From bf254f2a855ab9156a609acb0c3e977f1c2f6cc8 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] [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 beec73b59..c30d32039 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'
     }
 
@@ -463,7 +454,6 @@ 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",
-            "version": "1"
-        },
-        {
-            "crc32c": "68AEC241",
-            "sha1": "1296d3c9b98cef091f1aecd6d9df25fa7f780d5c",
-            "sha256": "c9cd608014bb3cfd7b0ab891cd597272f0e860f0d5e7f0eab38338d828ba2bec",
-            "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",
@@ -119,30 +11,6 @@
             "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"
         }
     ],
     "metadata": {
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	
@@ -1,149 +1,5 @@
 {
     "manifest": [
-        {
-            "crc32c": "A78360AF",
-            "sha1": "e71327f467a43cca405794f5bf59856d78d93243",
-            "sha256": "f3c7f5fa20f3a57093de7e3d4afebfe0e79e0fc4199787f0527b83cbd548a462",
-            "s3_etag": "06621a64a5764cd05279e6de5c45940d",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "cell_suspension_0.json",
-            "size": 1084,
-            "uuid": "23e6c6f8-8bc4-4f18-81fd-1803e5628f6e",
-            "version": "1"
-        },
-        {
-            "crc32c": "D8097612",
-            "sha1": "f7eef7c5deab2669f7f19bc8b136564481dce1fa",
-            "sha256": "13949d71db41b28215ef855e41b63c16b88908eda26a24de405955f678125632",
-            "s3_etag": "8bf3ce1178c2204273571e1b4840ae25",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "collection_protocol_0.json",
-            "size": 698,
-            "uuid": "49c1ee68-51ea-476e-8432-c7419adb366b",
-            "version": "1"
-        },
-        {
-            "crc32c": "8A734C29",
-            "sha1": "94744afce8a76a828338a74cd1e0448b37ed9968",
-            "sha256": "d0a8f924a7861d9022a2199f106e35a643a0d1d0bb5d56f6d1201cd2890a850d",
-            "s3_etag": "ee2968d79156fdb69de1a6ef61af7fea",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "dissociation_protocol_0.json",
-            "size": 759,
-            "uuid": "35cf0ab5-c983-4da8-bb1c-c6504d74db8e",
-            "version": "1"
-        },
-        {
-            "crc32c": "477C14C4",
-            "sha1": "69e19c2322780bb6c31140214036e7286a66c022",
-            "sha256": "17a1c4f8a5f28028654a3e279d97695c6f3387a6ce20dd744381a2d8d4beae2b",
-            "s3_etag": "ee99d4e6d6da4ffdf0b321cdcf9d229d",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "donor_organism_0.json",
-            "size": 1129,
-            "uuid": "b7ef3cae-d65e-474d-ab6c-adbed59ed1ff",
-            "version": "1"
-        },
-        {
-            "crc32c": "FCDAF214",
-            "sha1": "23f4a2abf4456b2f2939645c7a1b65de59f460e6",
-            "sha256": "ba0c9eaf5361a1b3b8ec71f0050c01951cf756aff725b7bbe8ca5ec08c2e8305",
-            "s3_etag": "918e63ffedd853d5cb5418c89ec71f3c",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "enrichment_protocol_0.json",
-            "size": 948,
-            "uuid": "67f56a17-0a66-42c6-aac6-5aebe13aaf89",
-            "version": "1"
-        },
-        {
-            "crc32c": "20D5D16C",
-            "sha1": "5ce58077eed436a134c1a4baf4a838269e74e8bc",
-            "sha256": "0efe158e06b9d22ba10c72173ba3d175c5d33f3e0b1665a88cb49a1e90bc19f6",
-            "s3_etag": "fa5cd0c751962d1691218e5a99b02b14",
-            "content-type": "application/json; dcp-type=\"metadata/json\"",
-            "indexed": true,
-            "name": "enrichment_protocol_1.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
--- 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
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@@ -408,18 +12,6 @@
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@@ -432,18 +24,6 @@
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@@ -456,78 +36,6 @@
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@@ -540,18 +48,6 @@
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@@ -564,18 +60,6 @@
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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	
@@ -1,113 +1,5 @@
 {
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@@ -119,30 +11,6 @@
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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	
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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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@@ -120,30 +12,6 @@
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@@ -156,18 +24,6 @@
