
-        "protocol_1.json": {
+        "protocol/a1c80daf-58b0-4b7a-8e29-d0130493c8e6": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "FACS sorting cells by surface markers",
@@ -480,7 +480,7 @@
                 "document_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6"
             }
         },
-        "protocol_2.json": {
+        "protocol/52d79a89-4b49-4c1b-b857-5cc5da07f643": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "Make/amplify cDNA for each cell",
@@ -501,7 +501,7 @@
                 "document_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643"
             }
         },
-        "protocol_3.json": {
+        "protocol/ca6096cf-13c1-4930-8308-6ab05865e2c9": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "Sequencing SmartSeq2 cells",
diff --git a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
index 9db2e962c..6c05e5811 100644
--- a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
+++ b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
@@ -158,7 +158,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/01ba6be9-ed4b-4c6b-ae05-2e06aadc2019": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.1.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -173,7 +173,7 @@
                 "update_date": "2019-05-14T12:00:06.941Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/74eb3cb5-918a-49fc-9e15-3ac49fd54caf": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.2.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -191,7 +191,7 @@
                 "update_date": "2019-05-14T11:46:47.512Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/63818269-c4d9-429b-85a3-db39c0dd7fa0": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.3.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -216,7 +216,7 @@
                 "update_date": "2019-05-14T11:29:50.173Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/61fd5348-92c5-446b-a57a-746330cebf76": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.0.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -230,7 +230,7 @@
                 "update_date": "2019-05-14T11:21:17.762Z"
             }
         },
-        "supplementary_file_0.json": {
+        "supplementary_file/e738a267-87fc-4070-abc7-b3be6442c6d0": {
             "describedBy": "https://schema.humancellatlas.org/type/file/2.0.0/supplementary_file",
             "schema_type": "file",
             "file_core": {
@@ -243,7 +243,7 @@
                 "update_date": "2019-05-14T11:01:15.816Z"
             }
         },
-        "supplementary_file_1.json": {
+        "supplementary_file/01a1d04b-05d0-4904-b627-68b0dc02bc17": {
             "describedBy": "https://schema.humancellatlas.org/type/file/2.0.0/supplementary_file",
             "schema_type": "file",
             "file_core": {
@@ -256,7 +256,7 @@
                 "update_date": "2019-05-14T11:01:09.564Z"
             }
         },
-        "project_0.json": {
+        "project/8c3c290d-dfff-4553-8868-54ce45f4ba7f": {
             "describedBy": "https://schema.humancellatlas.org/type/project/14.0.0/project",
             "schema_type": "project",
             "project_core": {
@@ -271,7 +271,7 @@
                 "update_date": "2019-05-14T11:20:51.382Z"
             }
         },
-        "process_0.json": {
+        "process/91f475ec-be51-4f1e-a904-74b10b7259f1": {
             "process_core": {
                 "process_id": "proc_21784_6#51"
             },
@@ -283,7 +283,7 @@
                 "update_date": "2019-05-14T12:10:53.274Z"
             }
         },
-        "process_1.json": {
+        "process/e521d67d-c134-4dbd-9555-29e23f0463c5": {
             "process_core": {
                 "process_id": "process_id_366"
             },
@@ -295,7 +295,7 @@
                 "update_date": "2019-05-14T12:27:20.135Z"
             }
         },
-        "process_2.json": {
+        "process/453a352c-94fb-4d3b-b609-df1e7abf8c09": {
             "process_core": {
                 "process_id": "process_id_24"
             },
diff --git a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
index 48c7229c8..ee5b99fb6 100644
--- a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
+++ b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
@@ -218,7 +218,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/e4c205cd-746f-4665-8c29-149c6e109e9d": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/11.0.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -258,7 +258,7 @@
                 "update_date": "2019-04-17T16:58:31.889Z"
             }
         },
-        "cell_line_0.json": {
+        "cell_line/961092cd-dcff-4b59-a0d2-ceeef0aece74": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/11.0.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -330,7 +330,7 @@
                 "update_date": "2019-04-17T16:57:09.605Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/a72a2ac2-c91b-406a-968c-28c8e15a2eaf": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/9.0.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -374,7 +374,7 @@
                 "update_date": "2019-04-17T16:55:13.039Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/6c6973d5-9b4a-426d-9d88-825b464500f8": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/14.0.7/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -412,7 +412,7 @@
                 "update_date": "2019-04-17T16:55:12.518Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/a31d51c9-7354-4c8c-91e6-a9d2a2e10616": {
             "describedBy": "https://schema.humancellatlas.org/type/file/8.0.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -426,7 +426,7 @@
                 "update_date": "2019-04-17T17:27:47.623Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/a2db643f-decd-426d-94db-13c3279ea80a": {
             "describedBy": "https://schema.humancellatlas.org/type/file/8.0.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -440,7 +440,7 @@
                 "update_date": "2019-04-17T17:27:46.767Z"
             }
         },
-        "project_0.json": {
+        "project/b6dc9b93-929a-45d0-beb2-5cf8e64872fe": {
             "describedBy": "https://schema.humancellatlas.org/type/project/11.1.0/project",
             "schema_type": "project",
             "project_core": {
@@ -684,7 +684,7 @@
                 "update_date": "2019-04-17T16:55:12.490Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/60085aee-e5a6-40ac-bda1-855c052550b5": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.0.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -712,7 +712,7 @@
                 "update_date": "2019-04-17T16:52:16.679Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/9ccabcf3-7203-4f07-837f-6dde903d4cec": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.0.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -737,7 +737,7 @@
                 "update_date": "2019-04-17T16:52:16.627Z"
             }
         },
-        "differentiation_protocol_0.json": {
+        "differentiation_protocol/348b04e9-d131-4d45-b198-0c75300ee4a3": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/1.3.3/differentiation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -752,7 +752,7 @@
                 "update_date": "2019-04-17T16:52:16.700Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/31b89ceb-0625-4f88-9623-85a18bbb84ee": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.0.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -771,7 +771,7 @@
                 "update_date": "2019-04-17T16:52:16.668Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/958d38c4-fd0a-4352-9b1d-d95e28e2085e": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/2.2.9/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -791,7 +791,7 @@
                 "update_date": "2019-04-17T16:52:16.605Z"
             }
         },
-        "process_0.json": {
+        "process/3d88118e-44df-4c1a-a364-bf92ff2ca0e6": {
             "process_core": {
                 "process_id": "D54Dn15E01"
             },
@@ -803,7 +803,7 @@
                 "update_date": "2019-04-17T17:02:01.452Z"
             }
         },
-        "process_1.json": {
+        "process/2fbc1012-55ae-4fde-9069-fbf5376ca535": {
             "process_core": {
                 "process_id": "process_id_601"
             },
@@ -815,7 +815,7 @@
                 "update_date": "2019-04-17T17:00:21.013Z"
             }
         },
-        "process_2.json": {
+        "process/466050f5-213c-4554-939e-4bb8298130dd": {
             "process_core": {
                 "process_id": "process_id_4"
             },
@@ -827,7 +827,7 @@
                 "update_date": "2019-04-17T16:59:59.704Z"
             }
         },
-        "process_3.json": {
+        "process/4276c1dd-50aa-4ffa-a618-dee757bff479": {
             "process_core": {
                 "process_id": "process_id_1"
             },
diff --git a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
index c1b4fb447..6114ac0e5 100644
--- a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
+++ b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
@@ -1034,7 +1034,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/9ea49dd1-7511-48f8-be12-237e3d0690c0": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.6.6/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1071,7 +1071,7 @@
                 "update_date": "2019-01-23T11:01:24.376Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/e7049663-aa57-4001-8bb4-870e341b4f0b": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/6.3.8/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1110,7 +1110,7 @@
                 "update_date": "2019-01-23T10:55:57.143Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/a879fffa-3b98-4204-ae5a-603180007ca0": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/12.0.5/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1148,7 +1148,7 @@
                 "update_date": "2019-01-23T10:40:40.695Z"
             }
         },
-        "analysis_file_0.json": {
+        "analysis_file/b91aca7b-e71b-4014-ab09-5d87e52bc305": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1161,7 +1161,7 @@
                 "update_date": "2019-02-02T06:49:43.861Z"
             }
         },
-        "analysis_file_1.json": {
+        "analysis_file/34e92010-0e2d-49af-b4b7-bed7a2c9e490": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1174,7 +1174,7 @@
                 "update_date": "2019-02-02T06:49:37.893Z"
             }
         },
-        "analysis_file_2.json": {
+        "analysis_file/3db4d80f-cbd5-45da-9048-6fe8e2e4d0d2": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1187,7 +1187,7 @@
                 "update_date": "2019-02-02T06:49:40.900Z"
             }
         },
-        "analysis_file_3.json": {
+        "analysis_file/ed37a61e-4449-4bce-a774-7cbd732781c8": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1200,7 +1200,7 @@
                 "update_date": "2019-02-02T06:49:40.853Z"
             }
         },
-        "analysis_file_4.json": {
+        "analysis_file/b70e4907-383c-4466-a244-3e7ce9890dae": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1213,7 +1213,7 @@
                 "update_date": "2019-02-02T06:49:43.860Z"
             }
         },
-        "analysis_file_5.json": {
+        "analysis_file/7ee496ab-286c-4962-919a-70244090e315": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1226,7 +1226,7 @@
                 "update_date": "2019-02-02T06:49:53.070Z"
             }
         },
-        "analysis_file_6.json": {
+        "analysis_file/c15427d1-e5b7-4bee-91fe-d98b04dc6a01": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1239,7 +1239,7 @@
                 "update_date": "2019-02-02T06:49:53.044Z"
             }
         },
-        "analysis_file_7.json": {
+        "analysis_file/b11e96c4-2472-4317-b45b-5bc1c9b55704": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1252,7 +1252,7 @@
                 "update_date": "2019-02-02T06:49:55.885Z"
             }
         },
-        "analysis_file_8.json": {
+        "analysis_file/828d7e40-4f6b-42e1-8cd2-6ddccb5b0e6c": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1265,7 +1265,7 @@
                 "update_date": "2019-02-02T06:49:55.882Z"
             }
         },
-        "analysis_file_9.json": {
+        "analysis_file/6804b943-fda7-4e8f-bfba-23e368843e63": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1278,7 +1278,7 @@
                 "update_date": "2019-02-02T06:49:58.883Z"
             }
         },
-        "analysis_file_10.json": {
+        "analysis_file/aeb5aebe-9e45-4c9d-931a-883f8fa71225": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1291,7 +1291,7 @@
                 "update_date": "2019-02-02T06:49:58.860Z"
             }
         },
-        "analysis_file_11.json": {
+        "analysis_file/7c5a87c1-e3b6-42aa-8d68-0f534ded7d2d": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1304,7 +1304,7 @@
                 "update_date": "2019-02-02T06:50:01.875Z"
             }
         },
-        "analysis_file_12.json": {
+        "analysis_file/87bd704c-3d36-4620-bdf2-5ad28c5a3d56": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1317,7 +1317,7 @@
                 "update_date": "2019-02-02T06:49:34.958Z"
             }
         },
-        "analysis_file_13.json": {
+        "analysis_file/0aa4b2f3-b969-40d7-97f9-f33af0088915": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1330,7 +1330,7 @@
                 "update_date": "2019-02-02T06:49:37.919Z"
             }
         },
-        "analysis_file_14.json": {
+        "analysis_file/697a869d-079b-48d4-9a7d-c04cf05dd0a9": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1343,7 +1343,7 @@
                 "update_date": "2019-02-02T06:49:46.903Z"
             }
         },
-        "analysis_file_15.json": {
+        "analysis_file/6d928f58-2e83-46a0-84a2-d08744a42abd": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1356,7 +1356,7 @@
                 "update_date": "2019-02-02T06:49:49.891Z"
             }
         },
-        "analysis_file_16.json": {
+        "analysis_file/cc958050-fd69-4919-8529-6f91552ce0ea": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1369,7 +1369,7 @@
                 "update_date": "2019-02-02T06:49:53.098Z"
             }
         },
-        "analysis_file_17.json": {
+        "analysis_file/0a5730dc-eeeb-4f25-bcc7-24cb7d15ac01": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1382,7 +1382,7 @@
                 "update_date": "2019-02-02T06:50:01.882Z"
             }
         },
-        "analysis_file_18.json": {
+        "analysis_file/42fffad8-d47d-4da5-8318-45b0f5577c08": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1395,7 +1395,7 @@
                 "update_date": "2019-02-02T06:50:04.892Z"
             }
         },
-        "analysis_file_19.json": {
+        "analysis_file/2842a995-c205-4d80-959f-fcb9ff8719ee": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1408,7 +1408,7 @@
                 "update_date": "2019-02-02T06:50:04.900Z"
             }
         },
-        "analysis_file_20.json": {
+        "analysis_file/90d148ed-a6eb-44c3-a398-df29459943ff": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1421,7 +1421,7 @@
                 "update_date": "2019-02-02T06:50:07.892Z"
             }
         },
-        "analysis_file_21.json": {
+        "analysis_file/269a143b-a2c2-40cd-9394-41a13321581d": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1434,7 +1434,7 @@
                 "update_date": "2019-02-02T06:50:10.886Z"
             }
         },
-        "analysis_file_22.json": {
+        "analysis_file/1dda8255-de1c-4bfa-aa79-dbc501d3a112": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1447,7 +1447,7 @@
                 "update_date": "2019-02-02T06:50:10.905Z"
             }
         },
-        "analysis_file_23.json": {
+        "analysis_file/d76f404c-d294-49f2-bfd5-d475e08fa783": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1460,7 +1460,7 @@
                 "update_date": "2019-02-02T06:50:13.892Z"
             }
         },
-        "analysis_file_24.json": {
+        "analysis_file/3f672b26-ea2f-4e94-ba77-f463c3cb7c38": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1473,7 +1473,7 @@
                 "update_date": "2019-02-02T06:50:13.961Z"
             }
         },
-        "analysis_file_25.json": {
+        "analysis_file/4bc5b41c-9fea-4baa-9bf9-75fa4f4a9818": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1486,7 +1486,7 @@
                 "update_date": "2019-02-02T06:50:13.945Z"
             }
         },
-        "analysis_file_26.json": {
+        "analysis_file/3e44e8f9-e76d-4158-a7af-eeb9602cf8cc": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1499,7 +1499,7 @@
                 "update_date": "2019-02-02T06:50:16.898Z"
             }
         },
-        "analysis_file_27.json": {
+        "analysis_file/3fe1e9e8-1b0f-4683-a402-ae970b33f144": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1512,7 +1512,7 @@
                 "update_date": "2019-02-02T06:50:16.905Z"
             }
         },
-        "analysis_file_28.json": {
+        "analysis_file/e53c14f5-1a4f-44d6-9773-53faac32233b": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1525,7 +1525,7 @@
                 "update_date": "2019-02-02T06:50:19.912Z"
             }
         },
-        "analysis_file_29.json": {
+        "analysis_file/7a26e63d-fcf2-419a-a945-bca9e539480f": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1538,7 +1538,7 @@
                 "update_date": "2019-02-02T06:50:19.912Z"
             }
         },
-        "analysis_file_30.json": {
+        "analysis_file/644b261b-450e-453c-bb5e-0498a1cf5804": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1551,7 +1551,7 @@
                 "update_date": "2019-02-02T06:50:22.891Z"
             }
         },
-        "analysis_file_31.json": {
+        "analysis_file/b367129a-e83f-4a2b-9278-b5f7930ad457": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1564,7 +1564,7 @@
                 "update_date": "2019-02-02T06:50:22.873Z"
             }
         },
-        "analysis_file_32.json": {
+        "analysis_file/6d4785d0-bd42-4f98-8f7a-ab9ca8fcab39": {
             "describedBy": "https://schema.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1577,7 +1577,7 @@
                 "update_date": "2019-02-02T06:50:25.954Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/c15ee840-4702-45f7-bb19-693de19a742a": {
             "describedBy": "https://schema.humancellatlas.org/type/file/7.0.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1595,7 +1595,7 @@
                 "update_date": "2019-01-23T16:20:56.497Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/5f5d9c84-3565-4398-886c-2e50ad4c3964": {
             "describedBy": "https://schema.humancellatlas.org/type/file/7.0.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1613,7 +1613,7 @@
                 "update_date": "2019-01-23T16:20:53.469Z"
             }
         },
-        "project_0.json": {
+        "project/aabbec1a-1215-43e1-8e42-6489af25c12c": {
             "describedBy": "https://schema.humancellatlas.org/type/project/9.0.8/project",
             "schema_type": "project",
             "project_core": {
@@ -1836,7 +1836,7 @@
                 "update_date": "2019-01-23T10:40:40.301Z"
             }
         },
-        "analysis_protocol_0.json": {
+        "analysis_protocol/bb17ee61-193e-4ae1-a014-4f1b1c19b8b7": {
             "computational_method": "SmartSeq2SingleCell",
             "describedBy": "https://schema.humancellatlas.org/type/protocol/analysis/8.0.3/analysis_protocol",
             "protocol_core": {
@@ -1852,7 +1852,7 @@
                 "update_date": "2019-02-02T06:45:04.641Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/edda2708-1172-47f0-9c8b-b6771f463db1": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/4.4.4/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1884,7 +1884,7 @@
                 "update_date": "2019-01-23T10:34:05.563Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/46f58d61-c784-47fb-9c75-7af37871810e": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/9.0.8/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1909,7 +1909,7 @@
                 "update_date": "2019-01-23T10:34:05.670Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/dcfe8429-af02-491e-96e9-4ac0569cd5d1": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/2.2.8/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1929,7 +1929,7 @@
                 "update_date": "2019-01-23T10:34:05.632Z"
             }
         },
-        "enrichment_protocol_1.json": {
+        "enrichment_protocol/55dd1cfc-cc9c-4a03-aa43-2cb92b843253": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/2.2.8/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1950,7 +1950,7 @@
                 "update_date": "2019-01-23T10:34:06.540Z"
             }
         },
-        "enrichment_protocol_2.json": {
+        "enrichment_protocol/3d2707fa-83ad-472b-8282-7b6191f96bc2": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/2.2.8/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1971,7 +1971,7 @@
                 "update_date": "2019-01-23T10:34:05.715Z"
             }
         },
-        "enrichment_protocol_3.json": {
+        "enrichment_protocol/88bd21a4-8d6c-48ce-ab57-8b5e0b582cca": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/2.2.8/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1992,7 +1992,7 @@
                 "update_date": "2019-01-23T10:34:05.783Z"
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/477b201f-67f0-4f97-86d5-de32a7afc267": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/8.2.10/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -2012,7 +2012,7 @@
                 "update_date": "2019-01-23T10:34:05.575Z"
             }
         },
-        "analysis_process_0.json": {
+        "analysis_process/d6c56c65-bed0-4d6e-bf89-7e0d71bd3026": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/8.0.3/analysis_process",
             "input_bundles": [
@@ -2456,7 +2456,7 @@
                 "update_date": "2019-02-02T06:45:04.794Z"
             }
         },
-        "process_0.json": {
+        "process/55faef19-0c09-41ef-b21c-ad25a89ea2e3": {
             "insdc_experiment": {
                 "insdc_experiment": "ERX2481489"
             },
@@ -2471,7 +2471,7 @@
                 "update_date": "2019-01-23T11:19:16.982Z"
             }
         },
-        "process_1.json": {
+        "process/e84cac5b-1467-4055-a029-48d67a5505d6": {
             "process_core": {
                 "process_id": "process_id_5845"
             },
@@ -2483,7 +2483,7 @@
                 "update_date": "2019-01-23T11:10:57.210Z"
             }
         },
-        "process_2.json": {
+        "process/832b39e3-ebba-4686-a724-52babb96056f": {
             "process_core": {
                 "process_id": "process_id_21"
             },
diff --git a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
index 89a5d0c41..67e2712d8 100644
--- a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
+++ b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
@@ -182,7 +182,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/ef97eef1-a436-4462-a152-1a2b86ee8831": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -217,7 +217,7 @@
                 "update_date": "2018-10-07T12:04:46.292Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/80cb479b-dcb4-4dbb-a75d-0249a964bb70": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -252,7 +252,7 @@
                 "update_date": "2018-10-07T12:01:39.672Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/6c992ba4-c132-4dd3-840e-13cf3f38243e": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -296,7 +296,7 @@
                 "update_date": "2018-10-07T12:00:40.749Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/f3d5c7cb-7ab4-4903-8e0e-dc942121fe27": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -314,7 +314,7 @@
                 "update_date": "2018-10-07T12:08:49.204Z"
             }
         },
-        "project_0.json": {
+        "project/519b58ef-6462-4ed3-8c0d-375b54f53c31": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/project/9.0.3/project",
             "schema_type": "project",
             "project_core": {
@@ -411,7 +411,7 @@
                 "update_date": "2018-10-07T12:00:40.290Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/5f82b9c4-f3d7-410c-b843-0e5cdec9efa5": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/4.3.3/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -446,7 +446,7 @@
                 "update_date": "2018-10-07T11:58:50.532Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/d678165b-2753-4393-bf3b-5e2a09ba892c": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -469,7 +469,7 @@
                 "update_date": "2018-10-07T11:58:50.511Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/920078d0-b17e-4f23-8cf6-0674b19e7bec": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -488,7 +488,7 @@
                 "update_date": "2018-10-07T11:58:50.432Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/644c5f2d-33c8-4bf4-b411-b2dbec8b8227": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -508,7 +508,7 @@
                 "update_date": "2018-10-07T11:58:50.413Z"
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/403b586f-fd8d-45f2-a431-4bb6cc33d7d4": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/8.2.6/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -527,7 +527,7 @@
                 "update_date": "2018-10-07T11:58:50.563Z"
             }
         },
-        "enrichment_protocol_1.json": {
+        "enrichment_protocol/9ab53e6a-464e-44b1-aa24-12daca989969": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -546,7 +546,7 @@
                 "update_date": "2018-10-07T11:58:50.474Z"
             }
         },
-        "process_0.json": {
+        "process/18d49b08-d095-4371-bb34-151037f9f461": {
             "insdc_experiment": {
                 "insdc_experiment": "SRX3366459"
             },
@@ -561,7 +561,7 @@
                 "update_date": "2018-10-07T12:08:28.754Z"
             }
         },
-        "process_1.json": {
+        "process/d13a5a85-b8c7-4a07-9c0c-9180bd0a78eb": {
             "process_core": {
                 "process_id": "process_id_2255"
             },
@@ -573,7 +573,7 @@
                 "update_date": "2018-10-07T12:06:52.636Z"
             }
         },
-        "process_2.json": {
+        "process/5a15ed38-5e37-44ff-ba35-0d17bb8564bd": {
             "process_core": {
                 "process_location": "Sri Lanka",
                 "process_id": "process_id_15"
diff --git a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
index b127a2a0d..0ebf42876 100644
--- a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
+++ b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
@@ -182,7 +182,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/a31a0e93-5be4-44b8-b152-9e25b066e1e5": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.4.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -197,7 +197,7 @@
                 "update_date": "2018-09-05T18:24:09.865Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/e964f81f-54d9-4600-a9e9-981b1f1a6ca2": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.2.7/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -234,7 +234,7 @@
                 "update_date": "2018-09-05T18:24:10.111Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/c6001597-990c-4753-80bb-c5a01c9dda0d": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.0.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -260,7 +260,7 @@
                 "update_date": "2018-09-05T18:24:09.957Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/20474552-c0a3-471e-8fa0-d3c5aa05c017": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/6.5.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -275,7 +275,7 @@
                 "update_date": "2018-09-05T18:25:10.415Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/177a9d2c-99d4-4fb6-aab7-5869923e9d6a": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/6.5.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -290,7 +290,7 @@
                 "update_date": "2018-09-05T18:25:10.316Z"
             }
         },
-        "project_0.json": {
+        "project/bedfd14f-cc98-4142-b627-d44dfec5aced": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/project/9.0.0/project",
             "schema_type": "project",
             "project_core": {
@@ -311,7 +311,7 @@
                 "update_date": "2018-09-05T18:24:10.105Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/f77e65be-ca7a-4711-a7a9-701ad372901a": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/4.3.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -334,7 +334,7 @@
                 "update_date": "2018-09-05T18:24:09.959Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/9d3c0c92-2716-410b-85c6-963a29c24fe0": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/9.0.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -354,7 +354,7 @@
                 "update_date": "2018-09-05T18:24:09.960Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/d08422cf-7d04-46cd-9452-394bb2864ba7": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.1/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -371,7 +371,7 @@
                 "update_date": "2018-09-05T18:24:10.036Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/f3304cfe-c133-444c-a2db-92294d3f6a4d": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.3/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -387,7 +387,7 @@
                 "update_date": "2018-09-05T18:24:09.887Z"
             }
         },
-        "process_0.json": {
+        "process/bf7360ae-511e-4803-821e-c03167107588": {
             "process_core": {
                 "process_id": "sequence_process_file_1"
             },
@@ -399,7 +399,7 @@
                 "update_date": "2018-09-05T18:24:09.872Z"
             }
         },
-        "process_1.json": {
+        "process/b78f4279-9c6f-49da-890f-98499d8fb84a": {
             "process_core": {
                 "process_id": "process_id_2"
             },
@@ -411,7 +411,7 @@
                 "update_date": "2018-09-05T18:24:09.856Z"
             }
         },
-        "process_2.json": {
+        "process/6284381f-de72-4015-ae51-fa17e13677f8": {
             "process_core": {
                 "process_id": "process_id_1"
             },
diff --git a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
index c8824d066..35df6b74a 100644
--- a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
+++ b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
@@ -5570,7 +5570,7 @@
         }
     ],
     "metadata": {
-        "imaged_specimen_0.json": {
+        "imaged_specimen/87f58f88-ef8b-4323-bd19-cde1a2497b59": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/2.0.7/imaged_specimen",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -5596,7 +5596,7 @@
                 "update_date": "2019-04-03T10:13:50.866Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/edd1d525-a6ae-4658-a6bf-6c31d7ab6948": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -5630,7 +5630,7 @@
                 "update_date": "2019-04-03T10:13:45.512Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/6cb9fc09-7755-4a35-b6b1-0d6fe696b2d4": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/14.0.7/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -5683,7 +5683,7 @@
                 "update_date": "2019-04-03T10:13:45.427Z"
             }
         },
-        "image_file_0.json": {
+        "image_file/6baa3aff-b2a5-4e49-82f7-25c108a6107a": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5696,7 +5696,7 @@
                 "update_date": "2019-04-03T10:15:44.995Z"
             }
         },
-        "image_file_1.json": {
+        "image_file/06dcfc33-21da-485f-8e50-49d294713a9e": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5709,7 +5709,7 @@
                 "update_date": "2019-04-03T10:15:44.993Z"
             }
         },
-        "image_file_2.json": {
+        "image_file/404dd50b-4bc9-4c82-8c18-f53c68eed2fc": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5722,7 +5722,7 @@
                 "update_date": "2019-04-03T10:15:51.032Z"
             }
         },
-        "image_file_3.json": {
+        "image_file/5ceb5dc3-9194-494a-b1df-42bb75ab1a04": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5735,7 +5735,7 @@
                 "update_date": "2019-04-03T10:15:47.812Z"
             }
         },
-        "image_file_4.json": {
+        "image_file/76e52f76-ede7-4088-b7f6-d6e5f6152292": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5748,7 +5748,7 @@
                 "update_date": "2019-04-03T10:15:51.115Z"
             }
         },
-        "image_file_5.json": {
+        "image_file/2e496fe6-f500-4e27-b7f5-3c87fe43bbe5": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5761,7 +5761,7 @@
                 "update_date": "2019-04-03T10:15:54.073Z"
             }
         },
-        "image_file_6.json": {
+        "image_file/be66141d-84a3-457d-a8d2-2f0da8c91dff": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5774,7 +5774,7 @@
                 "update_date": "2019-04-03T10:15:51.125Z"
             }
         },
-        "image_file_7.json": {
+        "image_file/680cf532-ef0c-4155-b44d-a6ec3920743a": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5787,7 +5787,7 @@
                 "update_date": "2019-04-03T10:15:50.982Z"
             }
         },
-        "image_file_8.json": {
+        "image_file/08609f14-cf43-4188-b743-4a0b55b17347": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5800,7 +5800,7 @@
                 "update_date": "2019-04-03T10:15:47.817Z"
             }
         },
-        "image_file_9.json": {
+        "image_file/d10827a1-38f7-457d-9c9f-695f2fc7689c": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5813,7 +5813,7 @@
                 "update_date": "2019-04-03T10:15:44.996Z"
             }
         },
-        "image_file_10.json": {
+        "image_file/6f8eb2e5-7a0c-4c98-8da0-276457357071": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5826,7 +5826,7 @@
                 "update_date": "2019-04-03T10:15:47.821Z"
             }
         },
-        "image_file_11.json": {
+        "image_file/ca480df3-71bb-4634-8f71-b6a75aeb9f05": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5839,7 +5839,7 @@
                 "update_date": "2019-04-03T10:15:47.796Z"
             }
         },
-        "image_file_12.json": {
+        "image_file/03ae5f5e-65ac-4491-b0ce-eefc940e0224": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5852,7 +5852,7 @@
                 "update_date": "2019-04-03T10:15:48.018Z"
             }
         },
-        "image_file_13.json": {
+        "image_file/ff117ecb-767e-4e72-baa9-2bda4fcd3e62": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5865,7 +5865,7 @@
                 "update_date": "2019-04-03T10:15:51.040Z"
             }
         },
-        "image_file_14.json": {
+        "image_file/887f3d73-94d2-44ac-9047-67aca5225882": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5878,7 +5878,7 @@
                 "update_date": "2019-04-03T10:15:51.029Z"
             }
         },
-        "image_file_15.json": {
+        "image_file/896dfacd-206b-4e4f-a846-ba5b070060d9": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5891,7 +5891,7 @@
                 "update_date": "2019-04-03T10:15:47.819Z"
             }
         },
-        "image_file_16.json": {
+        "image_file/23303c88-01b1-47d0-b770-dca6802caa13": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5904,7 +5904,7 @@
                 "update_date": "2019-04-03T10:15:47.812Z"
             }
         },
-        "image_file_17.json": {
+        "image_file/3c1a388d-0577-4417-9cd2-ff33bfed9140": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5917,7 +5917,7 @@
                 "update_date": "2019-04-03T10:15:47.821Z"
             }
         },
-        "image_file_18.json": {
+        "image_file/67e71b34-7157-4a37-b495-0d740772b480": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5930,7 +5930,7 @@
                 "update_date": "2019-04-03T10:15:51.111Z"
             }
         },
-        "image_file_19.json": {
+        "image_file/cd3e5e62-6145-42d9-9a5b-046e1b49cf26": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5943,7 +5943,7 @@
                 "update_date": "2019-04-03T10:15:51.054Z"
             }
         },
-        "image_file_20.json": {
+        "image_file/5fbcb75e-3ee3-4429-8ede-b243afa0789f": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5956,7 +5956,7 @@
                 "update_date": "2019-04-03T10:15:51.028Z"
             }
         },
-        "image_file_21.json": {
+        "image_file/09226b24-6b11-4e4f-8052-2b544be461aa": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5969,7 +5969,7 @@
                 "update_date": "2019-04-03T10:15:51.126Z"
             }
         },
-        "image_file_22.json": {
+        "image_file/f67473fd-fbf8-4d69-9db1-556938ab5b87": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5982,7 +5982,7 @@
                 "update_date": "2019-04-03T10:15:54.317Z"
             }
         },
-        "image_file_23.json": {
+        "image_file/16acc1f2-9f1c-43c8-8ffe-4a9ea674e6ff": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
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             "file_core": {
@@ -8075,7 +8075,7 @@
                 "update_date": "2019-04-03T10:15:57.644Z"
             }
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-        "image_file_184.json": {
+        "image_file/f5ce7a96-cfc0-42c4-852b-386f9a27111d": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8088,7 +8088,7 @@
                 "update_date": "2019-04-03T10:16:00.829Z"
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-        "image_file_185.json": {
+        "image_file/8bc05db7-bd23-4a10-9761-96be7b8ef9ee": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8101,7 +8101,7 @@
                 "update_date": "2019-04-03T10:16:00.329Z"
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         },
-        "image_file_186.json": {
+        "image_file/3dff4add-7d6f-418c-afba-e46864af51d2": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8114,7 +8114,7 @@
                 "update_date": "2019-04-03T10:16:00.156Z"
             }
         },
-        "image_file_187.json": {
+        "image_file/ab2b7c67-8f13-4388-acd7-e2abb0091f30": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8127,7 +8127,7 @@
                 "update_date": "2019-04-03T10:16:00.743Z"
             }
         },
-        "image_file_188.json": {
+        "image_file/d9912d93-3d92-48d2-9f75-826fbba3d94e": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8140,7 +8140,7 @@
                 "update_date": "2019-04-03T10:16:03.046Z"
             }
         },
-        "image_file_189.json": {
+        "image_file/8b37aba2-be5e-4963-8e6f-51a2df8e143e": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8153,7 +8153,7 @@
                 "update_date": "2019-04-03T10:16:00.282Z"
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-        "image_file_190.json": {
+        "image_file/81c0e4e2-9021-4c4d-9876-1ed5b78ca7a7": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8166,7 +8166,7 @@
                 "update_date": "2019-04-03T10:16:00.805Z"
             }
         },
-        "image_file_191.json": {
+        "image_file/2d7e88dd-bddd-4289-9556-27d301be0b83": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8179,7 +8179,7 @@
                 "update_date": "2019-04-03T10:16:03.188Z"
             }
         },
-        "image_file_192.json": {
+        "image_file/0c1c578d-d4cc-40bb-a54d-d1d4d004373f": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8192,7 +8192,7 @@
                 "update_date": "2019-04-03T10:16:03.221Z"
             }
         },
-        "image_file_193.json": {
+        "image_file/9dc0ead3-f17a-4bb8-88e2-87f779029ff8": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8205,7 +8205,7 @@
                 "update_date": "2019-04-03T10:16:00.822Z"
             }
         },
-        "image_file_194.json": {
+        "image_file/f618a8bc-5e07-477f-a6d3-1b0af8c81ff0": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8218,7 +8218,7 @@
                 "update_date": "2019-04-03T10:16:03.130Z"
             }
         },
-        "image_file_195.json": {
+        "image_file/e834d3df-8432-40ba-b67d-c7cd0bd7328d": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8231,7 +8231,7 @@
                 "update_date": "2019-04-03T10:16:03.234Z"
             }
         },
-        "image_file_196.json": {
+        "image_file/d8908d6d-5daa-454d-9082-726054cfddc1": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8244,7 +8244,7 @@
                 "update_date": "2019-04-03T10:16:03.189Z"
             }
         },
-        "image_file_197.json": {
+        "image_file/c5a7142e-4702-4e84-b7aa-239df2a71ba8": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8257,7 +8257,7 @@
                 "update_date": "2019-04-03T10:16:00.189Z"
             }
         },
-        "image_file_198.json": {
+        "image_file/f69e44ef-cf23-4571-8dad-e44222697974": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8270,7 +8270,7 @@
                 "update_date": "2019-04-03T10:16:03.186Z"
             }
         },
-        "image_file_199.json": {
+        "image_file/ea72f81c-2c58-43e2-acca-294254f470f7": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8283,7 +8283,7 @@
                 "update_date": "2019-04-03T10:16:03.138Z"
             }
         },
-        "image_file_200.json": {
+        "image_file/89d1d2b5-81d3-487d-9fc1-d8b1d8ac34ab": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8296,7 +8296,7 @@
                 "update_date": "2019-04-03T10:16:03.194Z"
             }
         },
-        "image_file_201.json": {
+        "image_file/6928ac1b-fd1d-436c-bfc6-4087c65809d7": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8309,7 +8309,7 @@
                 "update_date": "2019-04-03T10:16:03.234Z"
             }
         },
-        "image_file_202.json": {
+        "image_file/07a7b938-435b-4804-b140-c255957b6532": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8322,7 +8322,7 @@
                 "update_date": "2019-04-03T10:16:03.185Z"
             }
         },
-        "image_file_203.json": {
+        "image_file/3d532a7b-55e7-4461-afbc-65ef76403384": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8335,7 +8335,7 @@
                 "update_date": "2019-04-03T10:16:00.225Z"
             }
         },
-        "image_file_204.json": {
+        "image_file/bab40245-28bd-49a2-8be0-ba109fe41c91": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8348,7 +8348,7 @@
                 "update_date": "2019-04-03T10:16:03.171Z"
             }
         },
-        "image_file_205.json": {
+        "image_file/9d577bd4-3a27-48be-ad7c-8c44cf803cda": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8361,7 +8361,7 @@
                 "update_date": "2019-04-03T10:16:03.221Z"
             }
         },
-        "image_file_206.json": {
+        "image_file/c4de7605-fec5-4389-bb9e-f2ea0c41cdef": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8374,7 +8374,7 @@
                 "update_date": "2019-04-03T10:16:03.221Z"
             }
         },
-        "image_file_207.json": {
+        "image_file/21a043b6-6dde-41b9-b20e-74b961da8b88": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8387,7 +8387,7 @@
                 "update_date": "2019-04-03T10:16:03.210Z"
             }
         },
-        "image_file_208.json": {
+        "image_file/11280200-1803-4110-aa84-2808776c2d50": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8400,7 +8400,7 @@
                 "update_date": "2019-04-03T10:16:03.231Z"
             }
         },
-        "image_file_209.json": {
+        "image_file/86df5269-576b-4d18-a0ce-6e2b2a36d51b": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8413,7 +8413,7 @@
                 "update_date": "2019-04-03T10:16:03.201Z"
             }
         },
-        "image_file_210.json": {
+        "image_file/e524ff4e-95fa-4561-bfd3-276cba79e664": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8426,7 +8426,7 @@
                 "update_date": "2019-04-03T10:16:03.251Z"
             }
         },
-        "image_file_211.json": {
+        "image_file/3d5737da-b1ab-48cb-a26f-d420e53edccd": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8439,7 +8439,7 @@
                 "update_date": "2019-04-03T10:16:03.057Z"
             }
         },
-        "image_file_212.json": {
+        "image_file/44cf15ec-3d4e-4698-bb14-107c34891191": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8452,7 +8452,7 @@
                 "update_date": "2019-04-03T10:16:03.206Z"
             }
         },
-        "image_file_213.json": {
+        "image_file/6242cdf3-fd6d-4479-a08a-1747818fd978": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8465,7 +8465,7 @@
                 "update_date": "2019-04-03T10:16:03.054Z"
             }
         },
-        "image_file_214.json": {
+        "image_file/bc60bbd4-8b09-425c-b507-9da24a84f412": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8478,7 +8478,7 @@
                 "update_date": "2019-04-03T10:16:00.270Z"
             }
         },
-        "image_file_215.json": {
+        "image_file/1f054ccf-f8dd-4127-a6f8-c577d7dd93dc": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8491,7 +8491,7 @@
                 "update_date": "2019-04-03T10:16:03.187Z"
             }
         },
-        "image_file_216.json": {
+        "image_file/9954cb4b-b0a4-4479-b31d-0bee1e75d9c7": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8504,7 +8504,7 @@
                 "update_date": "2019-04-03T10:16:03.267Z"
             }
         },
-        "image_file_217.json": {
+        "image_file/5f67c32c-a154-4620-8603-0b64979b04a4": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8517,7 +8517,7 @@
                 "update_date": "2019-04-03T10:16:03.116Z"
             }
         },
-        "image_file_218.json": {
+        "image_file/7d5bffb2-8bf9-4366-a8b2-762ebb4d6c5d": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8530,7 +8530,7 @@
                 "update_date": "2019-04-03T10:16:00.148Z"
             }
         },
-        "image_file_219.json": {
+        "image_file/dcee6df0-9e87-4935-8873-f8d30d449d76": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8543,7 +8543,7 @@
                 "update_date": "2019-04-03T10:16:03.250Z"
             }
         },
-        "image_file_220.json": {
+        "image_file/7d6bdde6-523f-46cb-bed5-d6cfa8fea80c": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8556,7 +8556,7 @@
                 "update_date": "2019-04-03T10:16:03.126Z"
             }
         },
-        "image_file_221.json": {
+        "image_file/e6d00b0c-3641-4ec4-a553-8fd742193dba": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8569,7 +8569,7 @@
                 "update_date": "2019-04-03T10:16:03.321Z"
             }
         },
-        "image_file_222.json": {
+        "image_file/e5034863-0528-4f55-be95-c8501c29f9fe": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8582,7 +8582,7 @@
                 "update_date": "2019-04-03T10:16:03.187Z"
             }
         },
-        "image_file_223.json": {
+        "image_file/cc61b14a-59d9-477b-8cb1-43c4ee4cf434": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8595,7 +8595,7 @@
                 "update_date": "2019-04-03T10:16:03.190Z"
             }
         },
-        "image_file_224.json": {
+        "image_file/33d332c9-aefe-4db5-8830-b8daddaed0d2": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8608,7 +8608,7 @@
                 "update_date": "2019-04-03T10:16:03.189Z"
             }
         },
-        "image_file_225.json": {
+        "image_file/bb3b6fc7-0902-432d-bad1-6b3f61951314": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8621,7 +8621,7 @@
                 "update_date": "2019-04-03T10:15:51.086Z"
             }
         },
-        "image_file_226.json": {
+        "image_file/2b734e88-3a33-4c73-92bb-82e0b8f8c13b": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8634,7 +8634,7 @@
                 "update_date": "2019-04-03T10:16:00.280Z"
             }
         },
-        "project_0.json": {
+        "project/ae5237b4-633f-403a-afc6-cb87e6f90db1": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/project/11.0.1/project",
             "schema_type": "project",
             "project_core": {
@@ -8658,7 +8658,7 @@
                 "update_date": "2019-04-03T10:13:45.439Z"
             }
         },
-        "imaging_protocol_0.json": {
+        "imaging_protocol/96ecb94d-e848-4d7b-8df9-f19af6ab17b8": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/imaging/11.0.12/imaging_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -11609,7 +11609,7 @@
                 "update_date": "2019-04-03T10:13:45.902Z"
             }
         },
-        "imaging_preparation_protocol_0.json": {
+        "imaging_preparation_protocol/a6d431b0-4373-4eaf-a3af-8c3fe461ab38": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/imaging/2.0.3/imaging_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -11627,7 +11627,7 @@
                 "update_date": "2019-04-03T10:13:45.426Z"
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/caf94c25-8327-4379-b88e-2a6642cd7513": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/9.0.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -11646,7 +11646,7 @@
                 "update_date": "2019-04-03T10:13:45.505Z"
             }
         },
-        "process_0.json": {
+        "process/da265acd-5601-49c5-855e-d792d51b4042": {
             "process_core": {
                 "process_id": "zador_baristaseq_1"
             },
@@ -11658,7 +11658,7 @@
                 "update_date": "2019-04-03T10:14:03.513Z"
             }
         },
-        "process_1.json": {
+        "process/07acb7d0-3f1c-47f7-9ef9-851c4f1caaec": {
             "process_core": {
                 "process_id": "process_id_2"
             },
@@ -11670,7 +11670,7 @@
                 "update_date": "2019-04-03T10:13:53.863Z"
             }
         },
-        "process_2.json": {
+        "process/fee8a188-5783-44cd-a1c1-ed9d5d7c32a9": {
             "process_core": {
                 "process_id": "process_id_1"
             },
diff --git a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
index ee4eba07a..07903af74 100644
--- a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
+++ b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
@@ -218,7 +218,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/74a06f8b-dff1-44d2-b1a6-99e3d14b69d1": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -266,7 +266,7 @@
                 "update_date": "2019-03-17T22:01:03.482Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/f3531ee2-d408-4075-b63e-0d0e2b01116c": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/7.0.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -314,7 +314,7 @@
                 "update_date": "2019-03-17T22:01:03.535Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/20db3238-9ce6-4820-8495-6753e4147d51": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/14.0.3/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -397,7 +397,7 @@
                 "update_date": "2019-03-17T22:01:03.211Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/6380c3bc-8bc3-459b-aea3-05dd6c0842ef": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/7.0.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -417,7 +417,7 @@
                 "update_date": "2019-03-17T22:03:04.130Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/ceb4dfaa-ecaf-4757-ae54-9d83707f66cc": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/7.0.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -437,7 +437,7 @@
                 "update_date": "2019-03-17T22:03:06.010Z"
             }
         },
-        "sequence_file_2.json": {
+        "sequence_file/5201d410-d789-4df6-b3fd-9edac998e5f3": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/7.0.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -457,7 +457,7 @@
                 "update_date": "2019-03-17T22:03:03.738Z"
             }
         },
-        "project_0.json": {
+        "project/5014cd10-bbed-4e85-bc45-6fe3a8a0079b": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/project/11.0.0/project",
             "schema_type": "project",
             "project_core": {
@@ -516,7 +516,7 @@
                 "update_date": "2019-03-17T22:01:03.175Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/aa7e9a08-2a0c-4575-a9a9-13cab4e96e73": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/sequencing/4.4.6/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -557,7 +557,7 @@
                 "update_date": "2019-03-17T22:01:03.138Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/4bc436f7-e429-4355-8d6e-853d8e639b37": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/sequencing/9.0.11/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -591,7 +591,7 @@
                 "update_date": "2019-03-17T22:01:02.999Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/1e9abdf3-54da-4c73-9e57-1297ceb39399": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.8/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -613,7 +613,7 @@
                 "update_date": "2019-03-17T22:01:03.046Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/df679627-ccb6-426d-a709-c259db607d84": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.9/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -638,7 +638,7 @@
                 "update_date": "2019-03-17T22:01:03.051Z"
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/c3dabd8c-6f32-4c0b-a13b-11bb71cc95de": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/8.2.11/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -670,7 +670,7 @@
                 "update_date": "2019-03-17T22:01:03.060Z"
             }
         },
-        "process_0.json": {
+        "process/8a0879df-13e0-4dce-9776-20fb259796e9": {
             "process_core": {
                 "process_id": "bundle1"
             },
@@ -682,7 +682,7 @@
                 "update_date": "2019-03-17T22:01:03.421Z"
             }
         },
-        "process_1.json": {
+        "process/b2e86d49-6874-4522-a68c-43166e858bdd": {
             "process_core": {
                 "process_id": "process_id_2"
             },
@@ -694,7 +694,7 @@
                 "update_date": "2019-03-17T22:01:03.392Z"
             }
         },
-        "process_2.json": {
+        "process/b147df84-443b-4dd2-8327-7ea42adcd151": {
             "process_core": {
                 "process_id": "process_id_1"
             },
diff --git a/test/hca_metadata_api/test.py b/test/hca_metadata_api/test.py
index fd4b28e77..fa8398219 100644
--- a/test/hca_metadata_api/test.py
+++ b/test/hca_metadata_api/test.py
@@ -35,6 +35,9 @@
     one,
 )
 
+from azul.indexer.document import (
+    EntityReference,
+)
 from azul_test_case import (
     AzulUnitTestCase,
 )
@@ -573,10 +576,11 @@ def test_project_fields(self):
         uuid = '68bdc676-c442-4581-923e-319c1c2d9018'
         version = '2018-10-07T130111.835234Z'
         manifest, metadata, links = self._canned_bundle('staging', uuid, version)
+        project_id = '519b58ef-6462-4ed3-8c0d-375b54f53c31'
 
         def assert_bundle():
             bundle = Bundle(uuid, version, manifest, metadata, links)
-            project = bundle.projects[UUID('519b58ef-6462-4ed3-8c0d-375b54f53c31')]
+            project = bundle.projects[UUID(project_id)]
             self.assertEqual(len(project.publications), 1)
             publication = project.publications.pop()
             title = 'Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis.'
@@ -594,10 +598,10 @@ def assert_bundle():
             self.assertEqual(project.supplementary_links, supplementary_links)
 
         assert_bundle()
-
-        for publication in metadata['project_0.json']['publications']:
+        project_metadata = metadata[f'project/{project_id}']
+        for publication in project_metadata['publications']:
             self._rename_keys(publication, title='publication_title', url='publication_url')
-        for contributor in metadata['project_0.json']['contributors']:
+        for contributor in project_metadata['contributors']:
             if 'project_role' in contributor:
                 contributor['project_role'] = dict(text=contributor['project_role'])
 
@@ -607,10 +611,11 @@ def test_project_contact(self):
         uuid = '6b498499-c5b4-452f-9ff9-2318dbb86000'
         version = '2019-01-03T163633.780215Z'
         manifest, metadata, links = self._canned_bundle('prod', uuid, version)
+        project_id = 'd96c2451-6e22-441f-a3e6-70fd0878bb1b'
 
         def assert_bundle():
             bundle = Bundle(uuid, version, manifest, metadata, links)
-            project = bundle.projects[UUID('d96c2451-6e22-441f-a3e6-70fd0878bb1b')]
+            project = bundle.projects[UUID(project_id)]
             self.assertEqual(len(project.contributors), 5)
             expected_names = {
                 'Sabina,,Kanton',
@@ -625,7 +630,7 @@ def assert_bundle():
 
         assert_bundle()
 
-        for contributor in metadata['project_0.json']['contributors']:
+        for contributor in metadata[f'project/{project_id}']['contributors']:
             self._rename_keys(contributor, name='contact_name')
 
         assert_bundle()
@@ -648,8 +653,8 @@ def assert_bundle():
 
         assert_bundle()
 
-        for file_name, file_content in metadata.items():
-            if file_name.startswith('sequence_file_') or file_name.startswith('supplementary_file_'):
+        for ref, file_content in metadata.items():
+            if EntityReference.parse(ref).entity_type in {'sequence_file', 'supplementary_file_'}:
                 self._rename_keys(file_content['file_core'], format='file_format')
 