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@@ -180,18 +36,6 @@
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@@ -204,18 +48,6 @@
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@@ -252,18 +72,6 @@
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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
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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 0a1c182fb..590e31ac2 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
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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
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+++ 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
index ee5b99fb6..27c2bd7f1 100644
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+++ 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
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--- 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
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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
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+++ b/test/indexer/data/00f48893-5e9d-52cd-b32d-af88edccabfa.dss.hca.json
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@@ -513,16 +183,6 @@
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@@ -536,26 +196,6 @@
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@@ -567,26 +207,6 @@
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@@ -598,26 +218,6 @@
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@@ -631,26 +231,6 @@
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@@ -662,46 +242,6 @@
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@@ -715,56 +255,6 @@
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-            "version": "2019-09-13T08:37:53.853000Z",
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@@ -778,26 +268,6 @@
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@@ -820,16 +290,6 @@
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@@ -843,16 +303,6 @@
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@@ -865,96 +315,6 @@
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@@ -4803,7 +4163,6 @@
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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 @@
 {
     "manifest": [
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@@ -66,36 +26,6 @@
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-            "version": "2021-06-28T14:21:17.614000Z",
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@@ -122,36 +52,6 @@
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-            "uuid": "e6b8f32e-7c8e-4308-b596-91006cde4b51",
-            "version": "2021-06-28T14:21:17.006000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
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-            "version": "2021-06-28T14:21:17.599000Z",
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-            "uuid": "ee52ecd1-68c0-48dd-82c2-6d3e45869b38",
-            "version": "2021-06-28T14:21:17.545000Z",
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         {
             "name": "mouse_cortex_S2_L003_R1_001.fastq",
             "uuid": "fd13fc62-8767-45d7-aa48-8a140f9a5005",
@@ -3619,7 +3099,6 @@
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-
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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": "012af05a-4771-45e5-bb92-9b63fcbde822",
-            "version": "2021-05-10T23:24:56.488000Z",
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             "name": "Adult2_S35_L004_R1_001.fastq.gz",
             "uuid": "01d2d764-457f-44c5-8b18-a6fadf73c1f7",
@@ -75,36 +65,6 @@
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-            "version": "2021-05-10T23:25:00.590000Z",
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-            "version": "2021-05-10T23:24:58.005000Z",
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-            "version": "2021-05-10T23:24:58.932000Z",
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         {
             "name": "Young3_S10_L001_R1_001.fastq.gz",
             "uuid": "03815b54-b935-4f04-96ac-56f7c87d601d",
@@ -144,46 +104,6 @@
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-            "version": "2021-05-10T23:24:59.644000Z",
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-        {
-            "name": "donor_organism_0.json",
-            "uuid": "04240909-9185-48d3-a4e9-9eb71b3c6648",
-            "version": "2021-05-10T23:24:54.910000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