         assert_bundle()
diff --git a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
index 504a1f5f5..8c4d61d20 100644
--- a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
+++ b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
@@ -958,7 +958,7 @@
         }
     ],
     "metadata": {
-        "analysis_file_0.json": {
+        "analysis_file/43598186-06cd-5f4b-95d9-fecb0a35d3ab": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
             "file_core": {
                 "content_description": [],
@@ -971,7 +971,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_file_1.json": {
+        "analysis_file/4c866eb3-7470-5ee8-91b9-942246f19fde": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
             "file_core": {
                 "content_description": [],
@@ -984,7 +984,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_file_2.json": {
+        "analysis_file/70ff6783-333f-5c1b-8208-3b495df95620": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
             "file_core": {
                 "content_description": [],
@@ -997,7 +997,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_file_3.json": {
+        "analysis_file/759bad57-b725-5346-b3ff-9fb80b27cfe7": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
             "file_core": {
                 "content_description": [
@@ -1016,7 +1016,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_file_4.json": {
+        "analysis_file/7a96a0c2-e22a-57ad-ac46-4c2433a63d94": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
             "file_core": {
                 "content_description": [],
@@ -1029,7 +1029,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_file_5.json": {
+        "analysis_file/a7915c55-1d80-5724-9c81-6dd0a9130361": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
             "file_core": {
                 "content_description": [
@@ -1048,7 +1048,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_file_6.json": {
+        "analysis_file/b949e4b6-c3fb-58b4-865b-40cb3ef2b6c6": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
             "file_core": {
                 "content_description": [],
@@ -1061,7 +1061,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_file_7.json": {
+        "analysis_file/bc111cd3-bf54-57ce-8af1-88f5997a0a9d": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
             "file_core": {
                 "content_description": [
@@ -1080,7 +1080,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_file_8.json": {
+        "analysis_file/d90280cc-a294-57de-b350-5234a5278c19": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
             "file_core": {
                 "content_description": [
@@ -1099,7 +1099,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_file_9.json": {
+        "analysis_file/f51568e8-b84c-504b-82f0-3ad5975d4bcb": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
             "file_core": {
                 "content_description": [
@@ -1118,7 +1118,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_file_10.json": {
+        "analysis_file/fec17064-9014-50b0-9e1a-dfaef2fbb4fc": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
             "file_core": {
                 "content_description": [
@@ -1138,7 +1138,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_protocol_0.json": {
+        "analysis_protocol/289ec28b-ce11-5be8-89ab-92fbceb874a0": {
             "computational_method": "Optimus",
             "describedBy": "https://schema.humancellatlas.org/type/protocol/analysis/9.1.0/analysis_protocol",
             "protocol_core": {
@@ -1154,7 +1154,7 @@
                 "text": "analysis_protocol"
             }
         },
-        "analysis_protocol_1.json": {
+        "analysis_protocol/432a7422-59b5-5c46-8983-a7953f196781": {
             "computational_method": "optimus_post_processing_v1.0.0",
             "describedBy": "https://schema.humancellatlas.org/type/protocol/analysis/9.1.0/analysis_protocol",
             "protocol_core": {
@@ -1170,7 +1170,7 @@
                 "text": "analysis; merge matrices"
             }
         },
-        "analysis_process_0.json": {
+        "analysis_process/366c7a41-3b80-4c7d-af4b-20248e69425f": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
@@ -1470,7 +1470,7 @@
                 "text": "analysis"
             }
         },
-        "analysis_process_1.json": {
+        "analysis_process/3d7a4690-8760-491c-98f9-9a1aea3f79b5": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
@@ -1770,7 +1770,7 @@
                 "text": "analysis"
             }
         },
-        "analysis_process_2.json": {
+        "analysis_process/3f615b1d-d507-4912-82c5-9cb575cd19c1": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
@@ -2070,7 +2070,7 @@
                 "text": "analysis"
             }
         },
-        "analysis_process_3.json": {
+        "analysis_process/76502973-5eb8-40b1-a0dc-17c4f772edaa": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
@@ -2370,7 +2370,7 @@
                 "text": "analysis"
             }
         },
-        "analysis_process_4.json": {
+        "analysis_process/9b4ae2d9-d681-4f08-b111-6f1878145b35": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
@@ -2670,7 +2670,7 @@
                 "text": "analysis"
             }
         },
-        "analysis_process_5.json": {
+        "analysis_process/c8430132-0f12-43ec-8b8d-bbcfcd401dab": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [],
@@ -2690,7 +2690,7 @@
                 "text": "analysis; merge matrices"
             }
         },
-        "project_0.json": {
+        "project/8185730f-4113-40d3-9cc3-929271784c2b": {
             "describedBy": "https://schema.humancellatlas.org/type/project/14.1.0/project",
             "schema_type": "project",
             "project_core": {
@@ -3110,7 +3110,7 @@
                 "update_date": "2019-09-13T08:37:53.825Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/1016adeb-cdc3-47d6-a89e-771c763dd2e7": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3135,7 +3135,7 @@
                 "update_date": "2019-09-13T09:07:26.172Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/15f64718-69cf-462c-9704-e8a1f54c27c8": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3160,7 +3160,7 @@
                 "update_date": "2019-09-13T08:56:51.563Z"
             }
         },
-        "sequence_file_2.json": {
+        "sequence_file/30040306-be5c-48f9-b221-e666e279ab5b": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3185,7 +3185,7 @@
                 "update_date": "2019-09-13T08:43:56.724Z"
             }
         },
-        "sequence_file_3.json": {
+        "sequence_file/33682180-6cdf-4d0c-9fe0-e1c029ac13b2": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3210,7 +3210,7 @@
                 "update_date": "2019-09-13T08:53:16.964Z"
             }
         },
-        "sequence_file_4.json": {
+        "sequence_file/39255288-6791-45b0-ac7e-b3ef4c981a3b": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3235,7 +3235,7 @@
                 "update_date": "2019-09-13T08:54:00.067Z"
             }
         },
-        "sequence_file_5.json": {
+        "sequence_file/52149e21-dcd2-4288-a5eb-e526c3dcf745": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3260,7 +3260,7 @@
                 "update_date": "2019-09-13T09:01:51.268Z"
             }
         },
-        "sequence_file_6.json": {
+        "sequence_file/6bd884d2-fccf-4227-8efc-184751527dfb": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3285,7 +3285,7 @@
                 "update_date": "2019-09-13T08:56:00.663Z"
             }
         },
-        "sequence_file_7.json": {
+        "sequence_file/6d52232d-dc77-4070-bdb1-9bb0ee59d309": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3310,7 +3310,7 @@
                 "update_date": "2019-09-13T08:46:45.334Z"
             }
         },
-        "sequence_file_8.json": {
+        "sequence_file/799f314f-7c6c-4981-be36-8e1310bf38e6": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3335,7 +3335,7 @@
                 "update_date": "2019-09-13T08:42:35.822Z"
             }
         },
-        "sequence_file_9.json": {
+        "sequence_file/9f8f5212-0749-460b-9a46-2949dea45d52": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3360,7 +3360,7 @@
                 "update_date": "2019-09-13T08:57:01.788Z"
             }
         },
-        "sequence_file_10.json": {
+        "sequence_file/a7b21a25-e76e-420d-8892-538062bfefbf": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3385,7 +3385,7 @@
                 "update_date": "2019-09-13T08:53:56.305Z"
             }
         },
-        "sequence_file_11.json": {
+        "sequence_file/b01b2e61-3ebd-48cc-b071-f2e8cb42ff7c": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3410,7 +3410,7 @@
                 "update_date": "2019-09-13T08:54:12.962Z"
             }
         },
-        "sequence_file_12.json": {
+        "sequence_file/e0efcd8d-8433-4b40-9eee-11dafb699a5a": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3435,7 +3435,7 @@
                 "update_date": "2019-09-13T08:53:22.108Z"
             }
         },
-        "sequence_file_13.json": {
+        "sequence_file/e92c42c7-f238-44ea-b147-e199b768d450": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3460,7 +3460,7 @@
                 "update_date": "2019-09-13T09:07:14.915Z"
             }
         },
-        "sequence_file_14.json": {
+        "sequence_file/f6407a7a-eecc-4735-a96a-b8bb634118e4": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -3485,7 +3485,7 @@
                 "update_date": "2019-09-13T08:49:05.856Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/1dda6a28-cbaa-4506-be47-fa117e8f463c": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -3529,7 +3529,7 @@
                 "update_date": "2019-09-13T08:37:53.863Z"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/252b008d-8b5a-450c-a17c-4e779a17ff26": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -3573,7 +3573,7 @@
                 "update_date": "2019-09-13T08:37:53.886Z"
             }
         },
-        "specimen_from_organism_2.json": {
+        "specimen_from_organism/edc72947-b776-4150-8bfe-b7331acfa66f": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -3617,7 +3617,7 @@
                 "update_date": "2019-09-13T08:37:53.864Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/427c0a62-9baf-42ab-a3a3-f48d10544280": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -3661,7 +3661,7 @@
                 "update_date": "2019-09-13T08:37:53.845Z"
             }
         },
-        "donor_organism_1.json": {
+        "donor_organism/66b7152c-8e94-412b-b0e4-f8fbf554df5a": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -3705,7 +3705,7 @@
                 "update_date": "2019-09-13T08:37:53.837Z"
             }
         },
-        "donor_organism_2.json": {
+        "donor_organism/b8049daa-7458-47bf-8ec2-3f5c56d2cb34": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -3749,7 +3749,7 @@
                 "update_date": "2019-09-13T08:37:53.853Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/2509f42a-0328-4e33-8d21-79d37560d846": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -3768,7 +3768,7 @@
                 "update_date": "2019-09-13T08:37:53.822Z"
             }
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/0aabed05-6a89-4141-9384-828a33581419": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -3793,7 +3793,7 @@
                 "update_date": "2019-09-13T08:37:53.849Z"
             }
         },
-        "cell_suspension_1.json": {
+        "cell_suspension/1d3e48d7-d80f-4b99-85bd-04ff393288e7": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -3818,7 +3818,7 @@
                 "update_date": "2019-09-13T08:37:53.860Z"
             }
         },
-        "cell_suspension_2.json": {
+        "cell_suspension/932000d6-c63b-40f0-bdd5-469fa4db8be2": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -3843,7 +3843,7 @@
                 "update_date": "2019-09-13T08:37:53.868Z"
             }
         },
-        "cell_suspension_3.json": {
+        "cell_suspension/b1b6ea44-e0b7-425a-9faa-51ecff56783e": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -3868,7 +3868,7 @@
                 "update_date": "2019-09-13T08:37:53.838Z"
             }
         },
-        "cell_suspension_4.json": {
+        "cell_suspension/eb32bfc6-e7be-4093-8959-b8bf27f2404f": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -3893,7 +3893,7 @@
                 "update_date": "2019-09-13T08:37:53.864Z"
             }
         },
-        "process_0.json": {
+        "process/1116b396-448e-4dd1-b9c9-78357c511e15": {
             "process_core": {
                 "process_id": "Retina_2_repB"
             },
@@ -3905,7 +3905,7 @@
                 "update_date": "2019-09-13T08:37:57.269Z"
             }
         },
-        "process_1.json": {
+        "process/25999eea-6f12-40a8-aecf-d1524c7cf564": {
             "process_core": {
                 "process_id": "process_id_7"
             },
@@ -3917,7 +3917,7 @@
                 "update_date": "2019-09-13T08:37:57.270Z"
             }
         },
-        "process_2.json": {
+        "process/262f55a3-d03d-49ae-8080-1a6208fddb4f": {
             "process_core": {
                 "process_id": "Retina_3_repA"
             },
@@ -3929,7 +3929,7 @@
                 "update_date": "2019-09-13T08:37:57.205Z"
             }
         },
-        "process_3.json": {
+        "process/2f8a07c2-4a6b-47ac-a304-0dead66eee9e": {
             "process_core": {
                 "process_id": "Retina_1"
             },
@@ -3941,7 +3941,7 @@
                 "update_date": "2019-09-13T08:37:57.269Z"
             }
         },
-        "process_4.json": {
+        "process/3ad5d964-6c2c-4adc-badb-9100ceada68c": {
             "process_core": {
                 "process_id": "process_id_8"
             },
@@ -3953,7 +3953,7 @@
                 "update_date": "2019-09-13T08:37:57.203Z"
             }
         },
-        "process_5.json": {
+        "process/4054b722-a585-4e90-8d74-a02fb4d98202": {
             "process_core": {
                 "process_id": "process_id_5"
             },
@@ -3965,7 +3965,7 @@
                 "update_date": "2019-09-13T08:37:57.167Z"
             }
         },
-        "process_6.json": {
+        "process/48a0c58c-ea67-4014-8752-6339de02b70e": {
             "process_core": {
                 "process_id": "process_id_1"
             },
@@ -3977,7 +3977,7 @@
                 "update_date": "2019-09-13T08:37:57.186Z"
             }
         },
-        "process_7.json": {
+        "process/8b81f0c2-3b57-4072-8a10-c169fece543e": {
             "process_core": {
                 "process_id": "Retina_2_repA"
             },
@@ -3989,7 +3989,7 @@
                 "update_date": "2019-09-13T08:37:57.252Z"
             }
         },
-        "process_8.json": {
+        "process/98c88684-6469-4bb3-90aa-57a4ea101244": {
             "process_core": {
                 "process_id": "process_id_4"
             },
@@ -4001,7 +4001,7 @@
                 "update_date": "2019-09-13T08:37:57.171Z"
             }
         },
-        "process_9.json": {
+        "process/a5e37780-0b71-4610-8a7c-26142dedfcec": {
             "process_core": {
                 "process_id": "process_id_2"
             },
@@ -4013,7 +4013,7 @@
                 "update_date": "2019-09-13T08:37:57.174Z"
             }
         },
-        "process_10.json": {
+        "process/ad220152-0eb4-4f85-a03e-c7e81ea3f167": {
             "process_core": {
                 "process_id": "Retina_3_repB"
             },
@@ -4025,7 +4025,7 @@
                 "update_date": "2019-09-13T08:37:57.252Z"
             }
         },
-        "process_11.json": {
+        "process/b360251f-7550-4c08-b576-781858554ea1": {
             "process_core": {
                 "process_id": "process_id_6"
             },
@@ -4037,7 +4037,7 @@
                 "update_date": "2019-09-13T08:37:57.252Z"
             }
         },
-        "process_12.json": {
+        "process/e511e7ff-e67c-4eb3-b0db-13aecefb5486": {
             "process_core": {
                 "process_id": "process_id_3"
             },
@@ -4049,7 +4049,7 @@
                 "update_date": "2019-09-13T08:37:57.269Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/a166be3d-6e84-4058-a1bd-edf90cf3ee88": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -4079,7 +4079,7 @@
                 "update_date": "2019-09-13T08:37:53.815Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/ba595d79-aa43-4e3a-ad10-89f92ef4f22f": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -4099,7 +4099,7 @@
                 "update_date": "2019-09-13T08:37:53.832Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/fa99959f-faa2-4d69-a092-48333e59f5f3": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -4137,7 +4137,7 @@
                 "update_date": "2019-09-13T08:37:53.809Z"
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/3030903f-4a4b-4b30-ab93-3b10183181e0": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
diff --git a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
index c40636930..5322f72b4 100644
--- a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
+++ b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
@@ -795,7 +795,7 @@
         }
     ],
     "metadata": {
-        "process_0.json": {
+        "process/02e69c25-71e2-48ca-a87b-e256938c6a98": {
             "insdc_experiment": {
                 "insdc_experiment_accession": "SRX5499352"
             },
@@ -812,7 +812,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_1.json": {
+        "process/341460a3-edf2-4f77-9625-7c6b92ac863e": {
             "process_core": {
                 "process_id": "process_id_7"
             },
@@ -826,7 +826,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_2.json": {
+        "process/3798c749-7f72-4847-a9d1-d99112f98162": {
             "process_core": {
                 "process_id": "process_id_3"
             },
@@ -840,7 +840,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_3.json": {
+        "process/39fdb0ae-9a00-4829-a581-e7cb59798f02": {
             "insdc_experiment": {
                 "insdc_experiment_accession": "SRX5499353"
             },
@@ -857,7 +857,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_4.json": {
+        "process/4b963d42-aad1-4f26-94d2-c13c8321c09d": {
             "process_core": {
                 "process_id": "process_id_35"
             },
@@ -871,7 +871,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_5.json": {
+        "process/721fcf01-ab0d-4220-9dfc-396ca6991d1d": {
             "process_core": {
                 "process_id": "process_id_4"
             },
@@ -885,7 +885,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_6.json": {
+        "process/771e716e-9906-4f5d-b41a-2fa7cc9bd77b": {
             "process_core": {
                 "process_id": "process_id_1"
             },
@@ -899,7 +899,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_7.json": {
+        "process/7e90d996-b643-4732-af87-ac090325a6e8": {
             "process_core": {
                 "process_id": "process_id_2"
             },
@@ -913,7 +913,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_8.json": {
+        "process/9a8d9df1-c511-4b6b-b6d3-cacc0eaf76c1": {
             "process_core": {
                 "process_id": "process_id_8"
             },
@@ -927,7 +927,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_9.json": {
+        "process/a85ceb28-cdb0-4021-98c8-752b9d07170a": {
             "process_core": {
                 "process_id": "process_id_5"
             },
@@ -941,7 +941,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_10.json": {
+        "process/bd774f12-82e6-4036-8779-d8674bce9205": {
             "process_core": {
                 "process_id": "process_id_6"
             },
@@ -955,7 +955,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_11.json": {
+        "process/da317018-1b0b-4e4f-b508-2c1c7d049507": {
             "process_core": {
                 "process_id": "exp2"
             },
@@ -969,7 +969,7 @@
                 "schema_minor_version": 2
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/5608f2b1-d42f-4198-8d52-96e40e5239e4": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1014,7 +1014,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/5e9f5040-c83a-4442-8944-db144717107a": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1059,7 +1059,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_2.json": {
+        "specimen_from_organism/6254fedf-0978-45ee-af82-e7f30ffebf0c": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1104,7 +1104,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_3.json": {
+        "specimen_from_organism/63170a26-263d-4207-8eab-871b687e234d": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1149,7 +1149,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_4.json": {
+        "specimen_from_organism/9b1c871e-20db-487f-9acc-36740b75877b": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1194,7 +1194,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_5.json": {
+        "specimen_from_organism/b5a382bd-34e5-429d-9013-3ff025ab322a": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1239,7 +1239,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_6.json": {
+        "specimen_from_organism/b9a0edf6-77bc-4e4a-a200-5cda4f902c04": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1284,7 +1284,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_7.json": {
+        "specimen_from_organism/e6b8f32e-7c8e-4308-b596-91006cde4b51": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1329,7 +1329,7 @@
                 "schema_minor_version": 4
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/000d1e4b-4c1f-40de-8fd6-8a3d1a26e1d2": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1359,7 +1359,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/06d54587-f54b-490c-8d29-3d84025e3b14": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1389,7 +1389,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_2.json": {
+        "sequence_file/1697aa82-0910-44e6-ac07-2020248e1977": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1419,7 +1419,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_3.json": {
+        "sequence_file/49eefca3-6441-4a63-a0f0-178d6fc2573d": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1449,7 +1449,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_4.json": {
+        "sequence_file/6b94ce38-27b9-460e-ab1b-bceb18275c71": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1479,7 +1479,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_5.json": {
+        "sequence_file/7c1802b3-0be5-4202-b14e-141974ca7fb3": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1509,7 +1509,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_6.json": {
+        "sequence_file/9610cb70-57c1-466d-b9c9-faa22aa7b917": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1539,7 +1539,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_7.json": {
+        "sequence_file/989f8f5d-710f-4529-b89b-0bfbf592951c": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1569,7 +1569,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_8.json": {
+        "sequence_file/a97f4858-0f13-405a-8b28-98ee5f997999": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1599,7 +1599,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_9.json": {
+        "sequence_file/bca273dd-1758-4439-b7e0-745755dcffa0": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1629,7 +1629,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_10.json": {
+        "sequence_file/c87f6dbf-1062-4e72-a19d-db779f1d3e66": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1659,7 +1659,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_11.json": {
+        "sequence_file/d86c34c4-0aeb-4f50-a53e-5a0983c906b7": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1689,7 +1689,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_12.json": {
+        "sequence_file/dc5b2d96-ba74-4bd0-bcf0-747548e1c6d7": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1719,7 +1719,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_13.json": {
+        "sequence_file/eacaacbb-f514-49bb-bfbf-ccb123c5bf2e": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1749,7 +1749,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_14.json": {
+        "sequence_file/ee52ecd1-68c0-48dd-82c2-6d3e45869b38": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1779,7 +1779,7 @@
                 "schema_minor_version": 3
             }
         },
-        "analysis_protocol_0.json": {
+        "analysis_protocol/89808d14-a99e-47d2-82cd-ff9621a32206": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/analysis/9.2.0/analysis_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1806,7 +1806,7 @@
                 "schema_minor_version": 2
             }
         },
-        "project_0.json": {
+        "project/dc1a41f6-9e09-42a6-959e-3be23db6da56": {
             "contributors": [
                 {
                     "name": "Jellert,T,Gaublomme",
@@ -2008,7 +2008,7 @@
                 "schema_minor_version": 1
             }
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/db4b5711-0abd-44cd-ac94-cdaca0cb1de3": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -2037,7 +2037,7 @@
                 "schema_minor_version": 3
             }
         },
-        "analysis_file_0.json": {
+        "analysis_file/004d18f2-f23c-4fd1-af2e-f0a6a9e13cc9": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.3.0/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -2059,7 +2059,7 @@
                 "schema_minor_version": 3
             }
         },
-        "analysis_file_1.json": {
+        "analysis_file/4d64269d-bd3f-46c1-a179-1c27e1caeb30": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.3.0/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -2083,7 +2083,7 @@
                 "schema_minor_version": 3
             }
         },
-        "analysis_file_2.json": {
+        "analysis_file/6ccd1b16-d3a9-4ba4-9dda-99aa882dfc2c": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.3.0/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -2106,7 +2106,7 @@
                 "schema_minor_version": 3
             }
         },
-        "analysis_file_3.json": {
+        "analysis_file/ad3f7b5e-77ed-4df1-a9af-5355f7951af4": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.3.0/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -2128,7 +2128,7 @@
                 "schema_minor_version": 3
             }
         },
-        "analysis_file_4.json": {
+        "analysis_file/c61a76f4-aebe-4a18-b272-e2e78307bb4a": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.3.0/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -2150,7 +2150,7 @@
                 "schema_minor_version": 3
             }
         },
-        "analysis_file_5.json": {
+        "analysis_file/cde6359a-a2b0-421d-a898-c53278c21399": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.3.0/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -2172,7 +2172,7 @@
                 "schema_minor_version": 3
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/6a72730a-1485-48f4-9b26-adc87380ad9b": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -2215,7 +2215,7 @@
                 "schema_minor_version": 2
             }
         },
-        "library_preparation_protocol_1.json": {
+        "library_preparation_protocol/c375019a-ef94-452b-b111-32244bdc054a": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -2258,7 +2258,7 @@
                 "schema_minor_version": 2
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/d3372c5a-20ea-4239-bfef-c11894862897": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -2281,7 +2281,7 @@
                 "schema_minor_version": 1
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/ab3e3079-2eea-49cd-836f-5b9f4cf27b86": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -2301,7 +2301,7 @@
                 "schema_minor_version": 2
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/133e78ac-aa06-4a0b-b43f-0e9e2148d528": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -2322,7 +2322,7 @@
                 "schema_minor_version": 2
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/014494a0-adde-4ac6-90c1-2b5824a8717c": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -2374,7 +2374,7 @@
                 "schema_minor_version": 5
             }
         },
-        "donor_organism_1.json": {
+        "donor_organism/c10356c8-e081-4f97-8e85-0ea87b8eb84b": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -2426,7 +2426,7 @@
                 "schema_minor_version": 5
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/6b2c7ae7-1d15-4914-a9e9-14233afd5c3f": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
diff --git a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
index 73a3e138f..9dbf16470 100644
--- a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
+++ b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
@@ -8991,7 +8991,7 @@
         }
     ],
     "metadata": {
-        "sequence_file_0.json": {
+        "sequence_file/012af05a-4771-45e5-bb92-9b63fcbde822": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9020,7 +9020,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/0256729b-47ee-4ed3-adc7-2c0813bb99b9": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9049,7 +9049,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_2.json": {
+        "sequence_file/02cfb8bb-4eb6-4343-9381-007968f1feee": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9078,7 +9078,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_3.json": {
+        "sequence_file/035a00e0-02ca-46e8-bb76-9b2449ee922f": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9107,7 +9107,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_4.json": {
+        "sequence_file/04066a52-7468-4783-b49c-46e28b076739": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9136,7 +9136,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_5.json": {
+        "sequence_file/0506c2a0-ef2b-4850-8567-20d08046bdaa": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9165,7 +9165,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_6.json": {
+        "sequence_file/061936ce-8fbb-4576-8c0c-ed871767917f": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9194,7 +9194,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_7.json": {
+        "sequence_file/067d2b7b-127b-421f-91db-0acc05ad62ad": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9223,7 +9223,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_8.json": {
+        "sequence_file/0697146c-0105-4d6f-baff-d9147593eadb": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9252,7 +9252,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_9.json": {
+        "sequence_file/09610000-dc5c-4665-a72e-b0dad51edf6d": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9281,7 +9281,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_10.json": {
+        "sequence_file/09a53782-90ea-4911-a793-706e74127adb": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9310,7 +9310,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_11.json": {
+        "sequence_file/09b831a2-5b60-4753-864e-8af803024437": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9339,7 +9339,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_12.json": {
+        "sequence_file/09c0456a-ec0b-47e3-870d-4b47221a45a6": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9368,7 +9368,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_13.json": {
+        "sequence_file/0c577531-9218-444b-8094-85d8c6f5c73e": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9397,7 +9397,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_14.json": {
+        "sequence_file/0dbf8a13-52a5-48ad-b48e-9fb0ef358dfc": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9426,7 +9426,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_15.json": {
+        "sequence_file/0fa69e92-febb-4bab-857c-4b67a2b17ff6": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9455,7 +9455,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_16.json": {
+        "sequence_file/102b8410-1c0e-46f5-90fe-609ab117221c": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9484,7 +9484,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_17.json": {
+        "sequence_file/10b3b42b-3612-48fb-849b-bfc036c248a6": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9513,7 +9513,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_18.json": {
+        "sequence_file/110bb0f5-9d1a-4573-b711-6bee156d0eb8": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9542,7 +9542,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_19.json": {
+        "sequence_file/11d171f7-7775-40a4-90a4-df995775b1c4": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9571,7 +9571,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_20.json": {
+        "sequence_file/12826f14-2ef8-4069-a797-42d2f4c0937b": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9600,7 +9600,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_21.json": {
+        "sequence_file/130831cc-87b6-47fd-93a8-ae1890d365f2": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9629,7 +9629,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_22.json": {
+        "sequence_file/14795e28-bcee-4da3-83cf-bb2592b6c0d0": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9658,7 +9658,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_23.json": {
+        "sequence_file/154dffeb-efd7-4081-a73c-bf1b73ca9a90": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9687,7 +9687,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_24.json": {
+        "sequence_file/17883ec7-0ff4-4c57-b2d0-2ac130bd3ae8": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9716,7 +9716,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_25.json": {
+        "sequence_file/18d81f7f-94c8-4877-939a-b74ba802835a": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9745,7 +9745,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_26.json": {
+        "sequence_file/19eb5d2e-2224-4bb4-9f94-526a4c06f7a2": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9774,7 +9774,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_27.json": {
+        "sequence_file/1a589473-0047-4bca-afce-57c8448f0dc6": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9803,7 +9803,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_28.json": {
+        "sequence_file/1adbb95f-f5c3-41ce-8e16-7657d189de79": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9832,7 +9832,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_29.json": {
+        "sequence_file/1badbbc9-6b43-41f6-acad-36f09cff3d21": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9861,7 +9861,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_30.json": {
+        "sequence_file/1bbafb1c-50eb-40b4-ab71-dd5d6f1d3288": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9890,7 +9890,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_31.json": {
+        "sequence_file/1c95a589-205c-4d7c-9c56-c3de4f7dbb66": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9919,7 +9919,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_32.json": {
+        "sequence_file/1d77e73b-9bd3-499f-a0d0-86d9f7306a7e": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9948,7 +9948,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_33.json": {
+        "sequence_file/1f134dea-8f9b-4e90-a1af-80508f43f73c": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -9977,7 +9977,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_34.json": {
+        "sequence_file/1f5d640c-1ea0-4f8e-a9ce-036a8eb6e0a1": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -10006,7 +10006,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequence_file_35.json": {
+        "sequence_file/1ffc9c1e-5894-4d8e-9bb7-be6a41aaabec": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.3.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -10035,7 +10035,7 @@
                 "schema_minor_version": 3
             }
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@@ -11775,7 +11775,7 @@
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             "schema_type": "protocol",
             "protocol_core": {
@@ -20432,7 +20432,7 @@
                 "schema_minor_version": 2
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/0e1884e4-310f-4afb-9721-e0721a290498": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -20454,7 +20454,7 @@
                 "schema_minor_version": 2
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/24023592-6f24-47d3-98ea-3c9e03cf3fc4": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -20505,7 +20505,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/5bd31092-57c0-4d69-aa2b-72d902872cca": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -20555,7 +20555,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_2.json": {
+        "specimen_from_organism/6e669924-95c7-4aef-bd34-6dd28bf29fdd": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -20606,7 +20606,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_3.json": {
+        "specimen_from_organism/8df6ce25-29e1-41a9-af33-d665ff8ca4e7": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -20657,7 +20657,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_4.json": {
+        "specimen_from_organism/a9cc38f8-0a0e-488b-b0c7-2c77f091d0ce": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -20708,7 +20708,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_5.json": {
+        "specimen_from_organism/ae5b7895-01cf-4a6e-aee0-8b58e820313c": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -20759,7 +20759,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_6.json": {
+        "specimen_from_organism/b8edcc72-efe5-44da-b478-9761be75a127": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -20809,7 +20809,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_7.json": {
+        "specimen_from_organism/c86979f7-726d-441b-a525-1a3369492695": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -20859,7 +20859,7 @@
                 "schema_minor_version": 4
             }
         },
-        "specimen_from_organism_8.json": {
+        "specimen_from_organism/f55166a1-c4f0-4fda-ac9f-164489040ee5": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -20910,7 +20910,7 @@
                 "schema_minor_version": 4
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/48f7f503-d213-4447-9ee4-3602da1066d7": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -20933,7 +20933,7 @@
                 "schema_minor_version": 1
             }
         },
-        "analysis_protocol_0.json": {
+        "analysis_protocol/07f1f962-dd38-4a0b-b0b5-f4efe30d21e2": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/analysis/9.2.0/analysis_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -20964,7 +20964,7 @@
                 "schema_minor_version": 2
             }
         },
-        "project_0.json": {
+        "project/bd400331-54b9-4fcc-bff6-6bb8b079ee1f": {
             "contributors": [
                 {
                     "name": "Choon Boon,,Sim",
@@ -21243,7 +21243,7 @@
                 "schema_minor_version": 1
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/572a625b-119a-4099-b5eb-d2994f8846bf": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -21264,7 +21264,7 @@
                 "schema_minor_version": 2
             }
         },
-        "collection_protocol_1.json": {
+        "collection_protocol/67fa2c3e-ba97-4bc6-beb9-92ea33bec948": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -21285,7 +21285,7 @@
                 "schema_minor_version": 2
             }
         },
-        "collection_protocol_2.json": {
+        "collection_protocol/dbeb62b8-e3e8-40f4-a06d-477ed495dfd9": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -21306,7 +21306,7 @@
                 "schema_minor_version": 2
             }
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/2129a373-0919-4c91-bf59-adf4de6566f5": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -21335,7 +21335,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_1.json": {
+        "cell_suspension/3bb2457a-505f-4f04-b5f9-71e351be791f": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -21364,7 +21364,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_2.json": {
+        "cell_suspension/5e811f8c-aa77-43f5-9197-f69c067b6e83": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -21393,7 +21393,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_3.json": {
+        "cell_suspension/60e4296c-5d92-4c12-bf4e-f5fe08f01614": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -21422,7 +21422,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_4.json": {
+        "cell_suspension/871337d9-1c55-4c97-8f67-2da1fff00847": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -21451,7 +21451,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_5.json": {
+        "cell_suspension/92363365-2bef-43b5-bb58-7a66b7cf57dc": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -21480,7 +21480,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_6.json": {
+        "cell_suspension/f21781e9-e5c7-48ff-9d7d-0e3637968279": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -21509,7 +21509,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_7.json": {
+        "cell_suspension/fc1541f1-27bb-4cd1-be90-2b04c29a902e": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -21538,7 +21538,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_8.json": {
+        "cell_suspension/fdb8e413-a62a-4c6c-9890-3945c0f19ce8": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -21567,7 +21567,7 @@
                 "schema_minor_version": 3
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/63db242f-a88b-4deb-b1e4-3677ade32d18": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
diff --git a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
index bdf5655d1..e9b9ae267 100644
--- a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
+++ b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
@@ -178,7 +178,7 @@
         }
     ],
     "metadata": {
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/0a8112d1-d401-4c0d-8334-8cda8f8532c8": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "method": {
                 "ontology": "EFO:0011026",
@@ -206,7 +206,7 @@
                 "schema_minor_version": 2
             }
         },
-        "dissociation_protocol_1.json": {
+        "dissociation_protocol/59eeb73e-64d6-4959-9c69-b85570a20900": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -234,7 +234,7 @@
                 "schema_minor_version": 2
             }
         },
-        "cell_line_0.json": {
+        "cell_line/d91bbbd5-c2c1-4bb7-906f-494ee686658e": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/14.5.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -270,7 +270,7 @@
                 "schema_minor_version": 5
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/328e83cc-1e31-4d49-bf69-3504a7d1d4ba": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -296,7 +296,7 @@
                 "schema_minor_version": 1
             }
         },
-        "process_0.json": {
+        "process/0722b70c-6778-423d-8fe9-869e2a515d35": {
             "insdc_experiment": {
                 "insdc_experiment_accession": "SRX4511355"
             },
@@ -313,7 +313,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_1.json": {
+        "process/0d48b9ba-5fea-4260-abbc-2949ac357f75": {
             "insdc_experiment": {
                 "insdc_experiment_accession": "SRX4511355"
             },
@@ -330,7 +330,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_2.json": {
+        "process/70b02064-3cf5-4e97-88f8-731c6e246965": {
             "process_core": {
                 "process_id": "process_id_48"
             },
@@ -344,7 +344,7 @@
                 "schema_minor_version": 2
             }
         },
-        "project_0.json": {
+        "project/16ed4ad8-7319-46b2-8859-6fe1c1d73a82": {
             "contributors": [
                 {
                     "name": "Haojia,,Wu",
@@ -463,7 +463,7 @@
                 "schema_minor_version": 1
             }
         },
-        "differentiation_protocol_0.json": {
+        "differentiation_protocol/0078130e-8a91-47d0-9ff7-854ae772b8ea": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/2.2.0/differentiation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -483,7 +483,7 @@
                 "schema_minor_version": 2
             }
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/b2feeafc-bd19-4c54-b669-648ce3ee5b52": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -520,7 +520,7 @@
                 "schema_minor_version": 3
             }
         },
-        "organoid_0.json": {
+        "organoid/df23c109-59f0-46d3-bd09-660175b51bda": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/11.3.0/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -555,7 +555,7 @@
                 "schema_minor_version": 3
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/f4234276-bdac-4ad1-b4a0-4b5d595ae04c": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -577,7 +577,7 @@
                 "schema_minor_version": 1
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/54647cbb-7814-4d9a-b7f8-a6605c2f7aa6": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -603,7 +603,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/95595c66-2121-4ebc-9f2e-b5b61d193f25": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -629,7 +629,7 @@
                 "schema_minor_version": 2
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/ca16fcf2-48df-4b2a-bd48-a5fce6b0cd75": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
diff --git a/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json b/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
index 7a4c949ff..3268348f7 100644
--- a/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
+++ b/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
@@ -146,7 +146,7 @@
         }
     ],
     "metadata": {
-        "project_0.json": {
+        "project/6ec8e247-2eb0-42d1-823f-75facd03988d": {
             "content": {
                 "contributors": [
                     {
@@ -250,7 +250,7 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/a86b1fda-bb1d-4ef8-87d9-392517d4a937": {
             "content": {
                 "biomaterial_core": {
                     "has_input_biomaterial": "A1-Spl-0-TL5",
@@ -277,7 +277,7 @@
                 "document_id": "a86b1fda-bb1d-4ef8-87d9-392517d4a937"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/d231b8f3-8fa3-4f3b-a8e5-66eca6228ae7": {
             "content": {
                 "state_of_specimen": {
                     "ischemic_time": 7200,
@@ -320,7 +320,7 @@
                 "document_id": "d231b8f3-8fa3-4f3b-a8e5-66eca6228ae7"
             }
         },
-        "donor_organism_2.json": {
+        "donor_organism/9a7acc6d-8352-497e-b162-5e63b380366f": {
             "content": {
                 "is_living": false,
                 "death": {
@@ -381,7 +381,7 @@
                 "document_id": "9a7acc6d-8352-497e-b162-5e63b380366f"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/49fddace-4c59-41c1-8930-0707460132d7": {
             "content": {
                 "file_core": {
                     "file_name": "HCATisStabAug177078016_S1_L001_I1_001.fastq.gz",
@@ -397,7 +397,7 @@
                 "document_id": "49fddace-4c59-41c1-8930-0707460132d7"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/771d9bcb-a5ff-43b5-b3e8-e738cc4c05bf": {
             "content": {
                 "file_core": {
                     "file_name": "HCATisStabAug177078016_S1_L001_R1_001.fastq.gz",
@@ -413,7 +413,7 @@
                 "document_id": "771d9bcb-a5ff-43b5-b3e8-e738cc4c05bf"
             }
         },
-        "sequence_file_2.json": {
+        "sequence_file/8ebfd02e-2a74-4367-80db-48082f331625": {
             "content": {
                 "file_core": {
                     "file_name": "HCATisStabAug177078016_S1_L001_R2_001.fastq.gz",
@@ -429,7 +429,7 @@
                 "document_id": "8ebfd02e-2a74-4367-80db-48082f331625"
             }
         },
-        "sequence_file_3.json": {
+        "sequence_file/fea5cc65-6d94-4d1e-a807-ec248f79b83d": {
             "content": {
                 "file_core": {
                     "file_name": "HCATisStabAug177078016_S2_L001_I1_001.fastq.gz",
@@ -445,7 +445,7 @@
                 "document_id": "fea5cc65-6d94-4d1e-a807-ec248f79b83d"
             }
         },
-        "sequence_file_4.json": {
+        "sequence_file/cee5b925-919c-4c77-8ea2-be51a1728e2b": {
             "content": {
                 "file_core": {
                     "file_name": "HCATisStabAug177078016_S2_L001_R1_001.fastq.gz",
@@ -461,7 +461,7 @@
                 "document_id": "cee5b925-919c-4c77-8ea2-be51a1728e2b"
             }
         },
-        "sequence_file_5.json": {
+        "sequence_file/c548066c-9994-415a-98cb-3df2933937ff": {
             "content": {
                 "file_core": {
                     "file_name": "HCATisStabAug177078016_S2_L001_R2_001.fastq.gz",
@@ -477,7 +477,7 @@
                 "document_id": "c548066c-9994-415a-98cb-3df2933937ff"
             }
         },
-        "sequence_file_6.json": {
+        "sequence_file/b7d8d43c-bee6-48eb-bb36-0c07701c47b5": {
             "content": {
                 "file_core": {
                     "file_name": "HCATisStabAug177078016_S3_L001_I1_001.fastq.gz",
@@ -493,7 +493,7 @@
                 "document_id": "b7d8d43c-bee6-48eb-bb36-0c07701c47b5"
             }
         },
-        "sequence_file_7.json": {
+        "sequence_file/6bc5b7ef-68f8-445d-8460-f04180c4fae1": {
             "content": {
                 "file_core": {
                     "file_name": "HCATisStabAug177078016_S3_L001_R1_001.fastq.gz",
@@ -509,7 +509,7 @@
                 "document_id": "6bc5b7ef-68f8-445d-8460-f04180c4fae1"
             }
         },
-        "sequence_file_8.json": {
+        "sequence_file/17add91c-4063-4684-859d-d739baa4b9bb": {
             "content": {
                 "file_core": {
                     "file_name": "HCATisStabAug177078016_S3_L001_R2_001.fastq.gz",
@@ -525,7 +525,7 @@
                 "document_id": "17add91c-4063-4684-859d-d739baa4b9bb"
             }
         },
-        "sequence_file_9.json": {
+        "sequence_file/b7554cb7-dc5a-4b07-9c7a-c04466d30576": {
             "content": {
                 "file_core": {
                     "file_name": "HCATisStabAug177078016_S4_L001_I1_001.fastq.gz",
@@ -541,7 +541,7 @@
                 "document_id": "b7554cb7-dc5a-4b07-9c7a-c04466d30576"
             }
         },
-        "sequence_file_10.json": {
+        "sequence_file/5239e70b-7d8d-4285-971f-9a156441c2f2": {
             "content": {
                 "file_core": {
                     "file_name": "HCATisStabAug177078016_S4_L001_R1_001.fastq.gz",
@@ -557,7 +557,7 @@
                 "document_id": "5239e70b-7d8d-4285-971f-9a156441c2f2"
             }
         },
-        "sequence_file_11.json": {
+        "sequence_file/024c5cb6-f473-40c9-9eb3-da08caf3180e": {
             "content": {
                 "file_core": {
                     "file_name": "HCATisStabAug177078016_S4_L001_R2_001.fastq.gz",
@@ -573,7 +573,7 @@
                 "document_id": "024c5cb6-f473-40c9-9eb3-da08caf3180e"
             }
         },
-        "process_0.json": {
+        "process/7d3747dc-9e3a-4740-8504-82086ad1d63a": {
             "content": {
                 "process_core": {
                     "process_id": "wrapper_process_7"
@@ -588,7 +588,7 @@
                 "document_id": "7d3747dc-9e3a-4740-8504-82086ad1d63a"
             }
         },
-        "process_1.json": {
+        "process/8797a64c-b498-4de6-aea7-86401199bee4": {
             "content": {
                 "process_core": {
                     "process_id": "sampling_process_3"
@@ -603,7 +603,7 @@
                 "document_id": "8797a64c-b498-4de6-aea7-86401199bee4"
             }
         },
-        "library_preparation_process_2.json": {
+        "library_preparation_process/fa9febdf-425e-41bc-925f-b17f27b96e61": {
             "content": {
                 "input_nucleic_acid_molecule": {
                     "text": "polyA RNA",
@@ -636,7 +636,7 @@
                 "document_id": "fa9febdf-425e-41bc-925f-b17f27b96e61"
             }
         },
-        "sequencing_process_3.json": {
+        "sequencing_process/0c6332ef-633b-403b-b4ed-c61ccacf87c8": {
             "content": {
                 "process_core": {
                     "process_id": "sequencing_process_1",
@@ -657,7 +657,7 @@
                 "document_id": "0c6332ef-633b-403b-b4ed-c61ccacf87c8"
             }
         },
-        "protocol_0.json": {
+        "protocol/73b0c9ae-a5bb-446e-9c7b-d0954e6af425": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "10X Genomics protocol - including loading single cells and library prep",
diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
index 7f8f9aee6..d22dd3ee9 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
@@ -458,7 +458,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/906f8f09-deaa-40bb-bf50-27d2336b2dc4": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -491,7 +491,7 @@
                 "schema_minor_version": 3
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/d6a518a8-0c5d-4cb0-aed5-68f3455c2bda": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -537,7 +537,7 @@
                 "schema_minor_version": 4
             }
         },
-        "cell_line_0.json": {
+        "cell_line/70054038-cb12-429d-bb37-69185ff1deee": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/14.5.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -583,7 +583,7 @@
                 "schema_minor_version": 5
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/2b7adb0a-82a4-4319-80d1-4a73d879dec1": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -633,7 +633,7 @@
                 "schema_minor_version": 5
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/5f68ea73-350b-4d37-a341-3004139fb699": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -660,7 +660,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/23f8e139-f4fa-4476-ba59-ff5d37003c34": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -687,7 +687,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_2.json": {
+        "sequence_file/3c3d882a-cc38-4eea-ac53-0885f906852e": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -714,7 +714,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_3.json": {
+        "sequence_file/35e07477-76cb-4a92-99b6-7b3bbb02ec06": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -741,7 +741,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_4.json": {
+        "sequence_file/63051b9f-87d4-4853-a4a0-5cc742ef6e72": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -768,7 +768,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_5.json": {
+        "sequence_file/6ca8e43f-5f40-4eb9-bfa9-294c54dbeade": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -795,7 +795,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_6.json": {
+        "sequence_file/3dffc456-caaf-4823-9f65-fc0db7abacbc": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -822,7 +822,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_7.json": {
+        "sequence_file/a2f4b05d-0dae-4655-acfd-ef3b91ae0ad0": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -849,7 +849,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_8.json": {
+        "sequence_file/98ee0901-d34c-48a5-915a-0511bac325ec": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -876,7 +876,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_9.json": {
+        "sequence_file/27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -903,7 +903,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_10.json": {
+        "sequence_file/133f2a25-f3aa-49a7-b9b6-d185d302fb26": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -930,7 +930,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_11.json": {
+        "sequence_file/e46af70a-0396-41db-9b74-330cb8244124": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -957,7 +957,7 @@
                 "schema_minor_version": 2
             }
         },
-        "project_0.json": {
+        "project/116965f3-f094-4769-9d28-ae675c1b569c": {
             "describedBy": "https://schema.humancellatlas.org/type/project/14.1.0/project",
             "schema_type": "project",
             "project_core": {
@@ -1079,7 +1079,7 @@
                 "schema_minor_version": 1
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/2945bb1f-90de-42a3-afa1-f57a62c853f0": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1109,7 +1109,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/08b09d15-ef99-4278-9b88-65127adb51b9": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1142,7 +1142,7 @@
                 "schema_minor_version": 1
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/eaf15851-97e3-4e4b-b81b-0e625098f4d5": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1163,7 +1163,7 @@
                 "schema_minor_version": 2
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/345bcbd2-f3a7-4f57-a806-fbb0ce4a25da": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1185,7 +1185,7 @@
                 "schema_minor_version": 1
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/8612862e-beb1-416b-a807-0a83fae8d168": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1206,7 +1206,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_0.json": {
+        "process/15de6ce1-c185-4852-ade4-43614c5d048b": {
             "start_time": "2019.01.21",
             "process_core": {
                 "process_id": "IDC9"
@@ -1221,7 +1221,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_1.json": {
+        "process/47ca0565-ab7d-42bd-8731-ce5d30cfd6c7": {
             "process_core": {
                 "process_id": "process_id_6"
             },
@@ -1235,7 +1235,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_2.json": {
+        "process/df5114c9-9f52-451b-afde-3673392fc864": {
             "process_core": {
                 "process_id": "process_id_1"
             },
@@ -1249,7 +1249,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_3.json": {
+        "process/c5cf9180-535a-4d1c-bdee-4f6ce7845b1e": {
             "process_core": {
                 "process_id": "process_id_3"
             },
diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
index 2411d9a0d..b942c7df5 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
@@ -481,7 +481,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/906f8f09-deaa-40bb-bf50-27d2336b2dc4": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -514,7 +514,7 @@
                 "schema_minor_version": 3
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/d6a518a8-0c5d-4cb0-aed5-68f3455c2bda": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -560,7 +560,7 @@
                 "schema_minor_version": 4
             }
         },
-        "cell_line_0.json": {
+        "cell_line/70054038-cb12-429d-bb37-69185ff1deee": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/14.5.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -606,7 +606,7 @@
                 "schema_minor_version": 5
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/2b7adb0a-82a4-4319-80d1-4a73d879dec1": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -656,7 +656,7 @@
                 "schema_minor_version": 5
             }
         },
-        "sequence_file_6.json": {
+        "sequence_file/5f68ea73-350b-4d37-a341-3004139fb699": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -683,7 +683,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/23f8e139-f4fa-4476-ba59-ff5d37003c34": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -710,7 +710,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_4.json": {
+        "sequence_file/3c3d882a-cc38-4eea-ac53-0885f906852e": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -737,7 +737,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_3.json": {
+        "sequence_file/35e07477-76cb-4a92-99b6-7b3bbb02ec06": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -764,7 +764,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_7.json": {
+        "sequence_file/63051b9f-87d4-4853-a4a0-5cc742ef6e72": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -791,7 +791,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_8.json": {
+        "sequence_file/6ca8e43f-5f40-4eb9-bfa9-294c54dbeade": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -818,7 +818,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_5.json": {
+        "sequence_file/3dffc456-caaf-4823-9f65-fc0db7abacbc": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -845,7 +845,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_10.json": {
+        "sequence_file/a2f4b05d-0dae-4655-acfd-ef3b91ae0ad0": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -872,7 +872,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_9.json": {
+        "sequence_file/98ee0901-d34c-48a5-915a-0511bac325ec": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -899,7 +899,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_2.json": {
+        "sequence_file/27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -926,7 +926,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/133f2a25-f3aa-49a7-b9b6-d185d302fb26": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -953,7 +953,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_11.json": {
+        "sequence_file/e46af70a-0396-41db-9b74-330cb8244124": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -980,7 +980,7 @@
                 "schema_minor_version": 2
             }
         },
-        "project_0.json": {
+        "project/116965f3-f094-4769-9d28-ae675c1b569c": {
             "describedBy": "https://schema.humancellatlas.org/type/project/14.1.0/project",
             "schema_type": "project",
             "project_core": {
@@ -1102,7 +1102,7 @@
                 "schema_minor_version": 1
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/2945bb1f-90de-42a3-afa1-f57a62c853f0": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1132,7 +1132,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/08b09d15-ef99-4278-9b88-65127adb51b9": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1165,7 +1165,7 @@
                 "schema_minor_version": 1
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/eaf15851-97e3-4e4b-b81b-0e625098f4d5": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1186,7 +1186,7 @@
                 "schema_minor_version": 2
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/345bcbd2-f3a7-4f57-a806-fbb0ce4a25da": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1208,7 +1208,7 @@
                 "schema_minor_version": 1
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/8612862e-beb1-416b-a807-0a83fae8d168": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1229,7 +1229,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_0.json": {
+        "process/15de6ce1-c185-4852-ade4-43614c5d048b": {
             "start_time": "2019.01.21",
             "process_core": {
                 "process_id": "IDC9"
@@ -1244,7 +1244,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_1.json": {
+        "process/47ca0565-ab7d-42bd-8731-ce5d30cfd6c7": {
             "process_core": {
                 "process_id": "process_id_6"
             },
@@ -1258,7 +1258,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_3.json": {
+        "process/df5114c9-9f52-451b-afde-3673392fc864": {
             "process_core": {
                 "process_id": "process_id_1"
             },
@@ -1272,7 +1272,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_2.json": {
+        "process/c5cf9180-535a-4d1c-bdee-4f6ce7845b1e": {
             "process_core": {
                 "process_id": "process_id_3"
             },
@@ -1286,7 +1286,7 @@
                 "schema_minor_version": 2
             }
         },
-        "supplementary_file_0.json": {
+        "supplementary_file/22561f93-d5e0-57eb-a54e-2d9d565cc234": {
             "describedBy": "https://schema.humancellatlas.org/type/file/2.2.0/supplementary_file/supplementary_file",
             "schema_type": "file",
             "provenance": {
@@ -1298,7 +1298,7 @@
                 "format": "unknown"
             }
         },
-        "supplementary_file_1.json": {
+        "supplementary_file/507d2814-1688-54e7-b73e-2f831aa34368": {
             "describedBy": "https://schema.humancellatlas.org/type/file/2.2.0/supplementary_file/supplementary_file",
             "schema_type": "file",
             "provenance": {
@@ -1310,7 +1310,7 @@
                 "format": "unknown"
             }
         },
-        "supplementary_file_2.json": {
+        "supplementary_file/c343a47d-683f-571d-99c4-1331841b4e63": {
             "describedBy": "https://schema.humancellatlas.org/type/file/2.2.0/supplementary_file/supplementary_file",
             "schema_type": "file",
             "provenance": {
diff --git a/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json b/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
index 8ce0c37f3..22185e862 100644
--- a/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
+++ b/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
@@ -206,7 +206,7 @@
         }
     ],
     "metadata": {
-        "project_0.json": {
+        "project/90bf705c-d891-5ce2-aa54-094488b445c6": {
             "array_express_accessions": [
                 "E-MTAB-10026"
             ],
@@ -323,7 +323,7 @@
             ],
             "schema_type": "project"
         },
-        "process_0.json": {
+        "process/1ed68210-eaba-531d-ba9e-db80164d65ef": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -337,7 +337,7 @@
             },
             "schema_type": "process"
         },
-        "process_1.json": {
+        "process/37e91a9f-b04e-5313-bbc0-4c394406247e": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -351,7 +351,7 @@
             },
             "schema_type": "process"
         },
-        "process_2.json": {
+        "process/b0092a47-b19d-5b34-b004-cb8edd8c625b": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -365,7 +365,7 @@
             },
             "schema_type": "process"
         },
-        "process_3.json": {
+        "process/bd6a4a38-c44b-5d17-b2b1-d0d4c4531bf0": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -379,7 +379,7 @@
             },
             "schema_type": "process"
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/119c4135-7b77-5003-a150-f052e22c6834": {
             "biomaterial_core": {
                 "biomaterial_id": "AP2CS_pre",
                 "ncbi_taxon_id": [
@@ -411,7 +411,7 @@
                 }
             ]
         },
-        "cell_suspension_1.json": {
+        "cell_suspension/6ff38054-9296-5d4c-b238-6a3b01a15175": {
             "biomaterial_core": {
                 "biomaterial_id": "AP3CS",
                 "ncbi_taxon_id": [
@@ -443,7 +443,7 @@
                 }
             ]
         },
-        "sequence_file_0.json": {
+        "sequence_file/8da4bdb9-ab64-5a90-8bce-f0ed5106ea41": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/9.5.0/sequence_file",
             "file_core": {
                 "file_name": "Test_S1_L001_R2_001.fastq.gz",
@@ -459,7 +459,7 @@
             "read_index": "read2",
             "schema_type": "file"
         },
-        "sequence_file_1.json": {
+        "sequence_file/de17aa7d-be28-53c1-b7a3-1f4b3989e3e6": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/9.5.0/sequence_file",
             "file_core": {
                 "file_name": "Test_S1_L001_R1_001.fastq.gz",
@@ -475,7 +475,7 @@
             "read_index": "read1",
             "schema_type": "file"
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/767282b2-2fc1-5559-b020-29686b810206": {
             "cell_barcode": {
                 "barcode_length": 16,
                 "barcode_offset": 0,
@@ -512,7 +512,7 @@
                 "barcode_read": "Read 1"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/1b8dfafd-178f-5826-a661-8a022334aaeb": {
             "10x": {
                 "fastq_method": "Cellranger",
                 "fastq_method_version": "Cellranger 4.0",
@@ -543,7 +543,7 @@
             },
             "schema_type": "protocol"
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/3bee0c9a-aced-52f2-b97f-89518f826b36": {
             "biomaterial_core": {
                 "biomaterial_id": "AP2_specimen",
                 "biomaterial_name": "AP2_specimen",
@@ -580,7 +580,7 @@
             },
             "schema_type": "biomaterial"
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/46435803-7ee8-5157-8569-8a61ad50c315": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "method": {
                 "ontology": "EFO:0009337",
@@ -600,7 +600,7 @@
             },
             "schema_type": "protocol"
         },
-        "donor_organism_0.json": {
+        "donor_organism/5bc2bf2f-eb98-5510-a386-172cef38f2f2": {
             "biomaterial_core": {
                 "biomaterial_id": "AP2",
                 "biomaterial_name": "Sanger_AP2",
@@ -645,7 +645,7 @@
             "schema_type": "biomaterial",
             "sex": "unknown"
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/e7f864e3-6ba7-53c8-842f-2a05cb90e1b7": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "method": {
                 "ontology": "EFO:0009121",
diff --git a/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json b/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
index 4018030db..516e43b06 100644
--- a/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
+++ b/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
@@ -158,7 +158,7 @@
         }
     ],
     "metadata": {
-        "project_0.json": {
+        "project/90bf705c-d891-5ce2-aa54-094488b445c6": {
             "array_express_accessions": [
                 "E-MTAB-10026"
             ],
@@ -275,7 +275,7 @@
             ],
             "schema_type": "project"
         },
-        "process_0.json": {
+        "process/1f6afb64-fa14-5c6f-a474-a742540108a3": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -289,7 +289,7 @@
             },
             "schema_type": "process"
         },
-        "process_1.json": {
+        "process/ae8529dc-3bc9-5061-828a-3c5dfacded64": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -303,7 +303,7 @@
             },
             "schema_type": "process"
         },
-        "process_2.json": {
+        "process/c6b932ff-69f1-58b1-a6e6-30319f04541b": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -317,7 +317,7 @@
             },
             "schema_type": "process"
         },
-        "imaged_specimen_0.json": {
+        "imaged_specimen/0bf91a05-85df-5d7d-bcc0-a625c5921de2": {
             "biomaterial_core": {
                 "biomaterial_id": "AP3_imagedspecimen",
                 "biomaterial_name": "AP3_imagedspecimen",
@@ -336,7 +336,7 @@
             "schema_type": "biomaterial",
             "slice_thickness": 10.0
         },
-        "analysis_file_0.json": {
+        "analysis_file/2645ed0a-a291-5fe2-a262-7b796b05d647": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/6.5.0/analysis_file",
             "file_core": {
                 "content_description": [
@@ -359,7 +359,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_protocol_0.json": {
+        "analysis_protocol/5e1fa49c-f0e9-5c2c-be16-386ccd60dfd7": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/analysis/10.0.0/analysis_protocol",
             "protocol_core": {
                 "protocol_description": "10x Genomics Visium spatial sequencing samples were aligned to the human transcriptome GRCh38-3.0.0 reference (consistently with single-cell RNA-seq samples) using 10x Genomics SpaceRanger v.1.2.1 and exonic reads were used to produce mRNA count matrices for each sample. 10x Genomics SpaceRanger was also used to align paired histology images with mRNA capture spot positions in the Visium slide. The paired image was used to determine the average number of nuclei per Visium location in the tissue and used as a hyperparameter in the spatial mapping of cell type",
@@ -379,7 +379,7 @@
                 "text": "spatial analysis"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/83f14748-af1c-57aa-9088-6cb1cdd4bba4": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/sequencing/6.3.1/library_preparation_protocol",
             "end_bias": "3 prime end bias",
             "input_nucleic_acid_molecule": {
@@ -419,7 +419,7 @@
                 "barcode_read": "Read 1"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/9a0bb729-552a-5f6e-9ed6-1f988c259531": {
             "biomaterial_core": {
                 "biomaterial_id": "AP3_specimen",
                 "biomaterial_name": "AP2_specimen",
@@ -456,7 +456,7 @@
             },
             "schema_type": "biomaterial"
         },
-        "imaging_preparation_protocol_0.json": {
+        "imaging_preparation_protocol/7cd840db-f395-5a61-bd17-72c2b2319c23": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/imaging/2.3.0/imaging_preparation_protocol",
             "protocol_core": {
                 "protocol_description": "All tissues were sectioned using the Leica CX3050S cryostat and were cut at 10um. Tissue optimization was performed to obtain permeabilization time for fetal tissue (12 min).",
@@ -471,7 +471,7 @@
             },
             "schema_type": "protocol"
         },
-        "donor_organism_0.json": {
+        "donor_organism/2d7b50d8-cd06-5408-9fde-1faed01c9ab2": {
             "biomaterial_core": {
                 "biomaterial_id": "AP3",
                 "biomaterial_name": "Sanger_AP3",
@@ -514,7 +514,7 @@
             "schema_type": "biomaterial",
             "sex": "unknown"
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/c5752f73-3511-55e1-95af-040ab3924bce": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "method": {
                 "ontology": "EFO:0009121",
diff --git a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
index f8ae11f25..69f958021 100644
--- a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
+++ b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
@@ -169,7 +169,7 @@
         }
     ],
     "metadata": {
-        "process_0.json": {
+        "process/04446f99-f9ed-4a4a-82ec-203ed468cbc0": {
             "process_core": {
                 "process_id": "process_id_50"
             },
@@ -183,7 +183,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_1.json": {
+        "process/1fd499c5-f397-4bff-9af0-eb42c37d5fbe": {
             "insdc_experiment": {
                 "insdc_experiment_accession": "SRX4511357"
             },
@@ -200,7 +200,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_2.json": {
+        "process/5f1f265f-edd3-4172-b5ae-5b9d39a389d2": {
             "insdc_experiment": {
                 "insdc_experiment_accession": "SRX4511357"
             },
@@ -217,7 +217,7 @@
                 "schema_minor_version": 2
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/b111e5bf-e907-47f9-8eed-75b2ec5536c5": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -264,7 +264,7 @@
                 "schema_minor_version": 5
             }
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/d1bc1192-b584-41c2-8591-6cea79fb7729": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -292,7 +292,7 @@
                 "schema_minor_version": 3
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/70d2b85a-8055-4027-a0d9-29452a49d668": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -339,7 +339,7 @@
                 "schema_minor_version": 4
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/bf7e7b5d-2ffa-4fb7-977f-c42c5c334bbe": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -384,7 +384,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/0d352174-7bf3-44b3-9b7b-7ef3056ed085": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -410,7 +410,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/853dbcbd-8aaf-479d-8e57-134e11c61b72": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -436,7 +436,7 @@
                 "schema_minor_version": 2
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/acf142b9-0657-4ffb-b039-cd0dd5317e25": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -458,7 +458,7 @@
                 "schema_minor_version": 2
             }
         },
-        "project_0.json": {
+        "project/16ed4ad8-7319-46b2-8859-6fe1c1d73a82": {
             "contributors": [
                 {
                     "name": "Haojia,,Wu",
@@ -577,7 +577,7 @@
                 "schema_minor_version": 1
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/328e83cc-1e31-4d49-bf69-3504a7d1d4ba": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -603,7 +603,7 @@
                 "schema_minor_version": 1
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/ef41ddaf-a324-40da-a149-dd27c6bb5f04": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -631,7 +631,7 @@
                 "schema_minor_version": 2
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/fb9f9cf3-28f9-4903-b191-10217bc18da6": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
diff --git a/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json b/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
index 10d2338e7..a2ea38f31 100644
--- a/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
+++ b/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
@@ -2306,7 +2306,7 @@
         }
     ],
     "metadata": {
-        "project_0.json": {
+        "project/6504d48c-1610-43aa-8cf8-214a960e110c": {
             "content": {
                 "describedBy": "https://schema.humancellatlas.org/type/project/5.1.0/project",
                 "project_core": {
@@ -2435,7 +2435,7 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/6d98e8a4-dc7e-4ee8-aad6-9861b744e9fe": {
             "content": {
                 "genus_species": [
                     {
@@ -2467,7 +2467,7 @@
                 "document_id": "6d98e8a4-dc7e-4ee8-aad6-9861b744e9fe"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/78e48232-86ed-4b68-ae64-df114f02fa80": {
             "content": {
                 "organ": {
                     "text": "hematopoietic system",
@@ -2500,7 +2500,7 @@
                 "document_id": "78e48232-86ed-4b68-ae64-df114f02fa80"
             }
         },
-        "donor_organism_2.json": {
+        "donor_organism/7d2dcb65-b759-40b8-9eb0-7b9951b7c036": {
             "content": {
                 "is_living": true,
                 "biological_sex": "female",
@@ -2536,7 +2536,7 @@
                 "document_id": "7d2dcb65-b759-40b8-9eb0-7b9951b7c036"
             }
         },
-        "cell_suspension_3.json": {
+        "cell_suspension/01f2d4b7-7746-4dc0-88d7-4cb0b3dbb370": {
             "content": {
                 "genus_species": [
                     {
@@ -2568,7 +2568,7 @@
                 "document_id": "01f2d4b7-7746-4dc0-88d7-4cb0b3dbb370"
             }
         },
-        "specimen_from_organism_4.json": {
+        "specimen_from_organism/2fe26d80-85fb-4926-bad1-a92a6e8c20c1": {
             "content": {
                 "organ": {
                     "text": "hematopoietic system",
@@ -2601,7 +2601,7 @@
                 "document_id": "2fe26d80-85fb-4926-bad1-a92a6e8c20c1"
             }
         },
-        "donor_organism_5.json": {
+        "donor_organism/0a69e7c4-56a3-498e-a867-aaf84c1344c8": {
             "content": {
                 "is_living": true,
                 "biological_sex": "male",
@@ -2637,7 +2637,7 @@
                 "document_id": "0a69e7c4-56a3-498e-a867-aaf84c1344c8"
             }
         },
-        "cell_suspension_6.json": {
+        "cell_suspension/ed887207-2034-4c85-bbec-4e69a745d009": {
             "content": {
                 "genus_species": [
                     {
@@ -2669,7 +2669,7 @@
                 "document_id": "ed887207-2034-4c85-bbec-4e69a745d009"
             }
         },
-        "specimen_from_organism_7.json": {
+        "specimen_from_organism/24796176-5825-47a3-966a-38a865d541ab": {
             "content": {
                 "organ": {
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@@ -2702,7 +2702,7 @@
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+        "process/e77e933d-c2fc-4bad-a5f6-edc88d3c67d0": {
             "content": {
                 "process_core": {
                     "process_id": "sampling_process_88"
@@ -8807,7 +8807,7 @@
                 "document_id": "e77e933d-c2fc-4bad-a5f6-edc88d3c67d0"
             }
         },
-        "dissociation_process_52.json": {
+        "dissociation_process/7a225ade-f8e6-4af4-b0bf-f47bc06b5d4a": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8826,7 +8826,7 @@
                 "document_id": "7a225ade-f8e6-4af4-b0bf-f47bc06b5d4a"
             }
         },
-        "process_53.json": {
+        "process/9c6285c0-1c91-4850-a6a8-80efaa98d08f": {
             "content": {
                 "process_core": {
                     "process_id": "sampling_process_50"
@@ -8841,7 +8841,7 @@
                 "document_id": "9c6285c0-1c91-4850-a6a8-80efaa98d08f"
             }
         },
-        "dissociation_process_54.json": {
+        "dissociation_process/3ce935e9-281f-46ee-8613-29e931f00927": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8860,7 +8860,7 @@
                 "document_id": "3ce935e9-281f-46ee-8613-29e931f00927"
             }
         },
-        "process_55.json": {
+        "process/969de231-87de-4c29-a82c-8101024ba7ce": {
             "content": {
                 "process_core": {
                     "process_id": "sampling_process_43"
@@ -8875,7 +8875,7 @@
                 "document_id": "969de231-87de-4c29-a82c-8101024ba7ce"
             }
         },
-        "dissociation_process_56.json": {
+        "dissociation_process/580d8a8a-4c94-422f-8018-d1481c8ae353": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8894,7 +8894,7 @@
                 "document_id": "580d8a8a-4c94-422f-8018-d1481c8ae353"
             }
         },
-        "process_57.json": {
+        "process/143fa677-7e4b-43e0-9a12-a3e82b871acd": {
             "content": {
                 "process_core": {
                     "process_id": "sampling_process_98"
@@ -8909,7 +8909,7 @@
                 "document_id": "143fa677-7e4b-43e0-9a12-a3e82b871acd"
             }
         },
-        "dissociation_process_58.json": {
+        "dissociation_process/ef5baf40-74bc-4651-ab98-109129c09efe": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8928,7 +8928,7 @@
                 "document_id": "ef5baf40-74bc-4651-ab98-109129c09efe"
             }
         },
-        "process_59.json": {
+        "process/304714cd-63c6-4a5c-8756-43177eeb0fff": {
             "content": {
                 "process_core": {
                     "process_id": "sampling_process_108"
@@ -8943,7 +8943,7 @@
                 "document_id": "304714cd-63c6-4a5c-8756-43177eeb0fff"
             }
         },
-        "dissociation_process_60.json": {
+        "dissociation_process/1461d692-fc23-4076-9076-eabd324e3b72": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8962,7 +8962,7 @@
                 "document_id": "1461d692-fc23-4076-9076-eabd324e3b72"
             }
         },
-        "process_61.json": {
+        "process/cd56f223-2abb-434c-adff-d94d43057181": {
             "content": {
                 "process_core": {
                     "process_id": "sampling_process_46"
@@ -8977,7 +8977,7 @@
                 "document_id": "cd56f223-2abb-434c-adff-d94d43057181"
             }
         },
-        "dissociation_process_62.json": {
+        "dissociation_process/a91ab216-b367-48e4-9c0f-0911a3558fb6": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8996,7 +8996,7 @@
                 "document_id": "a91ab216-b367-48e4-9c0f-0911a3558fb6"
             }
         },
-        "process_63.json": {
+        "process/e2765760-381d-4aa7-bc0b-fd23b134d9fe": {
             "content": {
                 "process_core": {
                     "process_id": "sampling_process_12"
@@ -9011,7 +9011,7 @@
                 "document_id": "e2765760-381d-4aa7-bc0b-fd23b134d9fe"
             }
         },
-        "library_preparation_process_64.json": {
+        "library_preparation_process/12ea2953-06a4-4e80-8910-a27aba936b9c": {
             "content": {
                 "input_nucleic_acid_molecule": {
                     "text": "polyA RNA",
@@ -9048,7 +9048,7 @@
                 "document_id": "12ea2953-06a4-4e80-8910-a27aba936b9c"
             }
         },
-        "sequencing_process_65.json": {
+        "sequencing_process/8918d1f2-e5f9-44a7-a8c4-f743758f2464": {
             "content": {
                 "paired_ends": true,
                 "local_machine_name": "HXE",
@@ -9076,7 +9076,7 @@
                 "document_id": "8918d1f2-e5f9-44a7-a8c4-f743758f2464"
             }
         },
-        "protocol_0.json": {
+        "protocol/3cbebf0a-4aab-4525-80f4-222703d14b98": {
             "content": {
                 "protocol_core": {
                     "protocol_id": "dissociation_protocol_1"
@@ -9091,7 +9091,7 @@
                 "document_id": "3cbebf0a-4aab-4525-80f4-222703d14b98"
             }
         },
-        "protocol_1.json": {
+        "protocol/81b97ec1-f68c-4d69-be78-50d1aad7bbef": {
             "content": {
                 "protocol_core": {
                     "protocol_id": "library_preparation_protocol_1"
@@ -9110,7 +9110,7 @@
                 "document_id": "81b97ec1-f68c-4d69-be78-50d1aad7bbef"
             }
         },
-        "protocol_2.json": {
+        "protocol/e99eed63-5794-4d8d-baf9-9c6888e91e6d": {
             "content": {
                 "protocol_core": {
                     "protocol_id": "10x_v2_sequencing_protocol_1"
diff --git a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
index 4cb6e918f..3859c59bc 100644
--- a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
+++ b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
@@ -155,7 +155,7 @@
         }
     ],
     "metadata": {
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/c2f2fee0-c8dc-4511-9e4a-3db4ab6b2dce": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -187,7 +187,7 @@
                 "schema_minor_version": 1
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/948945f9-1a3e-4be0-9119-960cc008bfa9": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -209,7 +209,7 @@
                 "schema_minor_version": 1
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/7ec2d69f-714f-450e-a687-73c1c0c98b6f": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -269,7 +269,7 @@
                 "schema_minor_version": 5
             }
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/809b90b1-e216-46e9-b4e3-0c06ded1c344": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -314,7 +314,7 @@
                 "schema_minor_version": 3
             }
         },
-        "process_0.json": {
+        "process/2c7d06b8-658e-4c51-9de4-a768322f84c5": {
             "process_core": {
                 "process_id": "process_id_145"
             },
@@ -328,7 +328,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_1.json": {
+        "process/6f500f25-8ea3-46e6-a30b-c11bb991e3a2": {
             "process_core": {
                 "process_id": "process_id_7"
             },
@@ -342,7 +342,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_2.json": {
+        "process/bb7cdb75-8a5a-414b-a40b-d20dcbfa9b15": {
             "insdc_experiment": {
                 "insdc_experiment_accession": "SRX10375200"
             },
@@ -359,7 +359,7 @@
                 "schema_minor_version": 2
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/3c219f11-db59-48b9-987a-a827400b9c7a": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -406,7 +406,7 @@
                 "schema_minor_version": 4
             }
         },
-        "analysis_protocol_0.json": {
+        "analysis_protocol/d42d3386-e7b7-4a26-8477-8ba867d10e2e": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/analysis/9.2.0/analysis_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -433,7 +433,7 @@
                 "schema_minor_version": 2
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/5a1041e3-ef49-45c3-a14b-636d22aae731": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -454,7 +454,7 @@
                 "schema_minor_version": 2
             }
         },
-        "project_0.json": {
+        "project/50151324-f3ed-4358-98af-ec352a940a61": {
             "describedBy": "https://schema.humancellatlas.org/type/project/15.0.0/project",
             "schema_type": "project",
             "project_core": {
@@ -607,7 +607,7 @@
                 "schema_minor_version": 0
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/c44dab69-861e-45f2-abbf-f785a552b10a": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -629,7 +629,7 @@
                 "schema_minor_version": 2
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/56e28cda-b5a6-40e5-801e-221a7c49e47f": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -678,7 +678,7 @@
                 "schema_minor_version": 2
             }
         },
-        "analysis_file_0.json": {
+        "analysis_file/30038dc4-4de3-4fdb-abd3-a50ea36cb225": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.3.0/analysis_file",
             "schema_type": "file",
             "file_core": {
diff --git a/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json b/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
index 651581ca8..0b94b5ece 100644
--- a/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
+++ b/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
@@ -146,7 +146,7 @@
         }
     ],
     "metadata": {
-        "project_0.json": {
+        "project/90bf705c-d891-5ce2-aa54-094488b445c6": {
             "array_express_accessions": [
                 "E-MTAB-10026"
             ],
@@ -263,7 +263,7 @@
             ],
             "schema_type": "project"
         },
-        "process_0.json": {
+        "process/3ac62c33-93e1-56b4-b857-59497f5d942d": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -277,7 +277,7 @@
             },
             "schema_type": "process"
         },
-        "process_1.json": {
+        "process/ae8529dc-3bc9-5061-828a-3c5dfacded64": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -291,7 +291,7 @@
             },
             "schema_type": "process"
         },
-        "process_2.json": {
+        "process/c6b932ff-69f1-58b1-a6e6-30319f04541b": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -305,7 +305,7 @@
             },
             "schema_type": "process"
         },
-        "imaged_specimen_0.json": {
+        "imaged_specimen/0bf91a05-85df-5d7d-bcc0-a625c5921de2": {
             "biomaterial_core": {
                 "biomaterial_id": "AP3_imagedspecimen",
                 "biomaterial_name": "AP3_imagedspecimen",
@@ -324,7 +324,7 @@
             "schema_type": "biomaterial",
             "slice_thickness": 10.0
         },
-        "image_file_0.json": {
+        "image_file/b29a331e-2d7b-507f-8e47-d6151bfeeb21": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/2.5.0/image_file",
             "file_core": {
                 "content_description": [
@@ -347,7 +347,7 @@
             },
             "schema_type": "file"
         },
-        "imaging_protocol_0.json": {
+        "imaging_protocol/50150415-898c-5dff-826e-55f9cb937b93": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/imaging/11.4.0/imaging_protocol",
             "magnification": "40x",
             "microscopy_technique": {
@@ -372,7 +372,7 @@
             },
             "schema_type": "protocol"
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/9a0bb729-552a-5f6e-9ed6-1f988c259531": {
             "biomaterial_core": {
                 "biomaterial_id": "AP3_specimen",
                 "biomaterial_name": "AP2_specimen",
@@ -409,7 +409,7 @@
             },
             "schema_type": "biomaterial"
         },
-        "imaging_preparation_protocol_0.json": {
+        "imaging_preparation_protocol/7cd840db-f395-5a61-bd17-72c2b2319c23": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/imaging/2.3.0/imaging_preparation_protocol",
             "protocol_core": {
                 "protocol_description": "All tissues were sectioned using the Leica CX3050S cryostat and were cut at 10um. Tissue optimization was performed to obtain permeabilization time for fetal tissue (12 min).",
@@ -424,7 +424,7 @@
             },
             "schema_type": "protocol"
         },
-        "donor_organism_0.json": {
+        "donor_organism/2d7b50d8-cd06-5408-9fde-1faed01c9ab2": {
             "biomaterial_core": {
                 "biomaterial_id": "AP3",
                 "biomaterial_name": "Sanger_AP3",
@@ -467,7 +467,7 @@
             "schema_type": "biomaterial",
             "sex": "unknown"
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/c5752f73-3511-55e1-95af-040ab3924bce": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "method": {
                 "ontology": "EFO:0009121",
diff --git a/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
index 83d2ed630..3f690229b 100644
--- a/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
+++ b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
@@ -554,7 +554,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/74bc8f6d-ce89-4128-bb4e-f0d527e84e83": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -600,7 +600,7 @@
                 "update_date": "2018-11-02T17:38:46.014Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/20356094-b09a-4ed9-bc29-7629ab2c716c": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -647,7 +647,7 @@
                 "update_date": "2018-11-02T17:38:45.852Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/560dcb19-ddbb-4c8b-b2d9-fece4d167d7b": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -727,7 +727,7 @@
                 "update_date": "2018-11-02T17:38:45.792Z"
             }
         },
-        "analysis_file_0.json": {
+        "analysis_file/2e072336-b906-4c9b-a475-ca03f51c8452": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -740,7 +740,7 @@
                 "update_date": "2018-11-02T18:37:30.666Z"
             }
         },
-        "analysis_file_1.json": {
+        "analysis_file/2f7c43a5-30e5-443b-951b-b2b5d32bea06": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -753,7 +753,7 @@
                 "update_date": "2018-11-02T18:37:30.669Z"
             }
         },
-        "analysis_file_2.json": {
+        "analysis_file/052ee573-ff99-41b8-ad19-eea77a9cce7f": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -766,7 +766,7 @@
                 "update_date": "2018-11-02T18:37:30.669Z"
             }
         },
-        "analysis_file_3.json": {
+        "analysis_file/d2cc22c0-6281-4f31-9ca1-b6ab6f27d2b1": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -779,7 +779,7 @@
                 "update_date": "2018-11-02T18:37:33.661Z"
             }
         },
-        "analysis_file_4.json": {
+        "analysis_file/69559434-0da7-4bdd-a8f4-8be55cdcf45e": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -792,7 +792,7 @@
                 "update_date": "2018-11-02T18:37:21.650Z"
             }
         },
-        "analysis_file_5.json": {
+        "analysis_file/a1007d9b-6636-4909-9918-4aa85f99e9e7": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -805,7 +805,7 @@
                 "update_date": "2018-11-02T18:37:33.662Z"
             }
         },
-        "analysis_file_6.json": {
+        "analysis_file/265c105c-803e-4468-a67d-8ba10011fcf1": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -818,7 +818,7 @@
                 "update_date": "2018-11-02T18:37:27.648Z"
             }
         },
-        "analysis_file_7.json": {
+        "analysis_file/eb4073be-f278-47f3-9f41-8a6e7284b49d": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -831,7 +831,7 @@
                 "update_date": "2018-11-02T18:37:30.669Z"
             }
         },
-        "analysis_file_8.json": {
+        "analysis_file/487ccf21-6270-4880-b93d-6c80a7e03ca3": {
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             "file_core": {
@@ -844,7 +844,7 @@
                 "update_date": "2018-11-02T18:37:33.662Z"
             }
         },
-        "analysis_file_9.json": {
+        "analysis_file/2046e0bc-be29-4933-8f1a-094aa2bf3172": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
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@@ -857,7 +857,7 @@
                 "update_date": "2018-11-02T18:37:36.659Z"
             }
         },
-        "analysis_file_10.json": {
+        "analysis_file/f3049150-14c7-4dae-a76c-3a1af9e951a1": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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             "file_core": {
@@ -870,7 +870,7 @@
                 "update_date": "2018-11-02T18:37:36.660Z"
             }
         },
-        "analysis_file_11.json": {
+        "analysis_file/79dc63a1-8114-495f-80cb-b0c0003d1f5b": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -883,7 +883,7 @@
                 "update_date": "2018-11-02T18:37:39.656Z"
             }
         },
-        "analysis_file_12.json": {
+        "analysis_file/2097f789-3a94-44f0-adc0-b3e76233b5dc": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -896,7 +896,7 @@
                 "update_date": "2018-11-02T18:37:39.656Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/6f725a94-5c81-45e5-8d16-96520aa99703": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -915,7 +915,7 @@
                 "update_date": "2018-11-02T17:40:58.933Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/2db43e94-5208-405e-bc2a-ffade59b94c0": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -934,7 +934,7 @@
                 "update_date": "2018-11-02T17:40:59.927Z"
             }
         },
-        "sequence_file_2.json": {
+        "sequence_file/62d33b9a-d413-45d0-b8c7-c3135922b4b1": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/6.5.2/sequence_file",
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@@ -953,7 +953,7 @@
                 "update_date": "2018-11-02T17:40:58.349Z"
             }
         },
-        "project_0.json": {
+        "project/ed79221b-9713-44cd-94af-183f88c348cd": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/project/9.0.3/project",
             "schema_type": "project",
             "project_core": {
@@ -1003,7 +1003,7 @@
                 "update_date": "2018-11-02T17:38:45.615Z"
             }
         },
-        "analysis_protocol_0.json": {
+        "analysis_protocol/4d6f7580-ce81-4a81-9c2c-872fcb23b7cd": {
             "computational_method": "10x",
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/analysis/8.0.3/analysis_protocol",
             "protocol_core": {
@@ -1019,7 +1019,7 @@
                 "update_date": "2018-11-02T18:31:42.607Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/7d50cf99-37b1-413d-ab4f-37428f9ce723": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/4.3.3/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1058,7 +1058,7 @@
                 "update_date": "2018-11-02T17:38:45.659Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/94ca10f5-6937-4b13-b7ce-2935cad90f94": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/9.0.3/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1088,7 +1088,7 @@
                 "update_date": "2018-11-02T17:38:45.681Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/b0dac4c3-a81c-4241-ba52-3e468746618b": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1107,7 +1107,7 @@
                 "update_date": "2018-11-02T17:38:45.674Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/5077e4f3-3be8-463a-8cc9-024d7905c65e": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1130,7 +1130,7 @@
                 "update_date": "2018-11-02T17:38:45.601Z"
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/139304c2-732a-4603-97e5-2db92ab6ec9f": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/8.2.6/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1162,7 +1162,7 @@
                 "update_date": "2018-11-02T17:38:45.683Z"
             }
         },
-        "analysis_process_0.json": {
+        "analysis_process/b7a172d6-dbb1-41f3-8ae4-7807e1eca803": {
             "analysis_run_type": "run",
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/process/analysis/8.0.3/analysis_process",
             "input_bundles": [
@@ -1326,7 +1326,7 @@
                 "update_date": "2018-11-02T18:31:42.681Z"
             }
         },
-        "process_0.json": {
+        "process/8818b2e9-1c7d-4dd3-9acc-64de03c6f304": {
             "process_core": {
                 "process_id": "bundle1"
             },
@@ -1338,7 +1338,7 @@
                 "update_date": "2018-11-02T17:38:46.112Z"
             }
         },
-        "process_1.json": {
+        "process/3809cc86-0ccb-4d2e-8520-24dcd9eda874": {
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@@ -1350,7 +1350,7 @@
                 "update_date": "2018-11-02T17:38:45.753Z"
             }
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-        "process_2.json": {
+        "process/8fa0c554-2503-408b-9f3b-6145463db850": {
             "process_core": {
                 "process_id": "process_id_1"
             },
diff --git a/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
index 5459e5d70..59222f8ec 100644
--- a/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
+++ b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
@@ -998,7 +998,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/02201088-f3be-46ce-bb04-e7c464189900": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1022,7 +1022,7 @@
                 "update_date": "2018-10-16T08:05:07.167Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/4c2b6ea0-43eb-4e37-b973-f2bdbc724e92": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1057,7 +1057,7 @@
                 "update_date": "2018-10-16T08:03:01.801Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/d919428e-d58b-4815-b36a-c9f186df6582": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1103,7 +1103,7 @@
                 "update_date": "2018-10-16T07:55:45.931Z"
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         },
-        "analysis_file_0.json": {
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@@ -1116,7 +1116,7 @@
                 "update_date": "2018-10-24T23:40:09.753Z"
             }
         },
-        "analysis_file_1.json": {
+        "analysis_file/884d5482-3432-4259-b551-955ba35becc2": {
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             "schema_type": "file",
             "file_core": {
@@ -1129,7 +1129,7 @@
                 "update_date": "2018-10-24T23:40:06.755Z"
             }
         },
-        "analysis_file_2.json": {
+        "analysis_file/77d3b337-d169-44a5-9b6a-be1c6d1b31b7": {
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@@ -1142,7 +1142,7 @@
                 "update_date": "2018-10-24T23:40:09.754Z"
             }
         },
-        "analysis_file_3.json": {
+        "analysis_file/b115459d-d690-418c-a608-48ede1cc5a43": {
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             "schema_type": "file",
             "file_core": {
@@ -1155,7 +1155,7 @@
                 "update_date": "2018-10-24T23:40:06.755Z"
             }
         },
-        "analysis_file_4.json": {
+        "analysis_file/05ea34ca-995b-4c30-9f87-81ad07e61305": {
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             "schema_type": "file",
             "file_core": {
@@ -1168,7 +1168,7 @@
                 "update_date": "2018-10-24T23:40:12.765Z"
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-        "analysis_file_5.json": {
+        "analysis_file/03e676dd-1718-40e0-a246-f3c6a594e334": {
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@@ -1181,7 +1181,7 @@
                 "update_date": "2018-10-24T23:40:18.754Z"
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-        "analysis_file_6.json": {
+        "analysis_file/19fee968-3d70-43a1-a64a-a778d656bd2e": {
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             "file_core": {
@@ -1194,7 +1194,7 @@
                 "update_date": "2018-10-24T23:40:21.780Z"
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-        "analysis_file_7.json": {
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@@ -1207,7 +1207,7 @@
                 "update_date": "2018-10-24T23:40:21.759Z"
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-        "analysis_file_8.json": {
+        "analysis_file/e8972873-6e54-40d8-85ca-790a8d5688d0": {
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             "file_core": {
@@ -1220,7 +1220,7 @@
                 "update_date": "2018-10-24T23:40:21.780Z"
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-        "analysis_file_9.json": {
+        "analysis_file/babd98f7-c1ae-4a5d-bf85-7cb347a3ce96": {
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             "file_core": {
@@ -1233,7 +1233,7 @@
                 "update_date": "2018-10-24T23:40:24.806Z"
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-        "analysis_file_10.json": {
+        "analysis_file/3314dd32-6acf-4841-83a4-03d4807d1365": {
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@@ -1246,7 +1246,7 @@
                 "update_date": "2018-10-24T23:40:24.810Z"
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         },
-        "analysis_file_11.json": {
+        "analysis_file/f6e76583-bc31-41e1-8695-7198e7842ea0": {
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             "file_core": {
@@ -1259,7 +1259,7 @@
                 "update_date": "2018-10-24T23:40:24.812Z"
             }
         },
-        "analysis_file_12.json": {
+        "analysis_file/f2473460-2b19-4b16-97c7-6eaa9060df6f": {
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             "file_core": {
@@ -1272,7 +1272,7 @@
                 "update_date": "2018-10-24T23:40:12.765Z"
             }
         },
-        "analysis_file_13.json": {
+        "analysis_file/0fa2c00a-02e4-444d-998d-b812d647565f": {
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             "file_core": {
@@ -1285,7 +1285,7 @@
                 "update_date": "2018-10-24T23:40:06.756Z"
             }
         },
-        "analysis_file_14.json": {
+        "analysis_file/09989709-cca8-4f82-a07f-6fa6a9fa3e03": {
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             "schema_type": "file",
             "file_core": {
@@ -1298,7 +1298,7 @@
                 "update_date": "2018-10-24T23:40:27.764Z"
             }
         },
-        "analysis_file_15.json": {
+        "analysis_file/020634de-da4b-47bb-b084-8c2d7e70ae17": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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             "file_core": {
@@ -1311,7 +1311,7 @@
                 "update_date": "2018-10-24T23:40:15.768Z"
             }
         },
-        "analysis_file_16.json": {
+        "analysis_file/f6a47716-c494-4229-85e9-bd1f20afa5d1": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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             "file_core": {
@@ -1324,7 +1324,7 @@
                 "update_date": "2018-10-24T23:40:18.758Z"
             }
         },
-        "analysis_file_17.json": {
+        "analysis_file/c82423e7-a621-4fee-bed2-5efa916124e3": {
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             "file_core": {
@@ -1337,7 +1337,7 @@
                 "update_date": "2018-10-24T23:40:27.770Z"
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-        "analysis_file_18.json": {
+        "analysis_file/401a3d93-c4c9-4f59-960e-41de71839619": {
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@@ -1350,7 +1350,7 @@
                 "update_date": "2018-10-24T23:40:27.759Z"
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-        "analysis_file_19.json": {
+        "analysis_file/f06c17a5-8197-4b6f-928a-55ffa8d796d2": {
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             "file_core": {
@@ -1363,7 +1363,7 @@
                 "update_date": "2018-10-24T23:40:30.762Z"
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-        "analysis_file_20.json": {
+        "analysis_file/95bdd09a-cc14-4a7b-b0f8-96cd4d6dcb1c": {
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@@ -1376,7 +1376,7 @@
                 "update_date": "2018-10-24T23:40:30.757Z"
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-        "analysis_file_21.json": {
+        "analysis_file/a3d20426-80af-4c2b-90a6-6e6644539aad": {
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@@ -1389,7 +1389,7 @@
                 "update_date": "2018-10-24T23:40:30.762Z"
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-        "analysis_file_22.json": {
+        "analysis_file/f6cdb1dd-df7c-4dab-bdd1-4bb59a2044f7": {
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@@ -1402,7 +1402,7 @@
                 "update_date": "2018-10-24T23:40:33.825Z"
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-        "analysis_file_23.json": {
+        "analysis_file/4de506d4-78d1-4de2-9780-e91f8a9d7b6d": {
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             "file_core": {
@@ -1415,7 +1415,7 @@
                 "update_date": "2018-10-24T23:40:33.825Z"
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-        "analysis_file_24.json": {
+        "analysis_file/c8aa1527-f40c-4e50-b7ca-51646562422b": {
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@@ -1428,7 +1428,7 @@
                 "update_date": "2018-10-24T23:40:33.831Z"
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-        "analysis_file_25.json": {
+        "analysis_file/6cc5378a-295b-4e72-80a2-370434fd2b94": {
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             "file_core": {
@@ -1441,7 +1441,7 @@
                 "update_date": "2018-10-24T23:40:36.805Z"
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-        "analysis_file_26.json": {
+        "analysis_file/75178504-d0ef-4d32-a3e6-6faa1026be84": {
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@@ -1454,7 +1454,7 @@
                 "update_date": "2018-10-24T23:40:36.794Z"
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-        "analysis_file_27.json": {
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@@ -1467,7 +1467,7 @@
                 "update_date": "2018-10-24T23:40:36.798Z"
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@@ -1480,7 +1480,7 @@
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@@ -1493,7 +1493,7 @@
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@@ -1506,7 +1506,7 @@
                 "update_date": "2018-10-24T23:40:39.800Z"
             }
         },
-        "analysis_file_31.json": {
+        "analysis_file/08be64a7-9ef4-4d17-b7d8-41f79c24c987": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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@@ -1519,7 +1519,7 @@
                 "update_date": "2018-10-24T23:40:42.786Z"
             }
         },
-        "analysis_file_32.json": {
+        "analysis_file/770c9eb2-f63f-4bd2-94c1-e2b6da1feeac": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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@@ -1532,7 +1532,7 @@
                 "update_date": "2018-10-24T23:40:42.787Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/b66c9d19-322c-42d4-8b65-3478fd0afa6a": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/6.5.2/sequence_file",
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@@ -1550,7 +1550,7 @@
                 "update_date": "2018-10-16T08:27:14.280Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/02c8352d-b2ba-4de4-a574-335eb9a61e0e": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1568,7 +1568,7 @@
                 "update_date": "2018-10-16T08:27:16.223Z"
             }
         },
-        "project_0.json": {
+        "project/08e7b6ba-5825-47e9-be2d-7978533c5f8c": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/project/9.0.3/project",
             "schema_type": "project",
             "project_core": {
@@ -1636,7 +1636,7 @@
                 "update_date": "2018-10-16T07:55:45.727Z"
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-        "analysis_protocol_0.json": {
+        "analysis_protocol/7a56f120-c055-4b63-acdf-8cc80c3555c1": {
             "computational_method": "SmartSeq2SingleCell",
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/analysis/8.0.3/analysis_protocol",
             "protocol_core": {
@@ -1652,7 +1652,7 @@
                 "update_date": "2018-10-24T23:35:51.714Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/7faadd95-bcee-4627-8990-04b79cf617f9": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/4.3.3/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1680,7 +1680,7 @@
                 "update_date": "2018-10-16T07:54:00.211Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/dcf48263-da0f-4fb8-9af7-2cb0e3af5b09": {
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             "schema_type": "protocol",
             "protocol_core": {
@@ -1700,7 +1700,7 @@
                 "update_date": "2018-10-16T07:54:00.089Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/2f0c9a0e-bf38-4df9-ba9c-d3502b843e2b": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1721,7 +1721,7 @@
                 "update_date": "2018-10-16T07:54:00.103Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/d9fdfade-52d2-40df-b299-e9aa292ea120": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1739,7 +1739,7 @@
                 "update_date": "2018-10-16T07:54:00.229Z"
             }
         },
-        "analysis_process_0.json": {
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             "analysis_run_type": "run",
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/process/analysis/8.0.3/analysis_process",
             "input_bundles": [
@@ -2183,7 +2183,7 @@
                 "update_date": "2018-10-24T23:35:57.706Z"
             }
         },
-        "process_0.json": {
+        "process/33d33846-5287-425b-a94f-2c3ec14a323c": {
             "process_core": {
                 "process_id": "SRR3564380"
             },
@@ -2195,7 +2195,7 @@
                 "update_date": "2018-10-16T08:11:24.186Z"
             }
         },
-        "process_1.json": {
+        "process/34cb3bc6-661b-4bbd-b51c-0b5e6f5e248d": {
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@@ -2207,7 +2207,7 @@
                 "update_date": "2018-10-16T08:08:00.774Z"
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-        "process_2.json": {
+        "process/4a1432a1-ae18-45f2-b574-9869b7242289": {
             "process_core": {
                 "process_id": "process_id_8"
             },
diff --git a/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index 653d6ce95..529b21fa1 100644
--- a/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
+++ b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
@@ -914,7 +914,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
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             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -944,7 +944,7 @@
                 "update_date": "2018-10-11T21:18:13.146Z"
             }
         },
-        "organoid_0.json": {
+        "organoid/2d8282f0-6cbb-4d5a-822c-4b01718b4d0d": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.3.8/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -979,7 +979,7 @@
                 "update_date": "2018-10-11T21:18:12.864Z"
             }
         },
-        "organoid_1.json": {
+        "organoid/b7214641-1ac5-4f60-b795-cb33a7c25434": {
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             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1014,7 +1014,7 @@
                 "update_date": "2018-10-11T21:18:12.763Z"
             }
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-        "organoid_2.json": {
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             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1049,7 +1049,7 @@
                 "update_date": "2018-10-11T21:18:06.730Z"
             }
         },
-        "organoid_3.json": {
+        "organoid/73f10dad-afc5-4d1d-a71c-4a8b6fff9172": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.3.8/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1084,7 +1084,7 @@
                 "update_date": "2018-10-11T21:18:06.725Z"
             }
         },
-        "cell_line_0.json": {
+        "cell_line/c532cca7-67c6-4617-ac47-5b91652621a5": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1131,7 +1131,7 @@
                 "update_date": "2018-10-11T21:18:06.721Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/c8e14a8e-81f9-4109-bb27-4bb3029240c1": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1168,7 +1168,7 @@
                 "update_date": "2018-10-11T21:18:06.720Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/d4c29b1a-f23c-4511-a2ae-097772d90254": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1213,7 +1213,7 @@
                 "update_date": "2018-10-11T21:18:06.768Z"
             }
         },
-        "cell_line_1.json": {
+        "cell_line/e924c114-e3cd-4060-9c8e-3d980ec7fcbe": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1260,7 +1260,7 @@
                 "update_date": "2018-10-11T21:18:06.679Z"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/5bd6106c-0158-4c2c-8c60-32019c599c83": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1297,7 +1297,7 @@
                 "update_date": "2018-10-11T21:18:06.627Z"
             }
         },
-        "donor_organism_1.json": {
+        "donor_organism/ef7e6ac7-172a-4b24-9620-fc909a5e9c6c": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1342,7 +1342,7 @@
                 "update_date": "2018-10-11T21:18:06.720Z"
             }
         },
-        "cell_line_2.json": {
+        "cell_line/a3651f83-dee6-49b2-ba4e-0ce20f02467d": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1389,7 +1389,7 @@
                 "update_date": "2018-10-11T21:18:06.795Z"
             }
         },
-        "specimen_from_organism_2.json": {
+        "specimen_from_organism/8f328973-9bc0-46b9-8a1f-38893e77b3b5": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1426,7 +1426,7 @@
                 "update_date": "2018-10-11T21:18:06.643Z"
             }
         },
-        "donor_organism_2.json": {
+        "donor_organism/931528fa-820b-49ca-af1e-ae9a2c0ef551": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1471,7 +1471,7 @@
                 "update_date": "2018-10-11T21:18:06.762Z"
             }
         },
-        "cell_line_3.json": {
+        "cell_line/6a16de30-176d-4488-81de-9337a1a6d8c5": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1518,7 +1518,7 @@
                 "update_date": "2018-10-11T21:18:06.634Z"
             }
         },
-        "specimen_from_organism_3.json": {
+        "specimen_from_organism/82368936-7b99-4864-9f49-b8fee3906d47": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1555,7 +1555,7 @@
                 "update_date": "2018-10-11T21:18:06.743Z"
             }
         },
-        "donor_organism_3.json": {
+        "donor_organism/96757312-0221-447a-84f1-7a737b5afd01": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1600,7 +1600,7 @@
                 "update_date": "2018-10-11T21:18:06.767Z"
             }
         },
-        "analysis_file_0.json": {
+        "analysis_file/cf93f747-1392-4670-8eb3-3ac60a96855e": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1613,7 +1613,7 @@
                 "update_date": "2018-10-18T20:39:13.335Z"
             }
         },
-        "analysis_file_1.json": {
+        "analysis_file/477c0b3e-4a06-4214-8f27-58199ba63528": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1626,7 +1626,7 @@
                 "update_date": "2018-10-18T20:39:16.337Z"
             }
         },
-        "analysis_file_2.json": {
+        "analysis_file/ad6d5170-d74b-408c-af6b-25a14315c9da": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1639,7 +1639,7 @@
                 "update_date": "2018-10-18T20:39:25.337Z"
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-        "analysis_file_3.json": {
+        "analysis_file/50be9b67-fae5-4472-9719-478dd1303d6e": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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@@ -1652,7 +1652,7 @@
                 "update_date": "2018-10-18T20:39:22.340Z"
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-        "analysis_file_4.json": {
+        "analysis_file/fd16b62e-e540-4f03-8ba0-07d0c204e3c8": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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             "file_core": {
@@ -1665,7 +1665,7 @@
                 "update_date": "2018-10-18T20:37:28.333Z"
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-        "analysis_file_5.json": {
+        "analysis_file/3c41b5b6-f480-4d47-8c5e-155e7c1adf54": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1678,7 +1678,7 @@
                 "update_date": "2018-10-18T20:40:01.344Z"
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-        "analysis_file_6.json": {
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             "file_core": {
@@ -1691,7 +1691,7 @@
                 "update_date": "2018-10-18T20:45:01.366Z"
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-        "analysis_file_7.json": {
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             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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@@ -1704,7 +1704,7 @@
                 "update_date": "2018-10-18T20:39:10.339Z"
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-        "analysis_file_8.json": {
+        "analysis_file/af025a74-53f1-4972-b50d-53095b5ffac2": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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@@ -1717,7 +1717,7 @@
                 "update_date": "2018-10-18T20:39:40.335Z"
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         },
-        "analysis_file_9.json": {
+        "analysis_file/e8395271-7c8e-4ec4-9598-495df43fe5fd": {
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             "file_core": {
@@ -1730,7 +1730,7 @@
                 "update_date": "2018-10-18T20:39:55.336Z"
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-        "analysis_file_10.json": {
+        "analysis_file/211a8fbf-b190-4576-ac2f-2b1a91743abb": {
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@@ -1743,7 +1743,7 @@
                 "update_date": "2018-10-18T20:39:58.363Z"
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-        "analysis_file_11.json": {
+        "analysis_file/17222e3a-5757-45e9-9dfe-c4b6aa10f28a": {
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@@ -1756,7 +1756,7 @@
                 "update_date": "2018-10-18T20:39:58.363Z"
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-        "analysis_file_12.json": {
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@@ -1769,7 +1769,7 @@
                 "update_date": "2018-10-18T20:40:13.334Z"
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-        "sequence_file_0.json": {
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@@ -1786,7 +1786,7 @@
                 "update_date": "2018-10-18T20:32:16.894Z"
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@@ -1803,7 +1803,7 @@
                 "update_date": "2018-10-18T20:32:18.864Z"
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@@ -1820,7 +1820,7 @@
                 "update_date": "2018-10-18T20:32:20.845Z"
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@@ -1834,7 +1834,7 @@
                 "update_date": "2018-10-18T20:40:54.699Z"
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@@ -1848,7 +1848,7 @@
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@@ -1862,7 +1862,7 @@
                 "update_date": "2018-10-18T20:40:57.146Z"
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-        "project_0.json": {
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@@ -1923,7 +1923,7 @@
                 "update_date": "2018-10-11T21:18:06.651Z"
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-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/92277226-bf78-4df9-a594-5190a8790a14": {
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@@ -1964,7 +1964,7 @@
                 "update_date": "2018-10-11T21:18:12.704Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/102cdbf3-b0e5-4dd5-9168-51150a9ebb6b": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1988,7 +1988,7 @@
                 "update_date": "2018-10-11T21:18:12.667Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/755762e0-7aff-48ed-a7d4-d3ea4005758f": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
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@@ -2014,7 +2014,7 @@
                 "update_date": "2018-10-11T21:18:12.751Z"
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         },
-        "differentiation_protocol_0.json": {
+        "differentiation_protocol/8f4a8e7c-e7ee-44dc-8e09-f4012355060f": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/1.3.0/differentiation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -2038,7 +2038,7 @@
                 "update_date": "2018-10-11T21:18:12.764Z"
             }
         },
-        "ipsc_induction_protocol_0.json": {
+        "ipsc_induction_protocol/cdfe38f2-1d90-4700-a199-d8105ce299df": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.0.1/ipsc_induction_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -2061,7 +2061,7 @@
                 "update_date": "2018-10-11T21:18:06.713Z"
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-        "analysis_process_0.json": {
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@@ -2225,7 +2225,7 @@
                 "update_date": "2018-10-18T20:32:19.562Z"
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-        "process_0.json": {
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@@ -2237,7 +2237,7 @@
                 "update_date": "2018-10-11T21:18:12.743Z"
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-        "process_1.json": {
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@@ -2249,7 +2249,7 @@
                 "update_date": "2018-10-11T21:18:10.787Z"
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-        "process_2.json": {
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@@ -2261,7 +2261,7 @@
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-        "process_3.json": {
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             },
@@ -2273,7 +2273,7 @@
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-        "process_4.json": {
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             },
@@ -2285,7 +2285,7 @@
                 "update_date": "2018-10-11T21:18:10.611Z"
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-        "process_5.json": {
+        "process/d5ac7f5f-9a50-403e-9b8d-6e983a099826": {
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                 "process_id": "process_id_13"
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@@ -2297,7 +2297,7 @@
                 "update_date": "2018-10-11T21:18:11.909Z"
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-        "process_6.json": {
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             },
@@ -2309,7 +2309,7 @@
                 "update_date": "2018-10-11T21:18:10.866Z"
             }
         },
-        "process_7.json": {
+        "process/45c67d31-0b05-4d5e-b215-e50e1b2b125c": {
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                 "process_id": "process_id_2"
             },
@@ -2321,7 +2321,7 @@
                 "update_date": "2018-10-11T21:18:10.656Z"
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-        "process_8.json": {
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@@ -2333,7 +2333,7 @@
                 "update_date": "2018-10-11T21:18:10.879Z"
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-        "process_9.json": {
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             },
@@ -2345,7 +2345,7 @@
                 "update_date": "2018-10-11T21:18:10.699Z"
             }
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-        "process_10.json": {
+        "process/76e685c9-fcf2-4582-bbfa-5e0369eb5bdb": {
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@@ -2357,7 +2357,7 @@
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-        "process_11.json": {
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@@ -2369,7 +2369,7 @@
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-        "process_12.json": {
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@@ -2381,7 +2381,7 @@
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-        "process_13.json": {
+        "process/bb2365b9-5a5b-436f-92e3-4fc6d86a9efd": {
             "process_core": {
                 "process_id": "process_id_4"
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diff --git a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index c4507901f..c8712b690 100644
--- a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
+++ b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
@@ -914,7 +914,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
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@@ -944,7 +944,7 @@
                 "update_date": "2018-10-11T21:18:13.146Z"
             }
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-        "organoid_0.json": {
+        "organoid/2d8282f0-6cbb-4d5a-822c-4b01718b4d0d": {
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             "schema_type": "biomaterial",
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@@ -979,7 +979,7 @@
                 "update_date": "2018-10-11T21:18:12.864Z"
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-        "organoid_1.json": {
+        "organoid/b7214641-1ac5-4f60-b795-cb33a7c25434": {
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             "schema_type": "biomaterial",
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@@ -1014,7 +1014,7 @@
                 "update_date": "2018-10-11T21:18:12.763Z"
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-        "organoid_2.json": {
+        "organoid/308eea51-d14b-4036-8cd1-cfd81d7532c3": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.3.8/organoid",
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             "biomaterial_core": {
@@ -1049,7 +1049,7 @@
                 "update_date": "2018-10-11T21:18:06.730Z"
             }
         },
-        "organoid_3.json": {
+        "organoid/73f10dad-afc5-4d1d-a71c-4a8b6fff9172": {
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             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1084,7 +1084,7 @@
                 "update_date": "2018-10-11T21:18:06.725Z"
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         },
-        "cell_line_0.json": {
+        "cell_line/c532cca7-67c6-4617-ac47-5b91652621a5": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1131,7 +1131,7 @@
                 "update_date": "2018-10-11T21:18:06.721Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/c8e14a8e-81f9-4109-bb27-4bb3029240c1": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1168,7 +1168,7 @@
                 "update_date": "2018-10-11T21:18:06.720Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/d4c29b1a-f23c-4511-a2ae-097772d90254": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1213,7 +1213,7 @@
                 "update_date": "2018-10-11T21:18:06.768Z"
             }
         },
-        "cell_line_1.json": {
+        "cell_line/e924c114-e3cd-4060-9c8e-3d980ec7fcbe": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1260,7 +1260,7 @@
                 "update_date": "2018-10-11T21:18:06.679Z"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/5bd6106c-0158-4c2c-8c60-32019c599c83": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1297,7 +1297,7 @@
                 "update_date": "2018-10-11T21:18:06.627Z"
             }
         },
-        "donor_organism_1.json": {
+        "donor_organism/ef7e6ac7-172a-4b24-9620-fc909a5e9c6c": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1342,7 +1342,7 @@
                 "update_date": "2018-10-11T21:18:06.720Z"
             }
         },
-        "cell_line_2.json": {
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             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_line",
             "schema_type": "biomaterial",
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@@ -1389,7 +1389,7 @@
                 "update_date": "2018-10-11T21:18:06.795Z"
             }
         },
-        "specimen_from_organism_2.json": {
+        "specimen_from_organism/8f328973-9bc0-46b9-8a1f-38893e77b3b5": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
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             "biomaterial_core": {
@@ -1426,7 +1426,7 @@
                 "update_date": "2018-10-11T21:18:06.643Z"
             }
         },
-        "donor_organism_2.json": {
+        "donor_organism/931528fa-820b-49ca-af1e-ae9a2c0ef551": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1471,7 +1471,7 @@
                 "update_date": "2018-10-11T21:18:06.762Z"
             }
         },
-        "cell_line_3.json": {
+        "cell_line/6a16de30-176d-4488-81de-9337a1a6d8c5": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1518,7 +1518,7 @@
                 "update_date": "2018-10-11T21:18:06.634Z"
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         },
-        "specimen_from_organism_3.json": {
+        "specimen_from_organism/82368936-7b99-4864-9f49-b8fee3906d47": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1555,7 +1555,7 @@
                 "update_date": "2018-10-11T21:18:06.743Z"
             }
         },
-        "donor_organism_3.json": {
+        "donor_organism/96757312-0221-447a-84f1-7a737b5afd01": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1600,7 +1600,7 @@
                 "update_date": "2018-10-11T21:18:06.767Z"
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-        "analysis_file_0.json": {
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@@ -1613,7 +1613,7 @@
                 "update_date": "2018-10-18T20:39:13.335Z"
             }
         },
-        "analysis_file_1.json": {
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@@ -1626,7 +1626,7 @@
                 "update_date": "2018-10-18T20:39:16.337Z"
             }
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-        "analysis_file_2.json": {
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@@ -1639,7 +1639,7 @@
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-        "analysis_file_3.json": {
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@@ -1652,7 +1652,7 @@
                 "update_date": "2018-10-18T20:39:22.340Z"
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-        "analysis_file_4.json": {
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@@ -1665,7 +1665,7 @@
                 "update_date": "2018-10-18T20:37:28.333Z"
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-        "analysis_file_5.json": {
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@@ -1678,7 +1678,7 @@
                 "update_date": "2018-10-18T20:40:01.344Z"
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-        "analysis_file_6.json": {
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@@ -1691,7 +1691,7 @@
                 "update_date": "2018-10-18T20:45:01.366Z"
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-        "analysis_file_7.json": {
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@@ -1704,7 +1704,7 @@
                 "update_date": "2018-10-18T20:39:10.339Z"
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-        "analysis_file_8.json": {
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@@ -1717,7 +1717,7 @@
                 "update_date": "2018-10-18T20:39:40.335Z"
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-        "analysis_file_9.json": {
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@@ -1730,7 +1730,7 @@
                 "update_date": "2018-10-18T20:39:55.336Z"
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-        "analysis_file_10.json": {
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@@ -1743,7 +1743,7 @@
                 "update_date": "2018-10-18T20:39:58.363Z"
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-        "analysis_file_11.json": {
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@@ -1756,7 +1756,7 @@
                 "update_date": "2018-10-18T20:39:58.363Z"
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-        "analysis_file_12.json": {
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@@ -1769,7 +1769,7 @@
                 "update_date": "2018-10-18T20:40:13.334Z"
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-        "sequence_file_0.json": {
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@@ -1786,7 +1786,7 @@
                 "update_date": "2018-10-18T20:32:16.894Z"
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@@ -1803,7 +1803,7 @@
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@@ -1820,7 +1820,7 @@
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@@ -1834,7 +1834,7 @@
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diff --git a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
index 3676cbfc0..ab314980f 100644
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diff --git a/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json b/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json
index cb038433c..40fff54ea 100644
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@@ -2306,7 +2306,7 @@
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@@ -8875,7 +8875,7 @@
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@@ -8894,7 +8894,7 @@
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@@ -8909,7 +8909,7 @@
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@@ -8928,7 +8928,7 @@
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@@ -8943,7 +8943,7 @@
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@@ -8962,7 +8962,7 @@
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@@ -8977,7 +8977,7 @@
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@@ -8996,7 +8996,7 @@
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@@ -9011,7 +9011,7 @@
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@@ -9048,7 +9048,7 @@
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@@ -9076,7 +9076,7 @@
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@@ -9091,7 +9091,7 @@
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@@ -9110,7 +9110,7 @@
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diff --git a/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json b/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
index a74884da3..0791ca7f3 100644
--- a/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
+++ b/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
@@ -181,7 +181,7 @@
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@@ -204,7 +204,7 @@
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@@ -227,7 +227,7 @@
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@@ -250,7 +250,7 @@
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@@ -273,7 +273,7 @@
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@@ -296,7 +296,7 @@
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@@ -319,7 +319,7 @@
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@@ -342,7 +342,7 @@
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diff --git a/test/indexer/data/4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json b/test/indexer/data/4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json
index 0ed08faae..f3cc0def4 100644
--- a/test/indexer/data/4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json
+++ b/test/indexer/data/4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json
@@ -182,7 +182,7 @@
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@@ -299,7 +299,7 @@
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@@ -313,7 +313,7 @@
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@@ -327,7 +327,7 @@
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@@ -341,7 +341,7 @@
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@@ -373,7 +373,7 @@
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@@ -397,7 +397,7 @@
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@@ -428,7 +428,7 @@
                 "text": "enzymatic dissociation"
             }
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@@ -465,7 +465,7 @@
                 "barcode_read": "Read 1"
             }
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-        "specimen_from_organism_0.json": {
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@@ -502,7 +502,7 @@
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-        "enrichment_protocol_0.json": {
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@@ -523,7 +523,7 @@
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-        "enrichment_protocol_1.json": {
+        "enrichment_protocol/9462efe9-1b1a-5a18-81bb-e510137ae743": {
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@@ -543,7 +543,7 @@
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-        "treatment_protocol_0.json": {
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             "media": "RPMI 1640",
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@@ -574,7 +574,7 @@
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-        "donor_organism_0.json": {
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                 "biomaterial_name": "Sanger_AP1",
@@ -619,7 +619,7 @@
             "schema_type": "biomaterial",
             "sex": "unknown"
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-        "collection_protocol_0.json": {
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diff --git a/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json b/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json
index 097d41d96..95d3b67ec 100644
--- a/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json
+++ b/test/indexer/data/56a338fe-7554-4b5d-96a2-7df127a7640b.dss.hca.json
@@ -26,7 +26,7 @@
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@@ -43,7 +43,7 @@
                 "document_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127"
             }
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-        "protocol_1.json": {
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@@ -60,7 +60,7 @@
                 "document_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6"
             }
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-        "protocol_2.json": {
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@@ -81,7 +81,7 @@
                 "document_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643"
             }
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-        "protocol_3.json": {
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@@ -97,7 +97,7 @@
                 "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
             }
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-        "project_0.json": {
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@@ -221,7 +221,7 @@
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@@ -252,7 +252,7 @@
                 "document_id": "04e58fb0-384e-4997-a9e9-575d9887e737"
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-        "specimen_from_organism_1.json": {
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@@ -284,7 +284,7 @@
                 "document_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c"
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-        "donor_organism_2.json": {
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@@ -329,7 +329,7 @@
                 "document_id": "689311a2-bfaf-4196-a753-554e69ab59b2"
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@@ -347,7 +347,7 @@
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@@ -362,7 +362,7 @@
                 "document_id": "0763320a-e0c4-4c07-b150-b83650fbef68"
             }
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-        "enrichment_process_2.json": {
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@@ -379,7 +379,7 @@
                 "document_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4"
             }
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-        "library_preparation_process_3.json": {
+        "library_preparation_process/687065f3-c70f-46c3-8452-a5eead33a1bf": {
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@@ -408,7 +408,7 @@
                 "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
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@@ -433,7 +433,7 @@
                 "document_id": "4624400f-00c5-476a-9bd6-589e87ddb0fe"
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-        "sequence_file_0.json": {
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@@ -449,7 +449,7 @@
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diff --git a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
index fc7618848..190412c61 100644
--- a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
+++ b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
@@ -914,7 +914,7 @@
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@@ -929,7 +929,7 @@
                 "update_date": "2018-10-10T02:23:43.182Z"
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-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/b5894cf5-ecdc-4ea6-a0b9-5335ab678c7a": {
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@@ -966,7 +966,7 @@
                 "update_date": "2018-10-10T02:23:43.038Z"
             }
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-        "donor_organism_0.json": {
+        "donor_organism/242e38d2-c975-47ee-800a-6645b47e92d2": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
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@@ -997,7 +997,7 @@
                 "update_date": "2018-10-10T02:23:42.998Z"
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-        "analysis_file_0.json": {
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@@ -1010,7 +1010,7 @@
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+        "analysis_file/8b4ed86d-99a8-4665-8f56-5a54fac6cb12": {
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@@ -1023,7 +1023,7 @@
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@@ -1036,7 +1036,7 @@
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-        "analysis_file_3.json": {
+        "analysis_file/0b34a80b-c818-4010-b193-e44a77036e27": {
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@@ -1049,7 +1049,7 @@
                 "update_date": "2018-10-10T03:06:57.736Z"
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@@ -1062,7 +1062,7 @@
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+        "analysis_file/1d77c6c5-24b6-4d43-ad5d-b02fba050025": {
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@@ -1075,7 +1075,7 @@
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@@ -1088,7 +1088,7 @@
                 "update_date": "2018-10-10T03:07:05.571Z"
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@@ -1101,7 +1101,7 @@
                 "update_date": "2018-10-10T03:07:08.560Z"
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@@ -1114,7 +1114,7 @@
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@@ -1127,7 +1127,7 @@
                 "update_date": "2018-10-10T03:07:08.939Z"
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-        "analysis_file_10.json": {
+        "analysis_file/21319798-fe9e-40a4-bcdb-a4c0780ee7bf": {
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@@ -1140,7 +1140,7 @@
                 "update_date": "2018-10-10T03:07:09.968Z"
             }
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-        "analysis_file_11.json": {
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@@ -1153,7 +1153,7 @@
                 "update_date": "2018-10-10T03:07:11.061Z"
             }
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-        "analysis_file_12.json": {
+        "analysis_file/a5acdc07-18bf-4c06-b212-2b36e52173ef": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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@@ -1166,7 +1166,7 @@
                 "update_date": "2018-10-10T03:06:52.860Z"
             }
         },
-        "analysis_file_13.json": {
+        "analysis_file/da510e7a-5495-40c5-964d-b5291372102c": {
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@@ -1179,7 +1179,7 @@
                 "update_date": "2018-10-10T03:06:53.850Z"
             }
         },
-        "analysis_file_14.json": {
+        "analysis_file/14d63962-7cd3-43fc-a4d6-dc8f761c9ebd": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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@@ -1192,7 +1192,7 @@
                 "update_date": "2018-10-10T03:07:00.280Z"
             }
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-        "analysis_file_15.json": {
+        "analysis_file/b7f69b47-cbdf-4ec9-be6e-d316827aad8e": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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@@ -1205,7 +1205,7 @@
                 "update_date": "2018-10-10T03:07:03.278Z"
             }
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-        "analysis_file_16.json": {
+        "analysis_file/a3b39c62-3dd8-48f9-bcba-08a16f43a40b": {
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@@ -1218,7 +1218,7 @@
                 "update_date": "2018-10-10T03:07:03.879Z"
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@@ -1231,7 +1231,7 @@
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@@ -1244,7 +1244,7 @@
                 "update_date": "2018-10-10T03:07:14.068Z"
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@@ -1257,7 +1257,7 @@
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@@ -1270,7 +1270,7 @@
                 "update_date": "2018-10-10T03:07:15.121Z"
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-        "analysis_file_21.json": {
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@@ -1283,7 +1283,7 @@
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@@ -1296,7 +1296,7 @@
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-        "analysis_file_23.json": {
+        "analysis_file/c0da3d0b-128b-4b37-a3d6-9538ab29e9b6": {
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@@ -1309,7 +1309,7 @@
                 "update_date": "2018-10-10T03:07:19.076Z"
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@@ -1322,7 +1322,7 @@
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-        "analysis_file_25.json": {
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@@ -1335,7 +1335,7 @@
                 "update_date": "2018-10-10T03:07:20.313Z"
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-        "analysis_file_26.json": {
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@@ -1348,7 +1348,7 @@
                 "update_date": "2018-10-10T03:07:21.178Z"
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-        "analysis_file_27.json": {
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@@ -1361,7 +1361,7 @@
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-        "analysis_file_28.json": {
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@@ -1374,7 +1374,7 @@
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@@ -1387,7 +1387,7 @@
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-        "sequence_file_0.json": {
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@@ -1402,7 +1402,7 @@
                 "update_date": "2018-10-10T03:03:52.783Z"
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-        "sequence_file_1.json": {
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@@ -1417,7 +1417,7 @@
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-        "project_0.json": {
+        "project/6615efae-fca8-4dd2-a223-9cfcf30fe94d": {
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@@ -1447,7 +1447,7 @@
                 "update_date": "2018-10-10T02:23:47.926Z"
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-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/92bc8cf5-b595-4536-b0e8-46eb702b4f4f": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/protocol/sequencing/4.3.3/library_preparation_protocol",
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@@ -1470,7 +1470,7 @@
                 "update_date": "2018-10-10T02:23:47.924Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/da614ddd-0384-49ca-a6e1-2141ace13a01": {
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@@ -1490,7 +1490,7 @@
                 "update_date": "2018-10-10T02:23:47.923Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/63d78c21-061c-4e94-bb68-a5914f811447": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
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@@ -1507,7 +1507,7 @@
                 "update_date": "2018-10-10T02:23:47.925Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/d7820ce6-f0f4-4778-9353-423626dbd7c0": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
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@@ -1523,7 +1523,7 @@
                 "update_date": "2018-10-10T02:23:47.920Z"
             }
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-        "analysis_process_0.json": {
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             "describedBy": "http://schema.integration.data.humancellatlas.org/type/process/analysis/8.0.3/analysis_process",
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@@ -1943,7 +1943,7 @@
                 "update_date": "2018-10-10T03:03:55.832Z"
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-        "process_0.json": {
+        "process/5afa951e-1591-4bad-a4f8-2e13cbdb760c": {
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@@ -1955,7 +1955,7 @@
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-        "process_1.json": {
+        "process/27b9dad1-b670-4fc3-aad3-24e51e70dfba": {
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@@ -1967,7 +1967,7 @@
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-        "process_2.json": {
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diff --git a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
index 8b4844b98..4c858abfe 100644
--- a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
+++ b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
@@ -4096,7 +4096,7 @@
         }
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@@ -4109,7 +4109,7 @@
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@@ -4122,7 +4122,7 @@
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             "schema_type": "file"
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-        "analysis_file_2.json": {
+        "analysis_file/10439c86-98bb-5009-8374-577a41575424": {
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@@ -4135,7 +4135,7 @@
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-        "analysis_file_3.json": {
+        "analysis_file/1b675693-2615-519e-bfa7-cc008b0ff6e9": {
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@@ -4148,7 +4148,7 @@
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-        "analysis_file_4.json": {
+        "analysis_file/2b9f7c89-d1c2-53ef-a769-80fec2f7d9e6": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
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@@ -4167,7 +4167,7 @@
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             "schema_type": "file"
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-        "analysis_file_5.json": {
+        "analysis_file/32c69d68-1792-53af-9f42-0e97c9afc94b": {
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@@ -4186,7 +4186,7 @@
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+        "analysis_file/38a0ef48-9df1-5fef-8eb6-b32fbb67aabd": {
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@@ -4205,7 +4205,7 @@
             },
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-        "analysis_file_7.json": {
+        "analysis_file/3cd78fb7-b7bc-5ab1-b122-47585f0023d4": {
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@@ -4224,7 +4224,7 @@
             },
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-        "analysis_file_8.json": {
+        "analysis_file/3e9b54c2-4244-5549-a0ca-ea1524949a86": {
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@@ -4237,7 +4237,7 @@
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-        "analysis_file_9.json": {
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@@ -4250,7 +4250,7 @@
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-        "analysis_file_10.json": {
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@@ -4269,7 +4269,7 @@
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-        "analysis_file_11.json": {
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@@ -11755,7 +11755,7 @@
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@@ -11770,7 +11770,7 @@
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@@ -11785,7 +11785,7 @@
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@@ -11800,7 +11800,7 @@
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@@ -11815,7 +11815,7 @@
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@@ -11830,7 +11830,7 @@
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@@ -11845,7 +11845,7 @@
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@@ -11860,7 +11860,7 @@
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@@ -11875,7 +11875,7 @@
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@@ -11890,7 +11890,7 @@
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@@ -11905,7 +11905,7 @@
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@@ -11920,7 +11920,7 @@
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@@ -11935,7 +11935,7 @@
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@@ -11950,7 +11950,7 @@
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@@ -11965,7 +11965,7 @@
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@@ -11980,7 +11980,7 @@
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@@ -11995,7 +11995,7 @@
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@@ -12010,7 +12010,7 @@
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@@ -12025,7 +12025,7 @@
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@@ -12040,7 +12040,7 @@
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@@ -12055,7 +12055,7 @@
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@@ -12070,7 +12070,7 @@
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@@ -12085,7 +12085,7 @@
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@@ -12100,7 +12100,7 @@
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@@ -12115,7 +12115,7 @@
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@@ -12130,7 +12130,7 @@
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@@ -12145,7 +12145,7 @@
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@@ -12160,7 +12160,7 @@
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@@ -12175,7 +12175,7 @@
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@@ -12190,7 +12190,7 @@
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@@ -12205,7 +12205,7 @@
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@@ -12220,7 +12220,7 @@
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@@ -12235,7 +12235,7 @@
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@@ -12250,7 +12250,7 @@
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@@ -12265,7 +12265,7 @@
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@@ -12280,7 +12280,7 @@
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@@ -12295,7 +12295,7 @@
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@@ -12310,7 +12310,7 @@
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@@ -12325,7 +12325,7 @@
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@@ -12340,7 +12340,7 @@
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@@ -12355,7 +12355,7 @@
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@@ -12370,7 +12370,7 @@
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@@ -12385,7 +12385,7 @@
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@@ -12400,7 +12400,7 @@
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@@ -12415,7 +12415,7 @@
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@@ -12430,7 +12430,7 @@
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@@ -12445,7 +12445,7 @@
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@@ -12460,7 +12460,7 @@
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@@ -12475,7 +12475,7 @@
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@@ -12490,7 +12490,7 @@
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@@ -12505,7 +12505,7 @@
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@@ -12520,7 +12520,7 @@
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@@ -12535,7 +12535,7 @@
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@@ -12550,7 +12550,7 @@
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@@ -15020,7 +15020,7 @@
                 "update_date": "2019-10-22T17:46:02.024Z"
             }
         },
-        "specimen_from_organism_2.json": {
+        "specimen_from_organism/2cbca5ef-0850-4c4a-9d24-05454a1060e8": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -15070,7 +15070,7 @@
                 "update_date": "2019-10-22T17:46:02.166Z"
             }
         },
-        "specimen_from_organism_3.json": {
+        "specimen_from_organism/3f646bab-c762-4dbd-8f7b-b374427dac74": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -15120,7 +15120,7 @@
                 "update_date": "2019-10-22T17:46:02.079Z"
             }
         },
-        "specimen_from_organism_4.json": {
+        "specimen_from_organism/442f68c7-502a-4fc7-a3b8-94e9574cd22d": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -15160,7 +15160,7 @@
                 "update_date": "2019-10-22T17:46:02.057Z"
             }
         },
-        "specimen_from_organism_5.json": {
+        "specimen_from_organism/5fbd4bb4-e761-4345-99b8-bd5e141a8b94": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -15200,7 +15200,7 @@
                 "update_date": "2019-10-22T17:46:02.150Z"
             }
         },
-        "specimen_from_organism_6.json": {
+        "specimen_from_organism/8c0ef0ae-0687-4f2a-8a27-d833b7032a26": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -15250,7 +15250,7 @@
                 "update_date": "2019-10-22T17:46:02.099Z"
             }
         },
-        "specimen_from_organism_7.json": {
+        "specimen_from_organism/8c1b5489-7bf1-40c0-ba60-5e6b079e108a": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -15300,7 +15300,7 @@
                 "update_date": "2019-10-22T17:46:02.136Z"
             }
         },
-        "specimen_from_organism_8.json": {
+        "specimen_from_organism/a39685fd-b34a-4db7-b973-381919edb96e": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -15340,7 +15340,7 @@
                 "update_date": "2019-10-22T17:46:02.139Z"
             }
         },
-        "specimen_from_organism_9.json": {
+        "specimen_from_organism/c98d14ec-8761-45f7-8e86-e63c188bd97f": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -15390,7 +15390,7 @@
                 "update_date": "2019-10-22T17:46:02.055Z"
             }
         },
-        "specimen_from_organism_10.json": {
+        "specimen_from_organism/ddd10ecc-f7b7-4370-82cf-14e30987b751": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -15430,7 +15430,7 @@
                 "update_date": "2019-10-22T17:46:02.035Z"
             }
         },
-        "specimen_from_organism_11.json": {
+        "specimen_from_organism/ee2bfb40-7aa4-4c78-b78a-91aa69c7dc6e": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -15480,7 +15480,7 @@
                 "update_date": "2019-10-22T17:46:02.129Z"
             }
         },
-        "specimen_from_organism_12.json": {
+        "specimen_from_organism/f37a0dec-b7ba-4b34-8e51-732fb5ac7213": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -15520,7 +15520,7 @@
                 "update_date": "2019-10-22T17:46:01.985Z"
             }
         },
-        "specimen_from_organism_13.json": {
+        "specimen_from_organism/f47bb6a8-a753-4d40-8254-28fee9d03c1b": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -15570,7 +15570,7 @@
                 "update_date": "2019-10-22T17:46:02.025Z"
             }
         },
-        "specimen_from_organism_14.json": {
+        "specimen_from_organism/f5d590c5-b307-4b99-af98-8ddba1e2a266": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -15620,7 +15620,7 @@
                 "update_date": "2019-10-22T17:46:02.036Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/fe71fe4a-0903-42e0-9a65-d985abd943ca": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -15649,7 +15649,7 @@
                 "update_date": "2019-10-22T17:46:02.098Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/71efd7ce-0ec0-4423-9eb2-9bd42f40a33f": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
diff --git a/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json b/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
index 81c367be0..4c2a6e03e 100644
--- a/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
+++ b/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
@@ -182,7 +182,7 @@
         }
     ],
     "metadata": {
-        "project_0.json": {
+        "project/90bf705c-d891-5ce2-aa54-094488b445c6": {
             "array_express_accessions": [
                 "E-MTAB-10026"
             ],
@@ -299,7 +299,7 @@
             ],
             "schema_type": "project"
         },
-        "process_0.json": {
+        "process/37e91a9f-b04e-5313-bbc0-4c394406247e": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -313,7 +313,7 @@
             },
             "schema_type": "process"
         },
-        "process_1.json": {
+        "process/7a330531-ec7f-5aee-84d4-2ba24d66e93b": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -327,7 +327,7 @@
             },
             "schema_type": "process"
         },
-        "process_2.json": {
+        "process/b0092a47-b19d-5b34-b004-cb8edd8c625b": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -341,7 +341,7 @@
             },
             "schema_type": "process"
         },
-        "process_3.json": {
+        "process/bd6a4a38-c44b-5d17-b2b1-d0d4c4531bf0": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -355,7 +355,7 @@
             },
             "schema_type": "process"
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/119c4135-7b77-5003-a150-f052e22c6834": {
             "biomaterial_core": {
                 "biomaterial_id": "AP2CS_pre",
                 "ncbi_taxon_id": [
@@ -387,7 +387,7 @@
                 }
             ]
         },
-        "cell_suspension_1.json": {
+        "cell_suspension/6ff38054-9296-5d4c-b238-6a3b01a15175": {
             "biomaterial_core": {
                 "biomaterial_id": "AP3CS",
                 "ncbi_taxon_id": [
@@ -419,7 +419,7 @@
                 }
             ]
         },
-        "analysis_file_0.json": {
+        "analysis_file/caf6d2a8-2272-5689-b3d8-9c97370d6c29": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/6.5.0/analysis_file",
             "file_core": {
                 "content_description": [
@@ -443,7 +443,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_protocol_0.json": {
+        "analysis_protocol/811adf54-7f27-5aec-9ed7-c6084c4c3a1b": {
             "computational_method": "10x v3",
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/analysis/10.0.0/analysis_protocol",
             "matrix": {
@@ -474,7 +474,7 @@
                 "text": "enzymatic dissociation"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/767282b2-2fc1-5559-b020-29686b810206": {
             "cell_barcode": {
                 "barcode_length": 16,
                 "barcode_offset": 0,
@@ -511,7 +511,7 @@
                 "barcode_read": "Read 1"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/3bee0c9a-aced-52f2-b97f-89518f826b36": {
             "biomaterial_core": {
                 "biomaterial_id": "AP2_specimen",
                 "biomaterial_name": "AP2_specimen",
@@ -548,7 +548,7 @@
             },
             "schema_type": "biomaterial"
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/46435803-7ee8-5157-8569-8a61ad50c315": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "method": {
                 "ontology": "EFO:0009337",
@@ -568,7 +568,7 @@
             },
             "schema_type": "protocol"
         },
-        "donor_organism_0.json": {
+        "donor_organism/5bc2bf2f-eb98-5510-a386-172cef38f2f2": {
             "biomaterial_core": {
                 "biomaterial_id": "AP2",
                 "biomaterial_name": "Sanger_AP2",
@@ -613,7 +613,7 @@
             "schema_type": "biomaterial",
             "sex": "unknown"
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/e7f864e3-6ba7-53c8-842f-2a05cb90e1b7": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "method": {
                 "ontology": "EFO:0009121",
diff --git a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
index 711aaa080..b5e4efd52 100644
--- a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
+++ b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
@@ -254,7 +254,7 @@
         }
     ],
     "metadata": {
-        "analysis_protocol_0.json": {
+        "analysis_protocol/289ec28b-ce11-5be8-89ab-92fbceb874a0": {
             "computational_method": "Optimus",
             "describedBy": "https://schema.humancellatlas.org/type/protocol/analysis/9.1.0/analysis_protocol",
             "protocol_core": {
@@ -270,7 +270,7 @@
                 "text": "analysis_protocol"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/30040306-be5c-48f9-b221-e666e279ab5b": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -295,7 +295,7 @@
                 "update_date": "2019-09-13T08:43:56.724Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/39255288-6791-45b0-ac7e-b3ef4c981a3b": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -320,7 +320,7 @@
                 "update_date": "2019-09-13T08:54:00.067Z"
             }
         },
-        "sequence_file_2.json": {
+        "sequence_file/9f8f5212-0749-460b-9a46-2949dea45d52": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -345,7 +345,7 @@
                 "update_date": "2019-09-13T08:57:01.788Z"
             }
         },
-        "analysis_file_0.json": {
+        "analysis_file/b949e4b6-c3fb-58b4-865b-40cb3ef2b6c6": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
             "file_core": {
                 "content_description": [],
@@ -358,7 +358,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_file_1.json": {
+        "analysis_file/d90280cc-a294-57de-b350-5234a5278c19": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
             "file_core": {
                 "content_description": [
@@ -377,7 +377,7 @@
             },
             "schema_type": "file"
         },
-        "project_0.json": {
+        "project/8185730f-4113-40d3-9cc3-929271784c2b": {
             "describedBy": "https://schema.humancellatlas.org/type/project/14.1.0/project",
             "schema_type": "project",
             "project_core": {
@@ -797,7 +797,7 @@
                 "update_date": "2019-09-13T08:37:53.825Z"
             }
         },
-        "analysis_process_0.json": {
+        "analysis_process/3d7a4690-8760-491c-98f9-9a1aea3f79b5": {
             "analysis_run_type": "run",
             "describedBy": "https://schema.humancellatlas.org/type/process/analysis/12.0.0/analysis_process",
             "inputs": [
@@ -1097,7 +1097,7 @@
                 "text": "analysis"
             }
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/932000d6-c63b-40f0-bdd5-469fa4db8be2": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1122,7 +1122,7 @@
                 "update_date": "2019-09-13T08:37:53.868Z"
             }
         },
-        "process_0.json": {
+        "process/1116b396-448e-4dd1-b9c9-78357c511e15": {
             "process_core": {
                 "process_id": "Retina_2_repB"
             },
@@ -1134,7 +1134,7 @@
                 "update_date": "2019-09-13T08:37:57.269Z"
             }
         },
-        "process_1.json": {
+        "process/a5e37780-0b71-4610-8a7c-26142dedfcec": {
             "process_core": {
                 "process_id": "process_id_2"
             },
@@ -1146,7 +1146,7 @@
                 "update_date": "2019-09-13T08:37:57.174Z"
             }
         },
-        "process_2.json": {
+        "process/b360251f-7550-4c08-b576-781858554ea1": {
             "process_core": {
                 "process_id": "process_id_6"
             },
@@ -1158,7 +1158,7 @@
                 "update_date": "2019-09-13T08:37:57.252Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/ba595d79-aa43-4e3a-ad10-89f92ef4f22f": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1178,7 +1178,7 @@
                 "update_date": "2019-09-13T08:37:53.832Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/edc72947-b776-4150-8bfe-b7331acfa66f": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1222,7 +1222,7 @@
                 "update_date": "2019-09-13T08:37:53.864Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/b8049daa-7458-47bf-8ec2-3f5c56d2cb34": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1266,7 +1266,7 @@
                 "update_date": "2019-09-13T08:37:53.853Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/a166be3d-6e84-4058-a1bd-edf90cf3ee88": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1296,7 +1296,7 @@
                 "update_date": "2019-09-13T08:37:53.815Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/2509f42a-0328-4e33-8d21-79d37560d846": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1315,7 +1315,7 @@
                 "update_date": "2019-09-13T08:37:53.822Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/fa99959f-faa2-4d69-a092-48333e59f5f3": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1353,7 +1353,7 @@
                 "update_date": "2019-09-13T08:37:53.809Z"
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/3030903f-4a4b-4b30-ab93-3b10183181e0": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
diff --git a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
index fd7ce1a28..c38969247 100644
--- a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
+++ b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
@@ -179,7 +179,7 @@
         }
     ],
     "metadata": {
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/58612e7a-c83a-4c7d-ab53-974b207291eb": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -206,7 +206,7 @@
                 "schema_minor_version": 1
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/5b2453cf-dffd-42e4-8868-73aec60b1418": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -261,7 +261,7 @@
                 "schema_minor_version": 4
             }
         },
-        "process_0.json": {
+        "process/4ce6bcb3-6402-4265-b18e-fa3ebea6e786": {
             "process_core": {
                 "process_id": "process_id_3281"
             },
@@ -275,7 +275,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_1.json": {
+        "process/80baee6e-00a5-4fdc-bfe3-d339ff8a7178": {
             "process_core": {
                 "process_id": "SRR3937937.1"
             },
@@ -289,7 +289,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_2.json": {
+        "process/f188ad1d-17dc-4f21-a35d-c24a1d53e728": {
             "process_core": {
                 "process_id": "process_id_7"
             },
@@ -303,7 +303,7 @@
                 "schema_minor_version": 2
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/46299069-e6aa-4b95-b134-5dcbd4685cb3": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -325,7 +325,7 @@
                 "schema_minor_version": 1
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/64f1a275-671c-46a2-ba7f-6647e672c8d7": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -353,7 +353,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/e27de859-4b05-43d6-8437-7f7dfc0507d1": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -381,7 +381,7 @@
                 "schema_minor_version": 2
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/37aee665-8ee9-451c-b1ef-e998cc268481": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -402,7 +402,7 @@
                 "schema_minor_version": 2
             }
         },
-        "dissociation_protocol_1.json": {
+        "dissociation_protocol/97c799c5-5db6-4d57-8a03-0fb877039255": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -423,7 +423,7 @@
                 "schema_minor_version": 2
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/270341ef-ab2d-4e88-9ae1-b49684fc60e0": {
             "biomaterial_core": {
                 "biomaterial_description": "adult human glioblastoma patient",
                 "biomaterial_id": "D_BT_S6",
@@ -473,7 +473,7 @@
                 "schema_minor_version": 5
             }
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/38f53d63-e470-491a-a98a-83bf0c47b630": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -515,7 +515,7 @@
                 "schema_minor_version": 3
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/5f886847-ef33-4a9b-b971-f2fe9f429cc4": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -536,7 +536,7 @@
                 "schema_minor_version": 2
             }
         },
-        "project_0.json": {
+        "project/2d846095-8a33-4f3c-97d4-585bafac13b4": {
             "describedBy": "https://schema.humancellatlas.org/type/project/15.0.0/project",
             "schema_type": "project",
             "project_core": {
@@ -687,7 +687,7 @@
                 "schema_minor_version": 0
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/9b9f5554-0f48-4af5-a765-c45226e0531c": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
diff --git a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
index b7fb2ac93..2bb894db6 100644
--- a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
+++ b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
@@ -76,7 +76,7 @@
         }
     ],
     "metadata": {
-        "supplementary_file_0.json": {
+        "supplementary_file/538faa28-3235-5e4b-a998-5672e2d964e8": {
             "describedBy": "https://schema.humancellatlas.org/type/file/2.2.0/supplementary_file",
             "schema_type": "file",
             "schema_version": "2.2.0",
@@ -99,7 +99,7 @@
                 "update_date": "2020-12-03T10:39:17.144517Z"
             }
         },
-        "supplementary_file_1.json": {
+        "supplementary_file/6c142250-567c-5b63-bd4f-0d78499863f8": {
             "describedBy": "https://schema.humancellatlas.org/type/file/2.2.0/supplementary_file",
             "schema_type": "file",
             "schema_version": "2.2.0",
@@ -122,7 +122,7 @@
                 "update_date": "2020-12-03T10:39:17.144517Z"
             }
         },
-        "supplementary_file_2.json": {
+        "supplementary_file/8d2ba1c1-bc9f-5c2a-a74d-fe5e09bdfb18": {
             "describedBy": "https://schema.humancellatlas.org/type/file/2.2.0/supplementary_file",
             "schema_type": "file",
             "schema_version": "2.2.0",
@@ -145,7 +145,7 @@
                 "update_date": "2020-12-03T10:39:17.144517Z"
             }
         },
-        "project_0.json": {
+        "project/8185730f-4113-40d3-9cc3-929271784c2b": {
             "describedBy": "https://schema.humancellatlas.org/type/project/14.1.0/project",
             "schema_type": "project",
             "project_core": {
diff --git a/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json b/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
index 41ea4d045..ca1ff626e 100644
--- a/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
+++ b/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
@@ -26,7 +26,7 @@
         }
     ],
     "metadata": {
-        "project_0.json": {
+        "project/93f6a42f-1790-4af4-b5d1-8c436cb6feae": {
             "content": {
                 "describedBy": "https://schema.humancellatlas.org/type/project/5.1.0/project",
                 "project_core": {
@@ -150,7 +150,7 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/54a80c57-0409-4f57-9699-8a2f8cbace43": {
             "content": {
                 "genus_species": [
                     {
@@ -182,7 +182,7 @@
                 "document_id": "54a80c57-0409-4f57-9699-8a2f8cbace43"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/b3623b88-c369-46c9-a2e9-a16042d2c589": {
             "content": {
                 "organ": {
                     "text": "lymph node"
@@ -217,7 +217,7 @@
                 "document_id": "b3623b88-c369-46c9-a2e9-a16042d2c589"
             }
         },
-        "donor_organism_2.json": {
+        "donor_organism/665b75b4-8638-4a15-83e5-f3928dd29314": {
             "content": {
                 "is_living": false,
                 "mus_musculus_specific": {
@@ -262,7 +262,7 @@
                 "document_id": "665b75b4-8638-4a15-83e5-f3928dd29314"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/b2cd6fb7-6612-4ab9-a1c5-e475663437e3": {
             "content": {
                 "file_core": {
                     "file_name": "21935_7#154_1.fastq.gz",
@@ -278,7 +278,7 @@
                 "document_id": "b2cd6fb7-6612-4ab9-a1c5-e475663437e3"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/f599ea3f-14bb-4504-82ce-d9c1f26e55fa": {
             "content": {
                 "file_core": {
                     "file_name": "21935_7#154_2.fastq.gz",
@@ -294,7 +294,7 @@
                 "document_id": "f599ea3f-14bb-4504-82ce-d9c1f26e55fa"
             }
         },
-        "dissociation_process_0.json": {
+        "dissociation_process/b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -312,7 +312,7 @@
                 "document_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902"
             }
         },
-        "process_1.json": {
+        "process/7a408c1b-d2f2-49d8-b390-37ba6d61e692": {
             "content": {
                 "process_core": {
                     "process_id": "sampling_process_38"
@@ -327,7 +327,7 @@
                 "document_id": "7a408c1b-d2f2-49d8-b390-37ba6d61e692"
             }
         },
-        "enrichment_process_2.json": {
+        "enrichment_process/87beb50f-521d-4102-9cb0-ca7b6f151afc": {
             "content": {
                 "enrichment_method": "FACS",
                 "process_core": {
@@ -344,7 +344,7 @@
                 "document_id": "87beb50f-521d-4102-9cb0-ca7b6f151afc"
             }
         },
-        "enrichment_process_3.json": {
+        "enrichment_process/8caf3d2b-7dba-40ca-a2d7-c69b433ba70b": {
             "content": {
                 "enrichment_method": "FACS",
                 "process_core": {
@@ -361,7 +361,7 @@
                 "document_id": "8caf3d2b-7dba-40ca-a2d7-c69b433ba70b"
             }
         },
-        "enrichment_process_4.json": {
+        "enrichment_process/5a801f3d-12b0-4374-aed9-deee905b55ef": {
             "content": {
                 "enrichment_method": "FACS",
                 "process_core": {
@@ -378,7 +378,7 @@
                 "document_id": "5a801f3d-12b0-4374-aed9-deee905b55ef"
             }
         },
-        "library_preparation_process_5.json": {
+        "library_preparation_process/687065f3-c70f-46c3-8452-a5eead33a1bf": {
             "content": {
                 "input_nucleic_acid_molecule": {
                     "text": "polyA RNA",
@@ -407,7 +407,7 @@
                 "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
             }
         },
-        "sequencing_process_6.json": {
+        "sequencing_process/66551017-88b4-431d-ab33-c3a805f37bdf": {
             "content": {
                 "paired_ends": true,
                 "instrument_manufacturer_model": {
@@ -432,7 +432,7 @@
                 "document_id": "66551017-88b4-431d-ab33-c3a805f37bdf"
             }
         },
-        "protocol_0.json": {
+        "protocol/c9a1e203-bddc-45d3-87c4-6010be8e0127": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "Extracting cells from lymph nodes",
@@ -449,7 +449,7 @@
                 "document_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127"
             }
         },
-        "protocol_1.json": {
+        "protocol/a1c80daf-58b0-4b7a-8e29-d0130493c8e6": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "FACS sorting cells by surface markers",
@@ -466,7 +466,7 @@
                 "document_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6"
             }
         },
-        "protocol_2.json": {
+        "protocol/52d79a89-4b49-4c1b-b857-5cc5da07f643": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "Make/amplify cDNA for each cell",
@@ -487,7 +487,7 @@
                 "document_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643"
             }
         },
-        "protocol_3.json": {
+        "protocol/ca6096cf-13c1-4930-8308-6ab05865e2c9": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "Sequencing SmartSeq2 cells",
diff --git a/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json b/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
index 8f26b1b31..d2c2c780a 100644
--- a/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
+++ b/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
@@ -206,7 +206,7 @@
         }
     ],
     "metadata": {
-        "project_0.json": {
+        "project/90bf705c-d891-5ce2-aa54-094488b445c6": {
             "array_express_accessions": [
                 "E-MTAB-10026"
             ],
@@ -323,7 +323,7 @@
             ],
             "schema_type": "project"
         },
-        "process_0.json": {
+        "process/8c1773c3-1885-545f-9381-0dab1edf6074": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -337,7 +337,7 @@
             },
             "schema_type": "process"
         },
-        "process_1.json": {
+        "process/ae8529dc-3bc9-5061-828a-3c5dfacded64": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -351,7 +351,7 @@
             },
             "schema_type": "process"
         },
-        "process_2.json": {
+        "process/c6b932ff-69f1-58b1-a6e6-30319f04541b": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -365,7 +365,7 @@
             },
             "schema_type": "process"
         },
-        "imaged_specimen_0.json": {
+        "imaged_specimen/0bf91a05-85df-5d7d-bcc0-a625c5921de2": {
             "biomaterial_core": {
                 "biomaterial_id": "AP3_imagedspecimen",
                 "biomaterial_name": "AP3_imagedspecimen",
@@ -384,7 +384,7 @@
             "schema_type": "biomaterial",
             "slice_thickness": 10.0
         },
-        "sequence_file_0.json": {
+        "sequence_file/31786d8d-d046-58d1-b7b4-49bc1114a0f8": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/9.5.0/sequence_file",
             "file_core": {
                 "file_name": "6330STDY9479159_S1_L001_I1_001.fastq.gz",
@@ -400,7 +400,7 @@
             "read_index": "index1",
             "schema_type": "file"
         },
-        "sequence_file_1.json": {
+        "sequence_file/6a0e071d-9bfc-5e12-b1b9-e887885e12f6": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/9.5.0/sequence_file",
             "file_core": {
                 "file_name": "6330STDY9479159_S1_L001_R1_001.fastq.gz",
@@ -416,7 +416,7 @@
             "read_index": "read1",
             "schema_type": "file"
         },
-        "sequence_file_2.json": {
+        "sequence_file/f6abda5c-65f3-5015-8167-ae78b96f5693": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/9.5.0/sequence_file",
             "file_core": {
                 "file_name": "6330STDY9479159_S1_L001_R2_001.fastq.gz",
@@ -432,7 +432,7 @@
             "read_index": "read2",
             "schema_type": "file"
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/83f14748-af1c-57aa-9088-6cb1cdd4bba4": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/sequencing/6.3.1/library_preparation_protocol",
             "end_bias": "3 prime end bias",
             "input_nucleic_acid_molecule": {
@@ -472,7 +472,7 @@
                 "barcode_read": "Read 1"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/1b8dfafd-178f-5826-a661-8a022334aaeb": {
             "10x": {
                 "fastq_method": "Cellranger",
                 "fastq_method_version": "Cellranger 4.0",
@@ -503,7 +503,7 @@
             },
             "schema_type": "protocol"
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/9a0bb729-552a-5f6e-9ed6-1f988c259531": {
             "biomaterial_core": {
                 "biomaterial_id": "AP3_specimen",
                 "biomaterial_name": "AP2_specimen",
@@ -540,7 +540,7 @@
             },
             "schema_type": "biomaterial"
         },
-        "imaging_preparation_protocol_0.json": {
+        "imaging_preparation_protocol/7cd840db-f395-5a61-bd17-72c2b2319c23": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/imaging/2.3.0/imaging_preparation_protocol",
             "protocol_core": {
                 "protocol_description": "All tissues were sectioned using the Leica CX3050S cryostat and were cut at 10um. Tissue optimization was performed to obtain permeabilization time for fetal tissue (12 min).",
@@ -555,7 +555,7 @@
             },
             "schema_type": "protocol"
         },
-        "donor_organism_0.json": {
+        "donor_organism/2d7b50d8-cd06-5408-9fde-1faed01c9ab2": {
             "biomaterial_core": {
                 "biomaterial_id": "AP3",
                 "biomaterial_name": "Sanger_AP3",
@@ -598,7 +598,7 @@
             "schema_type": "biomaterial",
             "sex": "unknown"
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/c5752f73-3511-55e1-95af-040ab3924bce": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "method": {
                 "ontology": "EFO:0009121",
diff --git a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
index 1a3f56c0c..2b8bc08e2 100644
--- a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
+++ b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
@@ -542,7 +542,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/26dd8b99-f4ad-4802-8d6d-cf372c819dcc": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -577,7 +577,7 @@
                 "schema_minor_version": 3
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/efa34a7f-6a0b-4728-9038-b947d47a63c6": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -628,7 +628,7 @@
                 "schema_minor_version": 4
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/a53d95b5-d1c7-4548-b2c0-479788085ab8": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -684,7 +684,7 @@
                 "schema_minor_version": 5
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/c0a69095-57ba-4eca-8cc7-fed514f35f43": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -710,7 +710,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/4a9b689f-5aad-4c30-b347-7b0d52ab3ecb": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -736,7 +736,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_2.json": {
+        "sequence_file/6fc876bc-5a8a-445c-8b41-77526203973b": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -762,7 +762,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_3.json": {
+        "sequence_file/d47c381f-cef0-432a-b2bb-49fb7a546ac1": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -788,7 +788,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_4.json": {
+        "sequence_file/b2a466dd-9de4-428c-9eda-f779d9ad672f": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -814,7 +814,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_5.json": {
+        "sequence_file/86102761-0ba7-43b6-a442-666db1296154": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -840,7 +840,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_6.json": {
+        "sequence_file/0c4b6682-12ab-46e7-9756-07ec104b14b1": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -866,7 +866,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_7.json": {
+        "sequence_file/f31358bc-064c-4185-ae23-af044804d591": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -892,7 +892,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_8.json": {
+        "sequence_file/a652744c-2d55-4181-b903-db411fa589b4": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -918,7 +918,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_9.json": {
+        "sequence_file/da3b3aa5-3bea-441b-b1d0-022f842ddda6": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -944,7 +944,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_10.json": {
+        "sequence_file/96ae6850-32c6-4d89-87cb-2f5005ac65aa": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -970,7 +970,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_11.json": {
+        "sequence_file/bb4b0758-444b-48c3-89a6-9ddcf61fe912": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -996,7 +996,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_12.json": {
+        "sequence_file/b4308ad2-8a51-4b1e-95a3-da961a13dd70": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1022,7 +1022,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_13.json": {
+        "sequence_file/2fa236c1-deb5-48a8-9961-3e2ee5cae2db": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1048,7 +1048,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_14.json": {
+        "sequence_file/ff664ba7-b1f9-4fd2-b6ae-a12eb0111721": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1074,7 +1074,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_15.json": {
+        "sequence_file/899e967e-06c8-49d9-bd3f-4bef8d04e22b": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1100,7 +1100,7 @@
                 "schema_minor_version": 2
             }
         },
-        "project_0.json": {
+        "project/4e6f083b-5b9a-4393-9890-2a83da8188f1": {
             "describedBy": "https://schema.humancellatlas.org/type/project/14.1.0/project",
             "schema_type": "project",
             "project_core": {
@@ -1406,7 +1406,7 @@
                 "schema_minor_version": 1
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/58df9607-ab66-48e0-a47b-1f897baae139": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1454,7 +1454,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/6282594c-1b9d-4f26-a4f3-a26066878740": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1485,7 +1485,7 @@
                 "schema_minor_version": 1
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/acaf2d60-e6fb-4381-a81e-2fec565fc8fa": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1506,7 +1506,7 @@
                 "schema_minor_version": 2
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/1c9774bf-979a-4023-9756-b297cba4e371": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1528,7 +1528,7 @@
                 "schema_minor_version": 1
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/e95ebc23-53b9-48a0-acd4-185969122f2d": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1549,7 +1549,7 @@
                 "schema_minor_version": 2
             }
         },
-        "collection_protocol_1.json": {
+        "collection_protocol/6ec6ce63-3c6f-41d1-a616-5ebb20fe9a8b": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1570,7 +1570,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_0.json": {
+        "process/c56e2990-d6a0-40f5-add2-793bc1f12d69": {
             "process_core": {
                 "process_id": "Lib5-1"
             },
@@ -1584,7 +1584,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_1.json": {
+        "process/6a14efb0-0c28-421f-968b-5fc022df2395": {
             "process_core": {
                 "process_id": "process_id_37"
             },
@@ -1598,7 +1598,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_2.json": {
+        "process/055b2189-7f89-4392-be1d-28a7274fe563": {
             "process_core": {
                 "process_id": "process_id_12"
             },
diff --git a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
index c8e3d57e3..3799d9abb 100644
--- a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
+++ b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
@@ -5570,7 +5570,7 @@
         }
     ],
     "metadata": {
-        "imaged_specimen_0.json": {
+        "imaged_specimen/87f58f88-ef8b-4323-bd19-cde1a2497b59": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/2.0.7/imaged_specimen",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -5596,7 +5596,7 @@
                 "update_date": "2019-04-03T10:13:50.866Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/edd1d525-a6ae-4658-a6bf-6c31d7ab6948": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -5630,7 +5630,7 @@
                 "update_date": "2019-04-03T10:13:45.512Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/6cb9fc09-7755-4a35-b6b1-0d6fe696b2d4": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/14.0.7/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -5683,7 +5683,7 @@
                 "update_date": "2019-04-03T10:13:45.427Z"
             }
         },
-        "image_file_0.json": {
+        "image_file/6baa3aff-b2a5-4e49-82f7-25c108a6107a": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5696,7 +5696,7 @@
                 "update_date": "2019-04-03T10:15:44.995Z"
             }
         },
-        "image_file_1.json": {
+        "image_file/06dcfc33-21da-485f-8e50-49d294713a9e": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5709,7 +5709,7 @@
                 "update_date": "2019-04-03T10:15:44.993Z"
             }
         },
-        "image_file_2.json": {
+        "image_file/404dd50b-4bc9-4c82-8c18-f53c68eed2fc": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5722,7 +5722,7 @@
                 "update_date": "2019-04-03T10:15:51.032Z"
             }
         },
-        "image_file_3.json": {
+        "image_file/5ceb5dc3-9194-494a-b1df-42bb75ab1a04": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5735,7 +5735,7 @@
                 "update_date": "2019-04-03T10:15:47.812Z"
             }
         },
-        "image_file_4.json": {
+        "image_file/76e52f76-ede7-4088-b7f6-d6e5f6152292": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5748,7 +5748,7 @@
                 "update_date": "2019-04-03T10:15:51.115Z"
             }
         },
-        "image_file_5.json": {
+        "image_file/2e496fe6-f500-4e27-b7f5-3c87fe43bbe5": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5761,7 +5761,7 @@
                 "update_date": "2019-04-03T10:15:54.073Z"
             }
         },
-        "image_file_6.json": {
+        "image_file/be66141d-84a3-457d-a8d2-2f0da8c91dff": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5774,7 +5774,7 @@
                 "update_date": "2019-04-03T10:15:51.125Z"
             }
         },
-        "image_file_7.json": {
+        "image_file/680cf532-ef0c-4155-b44d-a6ec3920743a": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5787,7 +5787,7 @@
                 "update_date": "2019-04-03T10:15:50.982Z"
             }
         },
-        "image_file_8.json": {
+        "image_file/08609f14-cf43-4188-b743-4a0b55b17347": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5800,7 +5800,7 @@
                 "update_date": "2019-04-03T10:15:47.817Z"
             }
         },
-        "image_file_9.json": {
+        "image_file/d10827a1-38f7-457d-9c9f-695f2fc7689c": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5813,7 +5813,7 @@
                 "update_date": "2019-04-03T10:15:44.996Z"
             }
         },
-        "image_file_10.json": {
+        "image_file/6f8eb2e5-7a0c-4c98-8da0-276457357071": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5826,7 +5826,7 @@
                 "update_date": "2019-04-03T10:15:47.821Z"
             }
         },
-        "image_file_11.json": {
+        "image_file/ca480df3-71bb-4634-8f71-b6a75aeb9f05": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5839,7 +5839,7 @@
                 "update_date": "2019-04-03T10:15:47.796Z"
             }
         },
-        "image_file_12.json": {
+        "image_file/03ae5f5e-65ac-4491-b0ce-eefc940e0224": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5852,7 +5852,7 @@
                 "update_date": "2019-04-03T10:15:48.018Z"
             }
         },
-        "image_file_13.json": {
+        "image_file/ff117ecb-767e-4e72-baa9-2bda4fcd3e62": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5865,7 +5865,7 @@
                 "update_date": "2019-04-03T10:15:51.040Z"
             }
         },
-        "image_file_14.json": {
+        "image_file/887f3d73-94d2-44ac-9047-67aca5225882": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5878,7 +5878,7 @@
                 "update_date": "2019-04-03T10:15:51.029Z"
             }
         },
-        "image_file_15.json": {
+        "image_file/896dfacd-206b-4e4f-a846-ba5b070060d9": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5891,7 +5891,7 @@
                 "update_date": "2019-04-03T10:15:47.819Z"
             }
         },
-        "image_file_16.json": {
+        "image_file/23303c88-01b1-47d0-b770-dca6802caa13": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5904,7 +5904,7 @@
                 "update_date": "2019-04-03T10:15:47.812Z"
             }
         },
-        "image_file_17.json": {
+        "image_file/3c1a388d-0577-4417-9cd2-ff33bfed9140": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5917,7 +5917,7 @@
                 "update_date": "2019-04-03T10:15:47.821Z"
             }
         },
-        "image_file_18.json": {
+        "image_file/67e71b34-7157-4a37-b495-0d740772b480": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5930,7 +5930,7 @@
                 "update_date": "2019-04-03T10:15:51.111Z"
             }
         },
-        "image_file_19.json": {
+        "image_file/cd3e5e62-6145-42d9-9a5b-046e1b49cf26": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5943,7 +5943,7 @@
                 "update_date": "2019-04-03T10:15:51.054Z"
             }
         },
-        "image_file_20.json": {
+        "image_file/5fbcb75e-3ee3-4429-8ede-b243afa0789f": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5956,7 +5956,7 @@
                 "update_date": "2019-04-03T10:15:51.028Z"
             }
         },
-        "image_file_21.json": {
+        "image_file/09226b24-6b11-4e4f-8052-2b544be461aa": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5969,7 +5969,7 @@
                 "update_date": "2019-04-03T10:15:51.126Z"
             }
         },
-        "image_file_22.json": {
+        "image_file/f67473fd-fbf8-4d69-9db1-556938ab5b87": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5982,7 +5982,7 @@
                 "update_date": "2019-04-03T10:15:54.317Z"
             }
         },
-        "image_file_23.json": {
+        "image_file/16acc1f2-9f1c-43c8-8ffe-4a9ea674e6ff": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -5995,7 +5995,7 @@
                 "update_date": "2019-04-03T10:15:50.940Z"
             }
         },
-        "image_file_24.json": {
+        "image_file/017a2c88-4f6e-418e-bb96-f42f3a220f87": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -6008,7 +6008,7 @@
                 "update_date": "2019-04-03T10:15:50.977Z"
             }
         },
-        "image_file_25.json": {
+        "image_file/30305240-004d-4632-84d4-37d7e7378782": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -6021,7 +6021,7 @@
                 "update_date": "2019-04-03T10:15:51.136Z"
             }
         },
-        "image_file_26.json": {
+        "image_file/20c5a14a-aaf3-40e1-9ab7-f95c06ea4200": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -6034,7 +6034,7 @@
                 "update_date": "2019-04-03T10:15:51.052Z"
             }
         },
-        "image_file_27.json": {
+        "image_file/3fd2781b-6855-4eaa-b2fb-81db386adb18": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -6047,7 +6047,7 @@
                 "update_date": "2019-04-03T10:15:51.027Z"
             }
         },
-        "image_file_28.json": {
+        "image_file/40474d53-44a4-4ab2-9f20-61b71291f8aa": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -6060,7 +6060,7 @@
                 "update_date": "2019-04-03T10:15:47.810Z"
             }
         },
-        "image_file_29.json": {
+        "image_file/aaa97d47-7124-4763-a3fc-f6d66eb6d990": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
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@@ -6073,7 +6073,7 @@
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+        "image_file/8b37aba2-be5e-4963-8e6f-51a2df8e143e": {
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             "schema_type": "file",
             "file_core": {
@@ -8153,7 +8153,7 @@
                 "update_date": "2019-04-03T10:16:00.282Z"
             }
         },
-        "image_file_190.json": {
+        "image_file/81c0e4e2-9021-4c4d-9876-1ed5b78ca7a7": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8166,7 +8166,7 @@
                 "update_date": "2019-04-03T10:16:00.805Z"
             }
         },
-        "image_file_191.json": {
+        "image_file/2d7e88dd-bddd-4289-9556-27d301be0b83": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8179,7 +8179,7 @@
                 "update_date": "2019-04-03T10:16:03.188Z"
             }
         },
-        "image_file_192.json": {
+        "image_file/0c1c578d-d4cc-40bb-a54d-d1d4d004373f": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8192,7 +8192,7 @@
                 "update_date": "2019-04-03T10:16:03.221Z"
             }
         },
-        "image_file_193.json": {
+        "image_file/9dc0ead3-f17a-4bb8-88e2-87f779029ff8": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8205,7 +8205,7 @@
                 "update_date": "2019-04-03T10:16:00.822Z"
             }
         },
-        "image_file_194.json": {
+        "image_file/f618a8bc-5e07-477f-a6d3-1b0af8c81ff0": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8218,7 +8218,7 @@
                 "update_date": "2019-04-03T10:16:03.130Z"
             }
         },
-        "image_file_195.json": {
+        "image_file/e834d3df-8432-40ba-b67d-c7cd0bd7328d": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8231,7 +8231,7 @@
                 "update_date": "2019-04-03T10:16:03.234Z"
             }
         },
-        "image_file_196.json": {
+        "image_file/d8908d6d-5daa-454d-9082-726054cfddc1": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8244,7 +8244,7 @@
                 "update_date": "2019-04-03T10:16:03.189Z"
             }
         },
-        "image_file_197.json": {
+        "image_file/c5a7142e-4702-4e84-b7aa-239df2a71ba8": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8257,7 +8257,7 @@
                 "update_date": "2019-04-03T10:16:00.189Z"
             }
         },
-        "image_file_198.json": {
+        "image_file/f69e44ef-cf23-4571-8dad-e44222697974": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8270,7 +8270,7 @@
                 "update_date": "2019-04-03T10:16:03.186Z"
             }
         },
-        "image_file_199.json": {
+        "image_file/ea72f81c-2c58-43e2-acca-294254f470f7": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8283,7 +8283,7 @@
                 "update_date": "2019-04-03T10:16:03.138Z"
             }
         },
-        "image_file_200.json": {
+        "image_file/89d1d2b5-81d3-487d-9fc1-d8b1d8ac34ab": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8296,7 +8296,7 @@
                 "update_date": "2019-04-03T10:16:03.194Z"
             }
         },
-        "image_file_201.json": {
+        "image_file/6928ac1b-fd1d-436c-bfc6-4087c65809d7": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8309,7 +8309,7 @@
                 "update_date": "2019-04-03T10:16:03.234Z"
             }
         },
-        "image_file_202.json": {
+        "image_file/07a7b938-435b-4804-b140-c255957b6532": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8322,7 +8322,7 @@
                 "update_date": "2019-04-03T10:16:03.185Z"
             }
         },
-        "image_file_203.json": {
+        "image_file/3d532a7b-55e7-4461-afbc-65ef76403384": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8335,7 +8335,7 @@
                 "update_date": "2019-04-03T10:16:00.225Z"
             }
         },
-        "image_file_204.json": {
+        "image_file/bab40245-28bd-49a2-8be0-ba109fe41c91": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8348,7 +8348,7 @@
                 "update_date": "2019-04-03T10:16:03.171Z"
             }
         },
-        "image_file_205.json": {
+        "image_file/9d577bd4-3a27-48be-ad7c-8c44cf803cda": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8361,7 +8361,7 @@
                 "update_date": "2019-04-03T10:16:03.221Z"
             }
         },
-        "image_file_206.json": {
+        "image_file/c4de7605-fec5-4389-bb9e-f2ea0c41cdef": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8374,7 +8374,7 @@
                 "update_date": "2019-04-03T10:16:03.221Z"
             }
         },
-        "image_file_207.json": {
+        "image_file/21a043b6-6dde-41b9-b20e-74b961da8b88": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8387,7 +8387,7 @@
                 "update_date": "2019-04-03T10:16:03.210Z"
             }
         },
-        "image_file_208.json": {
+        "image_file/11280200-1803-4110-aa84-2808776c2d50": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8400,7 +8400,7 @@
                 "update_date": "2019-04-03T10:16:03.231Z"
             }
         },
-        "image_file_209.json": {
+        "image_file/86df5269-576b-4d18-a0ce-6e2b2a36d51b": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8413,7 +8413,7 @@
                 "update_date": "2019-04-03T10:16:03.201Z"
             }
         },
-        "image_file_210.json": {
+        "image_file/e524ff4e-95fa-4561-bfd3-276cba79e664": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8426,7 +8426,7 @@
                 "update_date": "2019-04-03T10:16:03.251Z"
             }
         },
-        "image_file_211.json": {
+        "image_file/3d5737da-b1ab-48cb-a26f-d420e53edccd": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8439,7 +8439,7 @@
                 "update_date": "2019-04-03T10:16:03.057Z"
             }
         },
-        "image_file_212.json": {
+        "image_file/44cf15ec-3d4e-4698-bb14-107c34891191": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8452,7 +8452,7 @@
                 "update_date": "2019-04-03T10:16:03.206Z"
             }
         },
-        "image_file_213.json": {
+        "image_file/6242cdf3-fd6d-4479-a08a-1747818fd978": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8465,7 +8465,7 @@
                 "update_date": "2019-04-03T10:16:03.054Z"
             }
         },
-        "image_file_214.json": {
+        "image_file/bc60bbd4-8b09-425c-b507-9da24a84f412": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8478,7 +8478,7 @@
                 "update_date": "2019-04-03T10:16:00.270Z"
             }
         },
-        "image_file_215.json": {
+        "image_file/1f054ccf-f8dd-4127-a6f8-c577d7dd93dc": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8491,7 +8491,7 @@
                 "update_date": "2019-04-03T10:16:03.187Z"
             }
         },
-        "image_file_216.json": {
+        "image_file/9954cb4b-b0a4-4479-b31d-0bee1e75d9c7": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8504,7 +8504,7 @@
                 "update_date": "2019-04-03T10:16:03.267Z"
             }
         },
-        "image_file_217.json": {
+        "image_file/5f67c32c-a154-4620-8603-0b64979b04a4": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8517,7 +8517,7 @@
                 "update_date": "2019-04-03T10:16:03.116Z"
             }
         },
-        "image_file_218.json": {
+        "image_file/7d5bffb2-8bf9-4366-a8b2-762ebb4d6c5d": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8530,7 +8530,7 @@
                 "update_date": "2019-04-03T10:16:00.148Z"
             }
         },
-        "image_file_219.json": {
+        "image_file/dcee6df0-9e87-4935-8873-f8d30d449d76": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8543,7 +8543,7 @@
                 "update_date": "2019-04-03T10:16:03.250Z"
             }
         },
-        "image_file_220.json": {
+        "image_file/7d6bdde6-523f-46cb-bed5-d6cfa8fea80c": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8556,7 +8556,7 @@
                 "update_date": "2019-04-03T10:16:03.126Z"
             }
         },
-        "image_file_221.json": {
+        "image_file/e6d00b0c-3641-4ec4-a553-8fd742193dba": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8569,7 +8569,7 @@
                 "update_date": "2019-04-03T10:16:03.321Z"
             }
         },
-        "image_file_222.json": {
+        "image_file/e5034863-0528-4f55-be95-c8501c29f9fe": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8582,7 +8582,7 @@
                 "update_date": "2019-04-03T10:16:03.187Z"
             }
         },
-        "image_file_223.json": {
+        "image_file/cc61b14a-59d9-477b-8cb1-43c4ee4cf434": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8595,7 +8595,7 @@
                 "update_date": "2019-04-03T10:16:03.190Z"
             }
         },
-        "image_file_224.json": {
+        "image_file/33d332c9-aefe-4db5-8830-b8daddaed0d2": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8608,7 +8608,7 @@
                 "update_date": "2019-04-03T10:16:03.189Z"
             }
         },
-        "image_file_225.json": {
+        "image_file/bb3b6fc7-0902-432d-bad1-6b3f61951314": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8621,7 +8621,7 @@
                 "update_date": "2019-04-03T10:15:51.086Z"
             }
         },
-        "image_file_226.json": {
+        "image_file/2b734e88-3a33-4c73-92bb-82e0b8f8c13b": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/1.0.4/image_file",
             "schema_type": "file",
             "file_core": {
@@ -8634,7 +8634,7 @@
                 "update_date": "2019-04-03T10:16:00.280Z"
             }
         },
-        "project_0.json": {
+        "project/ae5237b4-633f-403a-afc6-cb87e6f90db1": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/project/11.0.1/project",
             "schema_type": "project",
             "project_core": {
@@ -8658,7 +8658,7 @@
                 "update_date": "2019-04-03T10:13:45.439Z"
             }
         },
-        "imaging_protocol_0.json": {
+        "imaging_protocol/96ecb94d-e848-4d7b-8df9-f19af6ab17b8": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/imaging/11.0.12/imaging_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -11609,7 +11609,7 @@
                 "update_date": "2019-04-03T10:13:45.902Z"
             }
         },
-        "imaging_preparation_protocol_0.json": {