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-            "uuid": "04836733-0449-4e57-be2e-6f3b8fbdfb12",
-            "version": "2021-05-10T23:25:12.412000Z",
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-            "version": "2021-05-10T23:24:56.774000Z",
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         {
             "name": "Fetal3_S13_L004_I1_001.fastq.gz",
             "uuid": "05736d0e-ab04-4183-9c38-1bfdf028978f",
@@ -210,16 +130,6 @@
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             "uuid": "062700c0-e8ed-46e2-b7cd-7cc6d8c3fc85",
@@ -246,26 +156,6 @@
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-            "version": "2021-05-10T23:25:00.232000Z",
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         {
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             "uuid": "073edb43-47d2-45c7-bff2-76c503ebb951",
@@ -292,26 +182,6 @@
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-            "version": "2021-05-10T23:24:55.328000Z",
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-            "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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@@ -358,26 +208,6 @@
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             "uuid": "09be6713-f8fa-48a6-873e-d9524c526c8f",
@@ -391,16 +221,6 @@
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             "uuid": "09ffc9cf-6e64-4d47-8188-a8588ec39861",
@@ -440,36 +260,6 @@
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@@ -496,16 +286,6 @@
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@@ -519,36 +299,6 @@
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@@ -575,16 +325,6 @@
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@@ -598,46 +338,6 @@
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@@ -703,16 +403,6 @@
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@@ -726,46 +416,6 @@
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@@ -8530,16 +4550,6 @@
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@@ -8553,46 +4563,6 @@
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@@ -8619,46 +4589,6 @@
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@@ -8685,26 +4615,6 @@
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@@ -8744,56 +4654,6 @@
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@@ -8820,36 +4680,6 @@
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@@ -8863,36 +4693,6 @@
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@@ -8906,56 +4706,6 @@
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@@ -8968,26 +4718,6 @@
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@@ -38542,7 +34272,6 @@
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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 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 @@
 {
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@@ -75,106 +25,6 @@
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-        {
-            "name": "library_preparation_protocol_0.json",
-            "uuid": "ca16fcf2-48df-4b2a-bd48-a5fce6b0cd75",
-            "version": "2021-03-18T11:38:47.884000Z",
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "size": 1095,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "cell_line_0.json",
-            "uuid": "d91bbbd5-c2c1-4bb7-906f-494ee686658e",
-            "version": "2021-03-18T11:38:47.207000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 1047,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "organoid_0.json",
-            "uuid": "df23c109-59f0-46d3-bd09-660175b51bda",
-            "version": "2021-03-18T11:38:47.509000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 836,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "enrichment_protocol_0.json",
-            "uuid": "f4234276-bdac-4ad1-b4a0-4b5d595ae04c",
-            "version": "2021-03-18T11:38:47.863000Z",
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "size": 710,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
         }
     ],
     "metadata": {
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 @@
 {
     "manifest": [
-        {
-            "name": "cell_suspension_0.json",
-            "uuid": "906f8f09-deaa-40bb-bf50-27d2336b2dc4",
-            "version": "2019-09-20T13:43:52.387000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 1033,
-            "indexed": true,
-            "crc32c": "003027e8",
-            "sha1": "a4b1887a5eb4896ab39bf70526fc3a4de1365ed4",
-            "sha256": "d54eefb2f3a7f4f926dd6bc02c18bd4565f34fc45f2f748dfa04f16e52e238b5",