+        "imaging_preparation_protocol/a6d431b0-4373-4eaf-a3af-8c3fe461ab38": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/imaging/2.0.3/imaging_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -11627,7 +11627,7 @@
                 "update_date": "2019-04-03T10:13:45.426Z"
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/caf94c25-8327-4379-b88e-2a6642cd7513": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/9.0.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -11646,7 +11646,7 @@
                 "update_date": "2019-04-03T10:13:45.505Z"
             }
         },
-        "process_0.json": {
+        "process/da265acd-5601-49c5-855e-d792d51b4042": {
             "process_core": {
                 "process_id": "zador_baristaseq_1"
             },
@@ -11658,7 +11658,7 @@
                 "update_date": "2019-04-03T10:14:03.513Z"
             }
         },
-        "process_1.json": {
+        "process/07acb7d0-3f1c-47f7-9ef9-851c4f1caaec": {
             "process_core": {
                 "process_id": "process_id_2"
             },
@@ -11670,7 +11670,7 @@
                 "update_date": "2019-04-03T10:13:53.863Z"
             }
         },
-        "process_2.json": {
+        "process/fee8a188-5783-44cd-a1c1-ed9d5d7c32a9": {
             "process_core": {
                 "process_id": "process_id_1"
             },
diff --git a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
index bdec17aa3..b4759e65d 100644
--- a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
+++ b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
@@ -194,7 +194,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/5ea17576-5f1d-4879-97a1-6a868ccb2b0b": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -222,7 +222,7 @@
                 "schema_minor_version": 3
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/d9b27804-1763-410b-9f19-995a363fe488": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -261,7 +261,7 @@
                 "schema_minor_version": 4
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/587d1170-aa27-4b06-9c15-b51846d14588": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -317,7 +317,7 @@
                 "schema_minor_version": 5
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/430755e7-2263-4b5b-ad65-b3231c0eb61d": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -343,7 +343,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/d53454df-9542-4c64-9f84-0d798d923777": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -369,7 +369,7 @@
                 "schema_minor_version": 2
             }
         },
-        "project_0.json": {
+        "project/4e6f083b-5b9a-4393-9890-2a83da8188f1": {
             "describedBy": "https://schema.humancellatlas.org/type/project/14.1.0/project",
             "schema_type": "project",
             "project_core": {
@@ -675,7 +675,7 @@
                 "schema_minor_version": 1
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/58df9607-ab66-48e0-a47b-1f897baae139": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -723,7 +723,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/6282594c-1b9d-4f26-a4f3-a26066878740": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -754,7 +754,7 @@
                 "schema_minor_version": 1
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/3f9fda53-2b30-47bb-8c92-4e131920b2e3": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -775,7 +775,7 @@
                 "schema_minor_version": 2
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/e95ebc23-53b9-48a0-acd4-185969122f2d": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -796,7 +796,7 @@
                 "schema_minor_version": 2
             }
         },
-        "collection_protocol_1.json": {
+        "collection_protocol/4dfda495-6aeb-41d9-b995-04da33cd2810": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -817,7 +817,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_0.json": {
+        "process/bf65ea92-6949-491d-b25b-52d06045044a": {
             "process_core": {
                 "process_id": "E8.75_anterior_Rep1"
             },
@@ -831,7 +831,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_1.json": {
+        "process/11b9ffae-0643-425b-b120-85a7bd46c057": {
             "process_core": {
                 "process_id": "process_id_48"
             },
@@ -845,7 +845,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_2.json": {
+        "process/4c6d81f9-4f12-457e-89cd-6efb297ca848": {
             "process_core": {
                 "process_id": "process_id_21"
             },
diff --git a/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json b/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
index 28347ab78..d2e4f1d04 100644
--- a/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
+++ b/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
@@ -26,7 +26,7 @@
         }
     ],
     "metadata": {
-        "project_0.json": {
+        "project/93f6a42f-1790-4af4-b5d1-8c436cb6feae": {
             "content": {
                 "describedBy": "https://schema.humancellatlas.org/type/project/9.0.0/project",
                 "project_core": {
@@ -150,7 +150,7 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
         },
-        "sequence_file_0.json": {
+        "sequence_file/e080459e-e4ab-40ea-ab75-a2646b5fdd29": {
             "content": {
                 "file_core": {
                     "file_name": "22467_6#373_1.fastq.gz",
@@ -166,7 +166,7 @@
                 "document_id": "e080459e-e4ab-40ea-ab75-a2646b5fdd29"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/3417cdb5-5618-4c0c-bc27-62a4eb78916a": {
             "content": {
                 "file_core": {
                     "file_name": "22467_6#373_2.fastq.gz",
@@ -182,7 +182,7 @@
                 "document_id": "3417cdb5-5618-4c0c-bc27-62a4eb78916a"
             }
         },
-        "dissociation_process_0.json": {
+        "dissociation_process/b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -200,7 +200,7 @@
                 "document_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902"
             }
         },
-        "process_1.json": {
+        "process/0763320a-e0c4-4c07-b150-b83650fbef68": {
             "content": {
                 "process_core": {
                     "process_id": "sampling_process_12"
@@ -215,7 +215,7 @@
                 "document_id": "0763320a-e0c4-4c07-b150-b83650fbef68"
             }
         },
-        "enrichment_process_2.json": {
+        "enrichment_process/bcef348b-3915-48b8-bc09-d24a5bff76c4": {
             "content": {
                 "enrichment_method": "FACS",
                 "process_core": {
@@ -232,7 +232,7 @@
                 "document_id": "bcef348b-3915-48b8-bc09-d24a5bff76c4"
             }
         },
-        "library_preparation_process_3.json": {
+        "library_preparation_process/687065f3-c70f-46c3-8452-a5eead33a1bf": {
             "content": {
                 "input_nucleic_acid_molecule": {
                     "text": "polyA RNA",
@@ -261,7 +261,7 @@
                 "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
             }
         },
-        "sequencing_process_4.json": {
+        "sequencing_process/b8a6acbe-6b57-4efb-b6c7-bceaa6d9924d": {
             "content": {
                 "paired_ends": true,
                 "instrument_manufacturer_model": {
@@ -286,7 +286,7 @@
                 "document_id": "b8a6acbe-6b57-4efb-b6c7-bceaa6d9924d"
             }
         },
-        "protocol_0.json": {
+        "protocol/c9a1e203-bddc-45d3-87c4-6010be8e0127": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "Extracting cells from lymph nodes",
@@ -303,7 +303,7 @@
                 "document_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127"
             }
         },
-        "protocol_1.json": {
+        "protocol/a1c80daf-58b0-4b7a-8e29-d0130493c8e6": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "FACS sorting cells by surface markers",
@@ -320,7 +320,7 @@
                 "document_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6"
             }
         },
-        "protocol_2.json": {
+        "protocol/52d79a89-4b49-4c1b-b857-5cc5da07f643": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "Make/amplify cDNA for each cell",
@@ -341,7 +341,7 @@
                 "document_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643"
             }
         },
-        "protocol_3.json": {
+        "protocol/ca6096cf-13c1-4930-8308-6ab05865e2c9": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "Sequencing SmartSeq2 cells",
@@ -357,7 +357,7 @@
                 "document_id": "ca6096cf-13c1-4930-8308-6ab05865e2c9"
             }
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/f59292f0-318f-40d0-bce5-29413b59a790": {
             "content": {
                 "genus_species": [
                     {
@@ -388,7 +388,7 @@
                 "document_id": "f59292f0-318f-40d0-bce5-29413b59a790"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/ffb809dd-3139-4162-b9af-ec88e491ee9c": {
             "content": {
                 "biomaterial_core": {
                     "has_input_biomaterial": "1117",
@@ -420,7 +420,7 @@
                 "document_id": "ffb809dd-3139-4162-b9af-ec88e491ee9c"
             }
         },
-        "donor_organism_2.json": {
+        "donor_organism/689311a2-bfaf-4196-a753-554e69ab59b2": {
             "content": {
                 "is_living": false,
                 "mus_musculus_specific": {
diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
index fa7da5135..adc4a5b37 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
@@ -182,7 +182,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/412898c5-5b9b-4907-b07c-e9b89666e204": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -207,7 +207,7 @@
                 "update_date": "2018-11-02T10:10:10.908Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/a21dc760-a500-4236-bcff-da34a0e873d2": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -246,7 +246,7 @@
                 "update_date": "2018-11-02T10:09:26.517Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/7b07b9d0-cc0e-4098-9f64-f4a569f7d746": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -296,7 +296,7 @@
                 "update_date": "2018-11-02T10:07:39.622Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/70d1af4a-82c8-478a-8960-e9028b3616ca": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -314,7 +314,7 @@
                 "update_date": "2018-11-02T10:35:03.810Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -332,7 +332,7 @@
                 "update_date": "2018-11-02T10:35:07.705Z"
             }
         },
-        "project_0.json": {
+        "project/e8642221-4c2c-4fd7-b926-a68bce363c88": {
             "describedBy": "https://schema.humancellatlas.org/type/project/9.0.3/project",
             "schema_type": "project",
             "project_core": {
@@ -400,7 +400,7 @@
                 "update_date": "2018-11-02T10:07:39.499Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/9c32cf70-3ed7-4720-badc-5ee71e8a38af": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/4.3.3/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -429,7 +429,7 @@
                 "update_date": "2018-11-02T10:05:10.360Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/61e629ed-0135-4492-ac8a-5c4ab3ccca8a": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/9.0.3/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -452,7 +452,7 @@
                 "update_date": "2018-11-02T10:05:10.376Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/31e708d3-79df-49b8-a3df-b1d694963468": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -470,7 +470,7 @@
                 "update_date": "2018-11-02T10:05:10.315Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/5bd4ba68-4c0e-4d22-840d-afc025e7badc": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -489,7 +489,7 @@
                 "update_date": "2018-11-02T10:05:10.335Z"
             }
         },
-        "process_0.json": {
+        "process/771ddaf6-3a4f-4314-97fe-6294ff8e25a4": {
             "process_core": {
                 "process_id": "SRR3562915"
             },
@@ -501,7 +501,7 @@
                 "update_date": "2018-11-02T10:13:43.197Z"
             }
         },
-        "process_1.json": {
+        "process/4c28e079-59af-4bd3-8c8b-763ea0beba98": {
             "process_core": {
                 "process_id": "process_id_714"
             },
@@ -513,7 +513,7 @@
                 "update_date": "2018-11-02T10:12:21.545Z"
             }
         },
-        "process_2.json": {
+        "process/4674255d-5ecd-4860-9b8d-beae98772cd9": {
             "process_core": {
                 "process_id": "process_id_6"
             },
diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
index c2778bb99..ccadf904c 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
@@ -182,7 +182,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/412898c5-5b9b-4907-b07c-e9b89666e204": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -207,7 +207,7 @@
                 "update_date": "2018-11-04T10:10:10.908Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/a21dc760-a500-4236-bcff-da34a0e873d2": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -246,7 +246,7 @@
                 "update_date": "2018-11-04T10:09:26.517Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/7b07b9d0-cc0e-4098-9f64-f4a569f7d746": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -296,7 +296,7 @@
                 "update_date": "2018-11-04T10:07:39.622Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/70d1af4a-82c8-478a-8960-e9028b3616ca": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -314,7 +314,7 @@
                 "update_date": "2018-11-04T10:35:03.810Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -332,7 +332,7 @@
                 "update_date": "2018-11-04T10:35:07.705Z"
             }
         },
-        "project_0.json": {
+        "project/e8642221-4c2c-4fd7-b926-a68bce363c88": {
             "describedBy": "https://schema.humancellatlas.org/type/project/9.0.3/project",
             "schema_type": "project",
             "project_core": {
@@ -400,7 +400,7 @@
                 "update_date": "2018-11-04T10:07:39.499Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/9c32cf70-3ed7-4720-badc-5ee71e8a38af": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/4.3.3/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -429,7 +429,7 @@
                 "update_date": "2018-11-04T10:05:10.360Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/61e629ed-0135-4492-ac8a-5c4ab3ccca8a": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/9.0.3/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -452,7 +452,7 @@
                 "update_date": "2018-11-04T10:05:10.376Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/31e708d3-79df-49b8-a3df-b1d694963468": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -470,7 +470,7 @@
                 "update_date": "2018-11-04T10:05:10.315Z"
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/5bd4ba68-4c0e-4d22-840d-afc025e7badc": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/2.2.5/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -489,7 +489,7 @@
                 "update_date": "2018-11-04T10:05:10.335Z"
             }
         },
-        "process_0.json": {
+        "process/771ddaf6-3a4f-4314-97fe-6294ff8e25a4": {
             "process_core": {
                 "process_id": "SRR3562915"
             },
@@ -501,7 +501,7 @@
                 "update_date": "2018-11-04T10:13:43.197Z"
             }
         },
-        "process_1.json": {
+        "process/4c28e079-59af-4bd3-8c8b-763ea0beba98": {
             "process_core": {
                 "process_id": "process_id_714"
             },
@@ -513,7 +513,7 @@
                 "update_date": "2018-11-04T10:12:21.545Z"
             }
         },
-        "process_2.json": {
+        "process/4674255d-5ecd-4860-9b8d-beae98772cd9": {
             "process_core": {
                 "process_id": "process_id_6"
             },
diff --git a/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json b/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
index 3ba38f5c5..1e1e8b7a8 100644
--- a/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
+++ b/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
@@ -2306,7 +2306,7 @@
         }
     ],
     "metadata": {
-        "project_0.json": {
+        "project/6504d48c-1610-43aa-8cf8-214a960e110c": {
             "content": {
                 "describedBy": "https://schema.humancellatlas.org/type/project/5.1.0/project",
                 "project_core": {
@@ -2435,7 +2435,7 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/81bdd959-6a0c-45e8-a95f-9e94362ac234": {
             "content": {
                 "genus_species": [
                     {
@@ -2467,7 +2467,7 @@
                 "document_id": "81bdd959-6a0c-45e8-a95f-9e94362ac234"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/763da7c3-cf84-4dd1-9816-99387476f439": {
             "content": {
                 "organ": {
                     "text": "hematopoietic system",
@@ -2500,7 +2500,7 @@
                 "document_id": "763da7c3-cf84-4dd1-9816-99387476f439"
             }
         },
-        "donor_organism_2.json": {
+        "donor_organism/50df319c-ce04-45d3-bf61-72017700f4c7": {
             "content": {
                 "is_living": true,
                 "biological_sex": "male",
@@ -2536,7 +2536,7 @@
                 "document_id": "50df319c-ce04-45d3-bf61-72017700f4c7"
             }
         },
-        "cell_suspension_3.json": {
+        "cell_suspension/8a5f6526-b075-4dc6-911a-094c9e9df5b8": {
             "content": {
                 "genus_species": [
                     {
@@ -2568,7 +2568,7 @@
                 "document_id": "8a5f6526-b075-4dc6-911a-094c9e9df5b8"
             }
         },
-        "specimen_from_organism_4.json": {
+        "specimen_from_organism/ea978eed-c518-421b-9ff1-e9946e79285d": {
             "content": {
                 "organ": {
                     "text": "hematopoietic system",
@@ -2601,7 +2601,7 @@
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                     "process_id": "sampling_process_104"
@@ -8739,7 +8739,7 @@
                 "document_id": "fa2d3e8d-2ba5-4b69-902d-43b184458f11"
             }
         },
-        "dissociation_process_48.json": {
+        "dissociation_process/4e475c02-d356-41d3-9841-385c41b3ff03": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8758,7 +8758,7 @@
                 "document_id": "4e475c02-d356-41d3-9841-385c41b3ff03"
             }
         },
-        "process_49.json": {
+        "process/036c253c-6291-45fb-b576-fc0b409d31ba": {
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                 "process_core": {
                     "process_id": "sampling_process_4"
@@ -8773,7 +8773,7 @@
                 "document_id": "036c253c-6291-45fb-b576-fc0b409d31ba"
             }
         },
-        "dissociation_process_50.json": {
+        "dissociation_process/0768a4f7-4f01-4c12-a3cf-2d785caca462": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8792,7 +8792,7 @@
                 "document_id": "0768a4f7-4f01-4c12-a3cf-2d785caca462"
             }
         },
-        "process_51.json": {
+        "process/143b36e8-1817-4d71-93ef-cf34bd3ea260": {
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@@ -8807,7 +8807,7 @@
                 "document_id": "143b36e8-1817-4d71-93ef-cf34bd3ea260"
             }
         },
-        "dissociation_process_52.json": {
+        "dissociation_process/c2337757-6b6d-450b-9323-e1096aac8a8a": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8826,7 +8826,7 @@
                 "document_id": "c2337757-6b6d-450b-9323-e1096aac8a8a"
             }
         },
-        "process_53.json": {
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@@ -8841,7 +8841,7 @@
                 "document_id": "460d08b2-db32-4f65-9c19-37b46170df7d"
             }
         },
-        "dissociation_process_54.json": {
+        "dissociation_process/eec9006d-d288-4311-806f-35a155cdf4fd": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8860,7 +8860,7 @@
                 "document_id": "eec9006d-d288-4311-806f-35a155cdf4fd"
             }
         },
-        "process_55.json": {
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                 "process_core": {
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@@ -8875,7 +8875,7 @@
                 "document_id": "8a307f43-db3b-41de-8ef2-78f94c63353b"
             }
         },
-        "dissociation_process_56.json": {
+        "dissociation_process/9948f709-25ff-4e0c-89a7-e95260f97349": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8894,7 +8894,7 @@
                 "document_id": "9948f709-25ff-4e0c-89a7-e95260f97349"
             }
         },
-        "process_57.json": {
+        "process/24b49306-6de0-4312-b7c6-ca59ba5c0240": {
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                 "process_core": {
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@@ -8909,7 +8909,7 @@
                 "document_id": "24b49306-6de0-4312-b7c6-ca59ba5c0240"
             }
         },
-        "dissociation_process_58.json": {
+        "dissociation_process/5b9516d2-dc9a-437e-ac75-2a17e131557a": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8928,7 +8928,7 @@
                 "document_id": "5b9516d2-dc9a-437e-ac75-2a17e131557a"
             }
         },
-        "process_59.json": {
+        "process/a386d9df-39d1-4bbb-bd3f-5e0f1ff2c061": {
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                 "process_core": {
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@@ -8943,7 +8943,7 @@
                 "document_id": "a386d9df-39d1-4bbb-bd3f-5e0f1ff2c061"
             }
         },
-        "dissociation_process_60.json": {
+        "dissociation_process/7c156764-c910-4e89-9845-a2dbe567a60a": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8962,7 +8962,7 @@
                 "document_id": "7c156764-c910-4e89-9845-a2dbe567a60a"
             }
         },
-        "process_61.json": {
+        "process/9da0296c-d378-4ad4-94c7-d359fa7433d1": {
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                 "process_core": {
                     "process_id": "sampling_process_61"
@@ -8977,7 +8977,7 @@
                 "document_id": "9da0296c-d378-4ad4-94c7-d359fa7433d1"
             }
         },
-        "dissociation_process_62.json": {
+        "dissociation_process/029b7cf1-c7f8-4f0a-b20d-35c8158f64a6": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8996,7 +8996,7 @@
                 "document_id": "029b7cf1-c7f8-4f0a-b20d-35c8158f64a6"
             }
         },
-        "process_63.json": {
+        "process/c534bfdb-4b99-45ca-8bd9-e21ff354e988": {
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                 "process_core": {
                     "process_id": "sampling_process_9"
@@ -9011,7 +9011,7 @@
                 "document_id": "c534bfdb-4b99-45ca-8bd9-e21ff354e988"
             }
         },
-        "library_preparation_process_64.json": {
+        "library_preparation_process/12ea2953-06a4-4e80-8910-a27aba936b9c": {
             "content": {
                 "input_nucleic_acid_molecule": {
                     "text": "polyA RNA",
@@ -9048,7 +9048,7 @@
                 "document_id": "12ea2953-06a4-4e80-8910-a27aba936b9c"
             }
         },
-        "sequencing_process_65.json": {
+        "sequencing_process/05e446a2-88c1-465b-b56c-7caf6ad4c018": {
             "content": {
                 "paired_ends": true,
                 "local_machine_name": "HXJ",
@@ -9076,7 +9076,7 @@
                 "document_id": "05e446a2-88c1-465b-b56c-7caf6ad4c018"
             }
         },
-        "protocol_0.json": {
+        "protocol/3cbebf0a-4aab-4525-80f4-222703d14b98": {
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                 "protocol_core": {
                     "protocol_id": "dissociation_protocol_1"
@@ -9091,7 +9091,7 @@
                 "document_id": "3cbebf0a-4aab-4525-80f4-222703d14b98"
             }
         },
-        "protocol_1.json": {
+        "protocol/81b97ec1-f68c-4d69-be78-50d1aad7bbef": {
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                 "protocol_core": {
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@@ -9110,7 +9110,7 @@
                 "document_id": "81b97ec1-f68c-4d69-be78-50d1aad7bbef"
             }
         },
-        "protocol_2.json": {
+        "protocol/e99eed63-5794-4d8d-baf9-9c6888e91e6d": {
             "content": {
                 "protocol_core": {
                     "protocol_id": "10x_v2_sequencing_protocol_1"
diff --git a/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json b/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
index ba60102af..ba9375653 100644
--- a/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
+++ b/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
@@ -26,7 +26,7 @@
         }
     ],
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-        "project_0.json": {
+        "project/93f6a42f-1790-4af4-b5d1-8c436cb6feae": {
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                 "project_core": {
@@ -150,7 +150,7 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
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-        "cell_suspension_0.json": {
+        "cell_suspension/603a818f-dbe7-466a-8241-58b9c1618846": {
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@@ -181,7 +181,7 @@
                 "document_id": "603a818f-dbe7-466a-8241-58b9c1618846"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/4e41a067-dbb7-439f-b72f-80240ce858f6": {
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                 "biomaterial_core": {
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@@ -213,7 +213,7 @@
                 "document_id": "4e41a067-dbb7-439f-b72f-80240ce858f6"
             }
         },
-        "donor_organism_2.json": {
+        "donor_organism/bf8492ad-1d45-46aa-9fe9-67058b8c2410": {
             "content": {
                 "is_living": false,
                 "mus_musculus_specific": {
@@ -258,7 +258,7 @@
                 "document_id": "bf8492ad-1d45-46aa-9fe9-67058b8c2410"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/d2f32681-9c1a-4dfd-b506-c24327afb8d1": {
             "content": {
                 "file_core": {
                     "file_name": "22011_1#268_1.fastq.gz",
@@ -274,7 +274,7 @@
                 "document_id": "d2f32681-9c1a-4dfd-b506-c24327afb8d1"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/aa662c76-d220-49f4-8316-f4af5820d60b": {
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                 "file_core": {
                     "file_name": "22011_1#268_2.fastq.gz",
@@ -290,7 +290,7 @@
                 "document_id": "aa662c76-d220-49f4-8316-f4af5820d60b"
             }
         },
-        "dissociation_process_0.json": {
+        "dissociation_process/b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902": {
             "content": {
                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -308,7 +308,7 @@
                 "document_id": "b7bbb2dc-3131-47c3-bcb9-4b7e0eeed902"
             }
         },
-        "process_1.json": {
+        "process/f03590d8-4e65-478e-bc67-a8c64d2c93e9": {
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@@ -323,7 +323,7 @@
                 "document_id": "f03590d8-4e65-478e-bc67-a8c64d2c93e9"
             }
         },
-        "enrichment_process_2.json": {
+        "enrichment_process/2f2fb366-249f-49e3-b47d-a0bb39d9bc78": {
             "content": {
                 "enrichment_method": "FACS",
                 "process_core": {
@@ -340,7 +340,7 @@
                 "document_id": "2f2fb366-249f-49e3-b47d-a0bb39d9bc78"
             }
         },
-        "enrichment_process_3.json": {
+        "enrichment_process/a192f0d7-8e8e-48ae-b80d-3cb18acb3215": {
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                 "enrichment_method": "FACS",
                 "process_core": {
@@ -357,7 +357,7 @@
                 "document_id": "a192f0d7-8e8e-48ae-b80d-3cb18acb3215"
             }
         },
-        "library_preparation_process_4.json": {
+        "library_preparation_process/687065f3-c70f-46c3-8452-a5eead33a1bf": {
             "content": {
                 "input_nucleic_acid_molecule": {
                     "text": "polyA RNA",
@@ -386,7 +386,7 @@
                 "document_id": "687065f3-c70f-46c3-8452-a5eead33a1bf"
             }
         },
-        "sequencing_process_5.json": {
+        "sequencing_process/2580dcf9-3f7d-4421-b962-ab860e10d072": {
             "content": {
                 "paired_ends": true,
                 "instrument_manufacturer_model": {
@@ -411,7 +411,7 @@
                 "document_id": "2580dcf9-3f7d-4421-b962-ab860e10d072"
             }
         },
-        "protocol_0.json": {
+        "protocol/c9a1e203-bddc-45d3-87c4-6010be8e0127": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "Extracting cells from lymph nodes",
@@ -428,7 +428,7 @@
                 "document_id": "c9a1e203-bddc-45d3-87c4-6010be8e0127"
             }
         },
-        "protocol_1.json": {
+        "protocol/a1c80daf-58b0-4b7a-8e29-d0130493c8e6": {
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                 "protocol_core": {
                     "protocol_name": "FACS sorting cells by surface markers",
@@ -445,7 +445,7 @@
                 "document_id": "a1c80daf-58b0-4b7a-8e29-d0130493c8e6"
             }
         },
-        "protocol_2.json": {
+        "protocol/52d79a89-4b49-4c1b-b857-5cc5da07f643": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "Make/amplify cDNA for each cell",
@@ -466,7 +466,7 @@
                 "document_id": "52d79a89-4b49-4c1b-b857-5cc5da07f643"
             }
         },
-        "protocol_3.json": {
+        "protocol/ca6096cf-13c1-4930-8308-6ab05865e2c9": {
             "content": {
                 "protocol_core": {
                     "protocol_name": "Sequencing SmartSeq2 cells",
diff --git a/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
index cb8aed169..5049d85d9 100644
--- a/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
+++ b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
@@ -194,7 +194,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/1e07c7cf-66c3-4cd5-a061-71f3e89489ff": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -231,7 +231,7 @@
                 "update_date": "2018-09-11T16:53:41.273Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/39a16395-6e12-4ec1-8cff-b77dd23f7024": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -282,7 +282,7 @@
                 "update_date": "2018-09-11T16:53:07.436Z"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/1fe5d2c3-cf34-45ce-b1e4-dc8568ca5ab2": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -333,7 +333,7 @@
                 "update_date": "2018-09-11T16:53:10.431Z"
             }
         },
-        "specimen_from_organism_2.json": {
+        "specimen_from_organism/02f67508-6e87-42cf-9588-df49a4250a95": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -384,7 +384,7 @@
                 "update_date": "2018-09-11T16:53:12.111Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/ff15c305-fc63-419f-a0fd-84d123f9b975": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -432,7 +432,7 @@
                 "update_date": "2018-09-11T16:53:04.090Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/211d3f25-1253-4a01-aadf-08b6452de585": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -452,7 +452,7 @@
                 "update_date": "2018-09-11T17:04:35.520Z"
             }
         },
-        "project_0.json": {
+        "project/587fe7e4-0e41-42d6-976f-585345a51ba2": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/project/9.0.2/project",
             "schema_type": "project",
             "project_core": {
@@ -474,7 +474,7 @@
                 "update_date": "2018-09-11T16:53:03.974Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/3720c08b-f4b6-4bc7-a889-d4d3db602e7d": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/4.3.2/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -507,7 +507,7 @@
                 "update_date": "2018-09-11T16:40:47.185Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/3e11dd06-396b-4aaa-a6ae-3b6a26a1d9f0": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -529,7 +529,7 @@
                 "update_date": "2018-09-11T16:40:45.581Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/f90527fc-d710-414b-b185-0e9c5b4138af": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -547,7 +547,7 @@
                 "update_date": "2018-09-11T16:40:46.268Z"
             }
         },
-        "process_0.json": {
+        "process/78e53890-4a5c-423b-a7b9-aa3247ecf98b": {
             "process_core": {
                 "process_id": "process_id_9101"
             },
@@ -559,7 +559,7 @@
                 "update_date": "2018-09-11T17:11:53.151Z"
             }
         },
-        "process_1.json": {
+        "process/427f77a0-9fc5-4fea-a9bb-d05841fad71c": {
             "process_core": {
                 "process_id": "process_id_13"
             },
@@ -571,7 +571,7 @@
                 "update_date": "2018-09-11T17:05:50.325Z"
             }
         },
-        "process_2.json": {
+        "process/677e65b8-5a0d-4f5a-af89-7cca51bcd6c3": {
             "process_core": {
                 "process_id": "process_id_1"
             },
@@ -583,7 +583,7 @@
                 "update_date": "2018-09-11T17:05:50.149Z"
             }
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-        "process_3.json": {
+        "process/ac321e06-ec12-423a-bf12-5e0ec97f0fb1": {
             "process_core": {
                 "process_id": "process_id_2"
             },
@@ -595,7 +595,7 @@
                 "update_date": "2018-09-11T17:05:50.159Z"
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-        "process_4.json": {
+        "process/34aa8a89-27d0-4a03-8196-72da4d701efb": {
             "process_core": {
                 "process_id": "process_id_3"
             },
diff --git a/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json b/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
index 24f48db53..a5102aea5 100644
--- a/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
+++ b/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
@@ -2234,7 +2234,7 @@
         }
     ],
     "metadata": {
-        "project_0.json": {
+        "project/6504d48c-1610-43aa-8cf8-214a960e110c": {
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                 "project_core": {
@@ -2363,7 +2363,7 @@
             "schema_version": "5.1.0",
             "schema_type": "project_bundle"
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/511d4724-0b88-418d-bd22-5d6f986d6053": {
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                     {
@@ -2395,7 +2395,7 @@
                 "document_id": "511d4724-0b88-418d-bd22-5d6f986d6053"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/a673bfc0-7dd8-4010-a882-8fb3e6f553b1": {
             "content": {
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@@ -8587,7 +8587,7 @@
                 "document_id": "d6f3b423-67c4-460e-989c-39cd2e762a92"
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@@ -8602,7 +8602,7 @@
                 "document_id": "7c86261f-3112-4bc1-bd8d-8a94accf7478"
             }
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-        "dissociation_process_54.json": {
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                 "nucleic_acid_source": "single cell",
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@@ -8621,7 +8621,7 @@
                 "document_id": "c55b1216-dec4-41bd-b425-3e9e2708ec3d"
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@@ -8636,7 +8636,7 @@
                 "document_id": "a0232494-8018-4f79-add4-d7f822d883c2"
             }
         },
-        "dissociation_process_56.json": {
+        "dissociation_process/d3fbeb3c-623d-453a-9a85-559cf8fcce42": {
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                 "nucleic_acid_source": "single cell",
                 "process_core": {
@@ -8655,7 +8655,7 @@
                 "document_id": "d3fbeb3c-623d-453a-9a85-559cf8fcce42"
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-        "process_57.json": {
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@@ -8670,7 +8670,7 @@
                 "document_id": "ac142e9e-cf8d-4e77-bf36-30177c2931f3"
             }
         },
-        "dissociation_process_58.json": {
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                 "nucleic_acid_source": "single cell",
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@@ -8689,7 +8689,7 @@
                 "document_id": "ced1975a-38cb-47d8-a940-48c438b9fb7a"
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@@ -8704,7 +8704,7 @@
                 "document_id": "f353f6e5-9415-4476-923a-a3bfbde8987a"
             }
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-        "dissociation_process_60.json": {
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                 "nucleic_acid_source": "single cell",
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@@ -8723,7 +8723,7 @@
                 "document_id": "e3515c4a-944a-4f0e-aeff-e872fe44d677"
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-        "process_61.json": {
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@@ -8738,7 +8738,7 @@
                 "document_id": "d46f0814-1caf-4668-ab2e-cec3af24b1fb"
             }
         },
-        "library_preparation_process_62.json": {
+        "library_preparation_process/12ea2953-06a4-4e80-8910-a27aba936b9c": {
             "content": {
                 "input_nucleic_acid_molecule": {
                     "text": "polyA RNA",
@@ -8775,7 +8775,7 @@
                 "document_id": "12ea2953-06a4-4e80-8910-a27aba936b9c"
             }
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-        "sequencing_process_63.json": {
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                 "local_machine_name": "HXJ",
@@ -8803,7 +8803,7 @@
                 "document_id": "f179fd50-5552-4277-9933-4f37fe0fd8e1"
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-        "protocol_0.json": {
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@@ -8818,7 +8818,7 @@
                 "document_id": "3cbebf0a-4aab-4525-80f4-222703d14b98"
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-        "protocol_1.json": {
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@@ -8837,7 +8837,7 @@
                 "document_id": "81b97ec1-f68c-4d69-be78-50d1aad7bbef"
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-        "protocol_2.json": {
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             "content": {
                 "protocol_core": {
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diff --git a/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
index 11c229559..3026047d2 100644
--- a/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
+++ b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
@@ -206,7 +206,7 @@
         }
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@@ -246,7 +246,7 @@
                 "update_date": "2019-07-18T21:12:44.344Z"
             }
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-        "cell_line_0.json": {
+        "cell_line/4ccd163e-a630-4ede-bc0c-336ba044b783": {
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@@ -283,7 +283,7 @@
                 "update_date": "2019-07-18T21:12:44.526Z"
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-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/92254a9e-3a14-4760-b229-d914f3e8973f": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.2.1/specimen_from_organism",
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@@ -328,7 +328,7 @@
                 "update_date": "2019-07-18T21:12:44.655Z"
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-        "donor_organism_0.json": {
+        "donor_organism/39d1a24f-1785-476d-9c04-065be917e3ff": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.3.2/donor_organism",
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@@ -393,7 +393,7 @@
                 "update_date": "2019-07-18T21:12:44.591Z"
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-        "sequence_file_0.json": {
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             "describedBy": "https://schema.humancellatlas.org/type/file/9.1.0/sequence_file",
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@@ -411,7 +411,7 @@
                 "update_date": "2019-07-18T21:22:48.292Z"
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-        "sequence_file_1.json": {
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             "describedBy": "https://schema.humancellatlas.org/type/file/9.1.0/sequence_file",
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@@ -429,7 +429,7 @@
                 "update_date": "2019-07-18T21:25:28.971Z"
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-        "project_0.json": {
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             "schema_type": "project",
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@@ -521,7 +521,7 @@
                 "update_date": "2019-07-18T21:12:44.350Z"
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-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/dc19bb22-ae7b-431b-9b8b-7b49799a8fcd": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.1.1/library_preparation_protocol",
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@@ -573,7 +573,7 @@
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-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/461851b8-55a5-4ae6-a52a-5bca71a00beb": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.0.2/sequencing_protocol",
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@@ -597,7 +597,7 @@
                 "update_date": "2019-07-18T21:12:44.253Z"
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-        "collection_protocol_0.json": {
+        "collection_protocol/79f7c6ac-ada8-4c17-86ec-e73e87b94374": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.1.1/collection_protocol",
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@@ -615,7 +615,7 @@
                 "update_date": "2019-07-18T21:12:44.265Z"
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-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/5d9fc5a2-5516-4205-9d6e-8d0d674f146f": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.0.1/enrichment_protocol",
             "schema_type": "protocol",
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@@ -635,7 +635,7 @@
                 "update_date": "2019-07-18T21:12:44.344Z"
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-        "process_0.json": {
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@@ -652,7 +652,7 @@
                 "update_date": "2019-07-18T21:12:44.356Z"
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-        "process_1.json": {
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@@ -664,7 +664,7 @@
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-        "process_2.json": {
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@@ -676,7 +676,7 @@
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-        "process_3.json": {
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                 "location": "AllCells, LLC",
                 "process_id": "HS_BM_P3_Run1"
diff --git a/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
index 5ad13428b..a48a0e666 100644
--- a/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
+++ b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
@@ -9422,7 +9422,7 @@
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@@ -9456,7 +9456,7 @@
                 "update_date": "2018-10-01T19:29:15.926Z"
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-        "cell_suspension_1.json": {
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@@ -9490,7 +9490,7 @@
                 "update_date": "2018-10-01T19:29:16.215Z"
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-        "cell_suspension_2.json": {
+        "cell_suspension/d52cc98d-5b2e-40b7-9dfd-c255de73602d": {
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             "schema_type": "biomaterial",
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@@ -9524,7 +9524,7 @@
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-        "cell_suspension_3.json": {
+        "cell_suspension/462505d7-48e1-4d85-92e3-f768a93d4fca": {
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             "schema_type": "biomaterial",
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@@ -9558,7 +9558,7 @@
                 "update_date": "2018-10-01T19:29:16.669Z"
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-        "cell_suspension_4.json": {
+        "cell_suspension/090682b0-dc11-43d0-b6f5-cf3dee18533a": {
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             "schema_type": "biomaterial",
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@@ -9592,7 +9592,7 @@
                 "update_date": "2018-10-01T19:29:16.820Z"
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-        "cell_suspension_5.json": {
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@@ -9626,7 +9626,7 @@
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             "schema_type": "biomaterial",
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@@ -9660,7 +9660,7 @@
                 "update_date": "2018-10-01T19:29:17.938Z"
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-        "cell_suspension_7.json": {
+        "cell_suspension/1a6292df-a383-40c7-bc28-b8bf63e03967": {
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             "schema_type": "biomaterial",
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@@ -9694,7 +9694,7 @@
                 "update_date": "2018-10-01T19:29:18.379Z"
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-        "cell_suspension_8.json": {
+        "cell_suspension/4aad31c4-06fc-4af6-804b-f10afa1cae1d": {
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             "schema_type": "biomaterial",
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@@ -9728,7 +9728,7 @@
                 "update_date": "2018-10-01T19:29:18.539Z"
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-        "cell_suspension_9.json": {
+        "cell_suspension/2a630ecd-440d-43c3-9c9a-2a8ec98a1784": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
             "schema_type": "biomaterial",
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@@ -9762,7 +9762,7 @@
                 "update_date": "2018-10-01T19:29:18.676Z"
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-        "cell_suspension_10.json": {
+        "cell_suspension/b60a1acf-24f7-46a7-b276-39c48f3460e9": {
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             "schema_type": "biomaterial",
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@@ -9796,7 +9796,7 @@
                 "update_date": "2018-10-01T19:29:18.846Z"
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-        "cell_suspension_11.json": {
+        "cell_suspension/5db6e3cf-bb9a-430d-8e5a-1499088526fc": {
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             "schema_type": "biomaterial",
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@@ -9830,7 +9830,7 @@
                 "update_date": "2018-10-01T19:29:19.239Z"
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-        "cell_suspension_12.json": {
+        "cell_suspension/6ff20c11-cb2e-4ace-9b3a-48094ce7a231": {
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@@ -9864,7 +9864,7 @@
                 "update_date": "2018-10-01T19:29:19.442Z"
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-        "cell_suspension_13.json": {
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@@ -9898,7 +9898,7 @@
                 "update_date": "2018-10-01T19:29:20.110Z"
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-        "cell_suspension_14.json": {
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@@ -9932,7 +9932,7 @@
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@@ -9966,7 +9966,7 @@
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@@ -10000,7 +10000,7 @@
                 "update_date": "2018-10-01T19:29:22.646Z"
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-        "cell_suspension_17.json": {
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@@ -10034,7 +10034,7 @@
                 "update_date": "2018-10-01T19:29:23.378Z"
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-        "cell_suspension_18.json": {
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@@ -10068,7 +10068,7 @@
                 "update_date": "2018-10-01T19:29:23.730Z"
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-        "cell_suspension_19.json": {
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@@ -10102,7 +10102,7 @@
                 "update_date": "2018-10-01T19:29:25.363Z"
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@@ -10136,7 +10136,7 @@
                 "update_date": "2018-10-01T19:29:25.994Z"
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-        "cell_suspension_21.json": {
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             "schema_type": "biomaterial",
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@@ -10170,7 +10170,7 @@
                 "update_date": "2018-10-01T19:29:26.198Z"
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@@ -10204,7 +10204,7 @@
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diff --git a/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
index e4e69c1de..38d771b2a 100644
--- a/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
+++ b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
@@ -926,7 +926,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/13b00a71-4916-441c-a863-0204b40ba127": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -959,7 +959,7 @@
                 "update_date": "2018-09-06T17:43:49.418Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/131f2ca9-0a3e-4794-a6f6-0170884de3bf": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/biomaterial/6.3.1/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -989,7 +989,7 @@
                 "update_date": "2018-09-06T17:43:40.640Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/651a2e3a-80a6-4e3a-99d0-63224ee2ef02": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/biomaterial/10.1.1/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1012,7 +1012,7 @@
                 "update_date": "2018-09-06T17:43:29.851Z"
             }
         },
-        "analysis_file_0.json": {
+        "analysis_file/84d27b0a-348e-4af2-82cb-c37973a9fe17": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1025,7 +1025,7 @@
                 "update_date": "2018-09-06T18:51:18.929Z"
             }
         },
-        "analysis_file_1.json": {
+        "analysis_file/36671cf7-ab85-409f-a28b-27c489e2ab51": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1038,7 +1038,7 @@
                 "update_date": "2018-09-06T18:51:15.720Z"
             }
         },
-        "analysis_file_2.json": {
+        "analysis_file/4ba5d8f9-2d1c-432d-9fa5-7e22eff732f1": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1051,7 +1051,7 @@
                 "update_date": "2018-09-06T18:51:18.800Z"
             }
         },
-        "analysis_file_3.json": {
+        "analysis_file/f71ca185-a4d4-42ec-b6f0-dbb140cb2f23": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1064,7 +1064,7 @@
                 "update_date": "2018-09-06T18:51:21.934Z"
             }
         },
-        "analysis_file_4.json": {
+        "analysis_file/a0521704-08fa-4594-90da-0b29ee40dc0a": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1077,7 +1077,7 @@
                 "update_date": "2018-09-06T18:51:18.835Z"
             }
         },
-        "analysis_file_5.json": {
+        "analysis_file/8dfb781a-9fa1-488d-9ddc-e8272bef5fe0": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1090,7 +1090,7 @@
                 "update_date": "2018-09-06T18:51:18.753Z"
             }
         },
-        "analysis_file_6.json": {
+        "analysis_file/e80fdd63-3c87-45f9-b1f7-9d7b7122dfdf": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1103,7 +1103,7 @@
                 "update_date": "2018-09-06T18:51:19.110Z"
             }
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-        "analysis_file_7.json": {
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             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1116,7 +1116,7 @@
                 "update_date": "2018-09-06T18:51:27.808Z"
             }
         },
-        "analysis_file_8.json": {
+        "analysis_file/46dc4f0d-11c0-4000-b6e9-710553a2a9cc": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1129,7 +1129,7 @@
                 "update_date": "2018-09-06T18:51:21.984Z"
             }
         },
-        "analysis_file_9.json": {
+        "analysis_file/b78926da-4a2c-4af9-8cd8-4ae337336ccc": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1142,7 +1142,7 @@
                 "update_date": "2018-09-06T18:51:22.213Z"
             }
         },
-        "analysis_file_10.json": {
+        "analysis_file/a002691d-8568-40a3-9fd2-bae403916e08": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1155,7 +1155,7 @@
                 "update_date": "2018-09-06T18:51:24.731Z"
             }
         },
-        "analysis_file_11.json": {
+        "analysis_file/0963c920-cd31-45bd-8844-ff0200ff1667": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1168,7 +1168,7 @@
                 "update_date": "2018-09-06T18:51:24.951Z"
             }
         },
-        "analysis_file_12.json": {
+        "analysis_file/fff7c188-ff07-4014-83a5-3f90dfafc09a": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1181,7 +1181,7 @@
                 "update_date": "2018-09-06T18:51:27.830Z"
             }
         },
-        "analysis_file_13.json": {
+        "analysis_file/cf4782d0-79e1-43dc-8313-93447a35620b": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1194,7 +1194,7 @@
                 "update_date": "2018-09-06T18:51:30.824Z"
             }
         },
-        "analysis_file_14.json": {
+        "analysis_file/63cb3d77-fded-4235-87a2-50e5f756826b": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1207,7 +1207,7 @@
                 "update_date": "2018-09-06T18:51:27.727Z"
             }
         },
-        "analysis_file_15.json": {
+        "analysis_file/140c27ca-12de-4425-953b-b1d4c2c918fc": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1220,7 +1220,7 @@
                 "update_date": "2018-09-06T18:51:30.804Z"
             }
         },
-        "analysis_file_16.json": {
+        "analysis_file/38c67a5f-db0c-4d5f-839b-b061709d8be9": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1233,7 +1233,7 @@
                 "update_date": "2018-09-06T18:51:30.712Z"
             }
         },
-        "analysis_file_17.json": {
+        "analysis_file/9efb3c26-4fd8-4986-8a72-1507880e6ab7": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1246,7 +1246,7 @@
                 "update_date": "2018-09-06T18:51:33.849Z"
             }
         },
-        "analysis_file_18.json": {
+        "analysis_file/fff934f7-4a3e-442b-99b2-3479762db53c": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1259,7 +1259,7 @@
                 "update_date": "2018-09-06T18:51:33.768Z"
             }
         },
-        "analysis_file_19.json": {
+        "analysis_file/3268e4bf-591a-4ca3-b7ad-440f61460610": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1272,7 +1272,7 @@
                 "update_date": "2018-09-06T18:51:27.818Z"
             }
         },
-        "analysis_file_20.json": {
+        "analysis_file/68b243fc-c128-40ac-8e51-0383b4860c29": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1285,7 +1285,7 @@
                 "update_date": "2018-09-06T18:51:27.703Z"
             }
         },
-        "analysis_file_21.json": {
+        "analysis_file/4448df34-27c1-413d-bfc1-a508f238e2ed": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1298,7 +1298,7 @@
                 "update_date": "2018-09-06T18:51:24.861Z"
             }
         },
-        "analysis_file_22.json": {
+        "analysis_file/c2c8aec7-489b-4c2b-9b79-dc9f9a6d2d1d": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1311,7 +1311,7 @@
                 "update_date": "2018-09-06T18:51:48.751Z"
             }
         },
-        "analysis_file_23.json": {
+        "analysis_file/b4b3e436-19f2-4b56-b30c-dd22682e94fe": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1324,7 +1324,7 @@
                 "update_date": "2018-09-06T18:51:39.778Z"
             }
         },
-        "analysis_file_24.json": {
+        "analysis_file/477b3e82-552d-47dc-a27b-22d242298362": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1337,7 +1337,7 @@
                 "update_date": "2018-09-06T18:51:39.839Z"
             }
         },
-        "analysis_file_25.json": {
+        "analysis_file/e274e132-3fe1-44e9-879b-d6bc22cba2ab": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1350,7 +1350,7 @@
                 "update_date": "2018-09-06T18:51:42.713Z"
             }
         },
-        "analysis_file_26.json": {
+        "analysis_file/2c11a11d-840c-4a3d-b811-e0e03c2e0976": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1363,7 +1363,7 @@
                 "update_date": "2018-09-06T18:51:48.696Z"
             }
         },
-        "analysis_file_27.json": {
+        "analysis_file/f3ca70e5-f530-4890-be95-e3635dcf164a": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1376,7 +1376,7 @@
                 "update_date": "2018-09-06T18:51:42.746Z"
             }
         },
-        "analysis_file_28.json": {
+        "analysis_file/12bcb6de-0f5b-4581-8d02-4ed3c59c13ab": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1389,7 +1389,7 @@
                 "update_date": "2018-09-06T18:51:45.770Z"
             }
         },
-        "analysis_file_29.json": {
+        "analysis_file/e3a50ba8-8e82-4b7f-89de-b6f512037e3d": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1402,7 +1402,7 @@
                 "update_date": "2018-09-06T18:51:45.736Z"
             }
         },
-        "analysis_file_30.json": {
+        "analysis_file/cf3a255f-e731-4912-a7b1-cbec1b0d5239": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/5.2.1/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1415,7 +1415,7 @@
                 "update_date": "2018-09-06T18:51:48.711Z"
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/c5d76832-f738-43a0-afe7-f62aa53a7824": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1429,7 +1429,7 @@
                 "update_date": "2018-09-06T18:43:35.669Z"
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/be1f1c69-5ad5-4d2c-a86f-c43f1f003210": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/file/6.5.2/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -1443,7 +1443,7 @@
                 "update_date": "2018-09-06T18:43:35.937Z"
             }
         },
-        "project_0.json": {
+        "project/26f1d58f-b247-4e0b-a4a9-402e029e5ac8": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/project/9.0.2/project",
             "schema_type": "project",
             "project_core": {
@@ -1470,7 +1470,7 @@
                 "update_date": "2018-09-06T17:43:29.771Z"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/237048e6-dbd9-4a0b-b0cc-8085513c2944": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/protocol/sequencing/4.3.2/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1499,7 +1499,7 @@
                 "update_date": "2018-09-06T17:43:20.063Z"
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/f6527c69-b8bb-467a-af22-32a1b7863c65": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1520,7 +1520,7 @@
                 "update_date": "2018-09-06T17:43:20.475Z"
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/babc8692-6932-4c29-b33d-4d7b4deebe54": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1536,7 +1536,7 @@
                 "update_date": "2018-09-06T17:43:19.766Z"
             }
         },
-        "analysis_process_0.json": {
+        "analysis_process/2a4e1440-dab6-4b0b-8204-ebb270613cc1": {
             "analysis_run_type": "run",
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/process/analysis/8.0.0/analysis_process",
             "input_bundles": [
@@ -1979,7 +1979,7 @@
                 "update_date": "2018-09-06T18:43:37.650Z"
             }
         },
-        "process_0.json": {
+        "process/c8ac10c7-fa3a-4fbc-a9bd-55e767444773": {
             "process_core": {
                 "process_id": "seq_proc_187"
             },
@@ -1991,7 +1991,7 @@
                 "update_date": "2018-09-06T17:44:11.383Z"
             }
         },
-        "process_1.json": {
+        "process/94510a2b-edc8-4f14-ab1e-494732ccf80a": {
             "process_core": {
                 "process_id": "process_id_189"
             },
@@ -2003,7 +2003,7 @@
                 "update_date": "2018-09-06T17:43:58.660Z"
             }
         },
-        "process_2.json": {
+        "process/44edcce5-152d-401c-ba29-ed73cd9ec57f": {
             "process_core": {
                 "process_id": "process_id_1"
             },
diff --git a/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json b/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
index b9bf43801..bf3b5d476 100644
--- a/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
+++ b/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
@@ -194,7 +194,7 @@
         }
     ],
     "metadata": {
-        "project_0.json": {
+        "project/90bf705c-d891-5ce2-aa54-094488b445c6": {
             "array_express_accessions": [
                 "E-MTAB-10026"
             ],
@@ -311,7 +311,7 @@
             ],
             "schema_type": "project"
         },
-        "process_0.json": {
+        "process/37e91a9f-b04e-5313-bbc0-4c394406247e": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -325,7 +325,7 @@
             },
             "schema_type": "process"
         },
-        "process_1.json": {
+        "process/b8ec88d7-675c-54ff-8071-63255adc181b": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -339,7 +339,7 @@
             },
             "schema_type": "process"
         },
-        "process_2.json": {
+        "process/bd6a4a38-c44b-5d17-b2b1-d0d4c4531bf0": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -353,7 +353,7 @@
             },
             "schema_type": "process"
         },
-        "process_3.json": {
+        "process/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/process/9.2.0/process",
             "process_core": {
                 "process_id": "dummy_process"
@@ -367,7 +367,7 @@
             },
             "schema_type": "process"
         },
-        "cell_suspension_0.json": {
+        "cell_suspension/119c4135-7b77-5003-a150-f052e22c6834": {
             "biomaterial_core": {
                 "biomaterial_id": "AP2CS_pre",
                 "ncbi_taxon_id": [
@@ -399,7 +399,7 @@
                 }
             ]
         },
-        "cell_suspension_1.json": {
+        "cell_suspension/af3549f4-8632-58c2-9821-c6249c622b0a": {
             "biomaterial_core": {
                 "biomaterial_id": "AP2CS",
                 "ncbi_taxon_id": [
@@ -431,7 +431,7 @@
                 }
             ]
         },
-        "analysis_file_0.json": {
+        "analysis_file/f0c8ac7c-1c4a-5c9c-9286-c8b16208f9ae": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/file/6.5.0/analysis_file",
             "file_core": {
                 "content_description": [
@@ -455,7 +455,7 @@
             },
             "schema_type": "file"
         },
-        "analysis_protocol_0.json": {
+        "analysis_protocol/811adf54-7f27-5aec-9ed7-c6084c4c3a1b": {
             "computational_method": "10x v3",
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/analysis/10.0.0/analysis_protocol",
             "matrix": {
@@ -486,7 +486,7 @@
                 "text": "enzymatic dissociation"
             }
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/767282b2-2fc1-5559-b020-29686b810206": {
             "cell_barcode": {
                 "barcode_length": 16,
                 "barcode_offset": 0,
@@ -523,7 +523,7 @@
                 "barcode_read": "Read 1"
             }
         },
-        "treatment_protocol_0.json": {
+        "treatment_protocol/0f959f0b-5efa-5cc8-9c46-097b0cb574d5": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/1.0.0/treatment_protocol",
             "media": "RPMI 1640",
             "method": [
@@ -554,7 +554,7 @@
                 }
             ]
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/3bee0c9a-aced-52f2-b97f-89518f826b36": {
             "biomaterial_core": {
                 "biomaterial_id": "AP2_specimen",
                 "biomaterial_name": "AP2_specimen",
@@ -591,7 +591,7 @@
             },
             "schema_type": "biomaterial"
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/46435803-7ee8-5157-8569-8a61ad50c315": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "method": {
                 "ontology": "EFO:0009337",
@@ -611,7 +611,7 @@
             },
             "schema_type": "protocol"
         },
-        "donor_organism_0.json": {
+        "donor_organism/5bc2bf2f-eb98-5510-a386-172cef38f2f2": {
             "biomaterial_core": {
                 "biomaterial_id": "AP2",
                 "biomaterial_name": "Sanger_AP2",
@@ -656,7 +656,7 @@
             "schema_type": "biomaterial",
             "sex": "unknown"
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/e7f864e3-6ba7-53c8-842f-2a05cb90e1b7": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "method": {
                 "ontology": "EFO:0009121",
diff --git a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
index e71b4214b..fe1e5410a 100644
--- a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
+++ b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
@@ -914,7 +914,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/803fd65a-c578-4c4f-a39e-bedec24e2578": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -944,7 +944,7 @@
                 "update_date": "2018-10-11T21:18:13.146Z"
             }
         },
-        "organoid_0.json": {
+        "organoid/2d8282f0-6cbb-4d5a-822c-4b01718b4d0d": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.3.8/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -979,7 +979,7 @@
                 "update_date": "2018-10-11T21:18:12.864Z"
             }
         },
-        "organoid_1.json": {
+        "organoid/b7214641-1ac5-4f60-b795-cb33a7c25434": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.3.8/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1014,7 +1014,7 @@
                 "update_date": "2018-10-11T21:18:12.763Z"
             }
         },
-        "organoid_2.json": {
+        "organoid/308eea51-d14b-4036-8cd1-cfd81d7532c3": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.3.8/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1049,7 +1049,7 @@
                 "update_date": "2018-10-11T21:18:06.730Z"
             }
         },
-        "organoid_3.json": {
+        "organoid/73f10dad-afc5-4d1d-a71c-4a8b6fff9172": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.3.8/organoid",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1084,7 +1084,7 @@
                 "update_date": "2018-10-11T21:18:06.725Z"
             }
         },
-        "cell_line_0.json": {
+        "cell_line/c532cca7-67c6-4617-ac47-5b91652621a5": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1131,7 +1131,7 @@
                 "update_date": "2018-10-11T21:18:06.721Z"
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/c8e14a8e-81f9-4109-bb27-4bb3029240c1": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1168,7 +1168,7 @@
                 "update_date": "2018-10-11T21:18:06.720Z"
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/d4c29b1a-f23c-4511-a2ae-097772d90254": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1213,7 +1213,7 @@
                 "update_date": "2018-10-11T21:18:06.768Z"
             }
         },
-        "cell_line_1.json": {
+        "cell_line/e924c114-e3cd-4060-9c8e-3d980ec7fcbe": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1260,7 +1260,7 @@
                 "update_date": "2018-10-11T21:18:06.679Z"
             }
         },
-        "specimen_from_organism_1.json": {
+        "specimen_from_organism/5bd6106c-0158-4c2c-8c60-32019c599c83": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1297,7 +1297,7 @@
                 "update_date": "2018-10-11T21:18:06.627Z"
             }
         },
-        "donor_organism_1.json": {
+        "donor_organism/ef7e6ac7-172a-4b24-9620-fc909a5e9c6c": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1342,7 +1342,7 @@
                 "update_date": "2018-10-11T21:18:06.720Z"
             }
         },
-        "cell_line_2.json": {
+        "cell_line/a3651f83-dee6-49b2-ba4e-0ce20f02467d": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1389,7 +1389,7 @@
                 "update_date": "2018-10-11T21:18:06.795Z"
             }
         },
-        "specimen_from_organism_2.json": {
+        "specimen_from_organism/8f328973-9bc0-46b9-8a1f-38893e77b3b5": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1426,7 +1426,7 @@
                 "update_date": "2018-10-11T21:18:06.643Z"
             }
         },
-        "donor_organism_2.json": {
+        "donor_organism/931528fa-820b-49ca-af1e-ae9a2c0ef551": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1471,7 +1471,7 @@
                 "update_date": "2018-10-11T21:18:06.762Z"
             }
         },
-        "cell_line_3.json": {
+        "cell_line/6a16de30-176d-4488-81de-9337a1a6d8c5": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_line",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1518,7 +1518,7 @@
                 "update_date": "2018-10-11T21:18:06.634Z"
             }
         },
-        "specimen_from_organism_3.json": {
+        "specimen_from_organism/82368936-7b99-4864-9f49-b8fee3906d47": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/6.3.3/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1555,7 +1555,7 @@
                 "update_date": "2018-10-11T21:18:06.743Z"
             }
         },
-        "donor_organism_3.json": {
+        "donor_organism/96757312-0221-447a-84f1-7a737b5afd01": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/10.1.2/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -1600,7 +1600,7 @@
                 "update_date": "2018-10-11T21:18:06.767Z"
             }
         },
-        "analysis_file_0.json": {
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             "file_core": {
@@ -1613,7 +1613,7 @@
                 "update_date": "2018-10-18T20:39:13.335Z"
             }
         },
-        "analysis_file_1.json": {
+        "analysis_file/477c0b3e-4a06-4214-8f27-58199ba63528": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1626,7 +1626,7 @@
                 "update_date": "2018-10-18T20:39:16.337Z"
             }
         },
-        "analysis_file_2.json": {
+        "analysis_file/ad6d5170-d74b-408c-af6b-25a14315c9da": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1639,7 +1639,7 @@
                 "update_date": "2018-10-18T20:39:25.337Z"
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-        "analysis_file_3.json": {
+        "analysis_file/50be9b67-fae5-4472-9719-478dd1303d6e": {
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@@ -1652,7 +1652,7 @@
                 "update_date": "2018-10-18T20:39:22.340Z"
             }
         },
-        "analysis_file_4.json": {
+        "analysis_file/fd16b62e-e540-4f03-8ba0-07d0c204e3c8": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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             "file_core": {
@@ -1665,7 +1665,7 @@
                 "update_date": "2018-10-18T20:37:28.333Z"
             }
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-        "analysis_file_5.json": {
+        "analysis_file/3c41b5b6-f480-4d47-8c5e-155e7c1adf54": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1678,7 +1678,7 @@
                 "update_date": "2018-10-18T20:40:01.344Z"
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-        "analysis_file_6.json": {
+        "analysis_file/022a217c-384d-4d9d-8631-6397b6838e3a": {
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             "schema_type": "file",
             "file_core": {
@@ -1691,7 +1691,7 @@
                 "update_date": "2018-10-18T20:45:01.366Z"
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-        "analysis_file_7.json": {
+        "analysis_file/9b778e46-0c51-4260-8e3f-000ecc145f0a": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
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@@ -1704,7 +1704,7 @@
                 "update_date": "2018-10-18T20:39:10.339Z"
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-        "analysis_file_8.json": {
+        "analysis_file/af025a74-53f1-4972-b50d-53095b5ffac2": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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@@ -1717,7 +1717,7 @@
                 "update_date": "2018-10-18T20:39:40.335Z"
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         },
-        "analysis_file_9.json": {
+        "analysis_file/e8395271-7c8e-4ec4-9598-495df43fe5fd": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
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             "file_core": {
@@ -1730,7 +1730,7 @@
                 "update_date": "2018-10-18T20:39:55.336Z"
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-        "analysis_file_10.json": {
+        "analysis_file/211a8fbf-b190-4576-ac2f-2b1a91743abb": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/file/5.3.4/analysis_file",
             "schema_type": "file",
             "file_core": {
@@ -1743,7 +1743,7 @@
                 "update_date": "2018-10-18T20:39:58.363Z"
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-        "analysis_file_11.json": {
+        "analysis_file/17222e3a-5757-45e9-9dfe-c4b6aa10f28a": {
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             "file_core": {
@@ -1756,7 +1756,7 @@
                 "update_date": "2018-10-18T20:39:58.363Z"
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-        "analysis_file_12.json": {
+        "analysis_file/2fb8a975-b50c-4528-b850-838a19e19a1e": {
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             "file_core": {
@@ -1769,7 +1769,7 @@
                 "update_date": "2018-10-18T20:40:13.334Z"
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-        "sequence_file_0.json": {
+        "sequence_file/213381ea-6161-4159-853e-cfcae4968001": {
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@@ -1786,7 +1786,7 @@
                 "update_date": "2018-10-18T20:32:16.894Z"
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-        "sequence_file_1.json": {
+        "sequence_file/9ee3da9e-83ca-4c02-84d6-ac09702b12ba": {
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@@ -1803,7 +1803,7 @@
                 "update_date": "2018-10-18T20:32:18.864Z"
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-        "sequence_file_2.json": {
+        "sequence_file/330a08ca-ae8e-4f1f-aa03-970abcd27f39": {
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@@ -1820,7 +1820,7 @@
                 "update_date": "2018-10-18T20:32:20.845Z"
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-        "supplementary_file_0.json": {
+        "supplementary_file/281c2d08-9e43-47f9-b937-e733e3ba3322": {
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@@ -1834,7 +1834,7 @@
                 "update_date": "2018-10-18T20:40:54.699Z"
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-        "supplementary_file_1.json": {
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@@ -1848,7 +1848,7 @@
                 "update_date": "2018-10-18T20:40:55.940Z"
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-        "supplementary_file_2.json": {
+        "supplementary_file/f518a8cc-e1d9-4fc9-bc32-491dd8543902": {
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@@ -1862,7 +1862,7 @@
                 "update_date": "2018-10-18T20:40:57.146Z"
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-        "project_0.json": {
+        "project/2c4724a4-7252-409e-b008-ff5c127c7e89": {
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@@ -1923,7 +1923,7 @@
                 "update_date": "2018-10-11T21:18:06.651Z"
             }
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-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/92277226-bf78-4df9-a594-5190a8790a14": {
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             "protocol_core": {
@@ -1964,7 +1964,7 @@
                 "update_date": "2018-10-11T21:18:12.704Z"
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-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/102cdbf3-b0e5-4dd5-9168-51150a9ebb6b": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/sequencing/9.0.2/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -1988,7 +1988,7 @@
                 "update_date": "2018-10-11T21:18:12.667Z"
             }
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-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/755762e0-7aff-48ed-a7d4-d3ea4005758f": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/5.0.3/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -2014,7 +2014,7 @@
                 "update_date": "2018-10-11T21:18:12.751Z"
             }
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-        "differentiation_protocol_0.json": {
+        "differentiation_protocol/8f4a8e7c-e7ee-44dc-8e09-f4012355060f": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/1.3.0/differentiation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -2038,7 +2038,7 @@
                 "update_date": "2018-10-11T21:18:12.764Z"
             }
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-        "ipsc_induction_protocol_0.json": {
+        "ipsc_induction_protocol/cdfe38f2-1d90-4700-a199-d8105ce299df": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/protocol/biomaterial_collection/2.0.1/ipsc_induction_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -2061,7 +2061,7 @@
                 "update_date": "2018-10-11T21:18:06.713Z"
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-        "analysis_process_0.json": {
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@@ -2225,7 +2225,7 @@
                 "update_date": "2018-10-18T20:32:19.562Z"
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-        "process_0.json": {
+        "process/a2510b8c-8c92-4fe4-bc06-5e4e92093545": {
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@@ -2237,7 +2237,7 @@
                 "update_date": "2018-10-11T21:18:12.743Z"
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-        "process_1.json": {
+        "process/c7b6e9fe-6f08-41a9-8907-9c0347e6d604": {
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@@ -2249,7 +2249,7 @@
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-        "process_2.json": {
+        "process/0d1d507d-4246-4b1c-8836-261d42f784eb": {
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@@ -2297,7 +2297,7 @@
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@@ -2309,7 +2309,7 @@
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@@ -2321,7 +2321,7 @@
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@@ -2333,7 +2333,7 @@
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@@ -2345,7 +2345,7 @@
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@@ -2357,7 +2357,7 @@
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@@ -2369,7 +2369,7 @@
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diff --git a/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
index ef78a318b..fee499f6a 100644
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+++ b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
@@ -242,7 +242,7 @@
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@@ -263,7 +263,7 @@
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@@ -468,7 +468,7 @@
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@@ -612,7 +612,7 @@
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@@ -630,7 +630,7 @@
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@@ -651,7 +651,7 @@
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@@ -666,7 +666,7 @@
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diff --git a/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
index 643a84c16..2c7c08e60 100644
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+++ b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
@@ -998,7 +998,7 @@
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@@ -1022,7 +1022,7 @@
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@@ -1057,7 +1057,7 @@
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@@ -1103,7 +1103,7 @@
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@@ -1116,7 +1116,7 @@
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@@ -1129,7 +1129,7 @@
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@@ -1142,7 +1142,7 @@
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@@ -1155,7 +1155,7 @@
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@@ -1168,7 +1168,7 @@
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@@ -1181,7 +1181,7 @@
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@@ -1194,7 +1194,7 @@
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@@ -1207,7 +1207,7 @@
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@@ -1220,7 +1220,7 @@
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@@ -1233,7 +1233,7 @@
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@@ -1246,7 +1246,7 @@
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@@ -1259,7 +1259,7 @@
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@@ -1272,7 +1272,7 @@
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@@ -1285,7 +1285,7 @@
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@@ -1298,7 +1298,7 @@
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@@ -1311,7 +1311,7 @@
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@@ -1324,7 +1324,7 @@
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@@ -1337,7 +1337,7 @@
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@@ -1350,7 +1350,7 @@
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@@ -1363,7 +1363,7 @@
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@@ -1376,7 +1376,7 @@
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diff --git a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
index ee0385e96..08cea3d03 100644
--- a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
+++ b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
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@@ -7365,7 +7365,7 @@
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@@ -7378,7 +7378,7 @@
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@@ -7391,7 +7391,7 @@
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@@ -7404,7 +7404,7 @@
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@@ -7417,7 +7417,7 @@
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@@ -7430,7 +7430,7 @@
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@@ -7443,7 +7443,7 @@
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@@ -7456,7 +7456,7 @@
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@@ -7469,7 +7469,7 @@
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@@ -7482,7 +7482,7 @@
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@@ -7495,7 +7495,7 @@
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@@ -11505,7 +11505,7 @@
                 "update_date": "2019-07-18T21:12:44.498Z"
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-        "process_3.json": {
+        "process/8b1f44be-7eaa-4030-b6c5-697c5fc388eb": {
             "process_core": {
                 "location": "AllCells, LLC",
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diff --git a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
index 9563b6f1e..4e5fb7422 100644
--- a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
+++ b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
@@ -266,7 +266,7 @@
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+        "cell_suspension/0037c9eb-8038-432f-8d9d-13ee094e54ab": {
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@@ -300,7 +300,7 @@
                 "update_date": "2018-09-13T18:24:16.328Z"
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-        "cell_suspension_1.json": {
+        "cell_suspension/aaaaaaaa-8038-432f-8d9d-13ee094e54ab": {
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@@ -334,7 +334,7 @@
                 "update_date": "2018-09-13T18:24:16.328Z"
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-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/b4e55fe1-7bab-44ba-a81d-3d8cb3873244": {
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@@ -359,7 +359,7 @@
                 "update_date": "2018-09-13T18:18:32.288Z"
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@@ -384,7 +384,7 @@
                 "update_date": "2018-09-13T18:18:32.288Z"
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+        "donor_organism/89b50434-f831-4e15-a8c0-0d57e6baa94c": {
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@@ -432,7 +432,7 @@
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@@ -447,7 +447,7 @@
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@@ -462,7 +462,7 @@
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@@ -476,7 +476,7 @@
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@@ -490,7 +490,7 @@
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@@ -504,7 +504,7 @@
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@@ -618,7 +618,7 @@
                 "update_date": "2018-09-13T18:07:50.370Z"
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-        "library_preparation_protocol_0.json": {
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@@ -649,7 +649,7 @@
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@@ -672,7 +672,7 @@
                 "update_date": "2018-09-13T18:02:29.857Z"
             }
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-        "dissociation_protocol_0.json": {
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@@ -690,7 +690,7 @@
                 "update_date": "2018-09-13T18:02:29.781Z"
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-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/d3287615-b97a-4984-a8cf-30a1c30e4773": {
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@@ -708,7 +708,7 @@
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@@ -720,7 +720,7 @@
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@@ -732,7 +732,7 @@
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diff --git a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
index 9caadc848..c62f1f4c6 100644
--- a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
+++ b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
@@ -554,7 +554,7 @@
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@@ -602,7 +602,7 @@
                 "update_date": "2019-02-14T18:29:49.098Z"
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-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/58c60e15-e07c-4875-ac34-f026d6912f1c": {
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@@ -650,7 +650,7 @@
                 "update_date": "2019-02-14T18:29:49.006Z"
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-        "donor_organism_0.json": {
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@@ -733,7 +733,7 @@
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@@ -746,7 +746,7 @@
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@@ -759,7 +759,7 @@
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@@ -772,7 +772,7 @@
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@@ -785,7 +785,7 @@
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-        "analysis_file_4.json": {
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@@ -798,7 +798,7 @@
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@@ -811,7 +811,7 @@
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@@ -824,7 +824,7 @@
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@@ -837,7 +837,7 @@
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@@ -850,7 +850,7 @@
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@@ -863,7 +863,7 @@
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@@ -876,7 +876,7 @@
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@@ -889,7 +889,7 @@
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@@ -902,7 +902,7 @@
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@@ -922,7 +922,7 @@
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@@ -942,7 +942,7 @@
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@@ -962,7 +962,7 @@
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-        "project_0.json": {
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@@ -1021,7 +1021,7 @@
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@@ -1037,7 +1037,7 @@
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@@ -1077,7 +1077,7 @@
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@@ -1111,7 +1111,7 @@
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@@ -1133,7 +1133,7 @@
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@@ -1158,7 +1158,7 @@
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@@ -1190,7 +1190,7 @@
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@@ -1354,7 +1354,7 @@
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@@ -1366,7 +1366,7 @@
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@@ -1378,7 +1378,7 @@
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diff --git a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
index 1654e0ae7..97dd29d26 100644
--- a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
+++ b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
@@ -6593,7 +6593,7 @@
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@@ -6606,7 +6606,7 @@
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@@ -19678,7 +19678,7 @@
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@@ -19978,7 +19978,7 @@
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@@ -20278,7 +20278,7 @@
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@@ -20305,7 +20305,7 @@
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@@ -20332,7 +20332,7 @@
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@@ -20359,7 +20359,7 @@
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@@ -20413,7 +20413,7 @@
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@@ -20440,7 +20440,7 @@
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@@ -20467,7 +20467,7 @@
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@@ -20548,7 +20548,7 @@
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@@ -20575,7 +20575,7 @@
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@@ -20629,7 +20629,7 @@
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@@ -20737,7 +20737,7 @@
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@@ -20764,7 +20764,7 @@
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@@ -20791,7 +20791,7 @@
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@@ -20818,7 +20818,7 @@
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@@ -20845,7 +20845,7 @@
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@@ -20872,7 +20872,7 @@
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@@ -20899,7 +20899,7 @@
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@@ -20926,7 +20926,7 @@
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@@ -20953,7 +20953,7 @@
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@@ -20980,7 +20980,7 @@
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@@ -21007,7 +21007,7 @@
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@@ -21034,7 +21034,7 @@
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@@ -21061,7 +21061,7 @@
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@@ -21088,7 +21088,7 @@
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@@ -21115,7 +21115,7 @@
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@@ -21142,7 +21142,7 @@
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@@ -21169,7 +21169,7 @@
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@@ -21196,7 +21196,7 @@
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@@ -21223,7 +21223,7 @@
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@@ -21250,7 +21250,7 @@
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@@ -21277,7 +21277,7 @@
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@@ -21304,7 +21304,7 @@
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@@ -21331,7 +21331,7 @@
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@@ -21358,7 +21358,7 @@
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@@ -21412,7 +21412,7 @@
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@@ -21439,7 +21439,7 @@
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@@ -21466,7 +21466,7 @@
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@@ -21493,7 +21493,7 @@
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@@ -21520,7 +21520,7 @@
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@@ -21547,7 +21547,7 @@
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@@ -21574,7 +21574,7 @@
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@@ -21655,7 +21655,7 @@
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@@ -21682,7 +21682,7 @@
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@@ -21709,7 +21709,7 @@
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@@ -21736,7 +21736,7 @@
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@@ -21790,7 +21790,7 @@
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@@ -21817,7 +21817,7 @@
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         },
-        "cell_suspension_16.json": {
+        "cell_suspension/6194245b-1ce5-495e-8e85-d859b3fcce66": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26095,7 +26095,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_17.json": {
+        "cell_suspension/64713d72-8e8f-4350-a3ba-e1981c872100": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26121,7 +26121,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_18.json": {
+        "cell_suspension/6b34fa3f-1878-48ec-84c2-e2d8877903c4": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26147,7 +26147,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_19.json": {
+        "cell_suspension/700af591-d469-4a3d-a908-cff116f28242": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26173,7 +26173,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_20.json": {
+        "cell_suspension/7318a24c-7abf-445d-b4d2-2c5acc01e715": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26199,7 +26199,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_21.json": {
+        "cell_suspension/732d6ffa-1d89-4476-ad10-5ce9d83a78ad": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26225,7 +26225,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_22.json": {
+        "cell_suspension/74d1b609-5477-4ec3-840e-fa721ffa580f": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26251,7 +26251,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_23.json": {
+        "cell_suspension/7c2c2ced-a0e3-4df7-ae1d-890218465626": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26277,7 +26277,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_24.json": {
+        "cell_suspension/85a66538-6c12-4ab4-9679-b1f95001606d": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26303,7 +26303,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_25.json": {
+        "cell_suspension/85e09b5b-24a8-4eea-9b0a-8ca17f9db79d": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26329,7 +26329,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_26.json": {
+        "cell_suspension/8d7b1004-5265-40cd-8912-336d71e0f296": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26355,7 +26355,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_27.json": {
+        "cell_suspension/90ab9fe3-3847-4477-bff8-66db44610c92": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26381,7 +26381,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_28.json": {
+        "cell_suspension/91a5af73-4a8a-4285-bcbb-42344e18745f": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26407,7 +26407,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_29.json": {
+        "cell_suspension/a69fcb4d-a7ec-4101-9e5a-1959bc3265ae": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26433,7 +26433,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_30.json": {
+        "cell_suspension/a7738486-8b11-4e05-a004-6c931569972f": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26459,7 +26459,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_31.json": {
+        "cell_suspension/a8674039-068d-4560-aa99-b9481239d4fb": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26485,7 +26485,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_32.json": {
+        "cell_suspension/ae38fa93-e50c-4033-a1e9-ac404ede7380": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26511,7 +26511,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_33.json": {
+        "cell_suspension/b5e9df12-e333-4754-a01b-c83c4b8f644a": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26537,7 +26537,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_34.json": {
+        "cell_suspension/c57bdaec-21df-479e-857e-ddb6f5f78f95": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26563,7 +26563,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_35.json": {
+        "cell_suspension/c8d8c14f-4e5e-4911-a386-391fd1153969": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26589,7 +26589,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_36.json": {
+        "cell_suspension/d4b2569d-4f63-41c0-9a11-97068ee3ae68": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26615,7 +26615,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_37.json": {
+        "cell_suspension/d94541a9-1505-4a33-8ff5-fcb2b19b0d92": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26641,7 +26641,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_38.json": {
+        "cell_suspension/ef50dd96-a305-4edd-84e7-aae93377c488": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26667,7 +26667,7 @@
                 "schema_minor_version": 3
             }
         },
-        "cell_suspension_39.json": {
+        "cell_suspension/ffe830d9-c586-47d1-9bb4-33baed6dcdc7": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26693,7 +26693,7 @@
                 "schema_minor_version": 3
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/1b5a4bc7-5a90-4782-a657-536a8b533156": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26736,7 +26736,7 @@
                 }
             ]
         },
-        "donor_organism_1.json": {
+        "donor_organism/39046bdd-483c-44ad-9b50-dea608d34255": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26779,7 +26779,7 @@
                 }
             ]
         },
-        "donor_organism_2.json": {
+        "donor_organism/5baa7164-60f5-4b28-8bad-e9a0563cac70": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26822,7 +26822,7 @@
                 }
             ]
         },
-        "donor_organism_3.json": {
+        "donor_organism/793d9bf6-00cb-49e6-acc2-2cc724036645": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26865,7 +26865,7 @@
                 }
             ]
         },
-        "donor_organism_4.json": {
+        "donor_organism/85dc3748-6751-482b-b7cd-c1e08f7df5c0": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26908,7 +26908,7 @@
                 }
             ]
         },
-        "donor_organism_5.json": {
+        "donor_organism/8f63d864-87e5-40f3-8f68-936640010c7d": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26951,7 +26951,7 @@
                 }
             ]
         },
-        "donor_organism_6.json": {
+        "donor_organism/9417041b-2952-41d5-b0d8-b42694f4fd4a": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -26994,7 +26994,7 @@
                 }
             ]
         },
-        "donor_organism_7.json": {
+        "donor_organism/ae71343b-df16-49a3-829d-a6e61afdc079": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -27037,7 +27037,7 @@
                 }
             ]
         },
-        "donor_organism_8.json": {
+        "donor_organism/ba005942-3abb-4988-90a4-57747fb05b8b": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -27080,7 +27080,7 @@
                 }
             ]
         },
-        "donor_organism_9.json": {
+        "donor_organism/d0baedfe-0556-4c2b-a1a0-d1e28ef07bb5": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -27123,7 +27123,7 @@
                 }
             ]
         },
-        "donor_organism_10.json": {
+        "donor_organism/dd19fdc7-35a9-432f-9a97-670637433eda": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -27166,7 +27166,7 @@
                 }
             ]
         },
-        "donor_organism_11.json": {
+        "donor_organism/e8fbe9c1-ab25-4300-a40d-65d0e8f627e0": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -27209,7 +27209,7 @@
                 }
             ]
         },
-        "donor_organism_12.json": {
+        "donor_organism/eed4d335-880b-4735-9d04-cdbf706e3d44": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -27252,7 +27252,7 @@
                 }
             ]
         },
-        "donor_organism_13.json": {
+        "donor_organism/f2ed99b4-a68d-4d54-8c65-9534ad5931b5": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
diff --git a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
index 8451d28e2..7bdbb3fbd 100644
--- a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
+++ b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
@@ -194,7 +194,7 @@
         }
     ],
     "metadata": {
-        "cell_suspension_0.json": {
+        "cell_suspension/0432e9a5-604f-4cb7-8571-014eb5fd8ba2": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -221,7 +221,7 @@
                 "schema_minor_version": 3
             }
         },
-        "specimen_from_organism_0.json": {
+        "specimen_from_organism/caadf4b5-f5e4-4416-9f04-9c1f902cc601": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/10.4.0/specimen_from_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -269,7 +269,7 @@
                 "schema_minor_version": 4
             }
         },
-        "donor_organism_0.json": {
+        "donor_organism/e66ac278-96b3-4713-9c5f-5c70b1efb6e3": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/15.5.0/donor_organism",
             "schema_type": "biomaterial",
             "biomaterial_core": {
@@ -324,7 +324,7 @@
                 "schema_minor_version": 5
             }
         },
-        "sequence_file_0.json": {
+        "sequence_file/4015da8b-18d8-4f3c-b2b0-54f0b77ae80a": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -348,7 +348,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequence_file_1.json": {
+        "sequence_file/fa17159e-52ec-4a88-80cf-a3be5e2e9988": {
             "describedBy": "https://schema.humancellatlas.org/type/file/9.2.0/sequence_file",
             "schema_type": "file",
             "file_core": {
@@ -372,7 +372,7 @@
                 "schema_minor_version": 2
             }
         },
-        "project_0.json": {
+        "project/88ec040b-8705-4f77-8f41-f81e57632f7d": {
             "describedBy": "https://schema.humancellatlas.org/type/project/14.1.0/project",
             "schema_type": "project",
             "project_core": {
@@ -767,7 +767,7 @@
             },
             "hca_bionetworks": []
         },
-        "library_preparation_protocol_0.json": {
+        "library_preparation_protocol/76a9a285-f79c-4754-bd26-310b80965b8f": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/6.2.0/library_preparation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -805,7 +805,7 @@
                 "schema_minor_version": 2
             }
         },
-        "sequencing_protocol_0.json": {
+        "sequencing_protocol/63afce7b-829a-491d-a6ed-ab27bf3b4fbc": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/sequencing/10.1.0/sequencing_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -830,7 +830,7 @@
                 "schema_minor_version": 1
             }
         },
-        "dissociation_protocol_0.json": {
+        "dissociation_protocol/78b86ffb-3c85-4b24-81ae-af54815bf222": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/6.2.0/dissociation_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -851,7 +851,7 @@
                 "schema_minor_version": 2
             }
         },
-        "enrichment_protocol_0.json": {
+        "enrichment_protocol/8ec628d3-91d2-46f3-82aa-67c2b831160d": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/3.1.0/enrichment_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -873,7 +873,7 @@
                 "schema_minor_version": 1
             }
         },
-        "collection_protocol_0.json": {
+        "collection_protocol/a7257865-6a66-472c-bdd1-6314c8a7d4b0": {
             "describedBy": "https://schema.humancellatlas.org/type/protocol/biomaterial_collection/9.2.0/collection_protocol",
             "schema_type": "protocol",
             "protocol_core": {
@@ -894,7 +894,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_0.json": {
+        "process/74fa0d9c-438f-42b7-94c7-7dd63ab67c12": {
             "process_core": {
                 "process_id": "Cortex2.CCJ15ANXX.SM2_052318p4_D8"
             },
@@ -908,7 +908,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_1.json": {
+        "process/c6598ea5-a7d0-4898-a640-66eb7aba33a4": {
             "process_core": {
                 "process_id": "process_id_23"
             },
@@ -922,7 +922,7 @@
                 "schema_minor_version": 2
             }
         },
-        "process_2.json": {
+        "process/c7070951-ec8a-492f-a7be-354b5670c056": {
             "process_core": {
                 "process_id": "process_id_4"
             },
diff --git a/test/indexer/test_indexer.py b/test/indexer/test_indexer.py
index c88649c1a..df3c51516 100644
--- a/test/indexer/test_indexer.py
+++ b/test/indexer/test_indexer.py
@@ -246,9 +246,9 @@ def test_indexing(self):
                                         expected = bundle.links
                                     else:
                                         expected = one(
-                                            m
-                                            for m in bundle.metadata.values()
-                                            if m['provenance']['document_id'] == entity_id
+                                            v
+                                            for k, v in bundle.metadata.items()
+                                            if EntityReference.parse(k).entity_id == entity_id
                                         )
                                     # Replica contents should match the entity
                                     # metadata as supplied by the repository
@@ -396,9 +396,11 @@ def test_duplicate_notification(self):
         entity = next(e for e in tallies_1.keys() if e.entity_type != 'bundles')
         tallies_1.pop(entity)
 
-        entity_contents = bundle.metadata[
-            one(m for m in bundle.manifest if m['uuid'] == entity.entity_id)['name']
-        ]
+        entity_contents = one(
+            metadata
+            for ref, metadata in bundle.metadata.items()
+            if EntityReference.parse(ref).entity_id == entity.entity_id
+        )
         coordinates = [
             ContributionCoordinates(
                 entity=entity,
@@ -1845,7 +1847,9 @@ def assert_cell_suspension(expected: JSON, hits: list[JSON]):
         #
         target_metadata = has_cells_bundle.metadata
         source_metadata = no_cells_bundle.metadata
-        target_metadata['project_0.json'] = source_metadata['project_0.json']
+        target_project = 'project/ed79221b-9713-44cd-94af-183f88c348cd'
+        source_project = 'project/6615efae-fca8-4dd2-a223-9cfcf30fe94d'
+        target_metadata[target_project] = source_metadata[source_project]
         self._index_bundle(has_cells_bundle)
         expected = {
             'total_estimated_cells': 10000,
@@ -2171,7 +2175,7 @@ def test_disallow_manifest_column_joiner(self):
         bundle_fqid = self.bundle_fqid(uuid='1b6d8348-d6e9-406a-aa6a-7ee886e52bf9',
                                        version='2019-10-03T10:55:24.911627Z')
         bundle = self._load_canned_bundle(bundle_fqid)
-        project = bundle.metadata['project_0.json']
+        project = bundle.metadata['project/116965f3-f094-4769-9d28-ae675c1b569c']
         contributor = project['contributors'][0]
         assert contributor['institution'] == 'Lund University'
         contributor['institution'] += ' || LabMED'
diff --git a/test/integration_test.py b/test/integration_test.py
index 3d4970621..cb3a1c3fe 100644
--- a/test/integration_test.py
+++ b/test/integration_test.py
@@ -1943,13 +1943,12 @@ def _test_catalog(self, catalog: config.Catalog):
                 self.assertIsInstance(metadata, dict)
                 self.assertIsInstance(links, dict)
                 self.assertIsInstance(stitched, list)
-                manifest_files = sorted(e['name'] for e in manifest if e['indexed'])
-                metadata_files = sorted(metadata.keys())
-                self.assertListEqual(manifest_files, metadata_files)
+                manifest_ids = sorted(e['uuid'] for e in manifest if e['indexed'])
                 metadata_ids = {
-                    entry['provenance']['document_id']
-                    for entry in metadata.values()
+                    EntityReference.parse(ref).entity_id
+                    for ref in metadata.keys()
                 }
+                self.assertListEqual(manifest_ids, sorted(metadata_ids))
                 self.assertIsSubset(set(stitched), metadata_ids)
             elif metadata_plugin_name == 'anvil':
                 self.assertEqual({'entities', 'links'}, bundle_json.keys())
diff --git a/test/service/test_manifest.py b/test/service/test_manifest.py
index c6a1826aa..c4654d22a 100644
--- a/test/service/test_manifest.py
+++ b/test/service/test_manifest.py
@@ -70,6 +70,9 @@
 from azul.indexer import (
     SourcedBundleFQID,
 )
+from azul.indexer.document import (
+    EntityReference,
+)
 from azul.json import (
     copy_json,
     json_hash,
@@ -355,18 +358,19 @@ def _shared_file_bundle(self, bundle):
         type.
         """
         bundle = self._load_canned_bundle(bundle)
+        new_specimen_id = '5275e5a0-6043-4ec9-86a1-6c1140cbeede'
         old_to_new = {
             # process
             '4da04038-adab-59a9-b6c4-3a61242cc972': '61af0068-1418-46e7-88ef-ab310e0ceaf8',
             # cell_suspension
             'd9eaaffe-4c93-5503-984f-762e8dfddce4': 'd6b3d2ab-5715-4486-a544-ac09fafac279',
             # specimen
-            '224d3750-f1f7-5b04-bbce-e23f09eea7d7': '5275e5a0-6043-4ec9-86a1-6c1140cbeede',
+            '224d3750-f1f7-5b04-bbce-e23f09eea7d7': new_specimen_id
         }
         manifest = self._replace_uuids(bundle.manifest, old_to_new)
         metadata = self._replace_uuids(bundle.metadata, old_to_new)
         # Change organ to prevent cell_suspensions aggregating together
-        metadata['specimen_from_organism_0.json']['organ'] = {
+        metadata[f'specimen_from_organism/{new_specimen_id}']['organ'] = {
             'text': 'lung',
             'ontology': 'UBERON:0002048',
             'ontology_label': 'lung'
@@ -397,12 +401,13 @@ def _add_ageless_donor(self, bundle):
         bundle = self._load_canned_bundle(bundle)
         # Since most of the metadata is duplicated (including biomaterial_id)
         # the donor_count will not increase.
-        duplicate_donor = deepcopy(bundle.metadata['donor_organism_0.json'])
+        old_donor_id = '9173ee6a-f1b2-5762-9272-3433b5ef7530'
+        duplicate_donor = deepcopy(bundle.metadata[f'donor_organism/{old_donor_id}'])
         del duplicate_donor['organism_age']
         del duplicate_donor['organism_age_unit']
         donor_id = '0895599c-f57d-4843-963e-11eab29f883b'
         duplicate_donor['provenance']['document_id'] = donor_id
-        bundle.metadata['donor_organism_1.json'] = duplicate_donor
+        bundle.metadata[f'donor_organism/{donor_id}'] = duplicate_donor
         donor_link = one(ln for ln in bundle.links['links']
                          if one(ln['inputs'])['input_type'] == 'donor_organism')
         new_donor_reference = {
@@ -551,28 +556,28 @@ def test_compact_manifest(self):
         # Duplicate one of the files into a minimal mock bundle to test
         # redundant file contributions from different bundles (for example due
         # to stitching)
-        files_names = {
-            'supplementary_file_1.json',
-            'SmartSeq2_RTPCR_protocol.pdf',
-            'links.json',
-            'project_0.json'
+        entity_ids = {
+            '89e313db-4423-4d53-b17e-164949acfa8f',  # Supplementary file (metadata)
+            '5f9b45af-9a26-4b16-a785-7f2d1053dd7c',  # Supplementary file (data)
+            '67bc798b-a34a-4104-8cab-cad648471f69',  # Project
         }
         manifest = [
             entry
             for entry in bundle.manifest
-            if entry['name'] in files_names
+            if entry['uuid'] in entity_ids
         ]
         metadata = {
-            file_name: copy_json(content)
-            for file_name, content in bundle.metadata.items()
-            if file_name in files_names
+            ref: copy_json(content)
+            for ref, content in bundle.metadata.items()
+            if EntityReference.parse(ref).entity_id in entity_ids
         }
         # This is an older bundle so there are no supplementary file links.
         # The existing links reference entities that weren't copied to the mock bundle.
         links = bundle.links
         links['links'].clear()
-        self._index_bundle(DSSBundle(fqid=self.bundle_fqid(uuid='b81656cf-231b-47a3-9317-10f1e501a05c',
-                                                           version='2000-01-01T01:00:00.000000Z'),
+        new_bundle_fqid = self.bundle_fqid(uuid='b81656cf-231b-47a3-9317-10f1e501a05c',
+                                           version='2000-01-01T01:00:00.000000Z')
+        self._index_bundle(DSSBundle(fqid=new_bundle_fqid,
                                      manifest=manifest,
                                      metadata=metadata,
                                      links=links))
@@ -1341,16 +1346,16 @@ def test_verbatim_jsonl_manifest(self):
                 'type': 'links',
                 'value': bundle.links
             })
-            for replica_type, key in [
-                ('cell_suspension', 'cell_suspension_0.json'),
-                ('project', 'project_0.json'),
-                ('sequence_file', 'sequence_file_0.json'),
-                ('sequence_file', 'sequence_file_1.json'),
-                ('specimen_from_organism', 'specimen_from_organism_0.json')
+            for ref in [
+                'cell_suspension/412898c5-5b9b-4907-b07c-e9b89666e204',
+                'project/e8642221-4c2c-4fd7-b926-a68bce363c88',
+                'sequence_file/70d1af4a-82c8-478a-8960-e9028b3616ca',
+                'sequence_file/0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb',
+                'specimen_from_organism/a21dc760-a500-4236-bcff-da34a0e873d2'
             ]:
                 expected.append({
-                    'type': replica_type,
-                    'value': bundle.metadata[key],
+                    'type': EntityReference.parse(ref).entity_type,
+                    'value': bundle.metadata[ref],
                 })
 