-            "s3_etag": "26f61da5c684da885b60b361404a76bb"
-        },
-        {
-            "name": "specimen_from_organism_0.json",
-            "uuid": "d6a518a8-0c5d-4cb0-aed5-68f3455c2bda",
-            "version": "2019-09-20T13:43:52.654000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 1300,
-            "indexed": true,
-            "crc32c": "ef2adac7",
-            "sha1": "2270093c55e4e5d1cc6b68ef60cb6c8abd6127ae",
-            "sha256": "f4688fdb5c6b9b18c3993599c1d6a853070889eb702a06fae790409699c292c1",
-            "s3_etag": "3f17191e3721a119a85fc0ea784c0a81"
-        },
-        {
-            "name": "cell_line_0.json",
-            "uuid": "70054038-cb12-429d-bb37-69185ff1deee",
-            "version": "2019-09-20T13:43:52.455000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 1527,
-            "indexed": true,
-            "crc32c": "be0eeb22",
-            "sha1": "d74b73ac34bca57f9be0daa7de3dfc6174f23aae",
-            "sha256": "4353ba866910713ded6a370f3cf7a6cdd475f916076b2c0f4f1e28e17a162fe0",
-            "s3_etag": "d879779af504915743e70405db0a5b5f"
-        },
-        {
-            "name": "donor_organism_0.json",
-            "uuid": "2b7adb0a-82a4-4319-80d1-4a73d879dec1",
-            "version": "2019-09-20T13:43:52.612000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 1399,
-            "indexed": true,
-            "crc32c": "43523c47",
-            "sha1": "517eed8395bef0f81cd499a631c6ee52a0db6c24",
-            "sha256": "c3fcb0c8b9ce3362f6367caf12862cd98e3240919efd87c1ccea1c18e84a8722",
-            "s3_etag": "f6c5034159c6a90ab4eef05dea5eeb18"
-        },
-        {
-            "name": "sequence_file_0.json",
-            "uuid": "5f68ea73-350b-4d37-a341-3004139fb699",
-            "version": "2019-09-20T13:50:35.660000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 847,
-            "indexed": true,
-            "crc32c": "3738e610",
-            "sha1": "e8bd13021e8cb3b5b664a880121c00453a7614f9",
-            "sha256": "ec2be2132d617c2d49c5476617a8e0ddfbcd50d6ac5f91fafd27fa0aa5cecf38",
-            "s3_etag": "8223c2f0408ced259f5b593ff2976822"
-        },
-        {
-            "name": "sequence_file_1.json",
-            "uuid": "23f8e139-f4fa-4476-ba59-ff5d37003c34",
-            "version": "2019-09-20T13:50:08.455000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 847,
-            "indexed": true,
-            "crc32c": "4f88ffe0",
-            "sha1": "7fdda44357784f1546dce02df2c3644abe0a0065",
-            "sha256": "81baa638a51e1674133cc79a52f4fde8ffdfd14cb83d10371f0cc36768dd0c98",
-            "s3_etag": "9cef189ee5a9630507cdd119aa10eda4"
-        },
-        {
-            "name": "sequence_file_2.json",
-            "uuid": "3c3d882a-cc38-4eea-ac53-0885f906852e",
-            "version": "2019-09-20T13:52:19.666000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 847,
-            "indexed": true,
-            "crc32c": "68264895",
-            "sha1": "a5d03344222236ea519f2116778f14b2f04888a1",
-            "sha256": "8b4a636d29f780020ceea6d30cebe716646c41c7b044467f666d285ccded36f3",
-            "s3_etag": "c210b53e32b633f8522bb6be0c89e87b"
-        },
-        {
-            "name": "sequence_file_3.json",
-            "uuid": "35e07477-76cb-4a92-99b6-7b3bbb02ec06",
-            "version": "2019-09-20T13:49:42.254000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 847,
-            "indexed": true,
-            "crc32c": "8cb2ff3f",
-            "sha1": "7f00912ad99b75a511c35d5ce596ea29462d4fbe",
-            "sha256": "3073173c130a387570f53058bb206318fd967a2231d7c9a5eae4816ca3c7bf46",
-            "s3_etag": "3c39efa8a8b6c8546dccc9a030dfc187"
-        },
-        {
-            "name": "sequence_file_4.json",
-            "uuid": "63051b9f-87d4-4853-a4a0-5cc742ef6e72",
-            "version": "2019-09-20T13:50:59.836000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 847,
-            "indexed": true,
-            "crc32c": "9b1ec98b",
-            "sha1": "476e62c8a8ad159d508d97f5a4abfa18a419a761",
-            "sha256": "384e0b507d97c1bfaf0fa4e6587b80e1565850a0d713f591f1b36e31633df6e1",
-            "s3_etag": "aa2265b201e2abfd2ca8f3c3c8535238"
-        },
-        {
-            "name": "sequence_file_5.json",
-            "uuid": "6ca8e43f-5f40-4eb9-bfa9-294c54dbeade",
-            "version": "2019-09-20T13:52:17.560000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 847,
-            "indexed": true,
-            "crc32c": "a563fb6e",
-            "sha1": "922b78b501ff086677ab2481450f21e075180211",
-            "sha256": "52d4e678736191df3a299628c1ec8f34628ae7270860266f90d091e30c40e588",