         response = self._get_manifest(ManifestFormat.verbatim_jsonl, {})
diff --git a/test/service/test_response.py b/test/service/test_response.py
index 857f5cfdc..a7b236500 100644
--- a/test/service/test_response.py
+++ b/test/service/test_response.py
@@ -1835,7 +1835,7 @@ def test_contributors_order(self):
         # First assert the order of the contributors in the indexed bundle
         bundle = self.indexed_bundles[bundle_uuid]
         assert isinstance(bundle, HCABundle)
-        project = bundle.metadata['project_0.json']
+        project = bundle.metadata['project/250aef61-a15b-4d97-b8b4-54bb997c1d7d']
         self.assertEqual(project_id, project['provenance']['document_id'])
         actual = [c['email'] for c in project['contributors']]
         self.assertEqual(expected, actual)

From 5ff2e5073fa43dd233659350f5933525df4b6e73 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Fri, 16 Aug 2024 18:51:19 -0700
Subject: [PATCH 18/20] Remove synthetic file names from TDR bundle manifest
 entries

---
 .../plugins/repository/tdr_hca/__init__.py    |  8 +--
 ...8-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json | 58 +++++++++----------
 ...5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json | 40 ++++++-------
 3 files changed, 52 insertions(+), 54 deletions(-)

diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py
index 0cb76e5a3..401dbde71 100644
--- a/src/azul/plugins/repository/tdr_hca/__init__.py
+++ b/src/azul/plugins/repository/tdr_hca/__init__.py
@@ -184,14 +184,13 @@ def canning_qualifier(cls) -> str:
 
     def add_entity(self,
                    *,
-                   entity_key: str,
                    entity: EntityReference,
                    row: BigQueryRow,
                    is_stitched: bool
                    ) -> None:
         if is_stitched:
             self.stitched.add(entity.entity_id)
-        self._add_manifest_entry(name=entity_key,
+        self._add_manifest_entry(name='',
                                  uuid=entity.entity_id,
                                  version=TDRPlugin.format_version(row['version']),
                                  size=row['content_size'],
@@ -356,11 +355,10 @@ def _emulate_bundle(self, bundle_fqid: TDRBundleFQID) -> TDRHCABundle:
                     rows = future.result()
                     pk_column = entity_type + '_id'
                     rows.sort(key=itemgetter(pk_column))
-                    for i, row in enumerate(rows):
+                    for row in rows:
                         entity = EntityReference(entity_id=row[pk_column], entity_type=entity_type)
                         is_stitched = entity not in root_entities
-                        bundle.add_entity(entity_key=f'{entity_type}_{i}.json',
-                                          entity=entity,
+                        bundle.add_entity(entity=entity,
                                           row=row,
                                           is_stitched=is_stitched)
                 else:
diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
index b942c7df5..38715f55a 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
@@ -12,7 +12,7 @@
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_1d239f78-f3e6-5dfb-aeb0-f50d8d97b51c"
         },
         {
-            "name": "sequencing_protocol_0.json",
+            "name": "",
             "uuid": "08b09d15-ef99-4278-9b88-65127adb51b9",
             "version": "2019-09-20T13:43:51.921000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
@@ -35,7 +35,7 @@
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_c82292d3-61d1-5785-b8dc-24b9365df5bd"
         },
         {
-            "name": "project_0.json",
+            "name": "",
             "uuid": "116965f3-f094-4769-9d28-ae675c1b569c",
             "version": "2019-10-03T10:54:38.894000Z",
             "content-type": "application/json; dcp-type=\"metadata/project\"",
@@ -45,7 +45,7 @@
             "sha256": ""
         },
         {
-            "name": "sequence_file_0.json",
+            "name": "",
             "uuid": "133f2a25-f3aa-49a7-b9b6-d185d302fb26",
             "version": "2019-09-20T13:51:28.379000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -55,7 +55,7 @@
             "sha256": ""
         },
         {
-            "name": "process_0.json",
+            "name": "",
             "uuid": "15de6ce1-c185-4852-ade4-43614c5d048b",
             "version": "2019-09-20T13:43:52.606000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
@@ -102,7 +102,7 @@
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_83e89c54-4fc6-58b0-800c-3788539c41e7"
         },
         {
-            "name": "supplementary_file_0.json",
+            "name": "",
             "uuid": "22561f93-d5e0-57eb-a54e-2d9d565cc234",
             "version": "2019-09-24T09:35:06.958773Z",
             "size": 353,
@@ -112,7 +112,7 @@
             "sha256": ""
         },
         {
-            "name": "sequence_file_1.json",
+            "name": "",
             "uuid": "23f8e139-f4fa-4476-ba59-ff5d37003c34",
             "version": "2019-09-20T13:50:08.455000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -122,7 +122,7 @@
             "sha256": ""
         },
         {
-            "name": "sequence_file_2.json",
+            "name": "",
             "uuid": "27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6",
             "version": "2019-09-20T13:50:35.338000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -145,7 +145,7 @@
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_dba31e1c-1b9c-56ae-af74-16b00b8144d2"
         },
         {
-            "name": "library_preparation_protocol_0.json",
+            "name": "",
             "uuid": "2945bb1f-90de-42a3-afa1-f57a62c853f0",
             "version": "2019-09-20T13:43:52.178000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
@@ -155,7 +155,7 @@
             "sha256": ""
         },
         {
-            "name": "donor_organism_0.json",
+            "name": "",
             "uuid": "2b7adb0a-82a4-4319-80d1-4a73d879dec1",
             "version": "2019-09-20T13:43:52.612000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
@@ -165,7 +165,7 @@
             "sha256": ""
         },
         {
-            "name": "enrichment_protocol_0.json",
+            "name": "",
             "uuid": "345bcbd2-f3a7-4f57-a806-fbb0ce4a25da",
             "version": "2019-09-20T13:43:52.381000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
@@ -175,7 +175,7 @@
             "sha256": ""
         },
         {
-            "name": "sequence_file_3.json",
+            "name": "",
             "uuid": "35e07477-76cb-4a92-99b6-7b3bbb02ec06",
             "version": "2019-09-20T13:49:42.254000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -185,7 +185,7 @@
             "sha256": ""
         },
         {
-            "name": "sequence_file_4.json",
+            "name": "",
             "uuid": "3c3d882a-cc38-4eea-ac53-0885f906852e",
             "version": "2019-09-20T13:52:19.666000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -195,7 +195,7 @@
             "sha256": ""
         },
         {
-            "name": "sequence_file_5.json",
+            "name": "",
             "uuid": "3dffc456-caaf-4823-9f65-fc0db7abacbc",
             "version": "2019-09-20T13:49:42.771000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -205,7 +205,7 @@
             "sha256": ""
         },
         {
-            "name": "process_1.json",
+            "name": "",
             "uuid": "47ca0565-ab7d-42bd-8731-ce5d30cfd6c7",
             "version": "2019-09-20T13:43:52.438000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
@@ -215,7 +215,7 @@
             "sha256": ""
         },
         {
-            "name": "supplementary_file_1.json",
+            "name": "",
             "uuid": "507d2814-1688-54e7-b73e-2f831aa34368",
             "version": "2019-09-24T09:35:06.958773Z",
             "size": 353,
@@ -236,7 +236,7 @@
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_9d6f268f-f484-5381-9095-f0998fa0c961"
         },
         {
-            "name": "sequence_file_6.json",
+            "name": "",
             "uuid": "5f68ea73-350b-4d37-a341-3004139fb699",
             "version": "2019-09-20T13:50:35.660000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -246,7 +246,7 @@
             "sha256": ""
         },
         {
-            "name": "sequence_file_7.json",
+            "name": "",
             "uuid": "63051b9f-87d4-4853-a4a0-5cc742ef6e72",
             "version": "2019-09-20T13:50:59.836000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -256,7 +256,7 @@
             "sha256": ""
         },
         {
-            "name": "sequence_file_8.json",
+            "name": "",
             "uuid": "6ca8e43f-5f40-4eb9-bfa9-294c54dbeade",
             "version": "2019-09-20T13:52:17.560000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -266,7 +266,7 @@
             "sha256": ""
         },
         {
-            "name": "cell_line_0.json",
+            "name": "",
             "uuid": "70054038-cb12-429d-bb37-69185ff1deee",
             "version": "2019-09-20T13:43:52.455000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
@@ -276,7 +276,7 @@
             "sha256": ""
         },
         {
-            "name": "collection_protocol_0.json",
+            "name": "",
             "uuid": "8612862e-beb1-416b-a807-0a83fae8d168",
             "version": "2019-09-20T13:43:52.146000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
@@ -299,7 +299,7 @@
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_a5e4e698-1d4c-5a5d-8d7c-5c84ea0f30d8"
         },
         {
-            "name": "cell_suspension_0.json",
+            "name": "",
             "uuid": "906f8f09-deaa-40bb-bf50-27d2336b2dc4",
             "version": "2019-09-20T13:43:52.387000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
@@ -309,7 +309,7 @@
             "sha256": ""
         },
         {
-            "name": "sequence_file_9.json",
+            "name": "",
             "uuid": "98ee0901-d34c-48a5-915a-0511bac325ec",
             "version": "2019-09-20T13:53:16.941000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -319,7 +319,7 @@
             "sha256": ""
         },
         {
-            "name": "sequence_file_10.json",
+            "name": "",
             "uuid": "a2f4b05d-0dae-4655-acfd-ef3b91ae0ad0",
             "version": "2019-09-20T13:50:08.492000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -342,7 +342,7 @@
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_065dad63-3e05-5738-8ba5-9925d5d73d5e"
         },
         {
-            "name": "supplementary_file_2.json",
+            "name": "",
             "uuid": "c343a47d-683f-571d-99c4-1331841b4e63",
             "version": "2019-09-24T09:35:06.958773Z",
             "size": 353,
@@ -378,7 +378,7 @@
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_e6c1d2ce-d6ad-500e-8682-626a555992ab"
         },
         {
-            "name": "process_2.json",
+            "name": "",
             "uuid": "c5cf9180-535a-4d1c-bdee-4f6ce7845b1e",
             "version": "2019-09-20T13:43:52.368000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
@@ -388,7 +388,7 @@
             "sha256": ""
         },
         {
-            "name": "specimen_from_organism_0.json",
+            "name": "",
             "uuid": "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda",
             "version": "2019-09-20T13:43:52.654000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
@@ -411,7 +411,7 @@
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_bb455f5a-a70f-5155-85a0-46f475856e9f"
         },
         {
-            "name": "process_3.json",
+            "name": "",
             "uuid": "df5114c9-9f52-451b-afde-3673392fc864",
             "version": "2019-09-20T13:43:52.607000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
@@ -421,7 +421,7 @@
             "sha256": ""
         },
         {
-            "name": "sequence_file_11.json",
+            "name": "",
             "uuid": "e46af70a-0396-41db-9b74-330cb8244124",
             "version": "2019-09-20T13:52:19.118000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -444,7 +444,7 @@
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_f140bd59-16c2-5082-aaf6-1c929e7063c6"
         },
         {
-            "name": "dissociation_protocol_0.json",
+            "name": "",
             "uuid": "eaf15851-97e3-4e4b-b81b-0e625098f4d5",
             "version": "2019-09-20T13:43:52.177000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
diff --git a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
index ab314980f..a7ab1c01b 100644
--- a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
+++ b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
@@ -1,7 +1,7 @@
 {
     "manifest": [
         {
-            "name": "supplementary_file_0.json",
+            "name": "",
             "uuid": "01a1d04b-05d0-4904-b627-68b0dc02bc17",
             "version": "2019-05-14T11:01:09.564000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -11,7 +11,7 @@
             "sha256": ""
         },
         {
-            "name": "analysis_protocol_0.json",
+            "name": "",
             "uuid": "099457a1-a453-54c6-aae5-b70dafa33bbd",
             "version": "2020-08-10T21:24:26.174274Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
@@ -21,7 +21,7 @@
             "sha256": ""
         },
         {
-            "name": "project_0.json",
+            "name": "",
             "uuid": "116965f3-f094-4769-9d28-ae675c1b569c",
             "version": "2019-10-03T10:54:38.894000Z",
             "content-type": "application/json; dcp-type=\"metadata/project\"",
@@ -31,7 +31,7 @@
             "sha256": ""
         },
         {
-            "name": "cell_suspension_0.json",
+            "name": "",
             "uuid": "201ae4d0-c7c6-4777-947f-18f5268884b6",
             "version": "2019-05-14T12:06:23.503000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
@@ -52,7 +52,7 @@
             "sha256": "1bb86ee570e328dcd72a684689ddd87c966209cfc4b2b5c36e50dd0e4c156cab"
         },
         {
-            "name": "donor_organism_0.json",
+            "name": "",
             "uuid": "3211ef8f-a60c-4892-ae55-91d6752dcd75",
             "version": "2019-05-14T11:29:52.575000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
@@ -62,7 +62,7 @@
             "sha256": ""
         },
         {
-            "name": "process_0.json",
+            "name": "",
             "uuid": "33e31f6f-fe78-45bd-ae57-10d2d14253cf",
             "version": "2019-05-14T12:29:57.858000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
@@ -72,7 +72,7 @@
             "sha256": ""
         },
         {
-            "name": "library_preparation_protocol_0.json",
+            "name": "",
             "uuid": "5b503dcb-dca6-4e4f-988b-f7100c030dc5",
             "version": "2019-05-14T11:06:42.648000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
@@ -82,7 +82,7 @@
             "sha256": ""
         },
         {
-            "name": "specimen_from_organism_0.json",
+            "name": "",
             "uuid": "5d82b884-7db4-47fa-9ccd-03054065c509",
             "version": "2019-05-14T11:59:17.317000Z",
             "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
@@ -105,7 +105,7 @@
             "s3_etag": "7e892bf8f6aa489ccb08a995c7f017e1"
         },
         {
-            "name": "process_1.json",
+            "name": "",
             "uuid": "6f5ddf2c-382d-4c0a-a506-3a5286067c83",
             "version": "2019-05-14T12:20:34.464000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
@@ -115,7 +115,7 @@
             "sha256": ""
         },
         {
-            "name": "analysis_file_0.json",
+            "name": "",
             "uuid": "7a015307-6db9-541f-aaae-db9fdb41000f",
             "version": "2020-08-10T21:24:26.174274Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -125,7 +125,7 @@
             "sha256": ""
         },
         {
-            "name": "analysis_process_0.json",
+            "name": "",
             "uuid": "848c816e-4ae8-4c9a-9e3d-ebe447519ff4",
             "version": "2020-08-10T21:24:26.174274Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
@@ -135,7 +135,7 @@
             "sha256": ""
         },
         {
-            "name": "sequence_file_0.json",
+            "name": "",
             "uuid": "8f8b9587-237f-4995-9461-c96eac53d615",
             "version": "2019-05-14T12:18:53.532000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -145,7 +145,7 @@
             "sha256": ""
         },
         {
-            "name": "supplementary_file_1.json",
+            "name": "",
             "uuid": "a06cb5d5-2675-4d64-aeb8-79e0103715f3",
             "version": "2019-05-14T11:01:09.596000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -155,7 +155,7 @@
             "sha256": ""
         },
         {
-            "name": "analysis_file_1.json",
+            "name": "",
             "uuid": "b8b76328-854c-5862-a688-9b761a9cea86",
             "version": "2020-08-10T21:24:26.174274Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -178,7 +178,7 @@
             "s3_etag": "2742e1e78f6d4663bf41d3080396695c"
         },
         {
-            "name": "process_2.json",
+            "name": "",
             "uuid": "c0d18b81-0b54-4a11-864b-cd3f43b7e7bf",
             "version": "2019-05-14T12:26:53.666000Z",
             "content-type": "application/json; dcp-type=\"metadata/process\"",
@@ -212,7 +212,7 @@
             "s3_etag": "846fd9e6b98041df46a1ddb94e85b6b9"
         },
         {
-            "name": "enrichment_protocol_0.json",
+            "name": "",
             "uuid": "dd7f3d64-4b79-48f0-9d8c-4324594fe820",
             "version": "2019-05-14T11:06:42.695000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
@@ -222,7 +222,7 @@
             "sha256": ""
         },
         {
-            "name": "supplementary_file_2.json",
+            "name": "",
             "uuid": "e738a267-87fc-4070-abc7-b3be6442c6d0",
             "version": "2019-05-14T11:01:15.816000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -245,7 +245,7 @@
             "s3_etag": "8786a82f739d1848aa5be480faf65e70"
         },
         {
-            "name": "sequencing_protocol_0.json",
+            "name": "",
             "uuid": "eca2ab79-ad61-411f-815a-4f6d936d992b",
             "version": "2019-05-14T11:06:42.648000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",
@@ -255,7 +255,7 @@
             "sha256": ""
         },
         {
-            "name": "sequence_file_1.json",
+            "name": "",
             "uuid": "ee7404a4-c183-4a75-8bd1-34b5fc140e81",
             "version": "2019-05-14T12:13:41.926000Z",
             "content-type": "application/json; dcp-type=\"metadata/file\"",
@@ -278,7 +278,7 @@
             "s3_etag": "6aca4df2ef18b97243967887837c3bef"
         },
         {
-            "name": "dissociation_protocol_0.json",
+            "name": "",
             "uuid": "fcba26aa-658c-4120-ab31-cc5a5a00f759",
             "version": "2019-05-14T11:06:42.781000Z",
             "content-type": "application/json; dcp-type=\"metadata/protocol\"",

From cc88892898848fd43c41dc2820f614d6cf609a11 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Thu, 8 Aug 2024 13:06:01 -0700
Subject: [PATCH 19/20] [p] Remove manifest entries for HCA metadata entities
 (partial #6299)

---
 .../plugins/repository/tdr_hca/__init__.py    |   10 -
 .../data/metadata/helpers/staging_area.py     |   16 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |  132 -
 ...a3fb4204953.2018-08-03T082009.272868Z.json |  168 -
 ...a3fb4204953.2018-08-03T082009.272868Z.json |  516 -
 ...a3fb4204953.2018-08-03T082009.272868Z.json |  132 -
 ...a3fb4204953.2018-08-03T082009.272868Z.json |  144 -
 ...a3fb4204953.2018-08-03T082009.272868Z.json |  132 -
 ...a3fb4204953.2018-08-03T082009.272868Z.json |  216 -
 ...318dbb86000.2019-01-03T163633.780215Z.json |  512 -
 ...61d6da02d44.2019-09-20T103932.395795Z.json |  228 -
 ...a3fb4204953.2018-03-29T142048.835519Z.json |   60 -
 ...d019d1c9439.2019-05-15T222432.561000Z.json |  120 -
 ...08092b2dabe.2019-04-17T175706.867000Z.json |  192 -
 ...68e20ec4a2e.2019-02-02T065454.662896Z.json |  612 --
 ...19c1c2d9018.2018-10-07T130111.835234Z.json |  168 -
 ...406a478d5ab.2018-09-05T182535.846470Z.json |  156 -
 ...95a3f8deb9c.2019-04-03T103426.471000Z.json | 2844 -----
 ...720f33a5dde.2019-03-17T220646.332108Z.json |  180 -
 ...3-5e9d-52cd-b32d-af88edccabfa.dss.hca.json |  641 --
 ...5-71e2-48ca-a87b-e256938c6a98.dss.hca.json |  521 -
 ...3-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json | 4271 --------
 ...c-6778-423d-8fe9-869e2a515d35.dss.hca.json |  150 -
 ...8-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json |  313 -
 ...8-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json |  291 -
 ...0-eaba-531d-ba9e-db80164d65ef.dss.hca.json |  180 -
 ...4-fa14-5c6f-a474-a742540108a3.dss.hca.json |  144 -
 ...5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json |  141 -
 ...8-658e-4c51-9de4-a768322f84c5.dss.hca.json |  140 -
 ...3-93e1-56b4-b857-59497f5d942d.dss.hca.json |  132 -
 ...a-940e-49b1-9bcc-25699a55b295.dss.hca.json |  360 -
 ...f-61a7-4504-a57c-fc70f38d5b13.dss.hca.json |  576 -
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json |  684 --
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json |  684 --
 ...5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json |  200 -
 ...e-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json |   91 -
 ...8-adab-59a9-b6c4-3a61242cc972.dss.hca.json |  168 -
 ...4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json |  528 -
 ...0.2020-12-10T10:30:00.000000Z.dss.hca.json | 2611 -----
 ...1-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json |  168 -
 ...f-8346-5420-b7e4-b486f99451a8.dss.hca.json |  191 -
 ...e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json |  151 -
 ...1-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json |   41 -
 ...3-1885-545f-9381-0dab1edf6074.dss.hca.json |  168 -
 ...e-9a5d-4e3d-ada2-0414b666b880.dss.hca.json |  348 -
 ...2-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json | 2844 -----
 ...3-f0ac-417a-8a29-221c77debde8.dss.hca.json |  168 -
 ...d.2018-11-02T11:33:44.698028Z.dss.hca.json |  156 -
 ...d.2018-11-04T11:33:44.698028Z.dss.hca.json |  156 -
 ...e-9b7b-4800-8977-fe7c94e131df.dss.hca.json |  180 -
 ...4-dc9f-439e-af29-f8eb75b0729d.dss.hca.json |  180 -
 ...4-9a58-4763-9e66-59894efbdaa8.dss.hca.json | 9372 -----------------
 ...d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json |  528 -
 ...f-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json |  180 -
 ...1-4766-4210-966c-f9ee25d19190.dss.hca.json |  684 --
 ...a-2b51-4419-9cde-34df44c6458a.dss.hca.json |  216 -
 ...e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json |  576 -
 ...4-6b80-4eed-97c9-4984de81a47c.dss.hca.json | 3600 -------
 ...7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json |  206 +-
 ...b-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json |  360 -
 ...7-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json | 4152 +-------
 ...f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json |  168 -
 test/integration_test.py                      |    2 -
 test/service/test_manifest.py                 |    4 +-
 64 files changed, 9 insertions(+), 44154 deletions(-)

diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py
index 401dbde71..3ed3139e3 100644
--- a/src/azul/plugins/repository/tdr_hca/__init__.py
+++ b/src/azul/plugins/repository/tdr_hca/__init__.py
@@ -190,12 +190,6 @@ def add_entity(self,
                    ) -> None:
         if is_stitched:
             self.stitched.add(entity.entity_id)
-        self._add_manifest_entry(name='',
-                                 uuid=entity.entity_id,
-                                 version=TDRPlugin.format_version(row['version']),
-                                 size=row['content_size'],
-                                 content_type='application/json',
-                                 dcp_type=f'"metadata/{row["schema_type"]}"')
         if entity.entity_type.endswith('_file'):
             descriptor = json.loads(row['descriptor'])
             self._add_manifest_entry(name=row['file_name'],
@@ -212,9 +206,6 @@ def add_entity(self,
                                       else content)
 
     metadata_columns: ClassVar[set[str]] = {
-        'version',
-        'JSON_EXTRACT_SCALAR(content, "$.schema_type") AS schema_type',
-        'BYTE_LENGTH(content) AS content_size',
         'content'
     }
 
@@ -462,7 +453,6 @@ def _retrieve_entities(self,
             else TDRHCABundle.data_columns if entity_type.endswith('_file')
             else TDRHCABundle.metadata_columns
         )
-        assert version_column in non_pk_columns
         table_name = backtick(self._full_table_name(source, entity_type))
         entity_id_type = one(set(map(type, entity_ids)))
 
diff --git a/src/humancellatlas/data/metadata/helpers/staging_area.py b/src/humancellatlas/data/metadata/helpers/staging_area.py
index f9a970bc0..c6a0cd651 100644
--- a/src/humancellatlas/data/metadata/helpers/staging_area.py
+++ b/src/humancellatlas/data/metadata/helpers/staging_area.py
@@ -157,25 +157,11 @@ def get_bundle_parts(self, subgraph_id: str) -> tuple[str, MutableJSONs, Mutable
         entity_ids_by_type = self._entity_ids_by_type(subgraph_id)
         for entity_type, entity_ids in entity_ids_by_type.items():
             # Sort entity_ids to produce the same ordering on multiple runs
-            for i, entity_id in enumerate(sorted(entity_ids)):
-                json_file_name = f'{entity_type}_{i}.json'
+            for entity_id in sorted(entity_ids):
                 metadata_file = self.metadata[entity_id]
                 json_content = metadata_file.content
                 key = str(EntityReference(entity_type=entity_type, entity_id=entity_id))
                 metadata[key] = json_content
-                file_manifest = {
-                    'content-type': 'application/json;',
-                    'crc32c': '0' * 8,
-                    'indexed': True,
-                    'name': json_file_name,
-                    's3_etag': None,
-                    'sha1': None,
-                    'sha256': '0' * 64,
-                    'size': len(json.dumps(json_content)),
-                    'uuid': metadata_file.uuid,
-                    'version': metadata_file.version
-                }
-                manifest.append(file_manifest)
                 if entity_type.endswith('_file'):
                     file_manifest = self.descriptors[entity_id].manifest_entry
                     manifest.append(file_manifest)
diff --git a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 0dbe6df85..ed036c617 100644
--- a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -1,113 +1,5 @@
 {
     "manifest": [
-        {
-            "crc32c": "1C09FCE0",
-            "sha1": "f1aeb2b94ce28ee524388730c9b63b7dafc895c7",
-            "sha256": "b3f554280c892aecfc235a64f924843b2484f73cb0cd21aacdd1d796383a6d69",
-            "s3_etag": "bceb1c61bab478faf3f70e0ff832b4c0",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "cell_suspension_0.json",
-            "size": 770,
-            "uuid": "84354fad-8890-41df-b808-48f9ed4e1cc3",
-            "version": "1"
-        },
-        {
-            "crc32c": "28EA16F2",
-            "sha1": "7cc7ac34f3c2c00befb398a63b5303d636ca4711",
-            "sha256": "de429783e1308851f7f5e8320d8612e7c1ad90975698fec9a481c836db2e9543",
-            "s3_etag": "61eb8b831af8c1fdf1105ee9cb66fb16",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "dissociation_protocol_0.json",
-            "size": 711,
-            "uuid": "30cf9805-82f5-4725-a7ad-7411c276b4a9",
-            "version": "1"
-        },
-        {
-            "crc32c": "C2C08857",
-            "sha1": "8f1b7481a5dc77f3a6c90530a957952102a92e35",
-            "sha256": "94be68544f8a5a0171fd918e070150a29fa1c8f4380ec351a302bb56b980b491",
-            "s3_etag": "d98de4db8b42b8def2aa2591da2f8569",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "donor_organism_0.json",
-            "size": 1358,
-            "uuid": "491a22fb-3a6c-4a8f-9c5b-f009e080d280",
-            "version": "1"
-        },
-        {
-            "crc32c": "0B85C35C",
-            "sha1": "dd9a81c11165c742d94b1cb8561e3789854a8ca7",
-            "sha256": "e215aceb61560e510592eb1f4247c501ea0d756659bd781d995df0546ecb9696",
-            "s3_etag": "abc3a4a3dbec4beab0e2cacf50b831c4",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "library_preparation_protocol_0.json",
-            "size": 1087,
-            "uuid": "821601f1-64e8-4427-8680-34a743b35b69",
-            "version": "1"
-        },
-        {
-            "crc32c": "522D96A7",
-            "sha1": "9876adb67827ea0328566811a1304bcf49a31b02",
-            "sha256": "ecc1b1a2cd924933311c28e9b00f841c0beaa918f3c29722a36ff3fa6600440b",
-            "s3_etag": "4f939c7dae692b468e4741b56ccfbe3e",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "process_0.json",
-            "size": 386,
-            "uuid": "c4175b47-1767-48c5-b408-f9e97c01f94e",
-            "version": "1"
-        },
-        {
-            "crc32c": "51B043A0",
-            "sha1": "9b17c9cd8e3d7c3bc4685e24bbcba9e528792d05",
-            "sha256": "98d9878e05b6a56fed6d00153aa5c0664de07185994e2cf080ec1be4b4776933",
-            "s3_etag": "8ff1e91a29e51311d5252889599eb709",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "process_1.json",
-            "size": 386,
-            "uuid": "88b3b728-e9c6-4b1b-a030-97f6670469c2",
-            "version": "1"
-        },
-        {
-            "crc32c": "1FAD27D0",
-            "sha1": "b2a61619fa1922cb899d993aace4fa0f6b30a232",
-            "sha256": "31eab93a5c0e39c58ee16d16c0ce5331e2185cc271891fbd63e7f62a75336e4b",
-            "s3_etag": "a781ef10618d4bd5c11bf5bb923d4d12",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "process_2.json",
-            "size": 384,
-            "uuid": "317b3c35-e0f6-48d6-9154-80db47ff8f20",
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diff --git a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index c4a5b2b76..4562cd052 100644
--- a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
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diff --git a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 8684d8653..3c5bdfc06 100644
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+++ b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
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diff --git a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 64ededa29..59154afab 100644
--- a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
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diff --git a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 09aacf25f..1a9caa012 100644
--- a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -1,125 +1,5 @@
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diff --git a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 3ef7e9534..c5887a11d 100644
--- a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
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diff --git a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 84f4ad58f..39103a9a5 100644
--- a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
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@@ -276,18 +84,6 @@
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diff --git a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
index 790373aac..6b6f241fe 100644
--- a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
+++ b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
@@ -1,517 +1,5 @@
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index 0a1c182fb..590e31ac2 100644
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diff --git a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
index 848545261..7d7ed0794 100644
--- a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
+++ b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
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diff --git a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
index 6c05e5811..f7ed54de1 100644
--- a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
+++ b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
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diff --git a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
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diff --git a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
index 6114ac0e5..843085449 100644
--- a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
+++ b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
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diff --git a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
index 67e2712d8..206faab34 100644
--- a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
+++ b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
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diff --git a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
index 0ebf42876..8b230fe64 100644
--- a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
+++ b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
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diff --git a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
index 35df6b74a..c50b514f7 100644
--- a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
+++ b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
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diff --git a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
index 07903af74..30a021c6e 100644
--- a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
+++ b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
@@ -1,185 +1,5 @@
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diff --git a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
index 8c4d61d20..0827d6abb 100644
--- a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
+++ b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
@@ -26,46 +26,6 @@
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         {
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@@ -79,26 +39,6 @@
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@@ -110,46 +50,6 @@
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@@ -163,76 +63,6 @@
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diff --git a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
index 5322f72b4..2cd6968d4 100644
--- a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
+++ b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
@@ -1,45 +1,5 @@
 {
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@@ -257,36 +117,6 @@
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@@ -346,26 +156,6 @@
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@@ -379,46 +169,6 @@
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@@ -521,46 +221,6 @@
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-            "version": "2021-06-28T14:21:17.557000Z",
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         {
             "name": "mouse_cortex_R2.fastq",
             "uuid": "b5a30ee7-6c2f-452a-b2aa-f032731b8b17",
@@ -574,106 +234,6 @@
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-            "uuid": "b5a382bd-34e5-429d-9013-3ff025ab322a",
-            "version": "2021-06-28T14:21:16.961000Z",
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-            "version": "2021-06-28T14:21:16.940000Z",
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-            "version": "2021-06-28T14:21:17.481000Z",
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-            "uuid": "bd774f12-82e6-4036-8779-d8674bce9205",
-            "version": "2021-06-28T14:21:18.045000Z",
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-        {
-            "name": "donor_organism_1.json",
-            "uuid": "c10356c8-e081-4f97-8e85-0ea87b8eb84b",
-            "version": "2021-06-28T14:21:16.893000Z",
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-            "version": "2021-06-28T14:21:17.409000Z",
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-            "version": "2021-06-28T14:21:17.977000Z",
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-        {
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-            "uuid": "d3372c5a-20ea-4239-bfef-c11894862897",
-            "version": "2021-06-28T14:21:17.382000Z",
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         {
             "name": "mouse_cortex_S2_L002_I1_001.fastq",
             "uuid": "d3965eac-1d56-4809-bf64-8291c9bbdf2f",
@@ -700,86 +260,6 @@
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-            "version": "2021-06-28T14:21:17.582000Z",
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-            "version": "2021-06-28T14:21:18.755000Z",
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-            "version": "2021-06-28T14:21:17.282000Z",
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-            "version": "2021-06-22T08:36:39.408000Z",
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             "uuid": "fd13fc62-8767-45d7-aa48-8a140f9a5005",
@@ -3619,7 +3099,6 @@
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diff --git a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
index 9dbf16470..73ee6694a 100644
--- a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
+++ b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
@@ -39,16 +39,6 @@
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             "uuid": "01d2d764-457f-44c5-8b18-a6fadf73c1f7",
@@ -75,36 +65,6 @@
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-            "version": "2021-05-10T23:24:58.932000Z",
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         {
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             "uuid": "03815b54-b935-4f04-96ac-56f7c87d601d",
@@ -144,46 +104,6 @@
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-            "version": "2021-05-10T23:24:54.910000Z",
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-            "version": "2021-05-10T23:24:56.774000Z",
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         {
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             "uuid": "05736d0e-ab04-4183-9c38-1bfdf028978f",
@@ -210,16 +130,6 @@
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-            "version": "2021-05-10T23:25:05.832000Z",
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             "uuid": "062700c0-e8ed-46e2-b7cd-7cc6d8c3fc85",
@@ -246,26 +156,6 @@
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         {
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             "uuid": "073edb43-47d2-45c7-bff2-76c503ebb951",
@@ -292,26 +182,6 @@
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-            "uuid": "07f1f962-dd38-4a0b-b0b5-f4efe30d21e2",
-            "version": "2021-05-10T23:24:55.328000Z",
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-            "indexed": true,
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-            "uuid": "07fc08c2-8b57-45f6-afe8-eeed266c0809",
-            "version": "2021-05-10T23:25:12.039000Z",
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         {
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             "uuid": "091a1403-2320-4e38-8749-3088deb6da8b",
@@ -325,26 +195,6 @@
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-            "version": "2021-05-10T23:25:12.151000Z",
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         {
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@@ -358,26 +208,6 @@
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-            "version": "2021-05-10T23:24:57.193000Z",
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         {
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             "uuid": "09be6713-f8fa-48a6-873e-d9524c526c8f",
@@ -391,16 +221,6 @@
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-            "version": "2021-05-10T23:24:57.806000Z",
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         {
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             "uuid": "09ffc9cf-6e64-4d47-8188-a8588ec39861",
@@ -440,36 +260,6 @@
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-            "version": "2021-05-10T23:25:12.382000Z",
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             "uuid": "ffb352c5-f9e2-497c-940c-7cb5dd0eaa5e",
@@ -8968,26 +4718,6 @@
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-            "version": "2021-05-10T23:24:56.379000Z",
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-            "version": "2021-05-10T23:24:59.401000Z",
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@@ -38542,7 +34272,6 @@
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-
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diff --git a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
index e9b9ae267..14e5068a2 100644
--- a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
+++ b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
@@ -1,55 +1,5 @@
 {
     "manifest": [
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-            "uuid": "0078130e-8a91-47d0-9ff7-854ae772b8ea",
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@@ -75,106 +25,6 @@
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diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
index d22dd3ee9..79a81af43 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
@@ -1,317 +1,5 @@
 {
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-        },
-        {
-            "name": "project_0.json",
-            "uuid": "116965f3-f094-4769-9d28-ae675c1b569c",
-            "version": "2019-10-03T10:54:38.894000Z",
-            "content-type": "application/json; dcp-type=\"metadata/project\"",
-            "size": 5652,
-            "indexed": true,
-            "crc32c": "3da96875",
-            "sha1": "68a22a727f3a8439461734e7d2c192adfb971176",
-            "sha256": "0c44b89305a602e0d2e286ff34426e8b29485a0946e83f88162d0ccd0602ee5b",
-            "s3_etag": "6e84ee99cf58559e5019eb2f286f513a"
-        },
-        {
-            "name": "library_preparation_protocol_0.json",
-            "uuid": "2945bb1f-90de-42a3-afa1-f57a62c853f0",
-            "version": "2019-09-20T13:43:52.178000Z",
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "size": 1109,
-            "indexed": true,
-            "crc32c": "ae7642fe",
-            "sha1": "992cbb9e80c3784409c35f955e928c9e4c2d4af0",
-            "sha256": "f6ae67d590e44c0864b8aba0b422647b3219861a92a8cae53795d6895f27e780",
-            "s3_etag": "9eb8d4c59b32f96839e8e5f297d17f77"
-        },
-        {
-            "name": "sequencing_protocol_0.json",
-            "uuid": "08b09d15-ef99-4278-9b88-65127adb51b9",
-            "version": "2019-09-20T13:43:51.921000Z",
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "size": 1240,
-            "indexed": true,
-            "crc32c": "e0510554",
-            "sha1": "e0c8b5c1ac1978cfa269cc543262f2fc3db123bb",
-            "sha256": "402b5686d8a8e3333c224aa3acf28336a4071ad6fd669c80585181c13bbac3b1",
-            "s3_etag": "2416dcdbe9718f9c5c10e484a8f5838d"
-        },
-        {
-            "name": "dissociation_protocol_0.json",
-            "uuid": "eaf15851-97e3-4e4b-b81b-0e625098f4d5",
-            "version": "2019-09-20T13:43:52.177000Z",
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "size": 830,
-            "indexed": true,
-            "crc32c": "2f7ea2aa",
-            "sha1": "7097cc98132f2ae167dacb3308eaeba6c401c93e",
-            "sha256": "d717b374ecec8da288f29cfb7486421e98b482bbabb29d0df67ee64b2e861b64",
-            "s3_etag": "64c9ebfce772a52b0e61c56ddacc26be"
-        },
-        {
-            "name": "enrichment_protocol_0.json",
-            "uuid": "345bcbd2-f3a7-4f57-a806-fbb0ce4a25da",
-            "version": "2019-09-20T13:43:52.381000Z",
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "size": 947,
-            "indexed": true,
-            "crc32c": "05052102",
-            "sha1": "22840f7cf4b682f711b974e08e3c981db32d14f0",
-            "sha256": "48e1642e7796c0ecff97a38cdcee6d675fd8c795aec6306b1587d48a59fbe090",
-            "s3_etag": "c42fa2044dbeb71bbc1032bc85a6c7f0"
-        },
-        {
-            "name": "collection_protocol_0.json",
-            "uuid": "8612862e-beb1-416b-a807-0a83fae8d168",
-            "version": "2019-09-20T13:43:52.146000Z",
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "size": 1384,
-            "indexed": true,
-            "crc32c": "2662b17b",
-            "sha1": "e05886127a290633dd33f62b10d92ad26bf6a93d",
-            "sha256": "cb51583cbf6a2e314c3d39161d993d89ca119bca07498b0b2298abfddc18a90b",
-            "s3_etag": "4fe82f596c893e0824a6f220ec659ae9"
-        },
-        {
-            "name": "process_0.json",
-            "uuid": "15de6ce1-c185-4852-ade4-43614c5d048b",
-            "version": "2019-09-20T13:43:52.606000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 470,
-            "indexed": true,
-            "crc32c": "ea37b628",
-            "sha1": "9f277e043768cf031244bcd8b755711e822b2307",
-            "sha256": "818c1cd77dbcb601c8ff0e09879154ee4a3a3e64c5f3588bad68cfb50a3d4679",
-            "s3_etag": "74630b8d7357296546c853214cacb00c"
-        },
-        {
-            "name": "process_1.json",
-            "uuid": "47ca0565-ab7d-42bd-8731-ce5d30cfd6c7",
-            "version": "2019-09-20T13:43:52.438000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 446,
-            "indexed": true,
-            "crc32c": "d73a7fd3",
-            "sha1": "c1fc70df9d0f957d51b52a1942f32e6bfa32e7cc",
-            "sha256": "e81a24a2adbe5e84aefd03f48559eb515f8bb2970e94ee87ca64027646dc482e",
-            "s3_etag": "e67d7a369cbf5d5ed876f225134c4ca0"
-        },
-        {
-            "name": "process_2.json",
-            "uuid": "df5114c9-9f52-451b-afde-3673392fc864",
-            "version": "2019-09-20T13:43:52.607000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 446,
-            "indexed": true,
-            "crc32c": "44beb2a9",
-            "sha1": "b82da91c0f1d794d610e92ea3ea2328d22dd6700",
-            "sha256": "c3621f31bf31d551169fa39e186bc90849df26b966d5deffb0190c8c93dc080e",
-            "s3_etag": "7136ddbeda4ebbd0e28232508dc141f3"
-        },
-        {
-            "name": "process_3.json",
-            "uuid": "c5cf9180-535a-4d1c-bdee-4f6ce7845b1e",
-            "version": "2019-09-20T13:43:52.368000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 446,
-            "indexed": true,
-            "crc32c": "7e39a5b4",
-            "sha1": "71f626ba4c6605d2f0c824c0b37a7390d2ea29e4",
-            "sha256": "55b54e2b1001ad02aa4d319138aee07492653efb25df7c029d2ec915147bb0a7",
-            "s3_etag": "b275f550a67f0f13bd9d72b4c7ab2965"
-        },
         {
             "name": "IDC9_L001_I1.fastq.gz",
             "uuid": "08bc2234-5157-4f5c-b348-5d63cc9f14e1",
@@ -1359,6 +1047,5 @@
             }
         ]
     },
-
     "stitched": []
 }
\ No newline at end of file
diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
index 38715f55a..ae3e2bea6 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
@@ -11,16 +11,6 @@
             "sha256": "",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_1d239f78-f3e6-5dfb-aeb0-f50d8d97b51c"
         },
-        {
-            "name": "",
-            "uuid": "08b09d15-ef99-4278-9b88-65127adb51b9",
-            "version": "2019-09-20T13:43:51.921000Z",
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "size": 1036,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "IDC9_L001_I1.fastq.gz",
             "uuid": "08bc2234-5157-4f5c-b348-5d63cc9f14e1",
@@ -34,36 +24,6 @@
             "s3_etag": "4cc2f68ce54b988081c14118adc480c4-7",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_c82292d3-61d1-5785-b8dc-24b9365df5bd"
         },
-        {
-            "name": "",
-            "uuid": "116965f3-f094-4769-9d28-ae675c1b569c",
-            "version": "2019-10-03T10:54:38.894000Z",
-            "content-type": "application/json; dcp-type=\"metadata/project\"",
-            "size": 4304,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "133f2a25-f3aa-49a7-b9b6-d185d302fb26",
-            "version": "2019-09-20T13:51:28.379000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 645,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "15de6ce1-c185-4852-ade4-43614c5d048b",
-            "version": "2019-09-20T13:43:52.606000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 388,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "c343a47d-683f-571d-99c4-1331841b4e63_file_name.fmt",
             "uuid": "19617367-cda8-54e0-8296-84623ef58c3f",
@@ -101,36 +61,6 @@
             "s3_etag": "06705170a39d451d000c0143135fc5c3-64",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_83e89c54-4fc6-58b0-800c-3788539c41e7"
         },
-        {
-            "name": "",
-            "uuid": "22561f93-d5e0-57eb-a54e-2d9d565cc234",
-            "version": "2019-09-24T09:35:06.958773Z",
-            "size": 353,
-            "indexed": true,
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "23f8e139-f4fa-4476-ba59-ff5d37003c34",
-            "version": "2019-09-20T13:50:08.455000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 645,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6",
-            "version": "2019-09-20T13:50:35.338000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 645,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "IDC9_L002_R1.fastq.gz",
             "uuid": "292b2faf-0db3-4ba1-a6a5-cb7bdfa9313d",
@@ -144,86 +74,6 @@
             "s3_etag": "31985ad7f32b053fa97f05216c6e805e-20",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_dba31e1c-1b9c-56ae-af74-16b00b8144d2"
         },
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-            "name": "",
-            "uuid": "2945bb1f-90de-42a3-afa1-f57a62c853f0",
-            "version": "2019-09-20T13:43:52.178000Z",
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "size": 931,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "2b7adb0a-82a4-4319-80d1-4a73d879dec1",
-            "version": "2019-09-20T13:43:52.612000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 1041,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "345bcbd2-f3a7-4f57-a806-fbb0ce4a25da",
-            "version": "2019-09-20T13:43:52.381000Z",
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "size": 815,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "35e07477-76cb-4a92-99b6-7b3bbb02ec06",
-            "version": "2019-09-20T13:49:42.254000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 645,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "3c3d882a-cc38-4eea-ac53-0885f906852e",
-            "version": "2019-09-20T13:52:19.666000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 645,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "3dffc456-caaf-4823-9f65-fc0db7abacbc",
-            "version": "2019-09-20T13:49:42.771000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 645,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "47ca0565-ab7d-42bd-8731-ce5d30cfd6c7",
-            "version": "2019-09-20T13:43:52.438000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 368,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "507d2814-1688-54e7-b73e-2f831aa34368",
-            "version": "2019-09-24T09:35:06.958773Z",
-            "size": 353,
-            "indexed": true,
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "507d2814-1688-54e7-b73e-2f831aa34368_file_name.fmt",
             "uuid": "519ee493-0984-5b54-95ec-85452d506b00",
@@ -235,56 +85,6 @@
             "sha256": "",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_9d6f268f-f484-5381-9095-f0998fa0c961"
         },
-        {
-            "name": "",
-            "uuid": "5f68ea73-350b-4d37-a341-3004139fb699",
-            "version": "2019-09-20T13:50:35.660000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 645,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "63051b9f-87d4-4853-a4a0-5cc742ef6e72",
-            "version": "2019-09-20T13:50:59.836000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 645,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "6ca8e43f-5f40-4eb9-bfa9-294c54dbeade",
-            "version": "2019-09-20T13:52:17.560000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 645,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "70054038-cb12-429d-bb37-69185ff1deee",
-            "version": "2019-09-20T13:43:52.455000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 1207,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "8612862e-beb1-416b-a807-0a83fae8d168",
-            "version": "2019-09-20T13:43:52.146000Z",
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "size": 1256,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "IDC9_L003_R1.fastq.gz",
             "uuid": "87fb0ccd-07d9-4dde-bbb0-c61338e3127b",
@@ -298,36 +98,6 @@
             "s3_etag": "fc818501a59964e076aff1bc7f7068c6-20",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_a5e4e698-1d4c-5a5d-8d7c-5c84ea0f30d8"
         },
-        {
-            "name": "",
-            "uuid": "906f8f09-deaa-40bb-bf50-27d2336b2dc4",
-            "version": "2019-09-20T13:43:52.387000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 781,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "98ee0901-d34c-48a5-915a-0511bac325ec",
-            "version": "2019-09-20T13:53:16.941000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 645,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "a2f4b05d-0dae-4655-acfd-ef3b91ae0ad0",
-            "version": "2019-09-20T13:50:08.492000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 645,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "IDC9_L004_R2.fastq.gz",
             "uuid": "ae5d1035-8f2b-4355-a0ef-bbb99958b303",
@@ -341,16 +111,6 @@
             "s3_etag": "c92e5374ac0a53b228d4c1511c2d2842-63",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_065dad63-3e05-5738-8ba5-9925d5d73d5e"
         },
-        {
-            "name": "",
-            "uuid": "c343a47d-683f-571d-99c4-1331841b4e63",
-            "version": "2019-09-24T09:35:06.958773Z",
-            "size": 353,
-            "indexed": true,
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "IDC9_L001_R1.fastq.gz",
             "uuid": "c4288821-5775-4163-9543-5d29f847b03b",
@@ -377,26 +137,6 @@
             "s3_etag": "3188a7180ba75349ca223905e3f589c1-64",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_e6c1d2ce-d6ad-500e-8682-626a555992ab"
         },
-        {
-            "name": "",
-            "uuid": "c5cf9180-535a-4d1c-bdee-4f6ce7845b1e",
-            "version": "2019-09-20T13:43:52.368000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 368,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda",
-            "version": "2019-09-20T13:43:52.654000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 946,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "IDC9_L003_I1.fastq.gz",
             "uuid": "dd7d84d2-c515-489f-9ead-3f7df2c66848",
@@ -410,26 +150,6 @@
             "s3_etag": "d7046367bee15cd004af8f9882874042-7",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_bb455f5a-a70f-5155-85a0-46f475856e9f"
         },
-        {
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-            "uuid": "df5114c9-9f52-451b-afde-3673392fc864",
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@@ -443,16 +163,6 @@
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@@ -1517,6 +1227,5 @@
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-
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\ No newline at end of file
diff --git a/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json b/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
index 22185e862..d029c477e 100644
--- a/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
+++ b/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
@@ -1,101 +1,5 @@
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@@ -108,18 +12,6 @@
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@@ -131,78 +23,6 @@
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diff --git a/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json b/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
index 516e43b06..d9db1bd1b 100644
--- a/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
+++ b/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
@@ -1,77 +1,5 @@
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@@ -83,78 +11,6 @@
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diff --git a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
index 69f958021..a37ae2591 100644
--- a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
+++ b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
@@ -1,46 +1,5 @@
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@@ -54,76 +13,6 @@
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@@ -136,36 +25,6 @@
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diff --git a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
index 3859c59bc..1bdfee488 100644
--- a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
+++ b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
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index 0b94b5ece..261e65119 100644
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+++ b/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
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diff --git a/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
index 3f690229b..79c54d5e9 100644
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+++ b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
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diff --git a/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
index 59222f8ec..6cab99cd5 100644
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+++ b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
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diff --git a/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index 529b21fa1..22766ee75 100644
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+++ b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
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diff --git a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index c8712b690..3b81dcf53 100644
--- a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
+++ b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
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diff --git a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
index a7ab1c01b..032a1c97e 100644
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diff --git a/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json b/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
index 0791ca7f3..13df425de 100644
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index f3cc0def4..a8afbb205 100644
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+++ b/test/indexer/data/4da04038-adab-59a9-b6c4-3a61242cc972.dss.hca.json
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diff --git a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
index 190412c61..2328e97fd 100644
--- a/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
+++ b/test/indexer/data/587d74b4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json
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diff --git a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
index 4c858abfe..8a70324a6 100644
--- a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
+++ b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
@@ -1,75 +1,5 @@
 {
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@@ -96,56 +26,6 @@
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@@ -157,26 +37,6 @@
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@@ -201,16 +61,6 @@
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@@ -222,16 +72,6 @@
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@@ -245,16 +85,6 @@
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@@ -268,66 +98,6 @@
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-            "version": "2019-10-22T17:46:02.061000Z",
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@@ -341,66 +111,6 @@
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diff --git a/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json b/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
index 4c2a6e03e..9dfd6045e 100644
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+++ b/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
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diff --git a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
index b5e4efd52..442cae10b 100644
--- a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
+++ b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
@@ -1,15 +1,5 @@
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diff --git a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
index c38969247..a236da3ca 100644
--- a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
+++ b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
@@ -13,106 +13,6 @@
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diff --git a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
index 2bb894db6..c71a6074d 100644
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+++ b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
@@ -1,15 +1,5 @@
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diff --git a/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json b/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
index d2c2c780a..3645044d6 100644
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+++ b/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
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diff --git a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
index 2b8bc08e2..e19b32521 100644
--- a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
+++ b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
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diff --git a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
index 3799d9abb..ed470ffb1 100644
--- a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
+++ b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
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diff --git a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
index b4759e65d..1d3ad2d9f 100644
--- a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
+++ b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
@@ -1,173 +1,5 @@
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diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
index adc4a5b37..7006933cf 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
@@ -1,161 +1,5 @@
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diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
index ccadf904c..2e84ea6e9 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
@@ -1,161 +1,5 @@
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diff --git a/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
index 5049d85d9..2291d9783 100644
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+++ b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
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diff --git a/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
index 3026047d2..f5c4700ed 100644
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+++ b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
@@ -1,185 +1,5 @@
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diff --git a/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
index a48a0e666..dfc852edc 100644
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+++ b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
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diff --git a/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
index 38d771b2a..075390d03 100644
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+++ b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
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diff --git a/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json b/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
index bf3b5d476..67955da34 100644
--- a/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
+++ b/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
@@ -1,101 +1,5 @@
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diff --git a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
index fe1e5410a..1cc9b3a28 100644
--- a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
+++ b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
@@ -1,689 +1,5 @@
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diff --git a/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
index fee499f6a..7dd5e31d0 100644
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+++ b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
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diff --git a/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
index 2c7c08e60..de01304f7 100644
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+++ b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
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diff --git a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
index 08cea3d03..517dddd95 100644
--- a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
+++ b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
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diff --git a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
index 4e5fb7422..b683e3716 100644
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+++ b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
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-            "crc32c": "d17760bf",
-            "indexed": true,
-            "name": "process_2.json",
-            "s3_etag": "3b07b1ac3649f1d21d31ebc3606c31be",
-            "sha1": "0739d5adda8ca0311ab23595f8928a9156e1351d",
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@@ -812,4 +608,4 @@
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     "stitched": []
-}
+}
\ No newline at end of file
diff --git a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
index c62f1f4c6..5dcaa6fb6 100644
--- a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
+++ b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
@@ -1,365 +1,5 @@
 {
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-            "crc32c": "744b6296",
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-            "name": "process_2.json",
-            "s3_etag": "090d4f86fdd5d36e04fd771afc24f84d",
-            "sha1": "01f1515381d1258a57c62cef0e26c1dba726e4c6",
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-            "uuid": "85b60548-5e15-4efa-8baa-966f0de7d11c",
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diff --git a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
index 97dd29d26..d0772b9d5 100644
--- a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
+++ b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
@@ -1,35 +1,5 @@
 {
     "manifest": [
-        {
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-            "uuid": "003cb4a8-9871-488f-9042-820504991f17",
-            "version": "2020-08-13T10:24:31.885000Z",
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
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-            "version": "2021-02-09T01:30:00.000000Z",
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             "name": "FCAImmP7316894_S1_L001_I1_001.fastq.gz",
             "uuid": "01824e76-505c-4e99-9ffd-bc1b5f56f726",
@@ -43,36 +13,6 @@
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             "s3_etag": "2a0329a71e83818c5f8e51fa091c5d20-39"
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-            "version": "2020-08-13T10:24:31.566000Z",
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             "name": "FCAImmP7352193_S1_L001_R2_001.fastq.gz",
             "uuid": "0526e3df-0747-40fb-b4be-99c8813deefd",
@@ -86,66 +26,6 @@
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-            "version": "2020-08-13T10:24:32.576000Z",
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-            "version": "2020-08-13T10:24:32.055000Z",
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-            "version": "2021-02-09T01:30:00.000000Z",
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             "name": "FCAImmP7316890_S1_L001_R1_001.fastq.gz",
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@@ -159,46 +39,6 @@
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         {
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             "uuid": "0a80f21f-3212-596b-9367-f7211c554c7d",
@@ -221,26 +61,6 @@
             "crc32c": "792b4a5d",
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             "uuid": "0c3e7565-d5bc-44ed-8b1c-a9446150f274",
@@ -265,56 +85,6 @@
             "crc32c": "9a0339f5",
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-            "version": "2020-08-13T10:24:30.913000Z",
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@@ -339,46 +109,6 @@
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@@ -403,16 +133,6 @@
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@@ -426,36 +146,6 @@
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@@ -480,16 +170,6 @@
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@@ -514,36 +194,6 @@
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@@ -555,16 +205,6 @@
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@@ -576,26 +216,6 @@
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-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 327,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "analysis_file_80.json",
-            "uuid": "ff3b3d1c-2ba9-50a9-9ca7-0558012cbe7d",
-            "version": "2021-02-09T01:30:00.000000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 327,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "sequence_file_119.json",
-            "uuid": "ffba13e2-0937-49b3-961a-2ce3055ad5c6",
-            "version": "2020-08-13T10:24:32.637000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 614,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "cell_suspension_39.json",
-            "uuid": "ffe830d9-c586-47d1-9bb4-33baed6dcdc7",
-            "version": "2020-08-13T10:24:31.133000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 574,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
         }
     ],
     "metadata": {
diff --git a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
index 7bdbb3fbd..d3055ed30 100644
--- a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
+++ b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
@@ -1,173 +1,5 @@
 {
     "manifest": [
-        {
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "crc32c": "a6670814",
-            "indexed": true,
-            "name": "cell_suspension_0.json",
-            "s3_etag": "0e44168582f71d0f11b0481b90e825f2",
-            "sha1": "bb6f2ddc26ce22f8da7af9a0b275926580e19b55",
-            "sha256": "4e8fc47be35b4cddfb4b49050d019a0b37253c0d95f97de521891062b4987da5",
-            "size": 853,
-            "uuid": "0432e9a5-604f-4cb7-8571-014eb5fd8ba2",
-            "version": "2019-10-09T15:35:11.150000Z"
-        },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "crc32c": "828918a3",
-            "indexed": true,
-            "name": "specimen_from_organism_0.json",
-            "s3_etag": "e51e349c5b0d57f6ce0fb5ca9268aa4a",
-            "sha1": "09247e163e8b992baf4fa034daa368a10cddbe83",
-            "sha256": "db12c012b8074606a58528588ef674750911179a03383e882d5f5339381dfbc5",
-            "size": 1313,
-            "uuid": "caadf4b5-f5e4-4416-9f04-9c1f902cc601",
-            "version": "2019-10-09T15:32:51.765000Z"
-        },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "crc32c": "be5925f9",
-            "indexed": true,
-            "name": "donor_organism_0.json",
-            "s3_etag": "69dea7e9bf5a3430d75fee85d96a48bd",
-            "sha1": "b2bbc9b07ac554921368e6e8c0af9c9f306b0ba8",
-            "sha256": "c11243d3d24084e443d65aa382b616b67827c18f255e5d38198fbb72a852bcb1",
-            "size": 1519,
-            "uuid": "e66ac278-96b3-4713-9c5f-5c70b1efb6e3",
-            "version": "2019-10-09T15:32:49.737000Z"
-        },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "crc32c": "da02862e",
-            "indexed": true,
-            "name": "sequence_file_0.json",
-            "s3_etag": "274582e91de58e0657489afd7668a71a",
-            "sha1": "91da2798201d64313bbeab91df4058f79da6b75a",
-            "sha256": "6b2a6d9c4f844e810b0fca6a66252038e36860338d01135ce1868f92ecf2b9b8",
-            "size": 755,
-            "uuid": "4015da8b-18d8-4f3c-b2b0-54f0b77ae80a",
-            "version": "2019-10-09T15:52:46.609000Z"
-        },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "crc32c": "ca7c8c28",
-            "indexed": true,
-            "name": "sequence_file_1.json",
-            "s3_etag": "bba08b0b123558c57707122214718f75",
-            "sha1": "38f0d459ed890013739f0e346b05569b3b9d2f8d",
-            "sha256": "5979c6bd607180a39697403dd963771ce52151f6a412b29b014c1c1b2a78d7ea",
-            "size": 755,
-            "uuid": "fa17159e-52ec-4a88-80cf-a3be5e2e9988",
-            "version": "2019-10-09T15:52:49.512000Z"
-        },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/project\"",
-            "crc32c": "ef89ecd4",
-            "indexed": true,
-            "name": "project_0.json",
-            "s3_etag": "6f48b91d5fe66c2b679432e27b71e93b",
-            "sha1": "d95c316e832cc732d2bdcb5ea3bb87a8b957ffee",
-            "sha256": "65b93005fa5752fd6029c3721bf87617af494a494c53b0450000f57d83cde31f",
-            "size": 16327,
-            "uuid": "88ec040b-8705-4f77-8f41-f81e57632f7d",
-            "version": "2019-10-09T15:32:48.934000Z"
-        },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "crc32c": "71d800d1",
-            "indexed": true,
-            "name": "library_preparation_protocol_0.json",
-            "s3_etag": "e2703dd0dc102dc50c0b58ac53235ea2",
-            "sha1": "5ba1336c74d9e025e39fb50e9e7bac2aa6b0c430",
-            "sha256": "bf677b1ca98243a7dc5f173bff7e978fca4e71be34f051126c57aeeeb405d86e",
-            "size": 1220,
-            "uuid": "76a9a285-f79c-4754-bd26-310b80965b8f",
-            "version": "2019-10-09T15:31:15.989000Z"
-        },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "crc32c": "8282b050",
-            "indexed": true,
-            "name": "sequencing_protocol_0.json",
-            "s3_etag": "09a0e7171f3ea49fa441b8e09f0ac769",
-            "sha1": "12613e48c63f2ae8ec31344b165e3129d5040aad",
-            "sha256": "d71e202c9731a2b063376f143a52e44e96b2df28b02f72d3f8a46eb3581a20a5",
-            "size": 833,
-            "uuid": "63afce7b-829a-491d-a6ed-ab27bf3b4fbc",
-            "version": "2019-10-09T15:31:15.893000Z"
-        },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "crc32c": "6c31d2cc",
-            "indexed": true,
-            "name": "dissociation_protocol_0.json",
-            "s3_etag": "697080ed83400e4425fc1853d011f46f",
-            "sha1": "0423cfeef2250547c7e0c7f9b56c0fbcb880ec0a",
-            "sha256": "b806ee15d8ee2eb5ae37858cceb4f0ce4fe8af5dda45c96a4cdd4162f3ce4e13",
-            "size": 810,
-            "uuid": "78b86ffb-3c85-4b24-81ae-af54815bf222",
-            "version": "2019-10-09T15:31:16.106000Z"
-        },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "crc32c": "0e537f55",
-            "indexed": true,
-            "name": "enrichment_protocol_0.json",
-            "s3_etag": "30beafa88e211a28f48ffec5fa73c4e1",
-            "sha1": "def12f5f61990bdea742f5c73ebd5a7718c7f282",
-            "sha256": "e925667947e42905809ecfcb685d5f86d67ab22618bcdf0646c6f190d1609a46",
-            "size": 825,
-            "uuid": "8ec628d3-91d2-46f3-82aa-67c2b831160d",
-            "version": "2019-10-09T15:31:16.008000Z"
-        },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "crc32c": "bc14a506",
-            "indexed": true,
-            "name": "collection_protocol_0.json",
-            "s3_etag": "c39cdf83600485985f468f8545161d56",
-            "sha1": "9b572da3781bcd22bd1e423098931b9c3c7a2bba",
-            "sha256": "266025a360a2c77e292fb9d3ba8856463a83309a784d227cd3f72ec9c6d40479",
-            "size": 1434,
-            "uuid": "a7257865-6a66-472c-bdd1-6314c8a7d4b0",
-            "version": "2019-10-09T15:31:15.965000Z"
-        },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "crc32c": "78bd3ac9",
-            "indexed": true,
-            "name": "process_0.json",
-            "s3_etag": "da342d4085c06ce5e806a60049151754",
-            "sha1": "b74f143b0235d07e47defe87fd3e0d4c71fe577b",
-            "sha256": "e56163596ddc3938cfe86685cd68a1851ac6e7206614a3187e5a44837b2709bc",
-            "size": 467,
-            "uuid": "74fa0d9c-438f-42b7-94c7-7dd63ab67c12",
-            "version": "2019-10-09T15:38:24.184000Z"
-        },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "crc32c": "07b693bb",
-            "indexed": true,
-            "name": "process_1.json",
-            "s3_etag": "58b83e412e0c133863ff8bd647646ff5",
-            "sha1": "2b9b75100f0214be88d49ac6a2e3606710e0890e",
-            "sha256": "bf931deffb81e893a21a4af06014762f32741e5a718837b1723503ed163c7eb2",
-            "size": 447,
-            "uuid": "c6598ea5-a7d0-4898-a640-66eb7aba33a4",
-            "version": "2019-10-09T15:36:21.984000Z"
-        },
-        {
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "crc32c": "f1a3da0b",
-            "indexed": true,
-            "name": "process_2.json",
-            "s3_etag": "c6c6a8dbf6e40c37d4b2e2fad0ed8256",
-            "sha1": "c300798fad0d2fb6dc24e6775a19f0eac459ec85",
-            "sha256": "a4940fe935abba9fac026a81d602a05de686be873d36ae807b09a7f143e00d93",
-            "size": 446,
-            "uuid": "c7070951-ec8a-492f-a7be-354b5670c056",
-            "version": "2019-10-09T15:36:21.507000Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "49a9085f",
diff --git a/test/integration_test.py b/test/integration_test.py
index cb3a1c3fe..9807d488e 100644
--- a/test/integration_test.py
+++ b/test/integration_test.py
@@ -1943,12 +1943,10 @@ def _test_catalog(self, catalog: config.Catalog):
                 self.assertIsInstance(metadata, dict)
                 self.assertIsInstance(links, dict)
                 self.assertIsInstance(stitched, list)
-                manifest_ids = sorted(e['uuid'] for e in manifest if e['indexed'])
                 metadata_ids = {
                     EntityReference.parse(ref).entity_id
                     for ref in metadata.keys()
                 }
-                self.assertListEqual(manifest_ids, sorted(metadata_ids))
                 self.assertIsSubset(set(stitched), metadata_ids)
             elif metadata_plugin_name == 'anvil':
                 self.assertEqual({'entities', 'links'}, bundle_json.keys())
diff --git a/test/service/test_manifest.py b/test/service/test_manifest.py
index c4654d22a..a47c36e12 100644
--- a/test/service/test_manifest.py
+++ b/test/service/test_manifest.py
@@ -367,7 +367,6 @@ def _shared_file_bundle(self, bundle):
             # specimen
             '224d3750-f1f7-5b04-bbce-e23f09eea7d7': new_specimen_id
         }
-        manifest = self._replace_uuids(bundle.manifest, old_to_new)
         metadata = self._replace_uuids(bundle.metadata, old_to_new)
         # Change organ to prevent cell_suspensions aggregating together
         metadata[f'specimen_from_organism/{new_specimen_id}']['organ'] = {
@@ -376,10 +375,9 @@ def _shared_file_bundle(self, bundle):
             'ontology_label': 'lung'
         }
         links = self._replace_uuids(bundle.links, old_to_new)
-        assert isinstance(manifest, list)
         return DSSBundle(fqid=self.bundle_fqid(uuid=old_to_new[bundle.uuid],
                                                version=bundle.version),
-                         manifest=cast(MutableJSONs, manifest),
+                         manifest=cast(MutableJSONs, bundle.manifest),
                          metadata=metadata,
                          links=links)
 

From 4c70d10158ef0a64e489ba943ff8be7f217d66d4 Mon Sep 17 00:00:00 2001
From: Noa Aviel Dove <nadove@ucsc.edu>
Date: Thu, 22 Aug 2024 16:11:09 -0700
Subject: [PATCH 20/20] [p] Convert HCABundle.manifest to dictionary (partial
 #6299)

---
 src/azul/plugins/metadata/hca/bundle.py       |   5 +-
 src/azul/plugins/repository/dss/__init__.py   |   2 +-
 .../plugins/repository/tdr_hca/__init__.py    |  11 +-
 src/humancellatlas/data/metadata/api.py       |  35 +-
 .../data/metadata/helpers/staging_area.py     |   9 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   6 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   6 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |  16 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   6 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   6 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |   8 +-
 ...a3fb4204953.2018-08-03T082009.272868Z.json |  22 +-
 ...318dbb86000.2019-01-03T163633.780215Z.json |  16 +-
 ...61d6da02d44.2019-09-20T103932.395795Z.json |  18 +-
 ...a3fb4204953.2018-03-29T142048.835519Z.json |   8 +-
 ...d019d1c9439.2019-05-15T222432.561000Z.json |  10 +-
 ...08092b2dabe.2019-04-17T175706.867000Z.json |   8 +-
 ...68e20ec4a2e.2019-02-02T065454.662896Z.json |  74 +-
 ...19c1c2d9018.2018-10-07T130111.835234Z.json |   6 +-
 ...406a478d5ab.2018-09-05T182535.846470Z.json |   8 +-
 ...95a3f8deb9c.2019-04-03T103426.471000Z.json | 458 +++++------
 ...720f33a5dde.2019-03-17T220646.332108Z.json |  10 +-
 test/hca_metadata_api/test.py                 |  12 +-
 ...3-5e9d-52cd-b32d-af88edccabfa.dss.hca.json |  56 +-
 ...5-71e2-48ca-a87b-e256938c6a98.dss.hca.json |  47 +-
 ...3-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json | 730 +++++++++---------
 ...c-6778-423d-8fe9-869e2a515d35.dss.hca.json |   9 +-
 ...8-01a0-464a-9599-7375fda3353d.dss.hca.json |  28 +-
 ...8-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json |  29 +-
 ...8-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json |  34 +-
 ...0-eaba-531d-ba9e-db80164d65ef.dss.hca.json |   8 +-
 ...4-fa14-5c6f-a474-a742540108a3.dss.hca.json |   6 +-
 ...5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json |   9 +-
 ...c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json | 388 +++++-----
 ...8-658e-4c51-9de4-a768322f84c5.dss.hca.json |   7 +-
 ...3-93e1-56b4-b857-59497f5d942d.dss.hca.json |   6 +-
 ...a-940e-49b1-9bcc-25699a55b295.dss.hca.json |  37 +-
 ...f-61a7-4504-a57c-fc70f38d5b13.dss.hca.json |  75 +-
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json |  43 +-
 ...5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json |  43 +-
 ...5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json |  18 +-
 ...a-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json | 388 +++++-----
 ...e-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json |  20 +-
 ...8-adab-59a9-b6c4-3a61242cc972.dss.hca.json |   6 +-
 ...e-7554-4b5d-96a2-7df127a7640b.dss.hca.json |   8 +-
 ...4-1075-4bbf-b96a-4d1ede0481b2.dss.hca.json |  69 +-
 ...0.2020-12-10T10:30:00.000000Z.dss.hca.json | 246 +++---
 ...1-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json |   6 +-
 ...f-8346-5420-b7e4-b486f99451a8.dss.hca.json |  14 +-
 ...e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json |   8 +-
 ...1-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json |  10 +-
 ...f-4c01-48d5-a79f-1c5439659da3.dss.hca.json |   8 +-
 ...3-1885-545f-9381-0dab1edf6074.dss.hca.json |  10 +-
 ...e-9a5d-4e3d-ada2-0414b666b880.dss.hca.json |  37 +-
 ...2-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json | 459 +++++------
 ...3-f0ac-417a-8a29-221c77debde8.dss.hca.json |   9 +-
 ...6-ced8-448a-8e45-1fc7846d8995.dss.hca.json |   8 +-
 ...d.2018-11-02T11:33:44.698028Z.dss.hca.json |   9 +-
 ...d.2018-11-04T11:33:44.698028Z.dss.hca.json |   9 +-
 ...9-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json | 388 +++++-----
 ...8-7eaa-45f4-8077-5a3fb4204953.dss.hca.json |   8 +-
 ...e-9b7b-4800-8977-fe7c94e131df.dss.hca.json |   7 +-
 ...9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json | 376 ++++-----
 ...4-dc9f-439e-af29-f8eb75b0729d.dss.hca.json |   9 +-
 ...4-9a58-4763-9e66-59894efbdaa8.dss.hca.json |  13 +-
 ...d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json |  71 +-
 ...f-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json |   6 +-
 ...1-4766-4210-966c-f9ee25d19190.dss.hca.json |  43 +-
 ...a-2b51-4419-9cde-34df44c6458a.dss.hca.json |   9 +-
 ...e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json |  75 +-
 ...4-6b80-4eed-97c9-4984de81a47c.dss.hca.json | 575 +++++++-------
 ...7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json |  14 +-
 ...b-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json |  37 +-
 ...7-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json | 406 +++++-----
 ...f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json |   8 +-
 test/indexer/test_indexer.py                  |   2 +-
 test/integration_test.py                      |   2 +-
 test/service/test_manifest.py                 |  17 +-
 78 files changed, 2873 insertions(+), 2850 deletions(-)

diff --git a/src/azul/plugins/metadata/hca/bundle.py b/src/azul/plugins/metadata/hca/bundle.py
index 6af8e81fd..1bdb4597c 100644
--- a/src/azul/plugins/metadata/hca/bundle.py
+++ b/src/azul/plugins/metadata/hca/bundle.py
@@ -15,7 +15,6 @@
 from azul.types import (
     JSON,
     MutableJSON,
-    MutableJSONs,
 )
 
 log = logging.getLogger(__name__)
@@ -23,7 +22,7 @@
 
 @attrs.define(kw_only=True)
 class HCABundle(Bundle[BUNDLE_FQID], ABC):
-    manifest: MutableJSONs
+    manifest: MutableJSON
     """
     Each item of the `manifest` attribute's value has this shape:
     {
@@ -62,7 +61,7 @@ def from_json(cls, fqid: BUNDLE_FQID, json_: JSON) -> 'Bundle':
         metadata = json_['metadata']
         links = json_['links']
         stitched = json_['stitched']
-        assert isinstance(manifest, list), manifest
+        assert isinstance(manifest, dict), manifest
         assert isinstance(metadata, dict), metadata
         assert isinstance(links, dict), links
         assert isinstance(stitched, list), stitched
diff --git a/src/azul/plugins/repository/dss/__init__.py b/src/azul/plugins/repository/dss/__init__.py
index f250d46a5..43948604a 100644
--- a/src/azul/plugins/repository/dss/__init__.py
+++ b/src/azul/plugins/repository/dss/__init__.py
@@ -140,7 +140,7 @@ def list_bundles(self,
     def fetch_bundle(self, bundle_fqid: DSSBundleFQID) -> DSSBundle:
         assert False, 'DSS is EOL'
         # noinspection PyUnreachableCode
-        return DSSBundle(fqid=bundle_fqid, manifest=[], metadata={}, links={})
+        return DSSBundle(fqid=bundle_fqid, manifest={}, metadata={}, links={})
 
     def dss_subscription_query(self, prefix: str) -> JSON:
         return {
diff --git a/src/azul/plugins/repository/tdr_hca/__init__.py b/src/azul/plugins/repository/tdr_hca/__init__.py
index 3ed3139e3..f06b6526f 100644
--- a/src/azul/plugins/repository/tdr_hca/__init__.py
+++ b/src/azul/plugins/repository/tdr_hca/__init__.py
@@ -192,7 +192,8 @@ def add_entity(self,
             self.stitched.add(entity.entity_id)
         if entity.entity_type.endswith('_file'):
             descriptor = json.loads(row['descriptor'])
-            self._add_manifest_entry(name=row['file_name'],
+            self._add_manifest_entry(entity,
+                                     name=row['file_name'],
                                      uuid=descriptor['file_id'],
                                      version=descriptor['file_version'],
                                      size=descriptor['size'],
@@ -224,6 +225,7 @@ def add_entity(self,
     _suffix = 'tdr.'
 
     def _add_manifest_entry(self,
+                            entity: EntityReference,
                             *,
                             name: str,
                             uuid: str,
@@ -233,7 +235,7 @@ def _add_manifest_entry(self,
                             dcp_type: str,
                             checksums: Optional[Checksums] = None,
                             drs_uri: Optional[str] = None) -> None:
-        self.manifest.append({
+        self.manifest[str(entity)] = {
             'name': name,
             'uuid': uuid,
             'version': version,
@@ -250,7 +252,7 @@ def _add_manifest_entry(self,
                     **checksums.to_json()
                 }
             )
-        })
+        }
 
     def _parse_drs_uri(self,
                        file_id: Optional[str],
@@ -326,7 +328,7 @@ def _query_unique_sorted(self,
 
     def _emulate_bundle(self, bundle_fqid: TDRBundleFQID) -> TDRHCABundle:
         bundle = TDRHCABundle(fqid=bundle_fqid,
-                              manifest=[],
+                              manifest={},
                               metadata={},
                               links={})
         entities, root_entities, links_jsons = self._stitch_bundles(bundle)
@@ -356,7 +358,6 @@ def _emulate_bundle(self, bundle_fqid: TDRBundleFQID) -> TDRHCABundle:
                     log.error('TDR worker failed to retrieve entities of type %r',
                               entity_type, exc_info=e)
                     raise e
-        bundle.manifest.sort(key=itemgetter('uuid'))
         return bundle
 
     def _stitch_bundles(self,
diff --git a/src/humancellatlas/data/metadata/api.py b/src/humancellatlas/data/metadata/api.py
index 5aefe26d4..812b04156 100644
--- a/src/humancellatlas/data/metadata/api.py
+++ b/src/humancellatlas/data/metadata/api.py
@@ -34,6 +34,7 @@
 )
 from azul.collections import (
     OrderedSet,
+    adict,
     dict_merge,
 )
 
@@ -43,7 +44,6 @@
 from azul.types import (
     JSON,
     MutableJSON,
-    MutableJSONs,
     is_optional,
 )
 from humancellatlas.data.metadata.age_range import (
@@ -747,7 +747,7 @@ class File(LinkedEntity):
 
     def __init__(self,
                  json: JSON,
-                 manifest: Mapping[str, ManifestEntry]):
+                 manifest_entry: ManifestEntry):
         super().__init__(json)
         content = json.get('content', json)
         # '/' was once forbidden in file paths and was encoded with '!'. Now
@@ -756,7 +756,7 @@ def __init__(self,
         core = content['file_core']
         core['file_name'] = core['file_name'].replace('!', '/')
         self.format = lookup(core, 'format', 'file_format')
-        self.manifest_entry = manifest[core['file_name']]
+        self.manifest_entry = manifest_entry
         self.content_description = {ontology_label(cd) for cd in core.get('content_description', [])}
         self.file_source = core.get('file_source')
         self.from_processes = dict()
@@ -789,8 +789,8 @@ class SequenceFile(File):
 
     def __init__(self,
                  json: JSON,
-                 manifest: Mapping[str, ManifestEntry]):
-        super().__init__(json, manifest)
+                 manifest_entry: ManifestEntry):
+        super().__init__(json, manifest_entry)
         content = json.get('content', json)
         self.read_index = content['read_index']
         self.lane_index = content.get('lane_index')
@@ -807,8 +807,8 @@ class AnalysisFile(File):
 
     def __init__(self,
                  json: JSON,
-                 manifest: Mapping[str, ManifestEntry]):
-        super().__init__(json, manifest)
+                 manifest_entry: ManifestEntry):
+        super().__init__(json, manifest_entry)
         content = json.get('content', json)
         self.matrix_cell_count = content.get('matrix_cell_count')
 
@@ -914,29 +914,30 @@ class Bundle:
     def __init__(self,
                  uuid: str,
                  version: str,
-                 manifest: MutableJSONs,
-                 metadata: Mapping[str, JSON],
+                 manifest: Mapping[str, MutableJSON],
+                 metadata: Mapping[str, MutableJSON],
                  links_json: JSON,
                  stitched_entity_ids: Collection[str] = ()):
         self.uuid = UUID4(uuid)
         self.version = version
-        self.manifest = {m.name: m for m in map(ManifestEntry, manifest)}
+        self.manifest = {ref: ManifestEntry(e) for ref, e in manifest.items()}
         self.stitched = frozenset(map(UUID4, stitched_entity_ids))
 
-        json_by_core_cls: MutableMapping[type[E], list[JSON]] = defaultdict(list)
+        entity_args_by_core_cls: MutableMapping[type[E], list[dict]] = defaultdict(list)
         for key, json in metadata.items():
             schema_name = EntityReference.parse(key).entity_type
             entity_cls = entity_types[schema_name]
             core_cls = core_types[entity_cls]
-            json_by_core_cls[core_cls].append(json)
+            args = adict(json=json,
+                         manifest_entry=self.manifest.get(key))
+            entity_args_by_core_cls[core_cls].append(args)
 
         def from_json_vx(core_cls: type[E],
-                         **kwargs
                          ) -> MutableMapping[UUID4, E]:
-            json_entities = json_by_core_cls[core_cls]
+            args_list = entity_args_by_core_cls[core_cls]
             entities = (
-                core_cls.from_json(entity, **kwargs)
-                for entity in json_entities
+                core_cls.from_json(**args)
+                for args in args_list
             )
             return {entity.document_id: entity for entity in entities}
 
@@ -944,7 +945,7 @@ def from_json_vx(core_cls: type[E],
         self.biomaterials = from_json_vx(Biomaterial)
         self.processes = from_json_vx(Process)
         self.protocols = from_json_vx(Protocol)
-        self.files = from_json_vx(File, manifest=self.manifest)
+        self.files = from_json_vx(File)
 
         self.entities = {**self.projects, **self.biomaterials, **self.processes, **self.protocols, **self.files}
 
diff --git a/src/humancellatlas/data/metadata/helpers/staging_area.py b/src/humancellatlas/data/metadata/helpers/staging_area.py
index c6a0cd651..7bda07e3e 100644
--- a/src/humancellatlas/data/metadata/helpers/staging_area.py
+++ b/src/humancellatlas/data/metadata/helpers/staging_area.py
@@ -35,7 +35,6 @@
 from azul.types import (
     JSON,
     MutableJSON,
-    MutableJSONs,
 )
 from humancellatlas.data.metadata.api import (
     Bundle,
@@ -147,12 +146,14 @@ def get_bundle(self, subgraph_id: str) -> Bundle:
         version, manifest, metadata, links = self.get_bundle_parts(subgraph_id)
         return Bundle(subgraph_id, version, manifest, metadata, links)
 
-    def get_bundle_parts(self, subgraph_id: str) -> tuple[str, MutableJSONs, MutableJSON, MutableJSON]:
+    def get_bundle_parts(self,
+                         subgraph_id: str
+                         ) -> tuple[str, MutableJSON, MutableJSON, MutableJSON]:
         """
         Return the components to create a bundle from the staging area
         """
         links_file = self.links[subgraph_id]
-        manifest = []
+        manifest = {}
         metadata = {}
         entity_ids_by_type = self._entity_ids_by_type(subgraph_id)
         for entity_type, entity_ids in entity_ids_by_type.items():
@@ -164,7 +165,7 @@ def get_bundle_parts(self, subgraph_id: str) -> tuple[str, MutableJSONs, Mutable
                 metadata[key] = json_content
                 if entity_type.endswith('_file'):
                     file_manifest = self.descriptors[entity_id].manifest_entry
-                    manifest.append(file_manifest)
+                    manifest[key] = file_manifest
                 else:
                     pass
         return links_file.version, manifest, metadata, links_file.content
diff --git a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index ed036c617..5c2c197ca 100644
--- a/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/1M Immune Cells/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/36d7f891-8a43-4ae4-8472-a34dcb2be643": {
             "crc32c": "29B559F9",
             "sha1": "0587673d7d88efa40a6f4d25d34d2eba14cf8e8b",
             "sha256": "df8b88b6f32f494a53687f79724a6ebd8bbb9c5c0474b9a857d467a0bdb83c2d",
@@ -12,7 +12,7 @@
             "uuid": "c8a4ea32-6d66-48f3-b480-9421743b9c0a",
             "version": "1"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/7b53bae2-2424-44c0-9d80-ad72e8bca136": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 4562cd052..64cebd942 100644
--- a/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/CD4+ cytotoxic T lymphocytes/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/a5806f2e-3f85-486a-9015-e02e5c805285": {
             "crc32c": "E0404A01",
             "sha1": "2d85a788acb4a291d5d13fb918dfbb25d4205de9",
             "sha256": "895c57e9ca2bccbcd306086fd691c55b8e9303a864f1791d9a924b599a3c5313",
@@ -12,7 +12,7 @@
             "uuid": "6ac13e04-d123-42de-bed9-f874b0d2fed2",
             "version": "1"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/cc0d9bf0-6ad5-4489-994b-db26ff761c5a": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 3c5bdfc06..ce1cfe897 100644
--- a/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
+++ b/test/hca_metadata_api/cans/examples/HPSI_human_cerebral_organoids/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/740b2221-41c6-498d-87de-8b2937a5ebed": {
             "crc32c": "E9B38AA1",
             "sha1": "0cec1204162ddfbd3782a1aedce104b373163a9f",
             "sha256": "3f29407965e542a4787b6ab1f32ea3f4162017dc88e294ab3e48ddfe76d476e7",
@@ -12,7 +12,7 @@
             "uuid": "b9f26dd4-dddc-426d-97bb-674e8a0a26a2",
             "version": "1"
         },
-        {
+        "sequence_file/a3f614b3-e6cf-4751-a15d-ff623efea62a": {
             "crc32c": "59378C79",
             "sha1": "d982fed4c2cfd402a145637f1bc1d6364745a506",
             "sha256": "ff3118605c52fd9cb96cb17b96ecc8ec74b72cb75558305e8630568478c03547",
@@ -24,7 +24,7 @@
             "uuid": "1af1df49-a772-4645-bc0e-e8a599ab7121",
             "version": "1"
         },
-        {
+        "sequence_file/56c2a158-e389-40a3-97a7-0f2966a393b8": {
             "crc32c": "8F96945F",
             "sha1": "9cc9baf78624edf0e2c39e48ab7f559f32cfd7ca",
             "sha256": "5a4bc638c31346d1fc4cde4cc8bfaf2341e486ba377edbeafb42a12d49ab6ddc",
@@ -36,7 +36,7 @@
             "uuid": "53c4d13c-d3d3-4294-affe-fd1fecf9d1ef",
             "version": "1"
         },
-        {
+        "supplementary_file/a0eb3208-97e4-498c-993b-20757231b233": {
             "crc32c": "62D4DB03",
             "sha1": "32df780ee719286fccafae4d715607d4f05f3c40",
             "sha256": "6daea9af107bd45e2666ca2ccd1a2a3d98c42b892a7a783093b638508eccb158",
@@ -48,7 +48,7 @@
             "uuid": "c7555cbd-d66c-4f9a-b3f4-23e013da6910",
             "version": "1"
         },
-        {
+        "supplementary_file/e01ee650-58b3-4f3c-8da8-4483700a1eae": {
             "crc32c": "B9D38666",
             "sha1": "095ce1889337b2d8dd5ba3ce21ad85903ebda004",
             "sha256": "a8b3535da8ba62f83c31b238c86a6f4b9848f913c6d35824cef5f955748f1ab9",
@@ -60,7 +60,7 @@
             "uuid": "b5bc3187-6553-4410-b589-ac0f3bb6858f",
             "version": "1"
         },
-        {
+        "supplementary_file/5ab06a61-c66b-4d3d-9889-ab47371a65b0": {
             "crc32c": "47985515",
             "sha1": "b12c361c6d4ebb7c255ddb3e67e3babbd1fe0e25",
             "sha256": "492641dd1bc0004c879d9fe8599e03a455612892df4802f5a1e9c860216777f6",
@@ -72,7 +72,7 @@
             "uuid": "28aa156f-3eee-481b-8849-ab68ddf4b67d",
             "version": "1"
         }
-    ],
+    },
     "metadata": {
         "cell_line/304fadde-e22a-4ff9-9544-f8ec097b6135": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.2/cell_line",
diff --git a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 59154afab..e38da43d8 100644
--- a/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Healthy and type 2 diabetes pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/60471337-a47b-4b9c-95e7-4a19349a5e05": {
             "crc32c": "3D02CDD9",
             "sha1": "b2dad8a028624c456ba43f1f97ac20bba430af74",
             "sha256": "730386f5383a1c82f114ba6cc9ff381f2c47872d6edc4f1342b0b9df9a282795",
@@ -12,7 +12,7 @@
             "uuid": "32d60a94-9f0f-44e3-83c6-eb2d1c1177bd",
             "version": "1"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/1200f5bf-7d45-4f26-865e-b560797f1808": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 1a9caa012..96617dcbf 100644
--- a/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Mouse Melanoma/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/b93897c4-0681-407a-bc0c-fb791b919fa4": {
             "crc32c": "4AEB011B",
             "sha1": "7d5358d6a69ffc7e92ae1bae5e4ae6b9467bc8c5",
             "sha256": "d184ee1517a86acdf92d35e911db3effef0630ab40ef062b094d456d4e6084e1",
@@ -12,7 +12,7 @@
             "uuid": "b2b4819a-e22d-4ed4-a5c8-c04a1dec79eb",
             "version": "1"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/1446ca36-ba75-45ea-b6ab-a80641a88812": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index c5887a11d..1d47965c9 100644
--- a/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Single cell transcriptome analysis of human pancreas/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/baf745cd-9052-4a6c-8c1a-919390062c09": {
             "crc32c": "30F94925",
             "sha1": "472dd1bf4a1e942cbfc6ad79687e2a2ca8f72c74",
             "sha256": "b474913c2db1d26a3d8ab9f37c59ac7e1768b2c628b4e250d0dae0c942adc677",
@@ -12,7 +12,7 @@
             "uuid": "a4f16d4f-cdd7-46f4-8ead-42155d059f23",
             "version": "1"
         },
-        {
+        "sequence_file/0494ee09-b1e2-437a-986f-06d5df4a6858": {
             "crc32c": "3727801A",
             "sha1": "98b1bcf334aae2a06b973565497b16b092b5fc7e",
             "sha256": "a58cc9dff7f585b8ddc40c56c60219b9c61f76fe210e357d2761ca6cea0693f9",
@@ -24,7 +24,7 @@
             "uuid": "26f05d68-8700-40a4-8c5f-173cad377f22",
             "version": "1"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/c61125ab-d5e0-4d93-b0a7-2deac1729f65": {
             "describedBy": "http://schema.dev.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json
index 39103a9a5..4bb974624 100644
--- a/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
+++ b/test/hca_metadata_api/cans/examples/Tissue stability/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-08-03T082009.272868Z.json	
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/4d3839bf-e39f-4136-92a4-6f7009e88567": {
             "crc32c": "5E314552",
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@@ -12,7 +12,7 @@
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@@ -24,7 +24,7 @@
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@@ -36,7 +36,7 @@
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@@ -48,7 +48,7 @@
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@@ -60,7 +60,7 @@
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@@ -72,7 +72,7 @@
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@@ -84,7 +84,7 @@
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@@ -96,7 +96,7 @@
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@@ -108,7 +108,7 @@
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         }
-    ],
+    },
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diff --git a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
index 6b6f241fe..1904c588e 100644
--- a/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
+++ b/test/hca_metadata_api/cans/prod/6b498499-c5b4-452f-9ff9-2318dbb86000.2019-01-03T163633.780215Z.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
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+    "manifest": {
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@@ -12,7 +12,7 @@
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             "version": "2019-01-03T163557.783237Z"
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@@ -24,7 +24,7 @@
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@@ -36,7 +36,7 @@
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@@ -48,7 +48,7 @@
             "uuid": "83361a8e-5029-45fd-9705-68e5a9bb4074",
             "version": "2019-01-03T163558.501100Z"
         },
-        {
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@@ -60,7 +60,7 @@
             "uuid": "f633ef07-9c42-4771-9057-16f4adfb2350",
             "version": "2019-01-03T163558.748211Z"
         },
-        {
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@@ -72,7 +72,7 @@
             "uuid": "d2eedcf0-e06b-4975-99f8-f3c810ca1e39",
             "version": "2019-01-03T163559.110502Z"
         }
-    ],
+    },
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diff --git a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
index 590e31ac2..3b91c0675 100644
--- a/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
+++ b/test/hca_metadata_api/cans/prod/86e7b58e-b9f0-4020-8b34-c61d6da02d44.2019-09-20T103932.395795Z.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
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@@ -12,7 +12,7 @@
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@@ -24,7 +24,7 @@
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@@ -36,7 +36,7 @@
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         },
-        {
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@@ -48,7 +48,7 @@
             "uuid": "8e71749b-d445-409a-bc53-ba359438df69",
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-        {
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@@ -60,7 +60,7 @@
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@@ -72,7 +72,7 @@
             "uuid": "deb6c7db-8ed1-4c87-ab39-44c3499e8499",
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         },
-        {
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@@ -84,7 +84,7 @@
             "uuid": "58b2c404-62c7-46cc-912f-99a5731cd8e5",
             "version": "2019-09-20T104009.214107Z"
         }
-    ],
+    },
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diff --git a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
index 7d7ed0794..29664b620 100644
--- a/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
+++ b/test/hca_metadata_api/cans/prod/b2216048-7eaa-45f4-8077-5a3fb4204953.2018-03-29T142048.835519Z.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/d2f32681-9c1a-4dfd-b506-c24327afb8d1": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "f93b9d00",
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@@ -12,7 +12,7 @@
             "uuid": "d2f32681-9c1a-4dfd-b506-c24327afb8d1",
             "version": "2018-03-29T142044.370144Z"
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-        {
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@@ -24,7 +24,7 @@
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             "version": "2018-03-29T142045.025802Z"
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-    ],
+    },
     "metadata": {
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diff --git a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
index f7ed54de1..bb95ea3ca 100644
--- a/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
+++ b/test/hca_metadata_api/cans/prod/cc0b5aa4-9f66-48d2-aa4f-ed019d1c9439.2019-05-15T222432.561000Z.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
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+    "manifest": {
+        "sequence_file/61fd5348-92c5-446b-a57a-746330cebf76": {
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@@ -12,7 +12,7 @@
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             "version": "2019-05-16T015324.490566Z"
         },
-        {
+        "supplementary_file/e738a267-87fc-4070-abc7-b3be6442c6d0": {
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@@ -24,7 +24,7 @@
             "uuid": "6578c322-7060-4c82-8469-9e54100e6b44",
             "version": "2019-05-16T015325.007527Z"
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-        {
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@@ -36,7 +36,7 @@
             "uuid": "cd8e02d1-d0f9-4094-9a31-329931df60dc",
             "version": "2019-05-16T015325.251968Z"
         }
-    ],
+    },
     "metadata": {
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diff --git a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
index 27c2bd7f1..1fbfd0b77 100644
--- a/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
+++ b/test/hca_metadata_api/cans/prod/ffee3a9b-14de-4dda-980f-c08092b2dabe.2019-04-17T175706.867000Z.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
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+    "manifest": {
+        "sequence_file/a31d51c9-7354-4c8c-91e6-a9d2a2e10616": {
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             "crc32c": "9e612174",
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@@ -12,7 +12,7 @@
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-        {
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@@ -24,7 +24,7 @@
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+    },
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diff --git a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
index 843085449..8b3aa37ba 100644
--- a/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
+++ b/test/hca_metadata_api/cans/prod/ffee7f29-5c38-461a-8771-a68e20ec4a2e.2019-02-02T065454.662896Z.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
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+    "manifest": {
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             "crc32c": "82ad16f4",
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@@ -12,7 +12,7 @@
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             "version": "2019-02-02T065434.636713Z"
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-        {
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@@ -24,7 +24,7 @@
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             "version": "2019-02-02T065434.962270Z"
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-        {
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@@ -36,7 +36,7 @@
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-        {
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@@ -48,7 +48,7 @@
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+        "analysis_file/b70e4907-383c-4466-a244-3e7ce9890dae": {
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@@ -60,7 +60,7 @@
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@@ -72,7 +72,7 @@
             "uuid": "78e49bf5-c92b-4663-bc12-6e838ad63040",
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@@ -84,7 +84,7 @@
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             "content-type": "text/csv; dcp-type=data",
             "crc32c": "202ef83a",
             "indexed": false,
@@ -96,7 +96,7 @@
             "uuid": "b263ebdf-6585-473a-a3eb-a19588b43e35",
             "version": "2019-02-02T065437.247604Z"
         },
-        {
+        "analysis_file/828d7e40-4f6b-42e1-8cd2-6ddccb5b0e6c": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "0e0c45c6",
             "indexed": false,
@@ -108,7 +108,7 @@
             "uuid": "8fdc9b77-6b95-4149-91b6-1ed529eb75af",
             "version": "2019-02-02T065437.646451Z"
         },
-        {
+        "analysis_file/6804b943-fda7-4e8f-bfba-23e368843e63": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "cd082d61",
             "indexed": false,
@@ -120,7 +120,7 @@
             "uuid": "a08fbac2-47d0-426d-9b62-94f60792c554",
             "version": "2019-02-02T065438.217456Z"
         },
-        {
+        "analysis_file/aeb5aebe-9e45-4c9d-931a-883f8fa71225": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "4bb6bdc9",
             "indexed": false,
@@ -132,7 +132,7 @@
             "uuid": "e274aff4-2348-4d25-a69f-aa5e30f50529",
             "version": "2019-02-02T065438.572940Z"
         },
-        {
+        "analysis_file/7c5a87c1-e3b6-42aa-8d68-0f534ded7d2d": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "99822758",
             "indexed": false,
@@ -144,7 +144,7 @@
             "uuid": "b426e03c-0f98-4b9e-838b-b6fe67e35a0a",
             "version": "2019-02-02T065439.061311Z"
         },
-        {
+        "analysis_file/87bd704c-3d36-4620-bdf2-5ad28c5a3d56": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "d9e787ec",
             "indexed": false,
@@ -156,7 +156,7 @@
             "uuid": "f467b2b5-d0d5-4c2c-a253-1f9f64629e3b",
             "version": "2019-02-02T065439.579077Z"
         },
-        {
+        "analysis_file/0aa4b2f3-b969-40d7-97f9-f33af0088915": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "01716cae",
             "indexed": false,
@@ -168,7 +168,7 @@
             "uuid": "70d8b64f-a333-4ac3-8b63-17ba0fb8ef64",
             "version": "2019-02-02T065440.809043Z"
         },
-        {
+        "analysis_file/697a869d-079b-48d4-9a7d-c04cf05dd0a9": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "c2d024b3",
             "indexed": false,
@@ -180,7 +180,7 @@
             "uuid": "28d29046-bdb9-4b70-bb18-f4e8e577e26c",
             "version": "2019-02-02T065441.191549Z"
         },
-        {
+        "analysis_file/6d928f58-2e83-46a0-84a2-d08744a42abd": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "0d996a3f",
             "indexed": false,
@@ -192,7 +192,7 @@
             "uuid": "4bf077f4-ca44-48db-a1ec-fe8ee8a78ba6",
             "version": "2019-02-02T065442.065089Z"
         },
-        {
+        "analysis_file/cc958050-fd69-4919-8529-6f91552ce0ea": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "c9e4f397",
             "indexed": false,
@@ -204,7 +204,7 @@
             "uuid": "ee682f7d-5153-4383-8820-7c382fea111a",
             "version": "2019-02-02T065442.936752Z"
         },
-        {
+        "analysis_file/0a5730dc-eeeb-4f25-bcc7-24cb7d15ac01": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "f8813cc8",
             "indexed": false,
@@ -216,7 +216,7 @@
             "uuid": "1ac59e2e-ac4c-4bc0-a88a-fcfa8ff9e554",
             "version": "2019-02-02T065443.721413Z"
         },
-        {
+        "analysis_file/42fffad8-d47d-4da5-8318-45b0f5577c08": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "444a7707",
             "indexed": false,
@@ -228,7 +228,7 @@
             "uuid": "c736ed67-6c4e-4a9c-a4e0-42e1bb8e0fa7",
             "version": "2019-02-02T065444.065526Z"
         },
-        {
+        "analysis_file/2842a995-c205-4d80-959f-fcb9ff8719ee": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "f35d7e55",
             "indexed": false,
@@ -240,7 +240,7 @@
             "uuid": "f1db2924-0210-4e97-9a24-302c61ad237f",
             "version": "2019-02-02T065444.301965Z"
         },
-        {
+        "analysis_file/90d148ed-a6eb-44c3-a398-df29459943ff": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "067c801b",
             "indexed": false,
@@ -252,7 +252,7 @@
             "uuid": "271f3b5a-549a-41dc-be0f-31b024f8be2b",
             "version": "2019-02-02T065444.467750Z"
         },
-        {
+        "analysis_file/269a143b-a2c2-40cd-9394-41a13321581d": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "88068bce",
             "indexed": false,
@@ -264,7 +264,7 @@
             "uuid": "25122289-69e6-49ec-b2f7-34f8f0197fe1",
             "version": "2019-02-02T065444.766955Z"
         },
-        {
+        "analysis_file/1dda8255-de1c-4bfa-aa79-dbc501d3a112": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "5825e083",
             "indexed": false,
@@ -276,7 +276,7 @@
             "uuid": "45cc3e84-7d4f-4fdc-b3f1-4fe5f3913c81",
             "version": "2019-02-02T065444.968166Z"
         },
-        {
+        "analysis_file/d76f404c-d294-49f2-bfd5-d475e08fa783": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "38a3821e",
             "indexed": false,
@@ -288,7 +288,7 @@
             "uuid": "d8146b44-678e-4954-8a88-c796b21ff424",
             "version": "2019-02-02T065445.333721Z"
         },
-        {
+        "analysis_file/3f672b26-ea2f-4e94-ba77-f463c3cb7c38": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "afce17ed",
             "indexed": false,
@@ -300,7 +300,7 @@
             "uuid": "f4bb3e61-373c-4266-a55b-3c212a75d660",
             "version": "2019-02-02T065445.564680Z"
         },
-        {
+        "analysis_file/4bc5b41c-9fea-4baa-9bf9-75fa4f4a9818": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "c6565f75",
             "indexed": false,
@@ -312,7 +312,7 @@
             "uuid": "9f9fd74e-59e3-4f7b-be1a-13ab4fef6bfd",
             "version": "2019-02-02T065445.798613Z"
         },
-        {
+        "analysis_file/3e44e8f9-e76d-4158-a7af-eeb9602cf8cc": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "c0b4fc1c",
             "indexed": false,
@@ -324,7 +324,7 @@
             "uuid": "69635c16-9520-440e-a38e-3f618b1697d8",
             "version": "2019-02-02T065446.025189Z"
         },
-        {
+        "analysis_file/3fe1e9e8-1b0f-4683-a402-ae970b33f144": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "80af448b",
             "indexed": false,
@@ -336,7 +336,7 @@
             "uuid": "e0130298-cda9-412e-9c80-aad41273e0aa",
             "version": "2019-02-02T065446.267656Z"
         },
-        {
+        "analysis_file/e53c14f5-1a4f-44d6-9773-53faac32233b": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "f282f971",
             "indexed": false,
@@ -348,7 +348,7 @@
             "uuid": "1b685fee-669b-4f9d-b2d5-2f193e24fb29",
             "version": "2019-02-02T065446.482201Z"
         },
-        {
+        "analysis_file/7a26e63d-fcf2-419a-a945-bca9e539480f": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "b89e6723",
             "indexed": false,
@@ -360,7 +360,7 @@
             "uuid": "247a7408-946c-4d2e-bbda-e79f27541347",
             "version": "2019-02-02T065446.804119Z"
         },
-        {
+        "analysis_file/644b261b-450e-453c-bb5e-0498a1cf5804": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "38f2e38c",
             "indexed": false,
@@ -372,7 +372,7 @@
             "uuid": "133e7526-bc1e-4731-b304-942b2302b260",
             "version": "2019-02-02T065447.022845Z"
         },
-        {
+        "analysis_file/b367129a-e83f-4a2b-9278-b5f7930ad457": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "88035931",
             "indexed": false,
@@ -384,7 +384,7 @@
             "uuid": "30d5a0b7-f83c-4834-a708-bfa5f33a1e79",
             "version": "2019-02-02T065447.365605Z"
         },
-        {
+        "analysis_file/6d4785d0-bd42-4f98-8f7a-ab9ca8fcab39": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "d3733841",
             "indexed": false,
@@ -396,7 +396,7 @@
             "uuid": "e0c065fb-3297-44e8-ab6b-cb6aa461bedc",
             "version": "2019-02-02T065447.635894Z"
         },
-        {
+        "sequence_file/c15ee840-4702-45f7-bb19-693de19a742a": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "4df5f693",
             "indexed": false,
@@ -408,7 +408,7 @@
             "uuid": "e3a876c0-814d-48d0-ab33-5de0ca400125",
             "version": "2019-02-01T115352.287395Z"
         },
-        {
+        "sequence_file/5f5d9c84-3565-4398-886c-2e50ad4c3964": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "aa8d705d",
             "indexed": false,
@@ -420,7 +420,7 @@
             "uuid": "54d7fff5-6a9e-44c9-b515-ea28a9b1940f",
             "version": "2019-02-01T115352.858162Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/9ea49dd1-7511-48f8-be12-237e3d0690c0": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.6.6/cell_suspension",
diff --git a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
index 206faab34..10a4f1ed3 100644
--- a/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
+++ b/test/hca_metadata_api/cans/staging/68bdc676-c442-4581-923e-319c1c2d9018.2018-10-07T130111.835234Z.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/f3d5c7cb-7ab4-4903-8e0e-dc942121fe27": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "a3f89844",
             "indexed": false,
@@ -12,7 +12,7 @@
             "uuid": "9dee7111-d743-43a1-b768-118614bf7987",
             "version": "2018-10-07T130110.968810Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/ef97eef1-a436-4462-a152-1a2b86ee8831": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
index 8b230fe64..38fcbca31 100644
--- a/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
+++ b/test/hca_metadata_api/cans/staging/70184761-70fc-4b80-8c48-f406a478d5ab.2018-09-05T182535.846470Z.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/20474552-c0a3-471e-8fa0-d3c5aa05c017": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "4ef74578",
             "indexed": false,
@@ -12,7 +12,7 @@
             "uuid": "2580e8f2-f2f8-4292-b14d-c9ae8bd25a4e",
             "version": "2018-09-05T182535.418417Z"
         },
-        {
+        "sequence_file/177a9d2c-99d4-4fb6-aab7-5869923e9d6a": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "69987b3e",
             "indexed": false,
@@ -24,7 +24,7 @@
             "uuid": "a53ef014-85f1-4ea8-b24a-454328724e77",
             "version": "2018-09-05T182535.627826Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/a31a0e93-5be4-44b8-b152-9e25b066e1e5": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.4.0/cell_suspension",
diff --git a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
index c50b514f7..c861381dc 100644
--- a/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
+++ b/test/hca_metadata_api/cans/staging/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.2019-04-03T103426.471000Z.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "image_file/6baa3aff-b2a5-4e49-82f7-25c108a6107a": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "d1fbf93a",
             "indexed": false,
@@ -12,7 +12,7 @@
             "uuid": "34d230e7-dd9f-4a47-8d5b-23043fe43bc0",
             "version": "2019-04-03T105535.336469Z"
         },
-        {
+        "image_file/06dcfc33-21da-485f-8e50-49d294713a9e": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "88def662",
             "indexed": false,
@@ -24,7 +24,7 @@
             "uuid": "3db743f3-8235-4553-9a70-37dee987dd64",
             "version": "2019-04-03T105535.723353Z"
         },
-        {
+        "image_file/404dd50b-4bc9-4c82-8c18-f53c68eed2fc": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "ad2281ce",
             "indexed": false,
@@ -36,7 +36,7 @@
             "uuid": "13ce8b32-13df-411e-8874-810de85a6d51",
             "version": "2019-04-03T105536.220197Z"
         },
-        {
+        "image_file/5ceb5dc3-9194-494a-b1df-42bb75ab1a04": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "d8b5d806",
             "indexed": false,
@@ -48,7 +48,7 @@
             "uuid": "1eb42fec-c278-43a5-b3a3-b68d998b3a2a",
             "version": "2019-04-03T105536.479486Z"
         },
-        {
+        "image_file/76e52f76-ede7-4088-b7f6-d6e5f6152292": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "3b0cdc15",
             "indexed": false,
@@ -60,7 +60,7 @@
             "uuid": "fe9c7709-3a1c-4548-9578-01e4a63cc9d3",
             "version": "2019-04-03T105536.745978Z"
         },
-        {
+        "image_file/2e496fe6-f500-4e27-b7f5-3c87fe43bbe5": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "d1935fb2",
             "indexed": false,
@@ -72,7 +72,7 @@
             "uuid": "508e6ec1-6693-4ffb-aa0c-53940a9b1a30",
             "version": "2019-04-03T105537.018211Z"
         },
-        {
+        "image_file/be66141d-84a3-457d-a8d2-2f0da8c91dff": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "817e676f",
             "indexed": false,
@@ -84,7 +84,7 @@
             "uuid": "9d66777d-7af9-4cf2-bcd7-6d4b0cba8fab",
             "version": "2019-04-03T105537.249443Z"
         },
-        {
+        "image_file/680cf532-ef0c-4155-b44d-a6ec3920743a": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "b3be7c25",
             "indexed": false,
@@ -96,7 +96,7 @@
             "uuid": "50b7b8e6-16fa-4e0c-999a-42cab234b1db",
             "version": "2019-04-03T105537.599532Z"
         },
-        {
+        "image_file/08609f14-cf43-4188-b743-4a0b55b17347": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "acf4da3b",
             "indexed": false,
@@ -108,7 +108,7 @@
             "uuid": "c4be485e-8f30-454c-a641-7d0ff3cafb4a",
             "version": "2019-04-03T105537.940591Z"
         },
-        {
+        "image_file/d10827a1-38f7-457d-9c9f-695f2fc7689c": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "527eec28",
             "indexed": false,
@@ -120,7 +120,7 @@
             "uuid": "23fad5c1-d704-479d-b8cc-a629fee2b340",
             "version": "2019-04-03T105538.199379Z"
         },
-        {
+        "image_file/6f8eb2e5-7a0c-4c98-8da0-276457357071": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "60e20c9b",
             "indexed": false,
@@ -132,7 +132,7 @@
             "uuid": "4a9702b6-04e4-409b-a241-42540df7a07f",
             "version": "2019-04-03T105538.500545Z"
         },
-        {
+        "image_file/ca480df3-71bb-4634-8f71-b6a75aeb9f05": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "c031ab08",
             "indexed": false,
@@ -144,7 +144,7 @@
             "uuid": "bb22c7d2-a22e-4e97-ab75-5bf44d95aa47",
             "version": "2019-04-03T105538.750403Z"
         },
-        {
+        "image_file/03ae5f5e-65ac-4491-b0ce-eefc940e0224": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "46b7935c",
             "indexed": false,
@@ -156,7 +156,7 @@
             "uuid": "3047eca0-886e-4989-a220-c35ee497ed62",
             "version": "2019-04-03T105538.997194Z"
         },
-        {
+        "image_file/ff117ecb-767e-4e72-baa9-2bda4fcd3e62": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "6571f990",
             "indexed": false,
@@ -168,7 +168,7 @@
             "uuid": "86df917c-0969-4e27-8f29-ad2b73837818",
             "version": "2019-04-03T105539.261002Z"
         },
-        {
+        "image_file/887f3d73-94d2-44ac-9047-67aca5225882": {
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@@ -2448,7 +2448,7 @@
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@@ -2664,7 +2664,7 @@
             "uuid": "bba231df-4b9b-44fe-a9e9-df314fc8f75d",
             "version": "2019-04-03T105645.222571Z"
         },
-        {
+        "image_file/e5034863-0528-4f55-be95-c8501c29f9fe": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "bd266ca9",
             "indexed": false,
@@ -2676,7 +2676,7 @@
             "uuid": "6c85c7e1-832c-476c-add9-e2cc509f8de0",
             "version": "2019-04-03T105645.515825Z"
         },
-        {
+        "image_file/cc61b14a-59d9-477b-8cb1-43c4ee4cf434": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "1285ec2c",
             "indexed": false,
@@ -2688,7 +2688,7 @@
             "uuid": "9a71aa79-aa5e-41ca-89ed-2d5eaea98840",
             "version": "2019-04-03T105645.832519Z"
         },
-        {
+        "image_file/33d332c9-aefe-4db5-8830-b8daddaed0d2": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "ee12e15f",
             "indexed": false,
@@ -2700,7 +2700,7 @@
             "uuid": "bec2697f-31b6-4db5-888a-024379f3d13f",
             "version": "2019-04-03T105646.096587Z"
         },
-        {
+        "image_file/bb3b6fc7-0902-432d-bad1-6b3f61951314": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "d148a0e3",
             "indexed": false,
@@ -2712,7 +2712,7 @@
             "uuid": "194db0d1-dfca-44d7-9ad7-194a9e091d32",
             "version": "2019-04-03T105646.365296Z"
         },
-        {
+        "image_file/2b734e88-3a33-4c73-92bb-82e0b8f8c13b": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "3c1c81b7",
             "indexed": false,
@@ -2724,7 +2724,7 @@
             "uuid": "57e036f8-063a-47fe-b668-499222390e95",
             "version": "2019-04-03T105646.657106Z"
         }
-    ],
+    },
     "metadata": {
         "imaged_specimen/87f58f88-ef8b-4323-bd19-cde1a2497b59": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/2.0.7/imaged_specimen",
diff --git a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
index 30a021c6e..fce57ca57 100644
--- a/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
+++ b/test/hca_metadata_api/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde.2019-03-17T220646.332108Z.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/6380c3bc-8bc3-459b-aea3-05dd6c0842ef": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "da1a6040",
             "indexed": false,
@@ -12,7 +12,7 @@
             "uuid": "46ab4893-bb4a-43fa-bc86-22f0d89fddf6",
             "version": "2019-03-17T220644.137081Z"
         },
-        {
+        "sequence_file/ceb4dfaa-ecaf-4757-ae54-9d83707f66cc": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "0eee0a0a",
             "indexed": false,
@@ -24,7 +24,7 @@
             "uuid": "2a2b38af-9776-41c8-b643-2e094ac1c58b",
             "version": "2019-03-17T220644.507486Z"
         },
-        {
+        "sequence_file/5201d410-d789-4df6-b3fd-9edac998e5f3": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "51ffe105",
             "indexed": false,
@@ -36,7 +36,7 @@
             "uuid": "04a1ab2c-e522-4d73-a881-effa1d9492d1",
             "version": "2019-03-17T220644.766900Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/74a06f8b-dff1-44d2-b1a6-99e3d14b69d1": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_suspension",
diff --git a/test/hca_metadata_api/test.py b/test/hca_metadata_api/test.py
index fa8398219..6ae9ac707 100644
--- a/test/hca_metadata_api/test.py
+++ b/test/hca_metadata_api/test.py
@@ -391,7 +391,7 @@ def _assert_bundle(self, uuid, version, manifest, metadata, links,
         # fact that dict instances aren't hashable and to ensure that no
         # redundant copies are made.
         self.assertEqual(set(id(f.manifest_entry.json) for f in bundle.files.values()),
-                         set(id(me) for me in manifest if not me['indexed']))
+                         set(id(me) for me in manifest.values() if not me['indexed']))
 
         biomaterials = bundle.biomaterials.values()
 
@@ -695,8 +695,8 @@ def test_missing_mandatory_checksums(self):
             with self.assertRaises(TypeError) as cm:
                 Bundle(uuid=uuid,
                        version='',
-                       manifest=[
-                           {
+                       manifest={
+                           '': {
                                'uuid': uuid,
                                'version': '',
                                'name': '',
@@ -705,7 +705,7 @@ def test_missing_mandatory_checksums(self):
                                'content-type': '',
                                **case
                            }
-                       ],
+                       },
                        metadata={},
                        links_json={})
             self.assertEqual(cm.exception.args[0], 'Property cannot be absent or None')
@@ -717,7 +717,7 @@ def test_name_substitution(self):
         version = '2019-02-02T065454.662896Z'
         manifest, metadata, links = self._canned_bundle('prod', uuid, version)
 
-        files_before = [f['name'] for f in manifest]
+        files_before = [f['name'] for f in manifest.values()]
         with_bang_before = set(f for f in files_before if '!' in f)
         expected_bang_before = {
             '9ea49dd1-7511-48f8-be12-237e3d0690c0.zarr!.zattrs',
@@ -747,7 +747,7 @@ def test_name_substitution(self):
         entity_json_file_names = set(e.json['file_core']['file_name']
                                      for e in bundle.entities.values()
                                      if isinstance(e, (AnalysisFile, SequenceFile)))
-        for files_after in set(bundle.manifest.keys()), entity_json_file_names:
+        for files_after in {e.name for e in bundle.manifest.values()}, entity_json_file_names:
             with_bang_after = set(f1 for f1 in files_after if '!' in f1)
             self.assertEqual(set(), with_bang_after)
             with_slash_after = set(f1 for f1 in files_after if '/' in f1)
diff --git a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
index 0827d6abb..11f6fa185 100644
--- a/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
+++ b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/e0efcd8d-8433-4b40-9eee-11dafb699a5a": {
             "name": "Retina_Wong_scRNA_Sample5_I1.fastq.gz",
             "uuid": "07b45ad4-7797-4c16-bfae-493fb41d6600",
             "version": "2019-09-13T09:16:27.260339Z",
@@ -13,7 +13,7 @@
             "sha256": "cc6bf034743ed5bf781320deeceb119b4584a7854d922b59f05392d6cd5cc737",
             "s3_etag": "b9223d5e376a061971bd23fb78e25fd8-13"
         },
-        {
+        "sequence_file/6d52232d-dc77-4070-bdb1-9bb0ee59d309": {
             "name": "Retina_Wong_scRNA_Sample5_R1.fastq.gz",
             "uuid": "09eb8fc6-9e27-4f08-87c5-bfccf918ee12",
             "version": "2019-09-13T09:16:28.234453Z",
@@ -26,7 +26,7 @@
             "sha256": "62495704a4bb9a99543fd2143ec577d7b4c106c57b7de37d5c8ed9e002152e5d",
             "s3_etag": "e3b61e35217b7ed1526704c92446e18a-47"
         },
-        {
+        "sequence_file/30040306-be5c-48f9-b221-e666e279ab5b": {
             "name": "Retina_Wong_scRNA_Sample4_I1.fastq.gz",
             "uuid": "1985c53a-b78f-4d9e-9563-dffed8207efd",
             "version": "2019-09-13T09:16:23.710869Z",
@@ -39,7 +39,7 @@
             "sha256": "fbb183a7608f5c4b98e0d9a2f4f77b843d24dcd727f0d5e4ea8111de7d9b22b2",
             "s3_etag": "f393918b58d786a89c467455152aa66e-17"
         },
-        {
+        "analysis_file/7a96a0c2-e22a-57ad-ac46-4c2433a63d94": {
             "name": "262f55a3-d03d-49ae-8080-1a6208fddb4f.bam",
             "uuid": "20329887-aab3-55fb-ba2c-e3eb27a20f6d",
             "version": "2021-02-03T20:52:24.000000Z",
@@ -50,7 +50,7 @@
             "crc32c": "c844464d",
             "sha256": "7a1ae83ca759edadf571751156b4482f592bda1224ae3bf8c7baccd1a2373b80"
         },
-        {
+        "sequence_file/f6407a7a-eecc-4735-a96a-b8bb634118e4": {
             "name": "Retina_Wong_scRNA_Sample2_I1.fastq.gz",
             "uuid": "27622c20-c017-4a98-b62c-76035758bc09",
             "version": "2019-09-13T09:16:27.588981Z",
@@ -63,7 +63,7 @@
             "sha256": "4d2a000eb5fe6eac0926812796794f265f1a1438346c30a2d459ddd3a0f3362c",
             "s3_etag": "0f3a2d1294d0e1cb0a2f504adc2aefaf-34"
         },
-        {
+        "sequence_file/b01b2e61-3ebd-48cc-b071-f2e8cb42ff7c": {
             "name": "Retina_Wong_scRNA_Sample1_I1.fastq.gz",
             "uuid": "39ae3998-72a4-41ba-b00f-526bfecb8ca2",
             "version": "2019-09-13T09:16:26.837580Z",
@@ -76,7 +76,7 @@
             "sha256": "979ff8bf675f4a3d56bb83e80e64641656bbfd1b7bfc805023445cf53fdd5450",
             "s3_etag": "ad7a88538e8a9c00b6d904c7eb00318c-32"
         },
-        {
+        "analysis_file/43598186-06cd-5f4b-95d9-fecb0a35d3ab": {
             "name": "ad220152-0eb4-4f85-a03e-c7e81ea3f167.bam",
             "uuid": "3ac6d370-c10b-54a2-a1ed-52f661aae1d7",
             "version": "2021-02-03T20:52:32.000000Z",
@@ -87,7 +87,7 @@
             "crc32c": "f82a27d8",
             "sha256": "874aaeeaf5d963df1fdc30a399250427873d5594457eece6603ae5f085930320"
         },
-        {
+        "sequence_file/15f64718-69cf-462c-9704-e8a1f54c27c8": {
             "name": "Retina_Wong_scRNA_Sample3_R2.fastq.gz",
             "uuid": "3e2b02f8-5b3b-4ab2-8ef4-7ae8a856854e",
             "version": "2019-09-13T09:16:27.026166Z",
@@ -100,7 +100,7 @@
             "sha256": "33ed54a5916930322b59f2e66ef840b7ae347da5fdec6a2443e5dceeb577b8a9",
             "s3_etag": "7d5599e41f686131c8d7da5b5f69f80f-143"
         },
-        {
+        "sequence_file/a7b21a25-e76e-420d-8892-538062bfefbf": {
             "name": "Retina_Wong_scRNA_Sample3_R1.fastq.gz",
             "uuid": "3e3505f9-4f47-402f-bfb8-960af07f91da",
             "version": "2019-09-13T09:16:26.831163Z",
@@ -113,7 +113,7 @@
             "sha256": "d06f4c866cb6f475692f322ae7415a188ae13fc3c37965daa101f73b425a8a47",
             "s3_etag": "fd9244e048c7d9e1f63f113736701ed5-43"
         },
-        {
+        "analysis_file/a7915c55-1d80-5724-9c81-6dd0a9130361": {
             "name": "262f55a3-d03d-49ae-8080-1a6208fddb4f.loom",
             "uuid": "4b611790-d17b-5938-86c4-695480abb4ef",
             "version": "2021-02-03T21:06:32.000000Z",
@@ -124,7 +124,7 @@
             "crc32c": "a9fb633c",
             "sha256": "3acf571a7329dece2fa69d92663bf6ea1cfe662b22e0ac8ab46b89ea8b1b5ba8"
         },
-        {
+        "sequence_file/9f8f5212-0749-460b-9a46-2949dea45d52": {
             "name": "Retina_Wong_scRNA_Sample4_R2.fastq.gz",
             "uuid": "5140b603-8cc1-4566-9043-e68145efbbd6",
             "version": "2019-09-13T09:16:24.192766Z",
@@ -137,7 +137,7 @@
             "sha256": "76f22d617806fffc64137ef2449e1e827a6d889c0b8e6fc0e38274f68c9f556d",
             "s3_etag": "012e21be88b6293dfc864c018f67ccf5-147"
         },
-        {
+        "analysis_file/d90280cc-a294-57de-b350-5234a5278c19": {
             "name": "1116b396-448e-4dd1-b9c9-78357c511e15.loom",
             "uuid": "5a11ed4f-41d1-53b4-9e62-3c0bbd04b4b0",
             "version": "2021-02-03T21:08:31.000000Z",
@@ -148,7 +148,7 @@
             "crc32c": "9d1f0a8c",
             "sha256": "733a4a7db49e1ef08a7f5631f3e658f49233c1d468d6d3da0a3f7c02621fab27"
         },
-        {
+        "sequence_file/52149e21-dcd2-4288-a5eb-e526c3dcf745": {
             "name": "Retina_Wong_scRNA_Sample5_R2.fastq.gz",
             "uuid": "5ceca6a5-2bc0-4b38-908b-01d4fec71d9f",
             "version": "2019-09-13T09:16:28.462542Z",
@@ -161,7 +161,7 @@
             "sha256": "46cc1e1fdd748e40227ccbb1eabd5f6456c7ef31faa934cbcb68a0707cb25427",
             "s3_etag": "a32e912ba25ab2702a47e31082806ee5-189"
         },
-        {
+        "analysis_file/b949e4b6-c3fb-58b4-865b-40cb3ef2b6c6": {
             "name": "1116b396-448e-4dd1-b9c9-78357c511e15.bam",
             "uuid": "640e64f1-6ada-5d12-a772-fe4ed4eeecea",
             "version": "2021-02-03T20:52:27.000000Z",
@@ -172,7 +172,7 @@
             "crc32c": "2ad80e5f",
             "sha256": "45e831be417a5bbf75b7d0a0a1a024ac9d9f22971115fd56f5b0e5b346e87a71"
         },
-        {
+        "analysis_file/70ff6783-333f-5c1b-8208-3b495df95620": {
             "name": "8b81f0c2-3b57-4072-8a10-c169fece543e.bam",
             "uuid": "76fc7a86-572e-5e00-ac87-b55d81a8515d",
             "version": "2021-02-03T20:52:29.000000Z",
@@ -183,7 +183,7 @@
             "crc32c": "a8427ce7",
             "sha256": "7098a7b9661d3be54f376c0e8b63ec7efbf2bf88ec389b79efbd7956f930519d"
         },
-        {
+        "sequence_file/39255288-6791-45b0-ac7e-b3ef4c981a3b": {
             "name": "Retina_Wong_scRNA_Sample4_R1.fastq.gz",
             "uuid": "79f589cb-32a2-4ba6-a091-7c5d820d02df",
             "version": "2019-09-13T09:16:23.982952Z",
@@ -196,7 +196,7 @@
             "sha256": "bb61a115aed93057cbd1dc8fb08e68ed5615cc8dc926a9b3336ea0ad58eef648",
             "s3_etag": "be870140031523af537bbb3861fff77e-44"
         },
-        {
+        "analysis_file/4c866eb3-7470-5ee8-91b9-942246f19fde": {
             "name": "2f8a07c2-4a6b-47ac-a304-0dead66eee9e.bam",
             "uuid": "820c396e-248b-5b4e-91b9-d7801cd9725f",
             "version": "2021-02-03T20:52:12.000000Z",
@@ -207,7 +207,7 @@
             "crc32c": "a068a3b9",
             "sha256": "1ef67647e5113fcbebbf04fa7e57aaa220ae35229a9f28af289708ab4c975298"
         },
-        {
+        "analysis_file/bc111cd3-bf54-57ce-8af1-88f5997a0a9d": {
             "name": "ad220152-0eb4-4f85-a03e-c7e81ea3f167.loom",
             "uuid": "98ab4428-d66a-57b7-a802-83fdec68d744",
             "version": "2021-02-03T21:06:08.000000Z",
@@ -218,7 +218,7 @@
             "crc32c": "72dc7f49",
             "sha256": "c9f957119f9a7d5f7b05d338ea622a7c6f1384bcf6e72d290f1f7738df8f3f86"
         },
-        {
+        "sequence_file/6bd884d2-fccf-4227-8efc-184751527dfb": {
             "name": "Retina_Wong_scRNA_Sample2_R1.fastq.gz",
             "uuid": "9d720856-425d-404f-bb5b-51c225e92dd6",
             "version": "2019-09-13T09:16:27.766043Z",
@@ -231,7 +231,7 @@
             "sha256": "705302cc9b0e08a951d2cca198da496da212426e3f69153381245bbd9cbc2e20",
             "s3_etag": "8276b9dd2ef8b1174cb233d0aaf0f63a-91"
         },
-        {
+        "analysis_file/f51568e8-b84c-504b-82f0-3ad5975d4bcb": {
             "name": "2f8a07c2-4a6b-47ac-a304-0dead66eee9e.loom",
             "uuid": "a301dcb4-6a8f-5ef8-af7e-6a9fe44058e8",
             "version": "2021-02-03T21:12:10.000000Z",
@@ -242,7 +242,7 @@
             "crc32c": "3b799574",
             "sha256": "285d82ac997f24fcd3543a47407bb84ed18babeb0186ecda4b3b208ba98e7a09"
         },
-        {
+        "sequence_file/799f314f-7c6c-4981-be36-8e1310bf38e6": {
             "name": "Retina_Wong_scRNA_Sample3_I1.fastq.gz",
             "uuid": "ad5fed6e-b0e1-40a0-82e8-0cfc2eca0786",
             "version": "2019-09-13T09:16:26.425735Z",
@@ -255,7 +255,7 @@
             "sha256": "700d3f3197a2f3f24273ab664dfa8e06c7a97ee8108c09b01de9e85f04f5390d",
             "s3_etag": "fbb100a856afca4d91f70afb015c2b5b-16"
         },
-        {
+        "sequence_file/1016adeb-cdc3-47d6-a89e-771c763dd2e7": {
             "name": "Retina_Wong_scRNA_Sample2_R2.fastq.gz",
             "uuid": "b9ab7f46-071a-48cf-bc7f-fdb9c8dd0c22",
             "version": "2019-09-13T09:16:27.945734Z",
@@ -268,7 +268,7 @@
             "sha256": "ba581a5282522ad15266c7843b1d18181e923c44f6ad9840184842af252e8f10",
             "s3_etag": "e2d161f5590706c0128c1aa41cc9b3eb-313"
         },
-        {
+        "analysis_file/fec17064-9014-50b0-9e1a-dfaef2fbb4fc": {
             "name": "wong-retina-human-eye-10XV2.loom",
             "uuid": "bd98f428-881e-501a-ac16-24f27a68ce2f",
             "version": "2021-02-11T23:11:45.000000Z",
@@ -279,7 +279,7 @@
             "crc32c": "d1b06ce5",
             "sha256": "6a6483c2e78da77017e912a4d350f141bda1ec7b269f20ca718b55145ee5c83c"
         },
-        {
+        "analysis_file/759bad57-b725-5346-b3ff-9fb80b27cfe7": {
             "name": "8b81f0c2-3b57-4072-8a10-c169fece543e.loom",
             "uuid": "bdd02a5f-2007-56f9-abeb-8c2c5c99a08e",
             "version": "2021-02-03T21:08:27.000000Z",
@@ -290,7 +290,7 @@
             "crc32c": "567bee09",
             "sha256": "52d70178293e01248f66928edaa01191c204e5169fa2b66b2008ddb4b0d4a412"
         },
-        {
+        "sequence_file/33682180-6cdf-4d0c-9fe0-e1c029ac13b2": {
             "name": "Retina_Wong_scRNA_Sample1_R1.fastq.gz",
             "uuid": "d65c128c-3bb7-4da3-8d56-b60007cf8d15",
             "version": "2019-09-13T09:16:27.063168Z",
@@ -303,7 +303,7 @@
             "sha256": "1a22499817f26c307ffe7876e2be5a2bdc9ab8aee2da3c6ca89af2bf3ab903e1",
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             "uuid": "d94b88bc-3507-4644-a221-1c99861895e2",
             "version": "2019-09-13T09:16:27.300840Z",
@@ -316,7 +316,7 @@
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diff --git a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
index 2cd6968d4..94433205b 100644
--- a/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
+++ b/test/indexer/data/02e69c25-71e2-48ca-a87b-e256938c6a98.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
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+    "manifest": {
+        "sequence_file/c87f6dbf-1062-4e72-a19d-db779f1d3e66": {
+
             "name": "mouse_cortex_S2_L002_R1_001.fastq",
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@@ -13,7 +14,7 @@
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+        "analysis_file/c61a76f4-aebe-4a18-b272-e2e78307bb4a": {
             "name": "experiment2_mouse_pbs_scp_metadata.txt",
             "uuid": "04f754f4-1c3c-4eac-a64f-c1a0937cae06",
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@@ -26,7 +27,7 @@
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@@ -39,7 +40,7 @@
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@@ -52,7 +53,7 @@
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@@ -65,7 +66,7 @@
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@@ -78,7 +79,7 @@
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@@ -91,7 +92,7 @@
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             "uuid": "50d634ef-77b0-4339-a9c3-9a83bd9e5ab6",
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@@ -104,7 +105,7 @@
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             "uuid": "59822819-0515-4b9f-beb6-5836aa2df759",
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@@ -117,7 +118,7 @@
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@@ -130,7 +131,7 @@
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@@ -143,7 +144,7 @@
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@@ -156,7 +157,7 @@
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@@ -169,7 +170,7 @@
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@@ -182,7 +183,7 @@
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+        "analysis_file/4d64269d-bd3f-46c1-a179-1c27e1caeb30": {
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@@ -195,7 +196,7 @@
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@@ -208,7 +209,7 @@
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@@ -221,7 +222,7 @@
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@@ -234,7 +235,7 @@
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             "uuid": "d3965eac-1d56-4809-bf64-8291c9bbdf2f",
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@@ -247,7 +248,7 @@
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@@ -260,7 +261,7 @@
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@@ -273,7 +274,7 @@
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diff --git a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
index 73ee6694a..90c95400a 100644
--- a/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
+++ b/test/indexer/data/04836733-0449-4e57-be2e-6f3b8fbdfb12.dss.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
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+    "manifest": {
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@@ -13,7 +13,7 @@
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@@ -26,7 +26,7 @@
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@@ -39,7 +39,7 @@
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@@ -52,7 +52,7 @@
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@@ -65,7 +65,7 @@
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@@ -78,7 +78,7 @@
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@@ -91,7 +91,7 @@
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@@ -104,7 +104,7 @@
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@@ -117,7 +117,7 @@
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@@ -130,7 +130,7 @@
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@@ -143,7 +143,7 @@
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@@ -156,7 +156,7 @@
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@@ -4459,7 +4459,7 @@
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@@ -4472,7 +4472,7 @@
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@@ -4485,7 +4485,7 @@
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@@ -4498,7 +4498,7 @@
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@@ -4511,7 +4511,7 @@
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             "uuid": "f4b0febc-2a23-436f-916c-2ddb328dddd4",
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@@ -4524,7 +4524,7 @@
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@@ -4537,7 +4537,7 @@
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@@ -4550,7 +4550,7 @@
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@@ -4563,7 +4563,7 @@
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@@ -4576,7 +4576,7 @@
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@@ -4589,7 +4589,7 @@
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             "uuid": "f90ae5d8-e31a-4f6d-914e-f37d223ea9d1",
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@@ -4602,7 +4602,7 @@
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@@ -4615,7 +4615,7 @@
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             "uuid": "fa17dd22-2d46-44dd-bf29-7ba21c575a6c",
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@@ -4628,7 +4628,7 @@
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             "uuid": "fb59546f-ca17-40ae-b0b8-ca16c1b94de9",
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@@ -4641,7 +4641,7 @@
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             "uuid": "fb71e3ae-31d9-4ce1-8d14-25955525b515",
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@@ -4654,7 +4654,7 @@
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             "uuid": "fd5331f0-025b-4370-94bf-a2a2d1812704",
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@@ -4667,7 +4667,7 @@
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             "uuid": "fd563e44-5e1a-4dfc-bfbd-42ef32c62d69",
             "version": "2021-05-10T23:24:55.955000Z",
@@ -4680,7 +4680,7 @@
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             "uuid": "fe2c65ca-06af-4760-9df8-086a81611a31",
             "version": "2021-05-10T23:24:56.352000Z",
@@ -4693,7 +4693,7 @@
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-        {
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             "uuid": "fecea080-2c71-42f2-a2cd-3dbd89e04c80",
             "version": "2021-05-10T23:25:03.741000Z",
@@ -4706,7 +4706,7 @@
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             "uuid": "ffb352c5-f9e2-497c-940c-7cb5dd0eaa5e",
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@@ -4719,7 +4719,7 @@
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             "s3_etag": "2c00a99240b3e95beabeae164f463980-40"
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-    ],
+    },
     "metadata": {
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diff --git a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
index 14e5068a2..9aa2db7b4 100644
--- a/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
+++ b/test/indexer/data/0722b70c-6778-423d-8fe9-869e2a515d35.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/54647cbb-7814-4d9a-b7f8-a6605c2f7aa6": {
+
             "name": "SRR7648414_2.fastq.gz",
             "uuid": "297d6cef-d2dd-4eaf-bcd7-5abd0b27d556",
             "version": "2021-03-18T11:38:48.652000Z",
@@ -13,7 +14,7 @@
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-        {
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             "uuid": "2d392c72-e042-48f4-8d4c-02800e9303a5",
             "version": "2021-03-18T11:38:48.639000Z",
@@ -26,7 +27,7 @@
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-    ],
+    },
     "metadata": {
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diff --git a/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json b/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
index 3268348f7..03364d448 100644
--- a/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
+++ b/test/indexer/data/17a3d288-01a0-464a-9599-7375fda3353d.dss.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
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             "uuid": "6bc5b7ef-68f8-445d-8460-f04180c4fae1",
@@ -12,7 +12,7 @@
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-        {
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             "name": "HCATisStabAug177078016_S2_L001_R1_001.fastq.gz",
             "uuid": "cee5b925-919c-4c77-8ea2-be51a1728e2b",
@@ -24,7 +24,7 @@
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             "size": 1210026035
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             "name": "HCATisStabAug177078016_S1_L001_R1_001.fastq.gz",
             "uuid": "771d9bcb-a5ff-43b5-b3e8-e738cc4c05bf",
@@ -36,7 +36,7 @@
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             "name": "HCATisStabAug177078016_S3_L001_R2_001.fastq.gz",
             "uuid": "17add91c-4063-4684-859d-d739baa4b9bb",
@@ -48,7 +48,7 @@
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-        {
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             "name": "HCATisStabAug177078016_S4_L001_R2_001.fastq.gz",
             "uuid": "024c5cb6-f473-40c9-9eb3-da08caf3180e",
@@ -60,7 +60,7 @@
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-        {
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             "name": "HCATisStabAug177078016_S4_L001_I1_001.fastq.gz",
             "uuid": "b7554cb7-dc5a-4b07-9c7a-c04466d30576",
@@ -72,7 +72,7 @@
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             "name": "HCATisStabAug177078016_S2_L001_I1_001.fastq.gz",
             "uuid": "fea5cc65-6d94-4d1e-a807-ec248f79b83d",
@@ -84,7 +84,7 @@
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             "name": "HCATisStabAug177078016_S3_L001_I1_001.fastq.gz",
             "uuid": "b7d8d43c-bee6-48eb-bb36-0c07701c47b5",
@@ -96,7 +96,7 @@
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             "name": "HCATisStabAug177078016_S4_L001_R1_001.fastq.gz",
             "uuid": "5239e70b-7d8d-4285-971f-9a156441c2f2",
@@ -108,7 +108,7 @@
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-        {
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             "name": "HCATisStabAug177078016_S2_L001_R2_001.fastq.gz",
             "uuid": "c548066c-9994-415a-98cb-3df2933937ff",
@@ -120,7 +120,7 @@
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             "size": 2734648788
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-        {
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             "name": "HCATisStabAug177078016_S1_L001_R2_001.fastq.gz",
             "uuid": "8ebfd02e-2a74-4367-80db-48082f331625",
@@ -132,7 +132,7 @@
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             "size": 2188935776
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-        {
+        "sequence_file/49fddace-4c59-41c1-8930-0707460132d7": {
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             "name": "HCATisStabAug177078016_S1_L001_I1_001.fastq.gz",
             "uuid": "49fddace-4c59-41c1-8930-0707460132d7",
@@ -144,7 +144,7 @@
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             "size": 470883073
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-    ],
+    },
     "metadata": {
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diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
index 79a81af43..094ce59f4 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/5f68ea73-350b-4d37-a341-3004139fb699": {
+
             "name": "IDC9_L001_I1.fastq.gz",
             "uuid": "08bc2234-5157-4f5c-b348-5d63cc9f14e1",
             "version": "2019-09-24T09:35:07.310307Z",
@@ -12,7 +13,7 @@
             "sha256": "5a51c7ea8ce08cafb06d279041bd65f0759ab24bb6d2c25f2ca488d017cd2bc6",
             "s3_etag": "4cc2f68ce54b988081c14118adc480c4-7"
         },
-        {
+        "sequence_file/23f8e139-f4fa-4476-ba59-ff5d37003c34": {
             "name": "IDC9_L001_R1.fastq.gz",
             "uuid": "c4288821-5775-4163-9543-5d29f847b03b",
             "version": "2019-09-24T09:35:07.508582Z",
@@ -24,7 +25,7 @@
             "sha256": "c2910761bfe2eb3ec958d653bc518988a8ecc081628a07d11f3308e25fb8f05d",
             "s3_etag": "046326b00d6cc7485eba093190ee7610-20"
         },
-        {
+        "sequence_file/3c3d882a-cc38-4eea-ac53-0885f906852e": {
             "name": "IDC9_L001_R2.fastq.gz",
             "uuid": "1b9d4386-97ac-402d-a93d-40740b2c3c28",
             "version": "2019-09-24T09:35:07.677792Z",
@@ -36,7 +37,7 @@
             "sha256": "6d84bb5bcfec87db8480a01e0c65f44f7caf1af8668010cb825ef8114de130e7",
             "s3_etag": "06705170a39d451d000c0143135fc5c3-64"
         },
-        {
+        "sequence_file/35e07477-76cb-4a92-99b6-7b3bbb02ec06": {
             "name": "IDC9_L002_I1.fastq.gz",
             "uuid": "ed7405bd-c1d0-4501-9a7a-7e953d887322",
             "version": "2019-09-24T09:35:07.845958Z",
@@ -48,7 +49,7 @@
             "sha256": "45ada227726e92de0638c50f4c2ac20ff3e2250f1138b436112d91d20fed19a3",
             "s3_etag": "4077676da51c8b6eff706b1ebf43114c-7"
         },
-        {
+        "sequence_file/63051b9f-87d4-4853-a4a0-5cc742ef6e72": {
             "name": "IDC9_L002_R1.fastq.gz",
             "uuid": "292b2faf-0db3-4ba1-a6a5-cb7bdfa9313d",
             "version": "2019-09-24T09:35:08.157668Z",
@@ -60,7 +61,7 @@
             "sha256": "125e5c181744e2dacf0b156d4c0b82ce771701947b26ca738689edddfc3af97e",
             "s3_etag": "31985ad7f32b053fa97f05216c6e805e-20"
         },
-        {
+        "sequence_file/6ca8e43f-5f40-4eb9-bfa9-294c54dbeade": {
             "name": "IDC9_L002_R2.fastq.gz",
             "uuid": "ea44789f-43b3-4684-b515-800605394177",
             "version": "2019-09-24T09:35:08.227847Z",
@@ -72,7 +73,7 @@
             "sha256": "e65d5d070584e7b08847fac0be1f89b7760ee9b301df792a66e5698d7d76d7f5",
             "s3_etag": "29da5762d5a55b9ecbd14c8663039f11-62"
         },
-        {
+        "sequence_file/3dffc456-caaf-4823-9f65-fc0db7abacbc": {
             "name": "IDC9_L003_I1.fastq.gz",
             "uuid": "dd7d84d2-c515-489f-9ead-3f7df2c66848",
             "version": "2019-09-24T09:35:08.401689Z",
@@ -84,7 +85,7 @@
             "sha256": "17456db03c93cef439a31b1a43f3165db4f27a1dc93dbc76263beb5d002a0530",
             "s3_etag": "d7046367bee15cd004af8f9882874042-7"
         },
-        {
+        "sequence_file/a2f4b05d-0dae-4655-acfd-ef3b91ae0ad0": {
             "name": "IDC9_L003_R1.fastq.gz",
             "uuid": "87fb0ccd-07d9-4dde-bbb0-c61338e3127b",
             "version": "2019-09-24T09:35:08.661156Z",
@@ -96,7 +97,7 @@
             "sha256": "55bd588c98a7caa2089271d79b6e0838ea8036726a7e56619786d4a23afa53c9",
             "s3_etag": "fc818501a59964e076aff1bc7f7068c6-20"
         },
-        {
+        "sequence_file/98ee0901-d34c-48a5-915a-0511bac325ec": {
             "name": "IDC9_L003_R2.fastq.gz",
             "uuid": "c4613a58-8bfb-43c6-8901-35d579631859",
             "version": "2019-09-24T09:35:08.872601Z",
@@ -108,7 +109,7 @@
             "sha256": "3813e23040c8e6a26a43fd1f164b2ec1d118e8f52b9d4510640f990d8e969dd8",
             "s3_etag": "3188a7180ba75349ca223905e3f589c1-64"
         },
-        {
+        "sequence_file/27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6": {
             "name": "IDC9_L004_I1.fastq.gz",
             "uuid": "f0011946-dbea-4f87-9858-5e3fd32a9829",
             "version": "2019-09-24T09:35:09.172703Z",
@@ -120,7 +121,7 @@
             "sha256": "8af97d885b995e7239a409f490e915f4754e7d1902f4a620f464995a422fb61f",
             "s3_etag": "20497e6cbc5f671fa94cf69bf0febdad-7"
         },
-        {
+        "sequence_file/133f2a25-f3aa-49a7-b9b6-d185d302fb26": {
             "name": "IDC9_L004_R1.fastq.gz",
             "uuid": "1abc51fb-6b3a-45e9-8691-fc250b4e0509",
             "version": "2019-09-24T09:35:09.245235Z",
@@ -132,7 +133,7 @@
             "sha256": "439112aa9aebd86f7e6a0c2206e005c8824994105aad3844090d765397931ed2",
             "s3_etag": "c9c70827a7c5d23bb150105a14112af9-20"
         },
-        {
+        "sequence_file/e46af70a-0396-41db-9b74-330cb8244124": {
             "name": "IDC9_L004_R2.fastq.gz",
             "uuid": "ae5d1035-8f2b-4355-a0ef-bbb99958b303",
             "version": "2019-09-24T09:35:09.407370Z",
@@ -144,7 +145,7 @@
             "sha256": "4c9b22cfd3eb141a30a43fd52ce576b586279ca021444ff191c460a26cf1e4cc",
             "s3_etag": "c92e5374ac0a53b228d4c1511c2d2842-63"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/906f8f09-deaa-40bb-bf50-27d2336b2dc4": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
diff --git a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
index ae3e2bea6..9dd46a048 100644
--- a/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
+++ b/test/indexer/data/1b6d8348-d6e9-406a-aa6a-7ee886e52bf9.tdr.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "supplementary_file/22561f93-d5e0-57eb-a54e-2d9d565cc234": {
             "name": "22561f93-d5e0-57eb-a54e-2d9d565cc234_file_name.fmt",
             "uuid": "046a88ef-d19f-51ed-9003-14847dffc820",
             "size": 1024,
@@ -11,7 +11,7 @@
             "sha256": "",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_1d239f78-f3e6-5dfb-aeb0-f50d8d97b51c"
         },
-        {
+        "sequence_file/5f68ea73-350b-4d37-a341-3004139fb699": {
             "name": "IDC9_L001_I1.fastq.gz",
             "uuid": "08bc2234-5157-4f5c-b348-5d63cc9f14e1",
             "version": "2019-09-24T09:35:07.310307Z",
@@ -24,7 +24,7 @@
             "s3_etag": "4cc2f68ce54b988081c14118adc480c4-7",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_c82292d3-61d1-5785-b8dc-24b9365df5bd"
         },
-        {
+        "supplementary_file/c343a47d-683f-571d-99c4-1331841b4e63": {
             "name": "c343a47d-683f-571d-99c4-1331841b4e63_file_name.fmt",
             "uuid": "19617367-cda8-54e0-8296-84623ef58c3f",
             "size": 1024,
@@ -35,7 +35,7 @@
             "sha256": "",
             "drs_uri": null
         },
-        {
+        "sequence_file/133f2a25-f3aa-49a7-b9b6-d185d302fb26": {
             "name": "IDC9_L004_R1.fastq.gz",
             "uuid": "1abc51fb-6b3a-45e9-8691-fc250b4e0509",
             "version": "2019-09-24T09:35:09.245235Z",
@@ -48,7 +48,7 @@
             "s3_etag": "c9c70827a7c5d23bb150105a14112af9-20",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_385feda5-d1e3-5a51-8e55-f4f491a4e7bf"
         },
-        {
+        "sequence_file/3c3d882a-cc38-4eea-ac53-0885f906852e": {
             "name": "IDC9_L001_R2.fastq.gz",
             "uuid": "1b9d4386-97ac-402d-a93d-40740b2c3c28",
             "version": "2019-09-24T09:35:07.677792Z",
@@ -61,7 +61,7 @@
             "s3_etag": "06705170a39d451d000c0143135fc5c3-64",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_83e89c54-4fc6-58b0-800c-3788539c41e7"
         },
-        {
+        "sequence_file/63051b9f-87d4-4853-a4a0-5cc742ef6e72": {
             "name": "IDC9_L002_R1.fastq.gz",
             "uuid": "292b2faf-0db3-4ba1-a6a5-cb7bdfa9313d",
             "version": "2019-09-24T09:35:08.157668Z",
@@ -74,7 +74,7 @@
             "s3_etag": "31985ad7f32b053fa97f05216c6e805e-20",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_dba31e1c-1b9c-56ae-af74-16b00b8144d2"
         },
-        {
+        "supplementary_file/507d2814-1688-54e7-b73e-2f831aa34368": {
             "name": "507d2814-1688-54e7-b73e-2f831aa34368_file_name.fmt",
             "uuid": "519ee493-0984-5b54-95ec-85452d506b00",
             "size": 1024,
@@ -85,7 +85,7 @@
             "sha256": "",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_9d6f268f-f484-5381-9095-f0998fa0c961"
         },
-        {
+        "sequence_file/a2f4b05d-0dae-4655-acfd-ef3b91ae0ad0": {
             "name": "IDC9_L003_R1.fastq.gz",
             "uuid": "87fb0ccd-07d9-4dde-bbb0-c61338e3127b",
             "version": "2019-09-24T09:35:08.661156Z",
@@ -98,7 +98,7 @@
             "s3_etag": "fc818501a59964e076aff1bc7f7068c6-20",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_a5e4e698-1d4c-5a5d-8d7c-5c84ea0f30d8"
         },
-        {
+        "sequence_file/e46af70a-0396-41db-9b74-330cb8244124": {
             "name": "IDC9_L004_R2.fastq.gz",
             "uuid": "ae5d1035-8f2b-4355-a0ef-bbb99958b303",
             "version": "2019-09-24T09:35:09.407370Z",
@@ -111,7 +111,7 @@
             "s3_etag": "c92e5374ac0a53b228d4c1511c2d2842-63",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_065dad63-3e05-5738-8ba5-9925d5d73d5e"
         },
-        {
+        "sequence_file/23f8e139-f4fa-4476-ba59-ff5d37003c34": {
             "name": "IDC9_L001_R1.fastq.gz",
             "uuid": "c4288821-5775-4163-9543-5d29f847b03b",
             "version": "2019-09-24T09:35:07.508582Z",
@@ -124,7 +124,7 @@
             "s3_etag": "046326b00d6cc7485eba093190ee7610-20",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_93ce1f3e-a963-5463-948f-44751a37f48d"
         },
-        {
+        "sequence_file/98ee0901-d34c-48a5-915a-0511bac325ec": {
             "name": "IDC9_L003_R2.fastq.gz",
             "uuid": "c4613a58-8bfb-43c6-8901-35d579631859",
             "version": "2019-09-24T09:35:08.872601Z",
@@ -137,7 +137,7 @@
             "s3_etag": "3188a7180ba75349ca223905e3f589c1-64",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_e6c1d2ce-d6ad-500e-8682-626a555992ab"
         },
-        {
+        "sequence_file/3dffc456-caaf-4823-9f65-fc0db7abacbc": {
             "name": "IDC9_L003_I1.fastq.gz",
             "uuid": "dd7d84d2-c515-489f-9ead-3f7df2c66848",
             "version": "2019-09-24T09:35:08.401689Z",
@@ -150,7 +150,7 @@
             "s3_etag": "d7046367bee15cd004af8f9882874042-7",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_bb455f5a-a70f-5155-85a0-46f475856e9f"
         },
-        {
+        "sequence_file/6ca8e43f-5f40-4eb9-bfa9-294c54dbeade": {
             "name": "IDC9_L002_R2.fastq.gz",
             "uuid": "ea44789f-43b3-4684-b515-800605394177",
             "version": "2019-09-24T09:35:08.227847Z",
@@ -163,7 +163,7 @@
             "s3_etag": "29da5762d5a55b9ecbd14c8663039f11-62",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_f140bd59-16c2-5082-aaf6-1c929e7063c6"
         },
-        {
+        "sequence_file/35e07477-76cb-4a92-99b6-7b3bbb02ec06": {
             "name": "IDC9_L002_I1.fastq.gz",
             "uuid": "ed7405bd-c1d0-4501-9a7a-7e953d887322",
             "version": "2019-09-24T09:35:07.845958Z",
@@ -176,7 +176,7 @@
             "s3_etag": "4077676da51c8b6eff706b1ebf43114c-7",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_b644bacb-5e69-5f73-baaf-f32178b0d0fd"
         },
-        {
+        "sequence_file/27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6": {
             "name": "IDC9_L004_I1.fastq.gz",
             "uuid": "f0011946-dbea-4f87-9858-5e3fd32a9829",
             "version": "2019-09-24T09:35:09.172703Z",
@@ -189,7 +189,7 @@
             "s3_etag": "20497e6cbc5f671fa94cf69bf0febdad-7",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_a694f8a4-424d-56db-9329-d449667416ea"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/906f8f09-deaa-40bb-bf50-27d2336b2dc4": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
diff --git a/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json b/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
index d029c477e..3465220f8 100644
--- a/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
+++ b/test/indexer/data/1ed68210-eaba-531d-ba9e-db80164d65ef.dss.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/8da4bdb9-ab64-5a90-8bce-f0ed5106ea41": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "9d9e936d",
             "indexed": false,
@@ -12,7 +12,7 @@
             "uuid": "c88f5811-6b23-5f9c-951f-29b4a80e6b4b",
             "version": "2021-01-01T00:00:00.000000Z"
         },
-        {
+        "sequence_file/de17aa7d-be28-53c1-b7a3-1f4b3989e3e6": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "e30fa683",
             "indexed": false,
@@ -24,7 +24,7 @@
             "uuid": "14c05ce3-f946-5936-893c-ee0ddd7407fb",
             "version": "2021-01-01T00:00:00.000000Z"
         }
-    ],
+    },
     "metadata": {
         "project/90bf705c-d891-5ce2-aa54-094488b445c6": {
             "array_express_accessions": [
diff --git a/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json b/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
index d9db1bd1b..4ef571c91 100644
--- a/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
+++ b/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "analysis_file/2645ed0a-a291-5fe2-a262-7b796b05d647": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "3c9d7a23",
             "indexed": false,
@@ -12,7 +12,7 @@
             "uuid": "b706259c-7429-5f2f-8142-2b8e9a48db1f",
             "version": "2021-01-01T00:00:00.000000Z"
         }
-    ],
+    },
     "metadata": {
         "project/90bf705c-d891-5ce2-aa54-094488b445c6": {
             "array_express_accessions": [
diff --git a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
index a37ae2591..264584536 100644
--- a/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
+++ b/test/indexer/data/1fd499c5-f397-4bff-9af0-eb42c37d5fbe.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/0d352174-7bf3-44b3-9b7b-7ef3056ed085": {
+
             "name": "SRR7648416_2.fastq.gz",
             "uuid": "2761715a-8de8-4d66-8286-90d89436a83d",
             "version": "2021-03-18T11:38:48.691000Z",
@@ -13,7 +14,7 @@
             "sha256": "a5a2f1f0c3353ae1d871c97f0d5d5e57f045d947a8d4ca02faff64a47a370745",
             "s3_etag": "07aaf23698191a8a3163999a86fb849a-239"
         },
-        {
+        "sequence_file/853dbcbd-8aaf-479d-8e57-134e11c61b72": {
             "name": "SRR7648416_1.fastq.gz",
             "uuid": "c3b97a11-bba4-42e7-bfee-7dcfd8249462",
             "version": "2021-03-18T11:38:48.705000Z",
@@ -26,7 +27,7 @@
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diff --git a/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json b/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
index a2ea38f31..c18771c9a 100644
--- a/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
+++ b/test/indexer/data/2a87dc5c-0c3c-4d91-a348-5d784ab48b92.dss.hca.json
@@ -1,6 +1,6 @@
 {
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@@ -12,7 +12,7 @@
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@@ -24,7 +24,7 @@
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@@ -48,7 +48,7 @@
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@@ -84,7 +84,7 @@
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@@ -96,7 +96,7 @@
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@@ -120,7 +120,7 @@
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@@ -192,7 +192,7 @@
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@@ -204,7 +204,7 @@
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@@ -216,7 +216,7 @@
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@@ -228,7 +228,7 @@
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@@ -240,7 +240,7 @@
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@@ -252,7 +252,7 @@
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@@ -264,7 +264,7 @@
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@@ -276,7 +276,7 @@
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@@ -288,7 +288,7 @@
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@@ -300,7 +300,7 @@
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@@ -312,7 +312,7 @@
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@@ -324,7 +324,7 @@
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diff --git a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
index 1bdfee488..69e1f1427 100644
--- a/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
+++ b/test/indexer/data/2c7d06b8-658e-4c51-9de4-a768322f84c5.dss.hca.json
@@ -1,6 +1,7 @@
 {
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diff --git a/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json b/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
index 261e65119..a1a4fece1 100644
--- a/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
+++ b/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
@@ -1,6 +1,6 @@
 {
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@@ -12,7 +12,7 @@
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diff --git a/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
index 79c54d5e9..9d3d58622 100644
--- a/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
+++ b/test/indexer/data/3db604da-940e-49b1-9bcc-25699a55b295.dss.hca.json
@@ -1,6 +1,7 @@
 {
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+
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@@ -12,7 +13,7 @@
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@@ -36,7 +37,7 @@
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@@ -48,7 +49,7 @@
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@@ -60,7 +61,7 @@
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@@ -72,7 +73,7 @@
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@@ -84,7 +85,7 @@
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@@ -96,7 +97,7 @@
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@@ -108,7 +109,7 @@
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@@ -120,7 +121,7 @@
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@@ -132,7 +133,7 @@
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@@ -144,7 +145,7 @@
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@@ -156,7 +157,7 @@
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@@ -168,7 +169,7 @@
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@@ -180,7 +181,7 @@
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-        {
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@@ -192,7 +193,7 @@
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             "version": "2018-11-02T17:42:17.032860Z"
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-    ],
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diff --git a/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
index 6cab99cd5..aafd04031 100644
--- a/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
+++ b/test/indexer/data/3f8176ff-61a7-4504-a57c-fc70f38d5b13.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "analysis_file/3404deaa-6274-4b78-99ae-442dd401714c": {
+
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "7fea1984",
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@@ -12,7 +13,7 @@
             "uuid": "2fe3ebac-9fc0-43e0-a074-53ec9c85a1c6",
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-        {
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             "crc32c": "062bc010",
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@@ -24,7 +25,7 @@
             "uuid": "0462b8db-4623-48ff-bcfc-7ad963407262",
             "version": "2018-10-24T23:43:46.657440Z"
         },
-        {
+        "analysis_file/77d3b337-d169-44a5-9b6a-be1c6d1b31b7": {
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "8111810d",
             "indexed": false,
@@ -36,7 +37,7 @@
             "uuid": "a9c9e43c-30a5-40f4-98c0-85af056e0be0",
             "version": "2018-10-24T23:43:46.917923Z"
         },
-        {
+        "analysis_file/b115459d-d690-418c-a608-48ede1cc5a43": {
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "88dab227",
             "indexed": false,
@@ -48,7 +49,7 @@
             "uuid": "ad24bc8f-8e57-42d2-8395-4d3dcdc5e317",
             "version": "2018-10-24T23:43:47.714898Z"
         },
-        {
+        "analysis_file/05ea34ca-995b-4c30-9f87-81ad07e61305": {
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "cea14b5c",
             "indexed": false,
@@ -60,7 +61,7 @@
             "uuid": "5619210b-c8ac-4607-a2ce-493e781945c3",
             "version": "2018-10-24T23:43:48.004861Z"
         },
-        {
+        "analysis_file/03e676dd-1718-40e0-a246-f3c6a594e334": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "bfa0a411",
             "indexed": false,
@@ -72,7 +73,7 @@
             "uuid": "e0039f22-89b6-455b-988f-cb0ce8777315",
             "version": "2018-10-24T23:43:48.309842Z"
         },
-        {
+        "analysis_file/19fee968-3d70-43a1-a64a-a778d656bd2e": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "133298b0",
             "indexed": false,
@@ -84,7 +85,7 @@
             "uuid": "b6f0ab9a-1c3a-4256-93bb-3eaee3ce8789",
             "version": "2018-10-24T23:43:48.570816Z"
         },
-        {
+        "analysis_file/edd03152-3219-41cd-9129-62f2e8944e91": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "11810dd2",
             "indexed": false,
@@ -96,7 +97,7 @@
             "uuid": "e9bdf224-232e-4285-8521-18febe6031fa",
             "version": "2018-10-24T23:43:48.840471Z"
         },
-        {
+        "analysis_file/e8972873-6e54-40d8-85ca-790a8d5688d0": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "404e1d3d",
             "indexed": false,
@@ -108,7 +109,7 @@
             "uuid": "7de22c98-e613-419a-a063-463b009d9977",
             "version": "2018-10-24T23:43:49.459923Z"
         },
-        {
+        "analysis_file/babd98f7-c1ae-4a5d-bf85-7cb347a3ce96": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "a44f5276",
             "indexed": false,
@@ -120,7 +121,7 @@
             "uuid": "a4c71562-cc3a-4aee-950a-c4e3c168a466",
             "version": "2018-10-24T23:43:49.707708Z"
         },
-        {
+        "analysis_file/3314dd32-6acf-4841-83a4-03d4807d1365": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "433f461e",
             "indexed": false,
@@ -132,7 +133,7 @@
             "uuid": "fae742b9-62fe-45bb-8769-39c2c841f292",
             "version": "2018-10-24T23:43:50.045854Z"
         },
-        {
+        "analysis_file/f6e76583-bc31-41e1-8695-7198e7842ea0": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "d9724b31",
             "indexed": false,
@@ -144,7 +145,7 @@
             "uuid": "787b88b9-8f21-4a68-b8b6-3b31a9e7fd30",
             "version": "2018-10-24T23:43:50.368499Z"
         },
-        {
+        "analysis_file/f2473460-2b19-4b16-97c7-6eaa9060df6f": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "73d003d2",
             "indexed": false,
@@ -156,7 +157,7 @@
             "uuid": "4050cf25-f78a-49e2-9750-f339d459b76b",
             "version": "2018-10-24T23:43:50.747688Z"
         },
-        {
+        "analysis_file/0fa2c00a-02e4-444d-998d-b812d647565f": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "80815add",
             "indexed": false,
@@ -168,7 +169,7 @@
             "uuid": "dc11cd36-b5d1-465f-95ef-0609d7ab7cf9",
             "version": "2018-10-24T23:43:50.982201Z"
         },
-        {
+        "analysis_file/09989709-cca8-4f82-a07f-6fa6a9fa3e03": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "06d1e1c8",
             "indexed": false,
@@ -180,7 +181,7 @@
             "uuid": "2db1b81c-3070-472f-b8ab-071c4a38f830",
             "version": "2018-10-24T23:43:51.288002Z"
         },
-        {
+        "analysis_file/020634de-da4b-47bb-b084-8c2d7e70ae17": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "c7497587",
             "indexed": false,
@@ -192,7 +193,7 @@
             "uuid": "0c800745-b4d5-46ad-8a76-24c320b08b6b",
             "version": "2018-10-24T23:43:51.477217Z"
         },
-        {
+        "analysis_file/f6a47716-c494-4229-85e9-bd1f20afa5d1": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "7c9e2e1a",
             "indexed": false,
@@ -204,7 +205,7 @@
             "uuid": "044fddd5-1bee-4f6e-8214-231061631b7f",
             "version": "2018-10-24T23:43:51.945446Z"
         },
-        {
+        "analysis_file/c82423e7-a621-4fee-bed2-5efa916124e3": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "a2113239",
             "indexed": false,
@@ -216,7 +217,7 @@
             "uuid": "ca09473c-84b1-4ccd-9c14-e6b71bcf310a",
             "version": "2018-10-24T23:43:52.750795Z"
         },
-        {
+        "analysis_file/401a3d93-c4c9-4f59-960e-41de71839619": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "444a7707",
             "indexed": false,
@@ -228,7 +229,7 @@
             "uuid": "c42f9b25-fa4a-40e8-b9fd-69e987d28d47",
             "version": "2018-10-24T23:43:52.990198Z"
         },
-        {
+        "analysis_file/f06c17a5-8197-4b6f-928a-55ffa8d796d2": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "f35d7e55",
             "indexed": false,
@@ -240,7 +241,7 @@
             "uuid": "8f6beb7b-feff-4d5d-93d9-8294f96a9734",
             "version": "2018-10-24T23:43:53.140897Z"
         },
-        {
+        "analysis_file/95bdd09a-cc14-4a7b-b0f8-96cd4d6dcb1c": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "53d7c1b4",
             "indexed": false,
@@ -252,7 +253,7 @@
             "uuid": "19dfd30d-d489-4cc8-b3ef-af4d83281767",
             "version": "2018-10-24T23:43:53.389145Z"
         },
-        {
+        "analysis_file/a3d20426-80af-4c2b-90a6-6e6644539aad": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "88068bce",
             "indexed": false,
@@ -264,7 +265,7 @@
             "uuid": "3a0aaa8f-7a5a-4ba7-ac90-72d786c3b3c0",
             "version": "2018-10-24T23:43:53.732254Z"
         },
-        {
+        "analysis_file/f6cdb1dd-df7c-4dab-bdd1-4bb59a2044f7": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "f672e644",
             "indexed": false,
@@ -276,7 +277,7 @@
             "uuid": "5650bf89-3095-4d11-be7a-83af89e197c6",
             "version": "2018-10-24T23:43:53.874430Z"
         },
-        {
+        "analysis_file/4de506d4-78d1-4de2-9780-e91f8a9d7b6d": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "38a3821e",
             "indexed": false,
@@ -288,7 +289,7 @@
             "uuid": "f231c645-1ac0-460d-b4db-90d3b4eea222",
             "version": "2018-10-24T23:43:54.039310Z"
         },
-        {
+        "analysis_file/c8aa1527-f40c-4e50-b7ca-51646562422b": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "afce17ed",
             "indexed": false,
@@ -300,7 +301,7 @@
             "uuid": "6217ca7d-ebcc-4e0d-80db-0ee2c23ca6db",
             "version": "2018-10-24T23:43:54.263560Z"
         },
-        {
+        "analysis_file/6cc5378a-295b-4e72-80a2-370434fd2b94": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "c6565f75",
             "indexed": false,
@@ -312,7 +313,7 @@
             "uuid": "7b322881-afd7-4896-8d42-8c0ea2979dd0",
             "version": "2018-10-24T23:43:54.428325Z"
         },
-        {
+        "analysis_file/75178504-d0ef-4d32-a3e6-6faa1026be84": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "c0b4fc1c",
             "indexed": false,
@@ -324,7 +325,7 @@
             "uuid": "6c0d9f3f-3112-45af-9d54-37ceb7639564",
             "version": "2018-10-24T23:43:54.802055Z"
         },
-        {
+        "analysis_file/215add4a-6239-4443-9b0c-c5e2b6e7052f": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "80af448b",
             "indexed": false,
@@ -336,7 +337,7 @@
             "uuid": "31ef1fee-8185-4b0e-a540-c1ea108f5a44",
             "version": "2018-10-24T23:43:55.053768Z"
         },
-        {
+        "analysis_file/f894b6e3-98b3-4161-97e4-a8d4ac9ad677": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "f282f971",
             "indexed": false,
@@ -348,7 +349,7 @@
             "uuid": "69fa904c-cd11-4560-817b-e98b2775da88",
             "version": "2018-10-24T23:43:55.200260Z"
         },
-        {
+        "analysis_file/f909af01-995b-499a-9086-fd2a90123102": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "b89e6723",
             "indexed": false,
@@ -360,7 +361,7 @@
             "uuid": "436c0cd7-e202-4e40-85aa-cc15cca31f7a",
             "version": "2018-10-24T23:43:55.390923Z"
         },
-        {
+        "analysis_file/75d692f4-e796-453d-b260-44a42f126c93": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "fa0eba46",
             "indexed": false,
@@ -372,7 +373,7 @@
             "uuid": "37cc585b-10f2-4c7f-93be-f7ab4b291b3d",
             "version": "2018-10-24T23:43:55.557557Z"
         },
-        {
+        "analysis_file/08be64a7-9ef4-4d17-b7d8-41f79c24c987": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "88035931",
             "indexed": false,
@@ -384,7 +385,7 @@
             "uuid": "9bccc57c-8134-4c5f-a800-833645437fce",
             "version": "2018-10-24T23:43:55.823439Z"
         },
-        {
+        "analysis_file/770c9eb2-f63f-4bd2-94c1-e2b6da1feeac": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "8a0c3621",
             "indexed": false,
@@ -396,7 +397,7 @@
             "uuid": "5d9fe37c-c1d5-45e8-a5e1-98409b965b57",
             "version": "2018-10-24T23:43:55.982645Z"
         },
-        {
+        "sequence_file/b66c9d19-322c-42d4-8b65-3478fd0afa6a": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "970af885",
             "indexed": false,
@@ -408,7 +409,7 @@
             "uuid": "1f5f6803-ce1f-4a4b-b19a-4e6e73e23404",
             "version": "2018-10-23T09:40:22.461764Z"
         },
-        {
+        "sequence_file/02c8352d-b2ba-4de4-a574-335eb9a61e0e": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "02d2680e",
             "indexed": false,
@@ -420,7 +421,7 @@
             "uuid": "335a8e97-6534-47ea-abf4-6df0093f9b85",
             "version": "2018-10-23T09:40:22.722285Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/02201088-f3be-46ce-bb04-e7c464189900": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index 22766ee75..a28430432 100644
--- a/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
+++ b/test/indexer/data/411cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "analysis_file/cf93f747-1392-4670-8eb3-3ac60a96855e": {
+
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "e511d1cf",
             "indexed": false,
@@ -12,7 +13,7 @@
             "uuid": "58b69c85-f5f3-4b94-8933-5520a54a6b25",
             "version": "2018-10-18T20:46:12.510116Z"
         },
-        {
+        "analysis_file/477c0b3e-4a06-4214-8f27-58199ba63528": {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "7571fac9",
             "indexed": false,
@@ -24,7 +25,7 @@
             "uuid": "b372aac3-0e2a-4815-9cb8-06957c0034d7",
             "version": "2018-10-18T20:46:12.954781Z"
         },
-        {
+        "analysis_file/ad6d5170-d74b-408c-af6b-25a14315c9da": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "883bc27f",
             "indexed": false,
@@ -36,7 +37,7 @@
             "uuid": "c81783cd-0531-4f64-9eef-a3e622152aae",
             "version": "2018-10-18T20:46:13.142208Z"
         },
-        {
+        "analysis_file/50be9b67-fae5-4472-9719-478dd1303d6e": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "182c881d",
             "indexed": false,
@@ -48,7 +49,7 @@
             "uuid": "17456232-f453-4178-b6d4-4c28840e0e9f",
             "version": "2018-10-18T20:46:13.433149Z"
         },
-        {
+        "analysis_file/fd16b62e-e540-4f03-8ba0-07d0c204e3c8": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "d3902ae4",
             "indexed": false,
@@ -60,7 +61,7 @@
             "uuid": "4cca0b74-7bfb-45a5-8a26-7342151805c9",
             "version": "2018-10-18T20:46:14.214293Z"
         },
-        {
+        "analysis_file/3c41b5b6-f480-4d47-8c5e-155e7c1adf54": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "1462f373",
             "indexed": false,
@@ -72,7 +73,7 @@
             "uuid": "0664a03c-9199-430e-9df6-e83e4a77df16",
             "version": "2018-10-18T20:46:14.565244Z"
         },
-        {
+        "analysis_file/022a217c-384d-4d9d-8631-6397b6838e3a": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "63dd3167",
             "indexed": false,
@@ -84,7 +85,7 @@
             "uuid": "a12a783c-6b91-4788-80b3-f25dae7838ce",
             "version": "2018-10-18T20:46:14.923428Z"
         },
-        {
+        "analysis_file/9b778e46-0c51-4260-8e3f-000ecc145f0a": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "a40c0ecb",
             "indexed": false,
@@ -96,7 +97,7 @@
             "uuid": "52d08a61-8d7b-4fd6-98e6-0620f815ecc5",
             "version": "2018-10-18T20:46:15.089157Z"
         },
-        {
+        "analysis_file/af025a74-53f1-4972-b50d-53095b5ffac2": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "03eb39ec",
             "indexed": false,
@@ -108,7 +109,7 @@
             "uuid": "40bb9b37-9c3c-4be4-adf6-c8609493d223",
             "version": "2018-10-18T20:46:15.963496Z"
         },
-        {
+        "analysis_file/e8395271-7c8e-4ec4-9598-495df43fe5fd": {
             "content-type": "text/html; dcp-type=data",
             "crc32c": "d5973bce",
             "indexed": false,
@@ -120,7 +121,7 @@
             "uuid": "05311530-98da-4ac7-a4da-244c0a19ae4a",
             "version": "2018-10-18T20:46:17.373562Z"
         },
-        {
+        "analysis_file/211a8fbf-b190-4576-ac2f-2b1a91743abb": {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "7c54ea3d",
             "indexed": false,
@@ -132,7 +133,7 @@
             "uuid": "d0757b34-5974-44e3-a8ae-5b60f7691913",
             "version": "2018-10-18T20:46:18.194283Z"
         },
-        {
+        "analysis_file/17222e3a-5757-45e9-9dfe-c4b6aa10f28a": {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "7571fac9",
             "indexed": false,
@@ -144,7 +145,7 @@
             "uuid": "5d8aea02-2dff-4bda-a218-2ee4c5cabfb4",
             "version": "2018-10-18T20:46:18.594371Z"
         },
-        {
+        "analysis_file/2fb8a975-b50c-4528-b850-838a19e19a1e": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "283d035a",
             "indexed": false,
@@ -156,7 +157,7 @@
             "uuid": "934faa14-ec75-4171-8c08-5ab20cc6ebff",
             "version": "2018-10-18T20:46:18.842610Z"
         },
-        {
+        "sequence_file/213381ea-6161-4159-853e-cfcae4968001": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "e80c9f6f",
             "indexed": false,
@@ -168,7 +169,7 @@
             "uuid": "8a0670ac-e3bd-4d38-afdc-0cf6d85e6adf",
             "version": "2018-10-11T22:04:37.262084Z"
         },
-        {
+        "sequence_file/9ee3da9e-83ca-4c02-84d6-ac09702b12ba": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "17a27554",
             "indexed": false,
@@ -180,7 +181,7 @@
             "uuid": "d1e5058a-b53c-4e71-9cbc-1853d95b75bd",
             "version": "2018-10-11T22:04:37.518108Z"
         },
-        {
+        "sequence_file/330a08ca-ae8e-4f1f-aa03-970abcd27f39": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "577e04eb",
             "indexed": false,
@@ -192,7 +193,7 @@
             "uuid": "a36fe69b-874b-4b9b-8e77-68be23cf98cd",
             "version": "2018-10-11T22:04:37.811384Z"
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-        {
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@@ -204,7 +205,7 @@
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@@ -216,7 +217,7 @@
             "uuid": "05f653e7-2920-499b-95fe-455d585da2b7",
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@@ -228,7 +229,7 @@
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             "version": "2018-10-11T22:04:38.356356Z"
         }
-    ],
+    },
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diff --git a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
index 3b81dcf53..2d84ad087 100644
--- a/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
+++ b/test/indexer/data/412cd8d5-5990-43cd-84cc-6c7796b8a76d.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "analysis_file/cf93f747-1392-4670-8eb3-3ac60a96855e": {
+
             "content-type": "text/tab-separated-values; dcp-type=data",
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@@ -12,7 +13,7 @@
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@@ -24,7 +25,7 @@
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@@ -36,7 +37,7 @@
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@@ -48,7 +49,7 @@
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-        {
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@@ -60,7 +61,7 @@
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@@ -72,7 +73,7 @@
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@@ -84,7 +85,7 @@
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@@ -96,7 +97,7 @@
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@@ -108,7 +109,7 @@
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@@ -120,7 +121,7 @@
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@@ -132,7 +133,7 @@
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@@ -144,7 +145,7 @@
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@@ -156,7 +157,7 @@
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@@ -168,7 +169,7 @@
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@@ -180,7 +181,7 @@
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@@ -192,7 +193,7 @@
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@@ -204,7 +205,7 @@
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@@ -216,7 +217,7 @@
             "uuid": "05f653e7-2920-499b-95fe-455d585da2b7",
             "version": "2018-10-11T22:04:38.189879Z"
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-        {
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@@ -228,7 +229,7 @@
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             "version": "2018-10-11T22:04:38.356356Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/803fd65a-c578-4c4f-a39e-bedec24e2578": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
index 032a1c97e..d0c12eb9e 100644
--- a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
+++ b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
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             "uuid": "23b7f3f8-b707-5f3c-b8e6-9173efa9dcf8",
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@@ -11,7 +11,7 @@
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             "sha256": "1bb86ee570e328dcd72a684689ddd87c966209cfc4b2b5c36e50dd0e4c156cab"
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-        {
+        "supplementary_file/e738a267-87fc-4070-abc7-b3be6442c6d0": {
             "name": "TissueDissociationProtocol.pdf",
             "uuid": "6578c322-7060-4c82-8469-9e54100e6b44",
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@@ -24,7 +24,7 @@
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             "uuid": "bf92ef4a-c422-44fb-bfc1-c2f86528b86b",
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@@ -37,7 +37,7 @@
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@@ -48,7 +48,7 @@
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-        {
+        "supplementary_file/01a1d04b-05d0-4904-b627-68b0dc02bc17": {
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             "uuid": "cd8e02d1-d0f9-4094-9a31-329931df60dc",
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@@ -61,7 +61,7 @@
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             "uuid": "ebf2947d-76d2-405b-a559-68c6ebb1b2d5",
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@@ -74,7 +74,7 @@
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@@ -87,7 +87,7 @@
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     "metadata": {
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diff --git a/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json b/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json
index 40fff54ea..bd020732e 100644
--- a/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json
+++ b/test/indexer/data/4afbb0ea-81ad-49dc-9b12-9f77f4f50be8.dss.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
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@@ -12,7 +12,7 @@
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@@ -24,7 +24,7 @@
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@@ -36,7 +36,7 @@
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-        {
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             "uuid": "e5dffb26-e7c6-4188-b99e-73e5033e1617",
@@ -48,7 +48,7 @@
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-        {
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@@ -60,7 +60,7 @@
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-        {
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             "uuid": "fb3db3b3-4d84-4016-826d-65cee4cb330b",
@@ -72,7 +72,7 @@
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-        {
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             "uuid": "25879d3f-6595-43d3-a5ca-5cdecea9eb51",
@@ -84,7 +84,7 @@
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@@ -96,7 +96,7 @@
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@@ -108,7 +108,7 @@
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@@ -120,7 +120,7 @@
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@@ -132,7 +132,7 @@
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             "uuid": "53ca1f09-4985-4827-a3cb-5f53d2cc543e",
@@ -144,7 +144,7 @@
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index 13df425de..b632eb090 100644
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index a8afbb205..dc6fa6b4b 100644
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index 2328e97fd..6dd4463fb 100644
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+        "analysis_file/7ba06d4d-c134-4324-84e6-3a37e57af2ce": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "59d86b68",
             "indexed": false,
@@ -312,7 +313,7 @@
             "uuid": "a8f0dc39-6019-4fc7-899d-4e34a48d03e5",
             "version": "2018-10-10T03:10:40.113268Z"
         },
-        {
+        "analysis_file/7cd4f7cc-8712-4ffd-b91d-9cb7c6182f52": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "25d193cf",
             "indexed": false,
@@ -324,7 +325,7 @@
             "uuid": "68ba4711-1447-42ac-aa40-9c0e4cda1666",
             "version": "2018-10-10T03:10:40.583439Z"
         },
-        {
+        "analysis_file/54604922-909e-4094-83d7-9d8ac7e7cdbd": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "17a84191",
             "indexed": false,
@@ -336,7 +337,7 @@
             "uuid": "27e66328-e337-4bcd-ba15-7893ecaf841f",
             "version": "2018-10-10T03:10:40.801631Z"
         },
-        {
+        "analysis_file/e0fc82a4-9bc2-4219-b763-99c865e4f9c0": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "25d193cf",
             "indexed": false,
@@ -348,7 +349,7 @@
             "uuid": "2ab1a516-ef36-41b6-a78f-513361658feb",
             "version": "2018-10-10T03:10:40.958708Z"
         },
-        {
+        "analysis_file/5c3246df-9ee8-42fe-ab19-ddd0ddea3e15": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "bdc30523",
             "indexed": false,
@@ -360,7 +361,7 @@
             "uuid": "351970aa-bc4c-405e-a274-be9e08e42e98",
             "version": "2018-10-10T03:10:41.135992Z"
         },
-        {
+        "sequence_file/5f0cdf49-aabe-40f4-8af3-033115805bb0": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "4ef74578",
             "indexed": false,
@@ -372,7 +373,7 @@
             "uuid": "c005f647-b3fb-45a8-857a-8f5e6a878ccf",
             "version": "2018-10-10T02:38:11.612423Z"
         },
-        {
+        "sequence_file/74c8c730-139e-40a5-b77e-f46088fa4d95": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "69987b3e",
             "indexed": false,
@@ -384,7 +385,7 @@
             "uuid": "b764ce7d-3938-4451-b68c-678feebc8f2a",
             "version": "2018-10-10T02:38:11.851483Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/377f2f5a-4a45-4c62-8fb0-db9ef33f5cf0": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
index 8a70324a6..19b39d251 100644
--- a/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
+++ b/test/indexer/data/79fa91b4-f1fc-534b-a935-b57342804a70.2020-12-10T10:30:00.000000Z.dss.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/5be64c5b-766b-43ad-ab5a-467ef1c47cc4": {
             "name": "CZIKidney7587405_S1_L001_R1_001.fastq.gz",
             "uuid": "075284e4-6a7b-45ba-a990-112beefd1296",
             "version": "2019-10-23T14:49:35.991570Z",
@@ -13,7 +13,7 @@
             "sha256": "3dc835af365d10a8b6f86e9119e513a722551c756e8999fed4085394127c3689",
             "s3_etag": "880df531d0365e1b06973b93a1d15a5a-119"
         },
-        {
+        "sequence_file/5646ff87-0427-4af5-a1ad-e072e6187c23": {
             "name": "4834STDY7002876_S1_L001_R1_001.fastq.gz",
             "uuid": "07e479d6-d44a-444e-bd19-7b955e4d0b37",
             "version": "2019-10-23T14:49:36.039396Z",
@@ -26,7 +26,7 @@
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             "s3_etag": "2365f210fc1bab590021b2031d893706-522"
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-        {
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             "name": "51fb7eb7-a422-482e-a98e-c9e6f9628e97.bam",
             "uuid": "0d2f92fd-72da-53e6-8035-6b9b2b41a2f6",
             "version": "2021-02-04T15:19:30.000000Z",
@@ -37,7 +37,7 @@
             "crc32c": "1747a06c",
             "sha256": "2bb185ee6e44e7bf6a2768dbf4e0509cc79f7ee0f956cbdaf87977b0a1b8ca96"
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-        {
+        "analysis_file/10439c86-98bb-5009-8374-577a41575424": {
             "name": "0f14c412-5014-4ac0-9a71-858b2f047777.bam",
             "uuid": "0df377a4-119b-5600-a3e6-e7c1bc94033f",
             "version": "2021-02-04T15:10:36.000000Z",
@@ -48,7 +48,7 @@
             "crc32c": "ee74c898",
             "sha256": "e7effa40cbf6adeda081c14a9bfd90735bcb7d0aee66e563400ed378d1de3407"
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-        {
+        "sequence_file/2b8c990c-4b79-4536-bf5f-1c8e57bff598": {
             "name": "CZIKidney7632801_S1_L001_R2_001.fastq.gz",
             "uuid": "0e9affc6-0257-44d8-8e27-3c723b9c8443",
             "version": "2019-10-23T14:49:42.059197Z",
@@ -61,7 +61,7 @@
             "sha256": "dfeed362194feb9731fb01ddb194b5d32bef27aa71be1ac96145e99d89321092",
             "s3_etag": "aaab19ef6c64720286e392b72168b0a0-230"
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-        {
+        "analysis_file/9a41c791-004c-5d89-a10c-d58d2ef7eca3": {
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             "uuid": "0f2bdf51-97c6-5892-b9e7-ad826dbf1321",
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@@ -72,7 +72,7 @@
             "crc32c": "c3003233",
             "sha256": "b4c9abbc701054b0b8685c6567566df4f01180dcb83ba6bdb35d250167bb7ca1"
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-        {
+        "sequence_file/70d226a8-01f4-4955-8293-210a6ec78920": {
             "name": "CZIKidney7632802_S1_L001_R2_001.fastq.gz",
             "uuid": "0fadf81a-30b4-4e70-ba6f-028950d06ec4",
             "version": "2019-10-23T14:49:36.081789Z",
@@ -85,7 +85,7 @@
             "sha256": "f2743a5243764eb59f04f88f673abc500d0a4c5538ae03b2fb81634155eba960",
             "s3_etag": "afe7816bac5b09b8496366eda4bb52cd-197"
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-        {
+        "sequence_file/599a4315-3b4b-4c42-9d68-961a2396cae5": {
             "name": "CZIKidney7632803_S1_L001_R2_001.fastq.gz",
             "uuid": "10e05576-100a-48cc-aa83-a30f09514384",
             "version": "2019-10-23T14:49:36.882952Z",
@@ -98,7 +98,7 @@
             "sha256": "c85efb39f331adeb34c937226e6661a4a575259ec6e36e6e3d353d606cdbdfaf",
             "s3_etag": "dcfb4f63603f7909ea8f5f1b6e8f86e0-212"
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-        {
+        "sequence_file/c8758f13-7e9b-464a-bada-b41b8b9e925f": {
             "name": "CZIKidney7587408_S1_L001_R2_001.fastq.gz",
             "uuid": "1456adad-9a4b-4a80-b115-9813f7a6b93c",
             "version": "2019-10-23T14:49:39.474413Z",
@@ -111,7 +111,7 @@
             "sha256": "ff538f40e72691b1c6f581d401144cf11b885622428985b216d97c3e43e62ef3",
             "s3_etag": "fe9271acb1ebea16f8f12e1327310298-31"
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-        {
+        "sequence_file/3de452b4-1c2a-49d6-80c8-495715921447": {
             "name": "CZIKidney7587404_S1_L001_R2_001.fastq.gz",
             "uuid": "1841191a-cad6-4bb8-b174-f41d94bee738",
             "version": "2019-10-23T14:49:36.895477Z",
@@ -124,7 +124,7 @@
             "sha256": "8bf272444637c809139c82bc65a41e3f33648eaa2cd1ce5e87854e7d6d1009b7",
             "s3_etag": "939afb3b3e5fb7829889c6a2be427348-31"
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-        {
+        "analysis_file/509608f1-e1d5-561c-b0d6-54348f0adb29": {
             "name": "51fb7eb7-a422-482e-a98e-c9e6f9628e97.loom",
             "uuid": "18c7131a-6f18-50a0-a805-04e0f4e2d7aa",
             "version": "2021-02-04T15:38:21.000000Z",
@@ -135,7 +135,7 @@
             "crc32c": "30fda154",
             "sha256": "85c0cc9d33346a374c50580fd00fef3bac6e9da0317deec948c677fc8bd7619c"
         },
-        {
+        "sequence_file/1eb30a4b-d595-4142-ae68-0a4ff4281c8d": {
             "name": "FCAImmP7528293_S1_L001_I1_001.fastq.gz",
             "uuid": "1932be60-8d3d-412b-86ac-4186ea87326b",
             "version": "2019-10-23T14:49:36.297060Z",
@@ -148,7 +148,7 @@
             "sha256": "003d74031b80fda82d6a96efa149dd028f1e0d7983283a576eb7cb9e3acc7986",
             "s3_etag": "728d08481bad39fb75abb4d36471cd06-40"
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-        {
+        "supplementary_file/944589e7-48a4-4333-b773-8e632ccb8865": {
             "name": "fetal_kidney_collection.pdf",
             "uuid": "1a04d1fb-55cc-4fd2-810a-71cf26d1aee9",
             "version": "2019-10-23T14:49:37.778548Z",
@@ -161,7 +161,7 @@
             "sha256": "8e241b0143084993f50332fec9d85fba8ad09d745fe02b3962af55925099a947",
             "s3_etag": "cce74f82cc90c9e5059acd326513ae37"
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-        {
+        "sequence_file/6500ad38-5b46-4186-9208-6a9494679191": {
             "name": "FCAImmP7462243_S1_L001_R1_001.fastq.gz",
             "uuid": "1a625464-2ab2-4d39-a1a5-e4e2240aa1fc",
             "version": "2019-10-23T14:49:36.819981Z",
@@ -174,7 +174,7 @@
             "sha256": "4c559dba0abed8f728e89eb48325dce81263d818812f3c9fa5a0e5b807e8d0e9",
             "s3_etag": "dce00c3dcdf1725d7ae0fbc365c8dbcc-126"
         },
-        {
+        "sequence_file/d3ea1255-7208-4952-be7f-7372d2dc9466": {
             "name": "4834STDY7002881_S1_L001_R2_001.fastq.gz",
             "uuid": "1d428c59-694c-4596-a360-a5e857f90635",
             "version": "2019-10-23T14:49:36.110149Z",
@@ -187,7 +187,7 @@
             "sha256": "6cbfc8a7166eae65a0b1171a71f4aa560d160798b14bd55dcec7061573036394",
             "s3_etag": "93e305000c055a82867f8f05eff05d7a-669"
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-        {
+        "analysis_file/fbcc2483-8a75-50ec-8cb6-8148a5087dce": {
             "name": "d8c08782-6f69-4314-947c-1afe6928cbce.loom",
             "uuid": "1d8a4488-3c4c-52b1-9912-52f08da57022",
             "version": "2021-02-04T15:28:41.000000Z",
@@ -198,7 +198,7 @@
             "crc32c": "599e199f",
             "sha256": "4181f361b8385d423fe4efbbfed08e703092469c40b40a568352cb5bde9b11f9"
         },
-        {
+        "supplementary_file/53089129-f71b-412c-ae2d-f7e8e50044c3": {
             "name": "fetal_flow_enrichment_2.pdf",
             "uuid": "1e3c935e-a508-47e5-a1a1-da5ad78a4f36",
             "version": "2019-10-23T14:49:36.963262Z",
@@ -211,7 +211,7 @@
             "sha256": "573a10fd2924173e82f8a8f3fa0c5fb6c68ca9373f7e2cdfaf39e68086d8204b",
             "s3_etag": "641a7fe74d0dc149a65b51a1b753e4a9"
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-        {
+        "sequence_file/8f6318ea-e692-4085-a693-02f4ff3204b5": {
             "name": "CZIKidney7587408_S1_L001_I1_001.fastq.gz",
             "uuid": "210c7287-2f6e-4a93-8c63-202fa0b596b7",
             "version": "2019-10-23T14:49:38.876464Z",
@@ -224,7 +224,7 @@
             "sha256": "51344e0de3761e9d45ca83916b8cc63e1afd3ab28b01ddaff3db9857750fe497",
             "s3_etag": "57cb25ef7a42dd6da8500a352aeb3023-4"
         },
-        {
+        "sequence_file/7a058660-f594-4eb5-b02f-bace314f6d76": {
             "name": "CZIKidney7587406_S1_L001_R1_001.fastq.gz",
             "uuid": "247b3006-918e-49de-9797-df31ffcfe4ca",
             "version": "2019-10-23T14:49:35.241234Z",
@@ -237,7 +237,7 @@
             "sha256": "70549b60bd385959d8eaf74cacc634991f70319535ecb6c320033c1bb355da14",
             "s3_etag": "514631b815424e2129ddce60de417275-135"
         },
-        {
+        "sequence_file/9614720d-ed06-4e72-9a4f-cb62088ff608": {
             "name": "FCAImmP7528293_S1_L001_R2_001.fastq.gz",
             "uuid": "25f7e8ad-e20e-4b7a-99b5-1f3c5bbfdf18",
             "version": "2019-10-23T14:49:36.795211Z",
@@ -250,7 +250,7 @@
             "sha256": "4c4ae28aac14171aef0c080993a4a1d6495c3b0c64a3c127fff574bb62dad43b",
             "s3_etag": "4d58aa43c6228235a108c5ba906f4cdf-439"
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-        {
+        "sequence_file/e28e68a3-3042-45f6-a714-ba8622a4b34e": {
             "name": "FCAImmP7555850_S1_L001_R1_001.fastq.gz",
             "uuid": "29a8f5fb-43a8-4f18-9255-f7573e9c4600",
             "version": "2019-10-23T14:49:35.155466Z",
@@ -263,7 +263,7 @@
             "sha256": "2dc0672b9e2c56e0ededbc6b50d609a9eb87dc0776afedc5abeb8b55e317dcd5",
             "s3_etag": "80923baffe8ef38b23af2ce6d79b788c-131"
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-        {
+        "analysis_file/f9b8be35-2641-5f85-af13-c0390b7bfe23": {
             "name": "548a75b4-ba45-4700-b7bb-656c3995c316.loom",
             "uuid": "30e6964e-df3b-5f93-ae18-b49ba08aea26",
             "version": "2021-02-04T15:30:21.000000Z",
@@ -274,7 +274,7 @@
             "crc32c": "1303acc0",
             "sha256": "d9671d190632e21e328f77e3344c240408852ca5a94299daeb504d0472575590"
         },
-        {
+        "analysis_file/5bb0243e-0764-5a77-ae7d-1638ebfd27b0": {
             "name": "83b474d3-c20f-48f6-95a0-b0fa2269f14d.bam",
             "uuid": "313c30cb-6941-5c2e-8c3e-60c02df4b977",
             "version": "2021-02-04T15:18:45.000000Z",
@@ -285,7 +285,7 @@
             "crc32c": "ff8963ff",
             "sha256": "af03184af8db101077bf2f7426a985b5b0510fe8c18acc0b26ad21313847ed6c"
         },
-        {
+        "analysis_file/44175006-91f3-5d95-9a08-b33e08ed1ae3": {
             "name": "b3ce1085-08dc-42ff-a609-6968315327a8.loom",
             "uuid": "316010e4-fdb5-5628-9510-adba0ca80a29",
             "version": "2021-02-04T15:30:01.000000Z",
@@ -296,7 +296,7 @@
             "crc32c": "bdc8f0d2",
             "sha256": "244c3f8d43f3b3756ecfb5b993bf4a8a149fa1def6c8f791b4b504dfdae46a6a"
         },
-        {
+        "analysis_file/df5af5d4-56e1-517b-8f47-7bf4888c853a": {
             "name": "082e87ac-5cf6-4bad-bedb-5f6591b8f566.loom",
             "uuid": "37accfb7-029b-57ba-892f-716f718dc9d2",
             "version": "2021-02-04T15:36:40.000000Z",
@@ -307,7 +307,7 @@
             "crc32c": "7e417f16",
             "sha256": "f1df2d78c8ab3a16d2207c6c315222c85a7c311ce14f9442d04b046eb381d4c1"
         },
-        {
+        "analysis_file/f9bf5721-5ee8-5837-8eb9-da3810cf04f1": {
             "name": "2c2c943c-1c0e-462c-b630-8a91a1f0fb94.bam",
             "uuid": "3c480b25-d8d1-5516-96ea-be6547af82ca",
             "version": "2021-02-04T15:20:15.000000Z",
@@ -318,7 +318,7 @@
             "crc32c": "3d0fd311",
             "sha256": "f65d5d47cfcd5d3cb8da8bb278e844bcba3dd2a5e922106df162443eb8cc6476"
         },
-        {
+        "analysis_file/38a0ef48-9df1-5fef-8eb6-b32fbb67aabd": {
             "name": "dc31f31d-ab56-4025-9834-99be638a2d50.loom",
             "uuid": "41d76180-77ac-5cb3-92bd-eb867d8c52c9",
             "version": "2021-02-04T15:34:25.000000Z",
@@ -329,7 +329,7 @@
             "crc32c": "5fc8c565",
             "sha256": "2ed196acb07ca0835b88625e430f19582992588ab21f340eab60a52b67d5bc65"
         },
-        {
+        "analysis_file/50547806-882a-5915-b217-5bbc692239b9": {
             "name": "6d273f72-f55c-4c8e-b91e-29e762194c3f.loom",
             "uuid": "4246f2be-5949-525d-a4ba-491176f13f69",
             "version": "2021-02-04T15:42:04.000000Z",
@@ -340,7 +340,7 @@
             "crc32c": "67682c74",
             "sha256": "6a748a5cb0cb3f7de9b4e3bd6968f2b10dd8b2ec82ee9b030e18a9f97c43f533"
         },
-        {
+        "sequence_file/1f50a6ba-90e5-4162-b6ac-6f8d5bfe72cc": {
             "name": "FCAImmP7462243_S1_L001_I1_001.fastq.gz",
             "uuid": "4471ff2f-9528-4ab0-a422-78ed0852e4a5",
             "version": "2019-10-23T14:49:36.492952Z",
@@ -353,7 +353,7 @@
             "sha256": "aa4f17dac6909575af38011a162368df992236c9439f4c300583d42c43b6efd9",
             "s3_etag": "0b7e4f8ddf4324812b3cb9ee97335603-41"
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-        {
+        "sequence_file/4e80d841-15c5-4da1-9660-4400b41d0536": {
             "name": "CZIKidney7587404_S1_L001_I1_001.fastq.gz",
             "uuid": "44d21c39-6acb-483a-99be-8fe8e7a5d208",
             "version": "2019-10-23T14:49:36.319957Z",
@@ -366,7 +366,7 @@
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-        {
+        "sequence_file/8831df7b-25f6-482e-9e54-5c53bdda4d53": {
             "name": "FCAImmP7462242_S1_L001_I1_001.fastq.gz",
             "uuid": "475885e1-5b81-452f-a939-91dc9b207f5b",
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@@ -379,7 +379,7 @@
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@@ -1292,7 +1292,7 @@
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@@ -1303,7 +1303,7 @@
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@@ -1355,7 +1355,7 @@
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@@ -1368,7 +1368,7 @@
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@@ -1379,7 +1379,7 @@
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@@ -1392,7 +1392,7 @@
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@@ -1405,7 +1405,7 @@
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@@ -1418,7 +1418,7 @@
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@@ -1431,7 +1431,7 @@
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@@ -1444,7 +1444,7 @@
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@@ -1457,7 +1457,7 @@
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@@ -1470,7 +1470,7 @@
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@@ -1483,7 +1483,7 @@
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diff --git a/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json b/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
index 9dfd6045e..d77b01882 100644
--- a/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
+++ b/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
@@ -1,6 +1,6 @@
 {
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@@ -12,7 +12,7 @@
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diff --git a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
index 442cae10b..2f69465e1 100644
--- a/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
+++ b/test/indexer/data/7eb74d9f-8346-5420-b7e4-b486f99451a8.dss.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
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@@ -13,7 +13,7 @@
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@@ -26,7 +26,7 @@
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@@ -37,7 +37,7 @@
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@@ -48,7 +48,7 @@
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@@ -61,7 +61,7 @@
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diff --git a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
index a236da3ca..2f6db1b09 100644
--- a/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
+++ b/test/indexer/data/80baee6e-00a5-4fdc-bfe3-d339ff8a7178.dss.hca.json
@@ -1,6 +1,6 @@
 {
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@@ -13,7 +13,7 @@
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@@ -26,7 +26,7 @@
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diff --git a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
index c71a6074d..cebdf45be 100644
--- a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
+++ b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
@@ -1,6 +1,6 @@
 {
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@@ -11,7 +11,7 @@
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@@ -22,7 +22,7 @@
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@@ -33,7 +33,7 @@
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diff --git a/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json b/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
index ca1ff626e..61894ccc1 100644
--- a/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
+++ b/test/indexer/data/8543d32f-4c01-48d5-a79f-1c5439659da3.dss.hca.json
@@ -1,6 +1,6 @@
 {
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@@ -12,7 +12,7 @@
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@@ -24,7 +24,7 @@
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diff --git a/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json b/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
index 3645044d6..bb86b5ce8 100644
--- a/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
+++ b/test/indexer/data/8c1773c3-1885-545f-9381-0dab1edf6074.dss.hca.json
@@ -1,6 +1,6 @@
 {
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@@ -12,7 +12,7 @@
             "uuid": "92855c6f-2807-50b6-a2a4-19b13c71aa65",
             "version": "2021-01-01T00:00:00.000000Z"
         },
-        {
+        "sequence_file/6a0e071d-9bfc-5e12-b1b9-e887885e12f6": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "50660f48",
             "indexed": false,
@@ -24,7 +24,7 @@
             "uuid": "c2fe321a-487d-5e53-83d3-766aad105c4f",
             "version": "2021-01-01T00:00:00.000000Z"
         },
-        {
+        "sequence_file/f6abda5c-65f3-5015-8167-ae78b96f5693": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "50660f48",
             "indexed": false,
@@ -36,7 +36,7 @@
             "uuid": "b613022f-86b4-50ab-9ca2-7dfe2bc27bef",
             "version": "2021-01-01T00:00:00.000000Z"
         }
-    ],
+    },
     "metadata": {
         "project/90bf705c-d891-5ce2-aa54-094488b445c6": {
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diff --git a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
index e19b32521..aeb34aee4 100644
--- a/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
+++ b/test/indexer/data/8c90d4fe-9a5d-4e3d-ada2-0414b666b880.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/c0a69095-57ba-4eca-8cc7-fed514f35f43": {
+
             "name": "read-RA_si-AACCGTAA_lane-001-chunk-001_R1.fastq.gz",
             "uuid": "f4146a80-2737-4299-8d9a-0ec685dbac8b",
             "version": "2019-10-14T19:54:58.812291Z",
@@ -12,7 +13,7 @@
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-        {
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@@ -24,7 +25,7 @@
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@@ -36,7 +37,7 @@
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-        {
+        "sequence_file/d47c381f-cef0-432a-b2bb-49fb7a546ac1": {
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@@ -48,7 +49,7 @@
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-        {
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             "uuid": "2f66adc7-7d45-4c62-95e2-43ed081fa298",
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@@ -60,7 +61,7 @@
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@@ -72,7 +73,7 @@
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@@ -84,7 +85,7 @@
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@@ -96,7 +97,7 @@
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-        {
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@@ -108,7 +109,7 @@
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-        {
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             "uuid": "a01cfd2b-ae29-47c5-9dac-42b7faf6bedf",
             "version": "2019-10-14T19:55:00.441246Z",
@@ -120,7 +121,7 @@
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-        {
+        "sequence_file/96ae6850-32c6-4d89-87cb-2f5005ac65aa": {
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             "uuid": "9989c2fc-2220-498c-8063-a8e93f1ad563",
             "version": "2019-10-14T19:55:00.608106Z",
@@ -132,7 +133,7 @@
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-        {
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             "uuid": "b45a9d83-d09e-4177-8714-b495463d4596",
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@@ -144,7 +145,7 @@
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-        {
+        "sequence_file/b4308ad2-8a51-4b1e-95a3-da961a13dd70": {
             "name": "read-RA_si-TCGGCGTC_lane-001-chunk-001_R1.fastq.gz",
             "uuid": "1f6f344d-734d-47dd-8c0e-4a566aece198",
             "version": "2019-10-14T19:55:04.648167Z",
@@ -156,7 +157,7 @@
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-        {
+        "sequence_file/2fa236c1-deb5-48a8-9961-3e2ee5cae2db": {
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             "uuid": "3423f8f0-b9e2-4f31-941e-d811ebc810df",
             "version": "2019-10-14T19:55:04.933666Z",
@@ -168,7 +169,7 @@
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-        {
+        "sequence_file/ff664ba7-b1f9-4fd2-b6ae-a12eb0111721": {
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             "uuid": "29de4b2c-f375-4d33-8495-98f70d8580e0",
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@@ -180,7 +181,7 @@
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-        {
+        "sequence_file/899e967e-06c8-49d9-bd3f-4bef8d04e22b": {
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             "uuid": "ab7aec45-0a5e-4edb-bc77-748413fd0a36",
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@@ -192,7 +193,7 @@
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         }
-    ],
+    },
     "metadata": {
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diff --git a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
index ed470ffb1..1df521fb9 100644
--- a/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
+++ b/test/indexer/data/94f2ba52-30c8-4de0-a78e-f95a3f8deb9c.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "image_file/6baa3aff-b2a5-4e49-82f7-25c108a6107a": {
+
             "content-type": "application/json; dcp-type=data",
             "crc32c": "d1fbf93a",
             "indexed": false,
@@ -12,7 +13,7 @@
             "uuid": "34d230e7-dd9f-4a47-8d5b-23043fe43bc0",
             "version": "2019-04-03T10:55:35.336469Z"
         },
-        {
+        "image_file/06dcfc33-21da-485f-8e50-49d294713a9e": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "88def662",
             "indexed": false,
@@ -24,7 +25,7 @@
             "uuid": "3db743f3-8235-4553-9a70-37dee987dd64",
             "version": "2019-04-03T10:55:35.723353Z"
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-        {
+        "image_file/404dd50b-4bc9-4c82-8c18-f53c68eed2fc": {
             "content-type": "image/tiff; dcp-type=data",
             "crc32c": "ad2281ce",
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@@ -36,7 +37,7 @@
             "uuid": "13ce8b32-13df-411e-8874-810de85a6d51",
             "version": "2019-04-03T10:55:36.220197Z"
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-        {
+        "image_file/5ceb5dc3-9194-494a-b1df-42bb75ab1a04": {
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@@ -48,7 +49,7 @@
             "uuid": "1eb42fec-c278-43a5-b3a3-b68d998b3a2a",
             "version": "2019-04-03T10:55:36.479486Z"
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-        {
+        "image_file/76e52f76-ede7-4088-b7f6-d6e5f6152292": {
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             "crc32c": "3b0cdc15",
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@@ -60,7 +61,7 @@
             "uuid": "fe9c7709-3a1c-4548-9578-01e4a63cc9d3",
             "version": "2019-04-03T10:55:36.745978Z"
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-        {
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@@ -72,7 +73,7 @@
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-        {
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@@ -84,7 +85,7 @@
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@@ -96,7 +97,7 @@
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-        {
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@@ -108,7 +109,7 @@
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             "version": "2019-04-03T10:55:37.940591Z"
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-        {
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@@ -120,7 +121,7 @@
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             "version": "2019-04-03T10:55:38.199379Z"
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-        {
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@@ -132,7 +133,7 @@
             "uuid": "4a9702b6-04e4-409b-a241-42540df7a07f",
             "version": "2019-04-03T10:55:38.500545Z"
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-        {
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@@ -144,7 +145,7 @@
             "uuid": "bb22c7d2-a22e-4e97-ab75-5bf44d95aa47",
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@@ -156,7 +157,7 @@
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             "version": "2019-04-03T10:55:38.997194Z"
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@@ -168,7 +169,7 @@
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@@ -180,7 +181,7 @@
             "uuid": "25ce5f57-b9e8-4403-aa8d-6e0d69044683",
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@@ -192,7 +193,7 @@
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@@ -204,7 +205,7 @@
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@@ -216,7 +217,7 @@
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             "version": "2019-04-03T10:55:40.220248Z"
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-        {
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@@ -228,7 +229,7 @@
             "uuid": "6c37dc76-a843-4009-986e-90f28512e5ef",
             "version": "2019-04-03T10:55:40.469870Z"
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-        {
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@@ -240,7 +241,7 @@
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@@ -252,7 +253,7 @@
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@@ -264,7 +265,7 @@
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@@ -276,7 +277,7 @@
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@@ -288,7 +289,7 @@
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@@ -300,7 +301,7 @@
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@@ -312,7 +313,7 @@
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@@ -324,7 +325,7 @@
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@@ -336,7 +337,7 @@
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@@ -348,7 +349,7 @@
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@@ -360,7 +361,7 @@
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@@ -384,7 +385,7 @@
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@@ -408,7 +409,7 @@
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@@ -432,7 +433,7 @@
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@@ -852,7 +853,7 @@
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@@ -2448,7 +2449,7 @@
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@@ -2460,7 +2461,7 @@
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@@ -2544,7 +2545,7 @@
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@@ -2556,7 +2557,7 @@
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@@ -2568,7 +2569,7 @@
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@@ -2580,7 +2581,7 @@
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@@ -2628,7 +2629,7 @@
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@@ -2652,7 +2653,7 @@
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@@ -2664,7 +2665,7 @@
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@@ -2676,7 +2677,7 @@
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@@ -2688,7 +2689,7 @@
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@@ -2700,7 +2701,7 @@
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@@ -2712,7 +2713,7 @@
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@@ -2724,7 +2725,7 @@
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             "version": "2019-04-03T10:56:46.657106Z"
         }
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diff --git a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
index 1d3ad2d9f..9ed3612b5 100644
--- a/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
+++ b/test/indexer/data/97f0cc83-f0ac-417a-8a29-221c77debde8.dss.hca.json
@@ -1,6 +1,7 @@
 {
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+
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diff --git a/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json b/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
index d2e4f1d04..3bc66a996 100644
--- a/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
+++ b/test/indexer/data/9dec1bd6-ced8-448a-8e45-1fc7846d8995.dss.hca.json
@@ -1,6 +1,6 @@
 {
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@@ -12,7 +12,7 @@
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diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
index 7006933cf..76806fe5e 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.dss.hca.json
@@ -1,6 +1,7 @@
 {
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diff --git a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
index 2e84ea6e9..08403796b 100644
--- a/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
+++ b/test/indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-04T11:33:44.698028Z.dss.hca.json
@@ -1,6 +1,7 @@
 {
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diff --git a/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json b/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
index 1e1e8b7a8..1c73018c4 100644
--- a/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
+++ b/test/indexer/data/b0850e79-5544-49fe-b54d-e29b9fc3f61f.dss.hca.json
@@ -1,6 +1,6 @@
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@@ -132,7 +132,7 @@
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@@ -144,7 +144,7 @@
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@@ -156,7 +156,7 @@
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@@ -168,7 +168,7 @@
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@@ -180,7 +180,7 @@
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@@ -192,7 +192,7 @@
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@@ -204,7 +204,7 @@
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@@ -216,7 +216,7 @@
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@@ -228,7 +228,7 @@
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@@ -240,7 +240,7 @@
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@@ -264,7 +264,7 @@
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@@ -276,7 +276,7 @@
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@@ -288,7 +288,7 @@
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@@ -300,7 +300,7 @@
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diff --git a/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json b/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
index ba9375653..00eb291e7 100644
--- a/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
+++ b/test/indexer/data/b2216048-7eaa-45f4-8077-5a3fb4204953.dss.hca.json
@@ -1,6 +1,6 @@
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diff --git a/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
index 2291d9783..b1a62674f 100644
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+++ b/test/indexer/data/b7fc737e-9b7b-4800-8977-fe7c94e131df.dss.hca.json
@@ -1,6 +1,7 @@
 {
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+
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@@ -12,7 +13,7 @@
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diff --git a/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json b/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
index a5102aea5..69be95e30 100644
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+++ b/test/indexer/data/c94a43f9-257f-4cd0-b2fe-eaf6d5d37d18.dss.hca.json
@@ -1,6 +1,6 @@
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@@ -2112,7 +2112,7 @@
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@@ -2136,7 +2136,7 @@
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@@ -2148,7 +2148,7 @@
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@@ -2160,7 +2160,7 @@
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@@ -2172,7 +2172,7 @@
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@@ -2232,7 +2232,7 @@
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diff --git a/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
index f5c4700ed..488d1aac7 100644
--- a/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
+++ b/test/indexer/data/cfab8304-dc9f-439e-af29-f8eb75b0729d.dss.hca.json
@@ -1,6 +1,7 @@
 {
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+
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@@ -12,7 +13,7 @@
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@@ -24,7 +25,7 @@
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diff --git a/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
index dfc852edc..2b7651096 100644
--- a/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
+++ b/test/indexer/data/d0e17014-9a58-4763-9e66-59894efbdaa8.dss.hca.json
@@ -1,6 +1,7 @@
 {
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@@ -12,7 +13,7 @@
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diff --git a/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
index 075390d03..d22eb6192 100644
--- a/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
+++ b/test/indexer/data/d5e01f9d-615f-4153-8a56-f2317d7d9ce8.dss.hca.json
@@ -1,6 +1,7 @@
 {
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@@ -12,7 +13,7 @@
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@@ -24,7 +25,7 @@
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@@ -48,7 +49,7 @@
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@@ -60,7 +61,7 @@
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@@ -84,7 +85,7 @@
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@@ -96,7 +97,7 @@
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@@ -108,7 +109,7 @@
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@@ -120,7 +121,7 @@
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@@ -132,7 +133,7 @@
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@@ -144,7 +145,7 @@
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-        {
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@@ -156,7 +157,7 @@
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-        {
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@@ -168,7 +169,7 @@
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@@ -180,7 +181,7 @@
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-        {
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@@ -192,7 +193,7 @@
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@@ -204,7 +205,7 @@
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-        {
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@@ -216,7 +217,7 @@
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-        {
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@@ -228,7 +229,7 @@
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-        {
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@@ -240,7 +241,7 @@
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@@ -252,7 +253,7 @@
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@@ -264,7 +265,7 @@
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@@ -276,7 +277,7 @@
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@@ -288,7 +289,7 @@
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@@ -300,7 +301,7 @@
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-        {
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@@ -312,7 +313,7 @@
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@@ -324,7 +325,7 @@
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             "version": "2018-09-06T18:57:56.812784Z"
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-        {
+        "analysis_file/f3ca70e5-f530-4890-be95-e3635dcf164a": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "0f2e6a1c",
             "indexed": false,
@@ -336,7 +337,7 @@
             "uuid": "124ad630-ac99-4447-9114-8a383bcff077",
             "version": "2018-09-06T18:57:57.676451Z"
         },
-        {
+        "analysis_file/12bcb6de-0f5b-4581-8d02-4ed3c59c13ab": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "9a8ecacb",
             "indexed": false,
@@ -348,7 +349,7 @@
             "uuid": "cd228ff5-d05e-49af-91ab-57f6b8cea769",
             "version": "2018-09-06T18:57:57.964761Z"
         },
-        {
+        "analysis_file/e3a50ba8-8e82-4b7f-89de-b6f512037e3d": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "0d0c6dfb",
             "indexed": false,
@@ -360,7 +361,7 @@
             "uuid": "bb109a5e-525a-47ef-b20f-2bf4f37b3de3",
             "version": "2018-09-06T18:57:58.163443Z"
         },
-        {
+        "analysis_file/cf3a255f-e731-4912-a7b1-cbec1b0d5239": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "115ea372",
             "indexed": false,
@@ -372,7 +373,7 @@
             "uuid": "7a1cf419-f901-487f-994e-ff98ec7015da",
             "version": "2018-09-06T18:57:58.621633Z"
         },
-        {
+        "sequence_file/c5d76832-f738-43a0-afe7-f62aa53a7824": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "cfa3d5df",
             "indexed": false,
@@ -384,7 +385,7 @@
             "uuid": "4cb61abf-25eb-4779-a9fd-16ce3371d83f",
             "version": "2018-09-06T18:03:20.549271Z"
         },
-        {
+        "sequence_file/be1f1c69-5ad5-4d2c-a86f-c43f1f003210": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "d1c4cd35",
             "indexed": false,
@@ -396,7 +397,7 @@
             "uuid": "abced4f5-1949-4d83-8b28-254753582378",
             "version": "2018-09-06T18:03:20.906445Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/13b00a71-4916-441c-a863-0204b40ba127": {
             "describedBy": "http://schema.integration.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json b/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
index 67955da34..6e577926c 100644
--- a/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
+++ b/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "analysis_file/f0c8ac7c-1c4a-5c9c-9286-c8b16208f9ae": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "4dab8938",
             "indexed": false,
@@ -12,7 +12,7 @@
             "uuid": "121add5e-8ed0-5368-b2f9-6a4d7fec0393",
             "version": "2021-01-01T00:00:00.000000Z"
         }
-    ],
+    },
     "metadata": {
         "project/90bf705c-d891-5ce2-aa54-094488b445c6": {
             "array_express_accessions": [
diff --git a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
index 1cc9b3a28..55b07abb2 100644
--- a/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
+++ b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "analysis_file/cf93f747-1392-4670-8eb3-3ac60a96855e": {
+
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "e511d1cf",
             "indexed": false,
@@ -12,7 +13,7 @@
             "uuid": "58b69c85-f5f3-4b94-8933-5520a54a6b25",
             "version": "2018-10-18T20:46:12.510116Z"
         },
-        {
+        "analysis_file/477c0b3e-4a06-4214-8f27-58199ba63528": {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "7571fac9",
             "indexed": false,
@@ -24,7 +25,7 @@
             "uuid": "b372aac3-0e2a-4815-9cb8-06957c0034d7",
             "version": "2018-10-18T20:46:12.954781Z"
         },
-        {
+        "analysis_file/ad6d5170-d74b-408c-af6b-25a14315c9da": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "883bc27f",
             "indexed": false,
@@ -36,7 +37,7 @@
             "uuid": "c81783cd-0531-4f64-9eef-a3e622152aae",
             "version": "2018-10-18T20:46:13.142208Z"
         },
-        {
+        "analysis_file/50be9b67-fae5-4472-9719-478dd1303d6e": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "182c881d",
             "indexed": false,
@@ -48,7 +49,7 @@
             "uuid": "17456232-f453-4178-b6d4-4c28840e0e9f",
             "version": "2018-10-18T20:46:13.433149Z"
         },
-        {
+        "analysis_file/fd16b62e-e540-4f03-8ba0-07d0c204e3c8": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "d3902ae4",
             "indexed": false,
@@ -60,7 +61,7 @@
             "uuid": "4cca0b74-7bfb-45a5-8a26-7342151805c9",
             "version": "2018-10-18T20:46:14.214293Z"
         },
-        {
+        "analysis_file/3c41b5b6-f480-4d47-8c5e-155e7c1adf54": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "1462f373",
             "indexed": false,
@@ -72,7 +73,7 @@
             "uuid": "0664a03c-9199-430e-9df6-e83e4a77df16",
             "version": "2018-10-18T20:46:14.565244Z"
         },
-        {
+        "analysis_file/022a217c-384d-4d9d-8631-6397b6838e3a": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "63dd3167",
             "indexed": false,
@@ -84,7 +85,7 @@
             "uuid": "a12a783c-6b91-4788-80b3-f25dae7838ce",
             "version": "2018-10-18T20:46:14.923428Z"
         },
-        {
+        "analysis_file/9b778e46-0c51-4260-8e3f-000ecc145f0a": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "a40c0ecb",
             "indexed": false,
@@ -96,7 +97,7 @@
             "uuid": "52d08a61-8d7b-4fd6-98e6-0620f815ecc5",
             "version": "2018-10-18T20:46:15.089157Z"
         },
-        {
+        "analysis_file/af025a74-53f1-4972-b50d-53095b5ffac2": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "03eb39ec",
             "indexed": false,
@@ -108,7 +109,7 @@
             "uuid": "40bb9b37-9c3c-4be4-adf6-c8609493d223",
             "version": "2018-10-18T20:46:15.963496Z"
         },
-        {
+        "analysis_file/e8395271-7c8e-4ec4-9598-495df43fe5fd": {
             "content-type": "text/html; dcp-type=data",
             "crc32c": "d5973bce",
             "indexed": false,
@@ -120,7 +121,7 @@
             "uuid": "05311530-98da-4ac7-a4da-244c0a19ae4a",
             "version": "2018-10-18T20:46:17.373562Z"
         },
-        {
+        "analysis_file/211a8fbf-b190-4576-ac2f-2b1a91743abb": {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "7c54ea3d",
             "indexed": false,
@@ -132,7 +133,7 @@
             "uuid": "d0757b34-5974-44e3-a8ae-5b60f7691913",
             "version": "2018-10-18T20:46:18.194283Z"
         },
-        {
+        "analysis_file/17222e3a-5757-45e9-9dfe-c4b6aa10f28a": {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "7571fac9",
             "indexed": false,
@@ -144,7 +145,7 @@
             "uuid": "5d8aea02-2dff-4bda-a218-2ee4c5cabfb4",
             "version": "2018-10-18T20:46:18.594371Z"
         },
-        {
+        "analysis_file/2fb8a975-b50c-4528-b850-838a19e19a1e": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "283d035a",
             "indexed": false,
@@ -156,7 +157,7 @@
             "uuid": "934faa14-ec75-4171-8c08-5ab20cc6ebff",
             "version": "2018-10-18T20:46:18.842610Z"
         },
-        {
+        "sequence_file/213381ea-6161-4159-853e-cfcae4968001": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "e80c9f6f",
             "indexed": false,
@@ -168,7 +169,7 @@
             "uuid": "8a0670ac-e3bd-4d38-afdc-0cf6d85e6adf",
             "version": "2018-10-11T22:04:37.262084Z"
         },
-        {
+        "sequence_file/9ee3da9e-83ca-4c02-84d6-ac09702b12ba": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "17a27554",
             "indexed": false,
@@ -180,7 +181,7 @@
             "uuid": "d1e5058a-b53c-4e71-9cbc-1853d95b75bd",
             "version": "2018-10-11T22:04:37.518108Z"
         },
-        {
+        "sequence_file/330a08ca-ae8e-4f1f-aa03-970abcd27f39": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "577e04eb",
             "indexed": false,
@@ -192,7 +193,7 @@
             "uuid": "a36fe69b-874b-4b9b-8e77-68be23cf98cd",
             "version": "2018-10-11T22:04:37.811384Z"
         },
-        {
+        "supplementary_file/281c2d08-9e43-47f9-b937-e733e3ba3322": {
             "content-type": "application/pdf; dcp-type=data",
             "crc32c": "1e67ff31",
             "indexed": false,
@@ -204,7 +205,7 @@
             "uuid": "9485d3c7-55f6-49f5-9eb1-ff85d8e4ef9f",
             "version": "2018-10-11T22:04:38.049605Z"
         },
-        {
+        "supplementary_file/ae1d6fa7-964f-465a-8c78-565206827434": {
             "content-type": "application/pdf; dcp-type=data",
             "crc32c": "201fded1",
             "indexed": false,
@@ -216,7 +217,7 @@
             "uuid": "05f653e7-2920-499b-95fe-455d585da2b7",
             "version": "2018-10-11T22:04:38.189879Z"
         },
-        {
+        "supplementary_file/f518a8cc-e1d9-4fc9-bc32-491dd8543902": {
             "content-type": "application/pdf; dcp-type=data",
             "crc32c": "47441108",
             "indexed": false,
@@ -228,7 +229,7 @@
             "uuid": "5eca9eb4-f837-4aa4-98e1-172a7c6da7ee",
             "version": "2018-10-11T22:04:38.356356Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/803fd65a-c578-4c4f-a39e-bedec24e2578": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
index 7dd5e31d0..87f1f59b0 100644
--- a/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
+++ b/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/12b25cbd-8cfa-4f0e-818f-d6ba3e823af4": {
+
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "43d9f66a",
             "indexed": false,
@@ -12,7 +13,7 @@
             "uuid": "76889aa2-de8e-42dc-9eaa-0d947ccb2604",
             "version": "2018-12-05T23:08:45.431819Z"
         },
-        {
+        "sequence_file/65d3d936-ae9d-4a18-a8c7-73ce6132355e": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "dbb883d5",
             "indexed": false,
@@ -24,7 +25,7 @@
             "uuid": "4cf0a9a7-111c-4284-82b9-5ae7326f235e",
             "version": "2018-12-05T23:08:45.915531Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/d29c64bd-b8d2-4e72-abbc-5536a44eac12": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
index de01304f7..070e6834a 100644
--- a/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
+++ b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "analysis_file/f5f82e76-173c-4f95-b25a-4ddc80bd1f86": {
+
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "6bb92520",
             "indexed": false,
@@ -12,7 +13,7 @@
             "uuid": "d7408870-a345-4d5c-be33-edbd69385529",
             "version": "2018-10-24T23:42:14.573498Z"
         },
-        {
+        "analysis_file/9b32ad49-e38d-458c-8976-668daa24c30e": {
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "06cf46cb",
             "indexed": false,
@@ -24,7 +25,7 @@
             "uuid": "4754bb8b-fc1f-431d-b063-fdbc2930fbf3",
             "version": "2018-10-24T23:42:15.014013Z"
         },
-        {
+        "analysis_file/479b4d96-b76b-41a7-9606-a523d701ce0c": {
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "2d0486d5",
             "indexed": false,
@@ -36,7 +37,7 @@
             "uuid": "c594b1a2-6a72-4744-8fc4-07debf086cbf",
             "version": "2018-10-24T23:42:15.215728Z"
         },
-        {
+        "analysis_file/f0b686e9-7a26-40f1-bdb2-58a1414d77eb": {
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "e1c51bd2",
             "indexed": false,
@@ -48,7 +49,7 @@
             "uuid": "bb1b99aa-1343-4825-88c9-1b67400982fc",
             "version": "2018-10-24T23:42:15.408775Z"
         },
-        {
+        "analysis_file/30f8d79e-8a4d-4fd3-93af-b5346f16b640": {
             "content-type": "text/plain; dcp-type=data",
             "crc32c": "53c649b7",
             "indexed": false,
@@ -60,7 +61,7 @@
             "uuid": "58fb543a-1021-499c-a96d-aa49612ece44",
             "version": "2018-10-24T23:42:15.703115Z"
         },
-        {
+        "analysis_file/20a011f9-e862-413b-bf1c-b43f3c64b874": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "09e98693",
             "indexed": false,
@@ -72,7 +73,7 @@
             "uuid": "7270a312-321a-4c33-80f3-4b02580be397",
             "version": "2018-10-24T23:42:15.988377Z"
         },
-        {
+        "analysis_file/c8caa0c3-7e78-40ac-a7f9-6219cbc2ee50": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "6dface93",
             "indexed": false,
@@ -84,7 +85,7 @@
             "uuid": "4c7e9d51-cd0a-4a0e-82e3-4c70550be2f0",
             "version": "2018-10-24T23:42:16.282105Z"
         },
-        {
+        "analysis_file/bdea53d3-49a6-4f5c-8504-d74996fe0745": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "522a934d",
             "indexed": false,
@@ -96,7 +97,7 @@
             "uuid": "3b5057e7-d9fa-4c66-b172-66efb9d46c7f",
             "version": "2018-10-24T23:42:16.551760Z"
         },
-        {
+        "analysis_file/0d27455f-d951-472a-849a-e234efca42d6": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "3290e07b",
             "indexed": false,
@@ -108,7 +109,7 @@
             "uuid": "8f886981-71ca-4d50-945d-fcad7456dce7",
             "version": "2018-10-24T23:42:16.801147Z"
         },
-        {
+        "analysis_file/2da7e3ba-23f5-4e81-9c36-5106b55bcdce": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "2ca91ed2",
             "indexed": false,
@@ -120,7 +121,7 @@
             "uuid": "6a02ba20-ba21-4685-b616-2651ce61df5c",
             "version": "2018-10-24T23:42:17.068963Z"
         },
-        {
+        "analysis_file/8776d7ea-5e3e-49a0-bd97-a713e9a14f3e": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "78cad56f",
             "indexed": false,
@@ -132,7 +133,7 @@
             "uuid": "c64fddc4-47bb-4219-8e1f-2c9b05192c30",
             "version": "2018-10-24T23:42:17.343576Z"
         },
-        {
+        "analysis_file/4fb97024-86ac-4d01-907d-d9b3159cf4be": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "37833b4b",
             "indexed": false,
@@ -144,7 +145,7 @@
             "uuid": "d5dcc2ea-11a3-40f6-94bd-b58584b9b9ea",
             "version": "2018-10-24T23:42:17.572545Z"
         },
-        {
+        "analysis_file/e1982adb-80b9-4ea6-a616-9206b0846afd": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "d05e6e24",
             "indexed": false,
@@ -156,7 +157,7 @@
             "uuid": "0e537564-ae91-460c-8b64-db6736fd342f",
             "version": "2018-10-24T23:42:17.849582Z"
         },
-        {
+        "analysis_file/b9254ef6-3f3a-4259-8829-01a6006fe5e3": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "383a286e",
             "indexed": false,
@@ -168,7 +169,7 @@
             "uuid": "7e977e69-0abf-4e2e-925b-fd312a91996c",
             "version": "2018-10-24T23:42:17.966695Z"
         },
-        {
+        "analysis_file/4bdb540a-7189-490a-9823-0f5c67e146d4": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "8be628a6",
             "indexed": false,
@@ -180,7 +181,7 @@
             "uuid": "c5745a0b-01c4-42ec-a4a3-4de76b72e3c7",
             "version": "2018-10-24T23:42:18.360888Z"
         },
-        {
+        "analysis_file/02e4b9e0-0750-4a21-8b18-46df9f7c86b5": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "1fcc995f",
             "indexed": false,
@@ -192,7 +193,7 @@
             "uuid": "780a8a11-d536-42be-9c92-a408b23f13a0",
             "version": "2018-10-24T23:42:18.517550Z"
         },
-        {
+        "analysis_file/55a4c327-4ca0-400d-88b9-91ccd89cad31": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "27f749cf",
             "indexed": false,
@@ -204,7 +205,7 @@
             "uuid": "989f8eac-c511-49e2-b4eb-1c7fde939df6",
             "version": "2018-10-24T23:42:19.746293Z"
         },
-        {
+        "analysis_file/dd5a65c4-23fc-40ba-8caf-37393a059e0f": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "c597ac81",
             "indexed": false,
@@ -216,7 +217,7 @@
             "uuid": "bc155f7e-ed46-41f1-a54b-5d094e1e32f2",
             "version": "2018-10-24T23:42:20.467152Z"
         },
-        {
+        "analysis_file/bc051b66-16fd-49b0-aca7-d6b29c445f61": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "444a7707",
             "indexed": false,
@@ -228,7 +229,7 @@
             "uuid": "0878349d-9608-4389-9b34-ac17d641c396",
             "version": "2018-10-24T23:42:20.712048Z"
         },
-        {
+        "analysis_file/b104083d-c607-4ad5-993e-e97632c9e4d9": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "f35d7e55",
             "indexed": false,
@@ -240,7 +241,7 @@
             "uuid": "65cf94ff-f203-4b93-aca4-2ef7ad3f5aa0",
             "version": "2018-10-24T23:42:20.881581Z"
         },
-        {
+        "analysis_file/b6576e30-18a2-412c-846d-377ad50cceed": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "1563daec",
             "indexed": false,
@@ -252,7 +253,7 @@
             "uuid": "0bf15e1e-cc40-43e1-b01f-93f2e725fae7",
             "version": "2018-10-24T23:42:21.017096Z"
         },
-        {
+        "analysis_file/544245b6-180b-4765-b8d2-db9a07fd2790": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "88068bce",
             "indexed": false,
@@ -264,7 +265,7 @@
             "uuid": "fd42c155-6189-4789-83b1-c6f3a7706228",
             "version": "2018-10-24T23:42:21.309195Z"
         },
-        {
+        "analysis_file/bdfc95f5-452d-45f0-a539-03e70be04d73": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "ae799606",
             "indexed": false,
@@ -276,7 +277,7 @@
             "uuid": "3877ba3c-3db8-4538-b3c6-39a4d70269eb",
             "version": "2018-10-24T23:42:21.442289Z"
         },
-        {
+        "analysis_file/46742270-3e39-45a2-99d6-50c2e1277045": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "38a3821e",
             "indexed": false,
@@ -288,7 +289,7 @@
             "uuid": "aea258d4-650e-45c8-890a-d2179a76a326",
             "version": "2018-10-24T23:42:21.729567Z"
         },
-        {
+        "analysis_file/1251ee1c-3f6f-43ef-b540-c4a3f3461e78": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "afce17ed",
             "indexed": false,
@@ -300,7 +301,7 @@
             "uuid": "af1aec5c-e200-4d9b-8ea4-f55bc4285615",
             "version": "2018-10-24T23:42:21.861075Z"
         },
-        {
+        "analysis_file/ad5a0217-3f5e-4293-bf4e-d56f55453dd5": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "c6565f75",
             "indexed": false,
@@ -312,7 +313,7 @@
             "uuid": "efb0702d-9593-4199-8129-2a86a13600a9",
             "version": "2018-10-24T23:42:21.990379Z"
         },
-        {
+        "analysis_file/fc842ec4-3fdc-447c-82a3-b59584f6509f": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "c0b4fc1c",
             "indexed": false,
@@ -324,7 +325,7 @@
             "uuid": "7474a924-91db-4468-81cf-4a28e6dacda5",
             "version": "2018-10-24T23:42:22.121285Z"
         },
-        {
+        "analysis_file/858b76ef-bb5b-44e2-b6fa-09efd3430a98": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "80af448b",
             "indexed": false,
@@ -336,7 +337,7 @@
             "uuid": "09144ccc-8f59-47c3-960d-1f97cedc0ba6",
             "version": "2018-10-24T23:42:22.356058Z"
         },
-        {
+        "analysis_file/8c4c53c9-87a3-4f28-8c65-57090360a9dc": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "f282f971",
             "indexed": false,
@@ -348,7 +349,7 @@
             "uuid": "0ecd1e02-2cf6-4c71-af42-259036b78284",
             "version": "2018-10-24T23:42:22.492841Z"
         },
-        {
+        "analysis_file/ec81ed84-ba61-4361-b611-c2ab3bf3f08e": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "b89e6723",
             "indexed": false,
@@ -360,7 +361,7 @@
             "uuid": "e6bc21b2-fbbd-46f3-9b3a-df0d547a3142",
             "version": "2018-10-24T23:42:22.705276Z"
         },
-        {
+        "analysis_file/51adec61-135c-4a93-b3d2-50019c0f58ad": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "1c9916e8",
             "indexed": false,
@@ -372,7 +373,7 @@
             "uuid": "63818a29-a94e-49ca-8c83-15e7813510d9",
             "version": "2018-10-24T23:42:22.837521Z"
         },
-        {
+        "analysis_file/abfb543f-345d-4f01-8a3d-c9c02b87cd0b": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "88035931",
             "indexed": false,
@@ -384,7 +385,7 @@
             "uuid": "599c92d3-6d60-4f14-a0e4-f6970958ae5a",
             "version": "2018-10-24T23:42:23.188749Z"
         },
-        {
+        "analysis_file/1afd626b-6730-4cb6-92c1-3379e7944f66": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "af11e230",
             "indexed": false,
@@ -396,7 +397,7 @@
             "uuid": "5f87557b-8b9e-44e5-b3e5-f1a785530418",
             "version": "2018-10-24T23:42:23.363215Z"
         },
-        {
+        "sequence_file/c8ed5871-28e6-42e2-8ccf-caa586a72c9e": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "0515f3b7",
             "indexed": false,
@@ -408,7 +409,7 @@
             "uuid": "e4232d09-11b1-44b6-a1d5-2049f2d2ef2e",
             "version": "2018-10-23T09:40:41.472595Z"
         },
-        {
+        "sequence_file/6291c2e7-3cc4-4d87-9bf6-2d6f6b131628": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "e1a944cc",
             "indexed": false,
@@ -420,7 +421,7 @@
             "uuid": "8194adce-71ef-45aa-af5a-468fc0f88c1c",
             "version": "2018-10-23T09:40:41.717604Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/75d0f208-d856-4e12-8916-a84f8f0e5338": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
index 517dddd95..2775f81c5 100644
--- a/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
+++ b/test/indexer/data/f0731ab4-6b80-4eed-97c9-4984de81a47c.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "analysis_file/2afae9e4-be02-4d57-bc44-24931f71d54c": {
+
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "28590550",
             "indexed": false,
@@ -12,7 +13,7 @@
             "uuid": "9689a1ab-02c3-48a1-ac8c-c1e097445ed8",
             "version": "2019-07-23T06:45:56.193221Z"
         },
-        {
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             "content-type": "application/vnd.openxmlformats-officedocument.wordprocessingml.document; dcp-type=data",
             "crc32c": "56fa99fc",
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@@ -24,7 +25,7 @@
             "uuid": "787084e4-f61e-4a15-b6b9-56c87fb31410",
             "version": "2019-07-23T06:45:57.057500Z"
         },
-        {
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             "crc32c": "57fd2051",
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@@ -36,7 +37,7 @@
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             "version": "2019-07-23T06:45:57.870215Z"
         },
-        {
+        "analysis_file/433f86ab-0a07-4f8c-ac18-b4dec37fa434": {
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             "crc32c": "f65585b6",
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@@ -48,7 +49,7 @@
             "uuid": "205b6575-dde3-4b63-b78a-b290c5b87403",
             "version": "2019-07-23T06:45:58.105975Z"
         },
-        {
+        "analysis_file/5ec54ddd-c6d7-4ae6-a822-94720c7bdbd1": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "76be2773",
             "indexed": false,
@@ -60,7 +61,7 @@
             "uuid": "28dfb106-a259-44dd-bf8e-63683c0a6dec",
             "version": "2019-07-23T06:45:58.957224Z"
         },
-        {
+        "analysis_file/b7890117-4733-4979-91ec-ba0208e088e9": {
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             "crc32c": "d08eee5e",
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@@ -72,7 +73,7 @@
             "uuid": "ff45fad9-74ba-4530-87b7-aa9997f0c68a",
             "version": "2019-07-23T06:45:59.355450Z"
         },
-        {
+        "analysis_file/5350b852-077e-43e3-885b-d1b37b3d7a6e": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "2ec4881d",
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@@ -84,7 +85,7 @@
             "uuid": "e488bef5-04a9-4adb-bf6e-279b11daa7af",
             "version": "2019-07-23T06:45:59.571299Z"
         },
-        {
+        "analysis_file/2c0bc0eb-739f-42ea-a5df-7d2943977fab": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "444a7707",
             "indexed": false,
@@ -96,7 +97,7 @@
             "uuid": "edeec1a2-026e-4467-9f3d-7887a9adc91d",
             "version": "2019-07-23T06:45:59.857953Z"
         },
-        {
+        "analysis_file/93153632-bf8c-49bb-a283-00957c7f853c": {
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             "crc32c": "444a7707",
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@@ -108,7 +109,7 @@
             "uuid": "5c166087-c87f-45d6-a531-8ec6d29754dd",
             "version": "2019-07-23T06:46:00.049191Z"
         },
-        {
+        "analysis_file/01d206e5-47b4-48dd-b823-74e62e2325d1": {
             "content-type": "application/json; dcp-type=data",
             "crc32c": "e7b081a4",
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@@ -120,7 +121,7 @@
             "uuid": "c3ba2d3d-58fc-42b2-9c06-9fada43f41b7",
             "version": "2019-07-23T06:46:00.296986Z"
         },
-        {
+        "analysis_file/752857d0-35f9-46fa-9888-fde25f21195b": {
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             "crc32c": "ccf165e9",
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@@ -132,7 +133,7 @@
             "uuid": "623ff088-74c5-433c-bdba-51ca67b30836",
             "version": "2019-07-23T06:46:00.690112Z"
         },
-        {
+        "analysis_file/ded3278c-98d4-43d1-81ce-5233f7123842": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "83893f92",
             "indexed": false,
@@ -144,7 +145,7 @@
             "uuid": "f3e44bed-2460-4e2f-8dc6-e41d4e21510d",
             "version": "2019-07-23T06:46:01.081702Z"
         },
-        {
+        "analysis_file/2e205f24-56cc-40ec-81b1-c17ebd0a5047": {
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             "crc32c": "a7fc43c5",
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@@ -156,7 +157,7 @@
             "uuid": "69b77a38-5c23-4429-94c1-b17d7a4fec5c",
             "version": "2019-07-23T06:46:01.422111Z"
         },
-        {
+        "analysis_file/cc486886-d9a2-44e6-8bf3-84a84c035ff6": {
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             "crc32c": "59bc0aad",
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@@ -168,7 +169,7 @@
             "uuid": "08915e23-ccfe-4b46-a445-2f48630ae7a8",
             "version": "2019-07-23T06:46:01.821260Z"
         },
-        {
+        "analysis_file/20ac4de0-bb12-4f99-9e54-bd6f284c741a": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "0d8cd1ff",
             "indexed": false,
@@ -180,7 +181,7 @@
             "uuid": "2c701dff-a283-48f7-a67f-fd0708746605",
             "version": "2019-07-23T06:46:02.309624Z"
         },
-        {
+        "analysis_file/d6ccfc37-bccb-463f-bd96-53accf9b5803": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "7ec55cf8",
             "indexed": false,
@@ -192,7 +193,7 @@
             "uuid": "98e75dc0-0b26-41ed-b545-36e8b7d96df1",
             "version": "2019-07-23T06:46:02.789752Z"
         },
-        {
+        "analysis_file/12c88fdb-2350-498c-a51c-6f93fad50621": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "f45bde01",
             "indexed": false,
@@ -204,7 +205,7 @@
             "uuid": "09695392-cf77-47df-b296-1003c20bea08",
             "version": "2019-07-23T06:46:03.189471Z"
         },
-        {
+        "analysis_file/bf4431ba-80da-468c-852b-7dbe008519f6": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "0c5cd29d",
             "indexed": false,
@@ -216,7 +217,7 @@
             "uuid": "e6ef8ad5-928f-4cd2-b773-8e2d078e5d3e",
             "version": "2019-07-23T06:46:03.596186Z"
         },
-        {
+        "analysis_file/4018b8da-201c-423b-a26a-737549674742": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "ea6b1cc9",
             "indexed": false,
@@ -228,7 +229,7 @@
             "uuid": "d20d0b30-8455-4bf5-ab03-ad430b279590",
             "version": "2019-07-23T06:46:03.975997Z"
         },
-        {
+        "analysis_file/8be955e9-eb4e-4834-8576-0fd7ba1c672d": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "5a7101ed",
             "indexed": false,
@@ -240,7 +241,7 @@
             "uuid": "ce7dc85c-5745-4c7e-8f2c-433d5ef98ed0",
             "version": "2019-07-23T06:46:04.397849Z"
         },
-        {
+        "analysis_file/291bc053-766d-4b04-aa69-53a7d6a05366": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "dccd7461",
             "indexed": false,
@@ -252,7 +253,7 @@
             "uuid": "e685cbab-3147-42e9-a8d3-68e33836bcda",
             "version": "2019-07-23T06:46:04.746479Z"
         },
-        {
+        "analysis_file/80b4596c-4047-40f7-8e90-d7ba13c3aba4": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "89cf69cc",
             "indexed": false,
@@ -264,7 +265,7 @@
             "uuid": "e2c7fc43-37f1-46f6-abec-042005826967",
             "version": "2019-07-23T06:46:05.112784Z"
         },
-        {
+        "analysis_file/bd8f069d-1b75-4f7d-b10a-55efe37e4625": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "1e098ffe",
             "indexed": false,
@@ -276,7 +277,7 @@
             "uuid": "44b60b61-703a-48a5-a545-46d5473e1af1",
             "version": "2019-07-23T06:46:05.486422Z"
         },
-        {
+        "analysis_file/287203a8-b15c-4fc9-ade7-4bfa9b4928e7": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "f773b4da",
             "indexed": false,
@@ -288,7 +289,7 @@
             "uuid": "ae99c085-13d6-44a4-bb51-50541f17e527",
             "version": "2019-07-23T06:46:05.951288Z"
         },
-        {
+        "analysis_file/3574966b-2810-45e2-8a1f-bb20a183d9c2": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "154df4f9",
             "indexed": false,
@@ -300,7 +301,7 @@
             "uuid": "a4b0c103-b579-473b-aef7-44c83e0f69f4",
             "version": "2019-07-23T06:46:06.361917Z"
         },
-        {
+        "analysis_file/5a2aa294-f923-4331-98c0-e9556263252e": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "ea50f0f0",
             "indexed": false,
@@ -312,7 +313,7 @@
             "uuid": "4cbd242c-46d5-4443-913a-40b2f938726a",
             "version": "2019-07-23T06:46:06.714015Z"
         },
-        {
+        "analysis_file/1e84fd86-6cd6-4533-8b48-cd314820e9a9": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "79a47905",
             "indexed": false,
@@ -324,7 +325,7 @@
             "uuid": "bd2da24e-38f0-4760-9698-525a1012735a",
             "version": "2019-07-23T06:46:07.096624Z"
         },
-        {
+        "analysis_file/058de439-51f8-47d4-8e63-c98ea902e527": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "b136c528",
             "indexed": false,
@@ -336,7 +337,7 @@
             "uuid": "4199d988-dc7e-4ad5-b379-c08c7e1e246e",
             "version": "2019-07-23T06:46:07.436291Z"
         },
-        {
+        "analysis_file/f7ab60fb-4ffb-43d5-8ce3-1ce6559d97b5": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "c84608a9",
             "indexed": false,
@@ -348,7 +349,7 @@
             "uuid": "94d22b10-d6c7-4908-bc08-f3fca1a86d8f",
             "version": "2019-07-23T06:46:07.780637Z"
         },
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@@ -972,7 +973,7 @@
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@@ -1008,7 +1009,7 @@
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@@ -1068,7 +1069,7 @@
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@@ -1080,7 +1081,7 @@
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@@ -1104,7 +1105,7 @@
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@@ -1152,7 +1153,7 @@
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@@ -1164,7 +1165,7 @@
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@@ -1188,7 +1189,7 @@
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+        "analysis_file/2b264ded-d29d-43e2-8288-26ab7ab1406b": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "6d2df55e",
             "indexed": false,
@@ -3384,7 +3385,7 @@
             "uuid": "4dd0cd99-6901-49a4-b287-de8b21e31a93",
             "version": "2019-07-23T06:47:59.254679Z"
         },
-        {
+        "analysis_file/86db2ba1-16df-4d73-afea-18148d4e7faa": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "886c277d",
             "indexed": false,
@@ -3396,7 +3397,7 @@
             "uuid": "b9541a8c-8989-44fe-972b-0aa98a409f68",
             "version": "2019-07-23T06:47:59.463261Z"
         },
-        {
+        "sequence_file/3f193e72-8efe-4c2a-ace1-79140ca36477": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "64e45095",
             "indexed": false,
@@ -3408,7 +3409,7 @@
             "uuid": "d879f732-d8d4-4251-a2ca-a91a852a034b",
             "version": "2019-07-18T21:29:49.534039Z"
         },
-        {
+        "sequence_file/078b71eb-220a-43e5-a0fc-4f231e90f85f": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "7046ca69",
             "indexed": false,
@@ -3420,7 +3421,7 @@
             "uuid": "1e14d503-31b1-4db6-82ba-f8d83bd85b9b",
             "version": "2019-07-18T21:29:49.697974Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/13eab62e-0038-4997-aeab-aa3192cc090e": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.1.1/cell_suspension",
diff --git a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
index b683e3716..c9cb07493 100644
--- a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
+++ b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/6c946b6c-040e-45cc-9114-a8b1454c8d20": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "980453cc",
             "indexed": false,
@@ -12,7 +12,7 @@
             "uuid": "f2b6c6f0-8d25-4aae-b255-1974cc110cfe",
             "version": "2018-09-14T12:33:43.720332Z"
         },
-        {
+        "sequence_file/c86e42d7-854a-479b-a627-6be1b49c980c": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "d2417d49",
             "indexed": false,
@@ -24,7 +24,7 @@
             "uuid": "f6608ce9-a570-4d5d-bd1f-407454958424",
             "version": "2018-09-14T12:33:45.304412Z"
         },
-        {
+        "supplementary_file/eeea6514-bfdc-473b-a9ae-82b00ab30c38": {
             "content-type": "application/pdf; dcp-type=data",
             "crc32c": "847325b6",
             "indexed": false,
@@ -36,7 +36,7 @@
             "uuid": "156c15a3-3406-45d3-a25e-27179baf0c59",
             "version": "2018-09-14T12:33:46.866929Z"
         },
-        {
+        "supplementary_file/89e313db-4423-4d53-b17e-164949acfa8f": {
             "content-type": "application/pdf; dcp-type=data",
             "crc32c": "b9364bfa",
             "indexed": false,
@@ -48,7 +48,7 @@
             "uuid": "5f9b45af-9a26-4b16-a785-7f2d1053dd7c",
             "version": "2018-09-14T12:33:47.012715Z"
         },
-        {
+        "supplementary_file/bf7df45c-c2d5-49a8-8110-7e1f17ed0094": {
             "content-type": "application/pdf; dcp-type=data",
             "crc32c": "3658ec51",
             "indexed": false,
@@ -60,7 +60,7 @@
             "uuid": "0db87826-ea2d-422b-ba71-b15d0e4293ae",
             "version": "2018-09-14T12:33:47.221025Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/0037c9eb-8038-432f-8d9d-13ee094e54ab": {
             "describedBy": "http://schema.staging.data.humancellatlas.org/type/biomaterial/8.6.1/cell_suspension",
diff --git a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
index 5dcaa6fb6..e4929de1a 100644
--- a/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
+++ b/test/indexer/data/fa5be5eb-2d64-49f5-8ed8-bd627ac9bc7a.dss.hca.json
@@ -1,6 +1,7 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "analysis_file/bd1307b9-70b5-49e4-8e02-9d4ca0d64747": {
+
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "1e03bc76",
             "indexed": false,
@@ -12,7 +13,7 @@
             "uuid": "9d95b445-e164-43fe-b6cb-3e23f9b3a820",
             "version": "2019-02-14T19:24:27.695139Z"
         },
-        {
+        "analysis_file/cf3453a3-68fb-4156-bc3e-0f08f7e6512c": {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "7571fac9",
             "indexed": false,
@@ -24,7 +25,7 @@
             "uuid": "689e9d77-708d-4f02-b2a0-e5cac72ae2ab",
             "version": "2019-02-14T19:24:27.995928Z"
         },
-        {
+        "analysis_file/234b0359-3853-4df4-898f-5182f698d48b": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "e0b2ceae",
             "indexed": false,
@@ -36,7 +37,7 @@
             "uuid": "94677e48-adf8-4ea3-a42b-5a9ce8853b21",
             "version": "2019-02-14T19:24:28.245144Z"
         },
-        {
+        "analysis_file/d95392c5-1958-4825-9076-2a9c130c53f3": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "461eb1e9",
             "indexed": false,
@@ -48,7 +49,7 @@
             "uuid": "d15b6930-24cb-4217-a963-bf611d48c6e7",
             "version": "2019-02-14T19:24:28.654694Z"
         },
-        {
+        "analysis_file/b9609367-7006-4055-8815-1bad881a1502": {
             "content-type": "text/csv; dcp-type=data",
             "crc32c": "53e5ecf8",
             "indexed": false,
@@ -60,7 +61,7 @@
             "uuid": "7807d073-e9dd-4f1f-8053-b89b4d12ebfd",
             "version": "2019-02-14T19:24:29.157180Z"
         },
-        {
+        "analysis_file/ebb2ec91-2cd0-4ec4-ba2b-5a6d6630bc5a": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "8487a5ae",
             "indexed": false,
@@ -72,7 +73,7 @@
             "uuid": "0fff97fe-c879-421a-a8d4-f9c5e995b21b",
             "version": "2019-02-14T19:24:29.395814Z"
         },
-        {
+        "analysis_file/1ab612ca-2a5a-4443-8004-bb5f0f784c67": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "c3921ecb",
             "indexed": false,
@@ -84,7 +85,7 @@
             "uuid": "9ea1b54e-0679-4cdc-93ab-c584110168ac",
             "version": "2019-02-14T19:24:30.435350Z"
         },
-        {
+        "analysis_file/34c64244-d3ed-4841-84b7-aa4cbb9d794b": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "466576fa",
             "indexed": false,
@@ -96,7 +97,7 @@
             "uuid": "432b5918-90b1-4624-abe3-f6a7c83010a9",
             "version": "2019-02-14T19:24:32.112522Z"
         },
-        {
+        "analysis_file/71710439-3864-4fc6-bc48-ca2ac90f7ccf": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "b5e461a4",
             "indexed": false,
@@ -108,7 +109,7 @@
             "uuid": "c2e39ef9-91a8-43a0-9600-d05819e30213",
             "version": "2019-02-14T19:24:32.795784Z"
         },
-        {
+        "analysis_file/2ab5242e-f118-48e3-afe5-c2287fa2e2b1": {
             "content-type": "text/html; dcp-type=data",
             "crc32c": "acf47b9f",
             "indexed": false,
@@ -120,7 +121,7 @@
             "uuid": "4f99fb32-9aa4-49cf-b4af-244a804c1259",
             "version": "2019-02-14T19:24:33.308106Z"
         },
-        {
+        "analysis_file/6da39577-256d-43fd-97c4-a3bedaa54273": {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "7c54ea3d",
             "indexed": false,
@@ -132,7 +133,7 @@
             "uuid": "eada050f-188b-409b-bbf3-8d586d24dd59",
             "version": "2019-02-14T19:24:33.996677Z"
         },
-        {
+        "analysis_file/86a93e19-eb89-4c27-8b64-006f96bb2c83": {
             "content-type": "text/tab-separated-values; dcp-type=data",
             "crc32c": "7571fac9",
             "indexed": false,
@@ -144,7 +145,7 @@
             "uuid": "efbe3d47-8089-4685-835c-f5af0227c31f",
             "version": "2019-02-14T19:24:34.225601Z"
         },
-        {
+        "analysis_file/0f858ddb-6d93-404e-95fd-0c200921dd40": {
             "content-type": "application/octet-stream; dcp-type=data",
             "crc32c": "d04a1146",
             "indexed": false,
@@ -156,7 +157,7 @@
             "uuid": "c508f1f3-dc97-4378-8e81-1586a881f354",
             "version": "2019-02-14T19:24:34.551509Z"
         },
-        {
+        "sequence_file/7df5d656-43cb-49f9-b81d-86cca3c44a65": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "da1a6040",
             "indexed": false,
@@ -168,7 +169,7 @@
             "uuid": "34e5f1ed-299e-401d-a62b-abad1a4ad2ca",
             "version": "2019-02-14T18:34:20.147713Z"
         },
-        {
+        "sequence_file/acd7d986-73ab-4d0b-9ead-377f3a2d646d": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "0eee0a0a",
             "indexed": false,
@@ -180,7 +181,7 @@
             "uuid": "66ea0038-2481-4c53-8e2f-229b03851701",
             "version": "2019-02-14T18:34:20.351186Z"
         },
-        {
+        "sequence_file/f9a78d6a-7c80-4c45-bedf-4bc152dc172d": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "51ffe105",
             "indexed": false,
@@ -192,7 +193,7 @@
             "uuid": "1b8bd5ec-f0c2-45e5-8fc1-455b48d9b5d6",
             "version": "2019-02-14T18:34:20.730308Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/a9ae9936-c11b-4195-b63a-fa6cb9c78e4c": {
             "describedBy": "https://schema.staging.data.humancellatlas.org/type/biomaterial/9.0.0/cell_suspension",
diff --git a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
index d0772b9d5..8590fd87a 100644
--- a/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
+++ b/test/indexer/data/fce68057-b0f0-5d11-b9a7-30e8fa3259a8.dss.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/99985ea4-d29e-4357-9879-99440a002b49": {
             "name": "FCAImmP7316894_S1_L001_I1_001.fastq.gz",
             "uuid": "01824e76-505c-4e99-9ffd-bc1b5f56f726",
             "version": "2020-08-13T10:24:33.604000Z",
@@ -13,7 +13,7 @@
             "sha256": "5f6e2b3c8d6e00fd6dd51c301d1c97f2536a7887963e0365f215cd0f96d34f97",
             "s3_etag": "2a0329a71e83818c5f8e51fa091c5d20-39"
         },
-        {
+        "sequence_file/601bacd5-c250-4dd3-a83d-c9f31a1b0dd8": {
             "name": "FCAImmP7352193_S1_L001_R2_001.fastq.gz",
             "uuid": "0526e3df-0747-40fb-b4be-99c8813deefd",
             "version": "2020-08-13T10:24:34.163000Z",
@@ -26,7 +26,7 @@
             "sha256": "5eb3a3d3cd1d20a58fef44967e43cc3bab983017fed83619ce583a190f35fc0f",
             "s3_etag": "40155c79aec333af98e27949b87fae21-445"
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-        {
+        "sequence_file/455c6c50-9424-4dac-b67c-1be48276d5b5": {
             "name": "FCAImmP7316890_S1_L001_R1_001.fastq.gz",
             "uuid": "085e5f88-ab09-4d69-bc14-afa71e1ae17c",
             "version": "2020-08-13T10:24:33.458000Z",
@@ -39,7 +39,7 @@
             "sha256": "2c1bbc2263124703a0c818aa4c75f6cfaedd1b567ad15b80fe0c2d2d3004d20e",
             "s3_etag": "bb820841d613f555c098abebd67a620d-120"
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-        {
+        "analysis_file/63bee9b4-8743-5a13-b144-80cf68313083": {
             "name": "cfa1e5da-607e-49b6-aa0d-8f43702b971f.bam",
             "uuid": "0a80f21f-3212-596b-9367-f7211c554c7d",
             "version": "2021-02-09T10:00:00.000000Z",
@@ -50,7 +50,7 @@
             "crc32c": "f9e695e2",
             "sha256": "f3f032bc303a9b2cba8ce26f69370f2e1565ab2276a9140e4abcba3721c5e39c"
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-        {
+        "analysis_file/07a81052-3964-5b08-8f2d-066c1e29de7d": {
             "name": "1248ead2-3dd4-43fe-9f7c-9609ed77d9c2.loom",
             "uuid": "0aa3a582-3905-5cba-9dd1-d3cf58be18ce",
             "version": "2021-02-09T08:34:58.000000Z",
@@ -61,7 +61,7 @@
             "crc32c": "792b4a5d",
             "sha256": "b4d1cf6d019cfb4f27e501d567bd8e9543216037d18a455e32b2012f51dc89d2"
         },
-        {
+        "sequence_file/b61e4f40-1742-4bbb-a20d-78a934c5f8de": {
             "name": "FCAImmP7352192_S1_L001_I1_001.fastq.gz",
             "uuid": "0c3e7565-d5bc-44ed-8b1c-a9446150f274",
             "version": "2020-08-13T10:24:34.100000Z",
@@ -74,7 +74,7 @@
             "sha256": "eee0705784755c472ffe202927e18264aa1664c991c5a3483a3fa6f5216a9aed",
             "s3_etag": "bed37bb5bb430de9fa47a5e0b4c0bbcc-39"
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-        {
+        "analysis_file/07a18873-6df1-57a8-848c-980bfa29fbf5": {
             "name": "3381994d-5624-4f5f-a574-01ad099c448c.loom",
             "uuid": "0c410012-5563-5e9d-9841-a0232b69d43f",
             "version": "2021-02-09T08:26:46.000000Z",
@@ -85,7 +85,7 @@
             "crc32c": "9a0339f5",
             "sha256": "a06fa80743f30442e6fae4eb7d5e85354d11459783b2b52a84ffc4996b85825d"
         },
-        {
+        "sequence_file/71c8dfa2-0a8c-4ae0-8161-933454f56420": {
             "name": "FCAImmP7198629_S1_L001_R1_001.fastq.gz",
             "uuid": "0ea260e6-08d5-4488-86bb-8bf3412540ee",
             "version": "2020-08-13T10:24:32.650000Z",
@@ -98,7 +98,7 @@
             "sha256": "7aafb4ae24d84eefc436a6c4b21af230c384271e0615f5c4fdab0103ce3d8356",
             "s3_etag": "c05e8bf9ad17eaa5e548d6dc013b3a07-122"
         },
-        {
+        "analysis_file/1f43235c-6299-527b-b470-2b6638bdaf8b": {
             "name": "37925a3b-3bce-4876-bb29-745922b2c972.bam",
             "uuid": "0edf6004-84e5-5b8a-99e2-bb60390d9b17",
             "version": "2021-02-09T08:22:39.000000Z",
@@ -109,7 +109,7 @@
             "crc32c": "5c6fa039",
             "sha256": "c0231f78ab9909b02badc89a3e8dd44f06bba1658197974eaca1d5cc63c3053a"
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-        {
+        "analysis_file/91caea03-3c9a-5ba8-9acc-3685e3a6062e": {
             "name": "a9c40eb8-24b6-4436-a3d3-e8035e84f6ae.loom",
             "uuid": "111c2683-e0ab-5704-b51f-7b93e6717415",
             "version": "2021-02-09T08:58:27.000000Z",
@@ -120,7 +120,7 @@
             "crc32c": "cbc2c019",
             "sha256": "72f702a989236ac8ee3ab989b73399776a79230e2bf507614004de81b2260396"
         },
-        {
+        "sequence_file/c30c31d2-ccfb-4651-8b78-a25a23ab4e95": {
             "name": "4834STDY7002878_S1_L001_R2_001.fastq.gz",
             "uuid": "1147a7c1-2f32-4f13-9457-929b9bce46f0",
             "version": "2020-08-13T10:24:32.079000Z",
@@ -133,7 +133,7 @@
             "sha256": "79382722d3531de6d4da59335f18428ccaccf8c01688f986fe69aa3a0a5cc3aa",
             "s3_etag": "22910df9d0c6a3a7f75bddabb9ba6d32-707"
         },
-        {
+        "sequence_file/d7f0b745-c135-4594-9a4b-a4c66c8a1520": {
             "name": "4834STDY7002882_S1_L001_R1_001.fastq.gz",
             "uuid": "120e7f3e-597a-4119-a9d6-1624704666b4",
             "version": "2020-08-13T10:24:32.208000Z",
@@ -146,7 +146,7 @@
             "sha256": "6816fea09166fd064564088335450eaa5b1083f50519e9a21fa55353920d8f80",
             "s3_etag": "157095d69509e358dde9bb6e8e4283a9-411"
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-        {
+        "analysis_file/e6604cbc-c882-5f03-b4d0-807eb969a293": {
             "name": "bc583c0e-4336-43d4-a7da-dc7e1f72b50b.loom",
             "uuid": "139bca8f-674f-5dc9-953f-9cfbf91f3179",
             "version": "2021-02-09T08:45:17.000000Z",
@@ -157,7 +157,7 @@
             "crc32c": "b3564b89",
             "sha256": "69f1d8c80296feaa8532a9c5a57f8ec32b2daed104e6477f3bd01ac240c8bee7"
         },
-        {
+        "sequence_file/24c3ce12-e4f9-4299-a005-320d602716ce": {
             "name": "FCAImmP7579223_S1_L001_I1_001.fastq.gz",
             "uuid": "15087f54-4375-44ad-9aef-405e976767c0",
             "version": "2020-08-13T10:24:35.400000Z",
@@ -170,7 +170,7 @@
             "sha256": "c3a2884fb50fbe934094ded8c48f2cdc8e0f83be65d6754cb49ff72ebcc0eda0",
             "s3_etag": "a1f0b8682c661d898803cbcc8c6d08b2-36"
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-        {
+        "analysis_file/129bdef3-ae23-5273-920f-204cccd878fc": {
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             "uuid": "15c898b4-124d-5c7b-b297-6b21226d0bda",
             "version": "2021-02-09T08:43:11.000000Z",
@@ -181,7 +181,7 @@
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@@ -194,7 +194,7 @@
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@@ -205,7 +205,7 @@
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@@ -216,7 +216,7 @@
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@@ -229,7 +229,7 @@
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@@ -242,7 +242,7 @@
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@@ -255,7 +255,7 @@
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@@ -268,7 +268,7 @@
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@@ -279,7 +279,7 @@
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@@ -292,7 +292,7 @@
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@@ -305,7 +305,7 @@
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@@ -318,7 +318,7 @@
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@@ -331,7 +331,7 @@
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@@ -342,7 +342,7 @@
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@@ -355,7 +355,7 @@
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@@ -368,7 +368,7 @@
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@@ -379,7 +379,7 @@
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@@ -392,7 +392,7 @@
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@@ -405,7 +405,7 @@
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@@ -416,7 +416,7 @@
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@@ -427,7 +427,7 @@
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@@ -440,7 +440,7 @@
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@@ -464,7 +464,7 @@
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@@ -525,7 +525,7 @@
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@@ -575,7 +575,7 @@
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@@ -599,7 +599,7 @@
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@@ -610,7 +610,7 @@
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@@ -621,7 +621,7 @@
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@@ -632,7 +632,7 @@
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@@ -1578,7 +1578,7 @@
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@@ -1600,7 +1600,7 @@
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@@ -1789,7 +1789,7 @@
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@@ -1837,7 +1837,7 @@
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@@ -1848,7 +1848,7 @@
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@@ -1859,7 +1859,7 @@
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@@ -1896,7 +1896,7 @@
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@@ -1907,7 +1907,7 @@
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@@ -1918,7 +1918,7 @@
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@@ -1942,7 +1942,7 @@
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@@ -1968,7 +1968,7 @@
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@@ -1981,7 +1981,7 @@
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             "version": "2020-08-13T10:24:33.664000Z",
@@ -2451,7 +2451,7 @@
             "sha256": "6f492eed4c3dce56c23be051c2280c0d02082764cc12eee0d78ec053575e33c8",
             "s3_etag": "01f727a9513e37db4f9127dddaa83443-439"
         }
-    ],
+    },
     "metadata": {
         "analysis_file/00dbea45-4e4d-5220-985e-afd8dcfce0b5": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.2.0/analysis_file",
diff --git a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
index d3055ed30..531a7b240 100644
--- a/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
+++ b/test/indexer/data/ffac201f-4b1c-4455-bd58-19c1a9e863b4.dss.hca.json
@@ -1,6 +1,6 @@
 {
-    "manifest": [
-        {
+    "manifest": {
+        "sequence_file/4015da8b-18d8-4f3c-b2b0-54f0b77ae80a": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "49a9085f",
             "indexed": false,
@@ -12,7 +12,7 @@
             "uuid": "a8b8479d-cfa9-4f74-909f-49552439e698",
             "version": "2019-10-09T17:22:51.560099Z"
         },
-        {
+        "sequence_file/fa17159e-52ec-4a88-80cf-a3be5e2e9988": {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "dd098625",
             "indexed": false,
@@ -24,7 +24,7 @@
             "uuid": "7338932d-edc9-49a9-8dbf-e459a465800f",
             "version": "2019-10-09T17:22:52.628550Z"
         }
-    ],
+    },
     "metadata": {
         "cell_suspension/0432e9a5-604f-4cb7-8571-014eb5fd8ba2": {
             "describedBy": "https://schema.humancellatlas.org/type/biomaterial/13.3.0/cell_suspension",
diff --git a/test/indexer/test_indexer.py b/test/indexer/test_indexer.py
index df3c51516..34c395d77 100644
--- a/test/indexer/test_indexer.py
+++ b/test/indexer/test_indexer.py
@@ -583,7 +583,7 @@ def _patch_bundle(self, bundle: Bundle) -> str:
         new_file_uuid = str(uuid4())
         bundle.manifest = deepcopy(bundle.manifest)
         file_name = '21935_7#154_2.fastq.gz'
-        for file in bundle.manifest:
+        for file in bundle.manifest.values():
             if file['name'] == file_name:
                 old_file_uuid = file['uuid']
                 file['uuid'] = new_file_uuid
diff --git a/test/integration_test.py b/test/integration_test.py
index 9807d488e..9ab465812 100644
--- a/test/integration_test.py
+++ b/test/integration_test.py
@@ -1939,7 +1939,7 @@ def _test_catalog(self, catalog: config.Catalog):
                 metadata = bundle_json['metadata']
                 links = bundle_json['links']
                 stitched = bundle_json['stitched']
-                self.assertIsInstance(manifest, list)
+                self.assertIsInstance(manifest, dict)
                 self.assertIsInstance(metadata, dict)
                 self.assertIsInstance(links, dict)
                 self.assertIsInstance(stitched, list)
diff --git a/test/service/test_manifest.py b/test/service/test_manifest.py
index a47c36e12..4513bbbe7 100644
--- a/test/service/test_manifest.py
+++ b/test/service/test_manifest.py
@@ -29,7 +29,6 @@
 )
 from typing import (
     Optional,
-    cast,
 )
 from unittest.mock import (
     MagicMock,
@@ -111,7 +110,6 @@
     JSON,
     JSONs,
     MutableJSON,
-    MutableJSONs,
 )
 from indexer import (
     AnvilCannedBundleTestCase,
@@ -377,7 +375,7 @@ def _shared_file_bundle(self, bundle):
         links = self._replace_uuids(bundle.links, old_to_new)
         return DSSBundle(fqid=self.bundle_fqid(uuid=old_to_new[bundle.uuid],
                                                version=bundle.version),
-                         manifest=cast(MutableJSONs, bundle.manifest),
+                         manifest=bundle.manifest,
                          metadata=metadata,
                          links=links)
 
@@ -555,15 +553,14 @@ def test_compact_manifest(self):
         # redundant file contributions from different bundles (for example due
         # to stitching)
         entity_ids = {
-            '89e313db-4423-4d53-b17e-164949acfa8f',  # Supplementary file (metadata)
-            '5f9b45af-9a26-4b16-a785-7f2d1053dd7c',  # Supplementary file (data)
+            '89e313db-4423-4d53-b17e-164949acfa8f',  # Supplementary file
             '67bc798b-a34a-4104-8cab-cad648471f69',  # Project
         }
-        manifest = [
-            entry
-            for entry in bundle.manifest
-            if entry['uuid'] in entity_ids
-        ]
+        manifest = {
+            ref: entry
+            for ref, entry in bundle.manifest.items()
+            if EntityReference.parse(ref).entity_id in entity_ids
+        }
         metadata = {
             ref: copy_json(content)
             for ref, content in bundle.metadata.items()