-            "s3_etag": "c818db35352e2230dd1b2b9e1b61b839"
-        },
-        {
-            "name": "sequence_file_6.json",
-            "uuid": "3dffc456-caaf-4823-9f65-fc0db7abacbc",
-            "version": "2019-09-20T13:49:42.771000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 847,
-            "indexed": true,
-            "crc32c": "969b6567",
-            "sha1": "acd83c3e3c7131a44cccfbf7fa4351d34b600301",
-            "sha256": "77e6413b121680434e226ab43d493abdb44b9839b12d29102d5257254871e865",
-            "s3_etag": "cf78c04caea2783c2f61a8876cf7115a"
-        },
-        {
-            "name": "sequence_file_7.json",
-            "uuid": "a2f4b05d-0dae-4655-acfd-ef3b91ae0ad0",
-            "version": "2019-09-20T13:50:08.492000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 847,
-            "indexed": true,
-            "crc32c": "b993bbe6",
-            "sha1": "489e857a10d71a46b5efa07816b7569de243ce5e",
-            "sha256": "4f4dcadd10f72198c1e3e675f4def3bcd88d8b03da4ce47f8d06fb441131b0fd",
-            "s3_etag": "9895d1814034cbc382d58fb93407aef2"
-        },
-        {
-            "name": "sequence_file_8.json",
-            "uuid": "98ee0901-d34c-48a5-915a-0511bac325ec",
-            "version": "2019-09-20T13:53:16.941000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 847,
-            "indexed": true,
-            "crc32c": "c67706ab",
-            "sha1": "bba5f91afcdc8e6622f2d76dc5b5dbeba3345caf",
-            "sha256": "b900cb7f3bf45fc4420a24acb1108d63c768b0cfc1b95bd7f26f0a222ea953db",
-            "s3_etag": "b6dcb7ec07332207b959d32822b00e0a"
-        },
-        {
-            "name": "sequence_file_9.json",
-            "uuid": "27fc1a2e-d70e-47ee-a4b7-92bf57e5b7a6",
-            "version": "2019-09-20T13:50:35.338000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 847,
-            "indexed": true,
-            "crc32c": "ec844324",
-            "sha1": "fea8b934f9869efebbcfacb3fd2fb782e34dad29",
-            "sha256": "71975b4328e5d0cf04bbd89242a484694e4ad3d91279e67c90212db9ac6ce4a8",
-            "s3_etag": "fbfed57ac71437dad8fb0d5de9f1a041"
-        },
-        {
-            "name": "sequence_file_10.json",
-            "uuid": "133f2a25-f3aa-49a7-b9b6-d185d302fb26",
-            "version": "2019-09-20T13:51:28.379000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 847,
-            "indexed": true,
-            "crc32c": "b68d086e",
-            "sha1": "58b74845529443d726ba4405c7bf4d1db5eaa00e",
-            "sha256": "4bcc03518394b442cf64738ee8d02e5ec31307d7044e5a4002a029a94cae5ad6",
-            "s3_etag": "5a675c82b3edfd124810ebfe9a0eab96"
-        },
-        {
-            "name": "sequence_file_11.json",
-            "uuid": "e46af70a-0396-41db-9b74-330cb8244124",
-            "version": "2019-09-20T13:52:19.118000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 847,
-            "indexed": true,
-            "crc32c": "85291395",
-            "sha1": "1ce811c5fab68ce865f88aed5942db1f627d8038",
-            "sha256": "0aeeab0a48f81e883ad334c52892b13e0ab9cba1e856f9766dbb908c0777fd01",
-            "s3_etag": "3d009b3c7aa9fc36ba424022fc2f3c0b"
-        },
-        {
-            "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"
         },
-        {
-            "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"
         },
-        {
-            "name": "",
-            "uuid": "df5114c9-9f52-451b-afde-3673392fc864",
-            "version": "2019-09-20T13:43:52.607000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 368,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "",
-            "uuid": "e46af70a-0396-41db-9b74-330cb8244124",
-            "version": "2019-09-20T13:52:19.118000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 645,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "IDC9_L002_R2.fastq.gz",
             "uuid": "ea44789f-43b3-4684-b515-800605394177",
@@ -443,16 +163,6 @@
             "s3_etag": "29da5762d5a55b9ecbd14c8663039f11-62",
             "drs_uri": "drs://mock_tdr.lan/v1_d8c20944-739f-4e7d-9161-b720953432ce_f140bd59-16c2-5082-aaf6-1c929e7063c6"
         },
-        {
-            "name": "",
-            "uuid": "eaf15851-97e3-4e4b-b81b-0e625098f4d5",
-            "version": "2019-09-20T13:43:52.177000Z",
-            "content-type": "application/json; dcp-type=\"metadata/protocol\"",
-            "size": 702,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "IDC9_L002_I1.fastq.gz",
             "uuid": "ed7405bd-c1d0-4501-9a7a-7e953d887322",
@@ -1517,6 +1227,5 @@
             }
         ]
     },
-
     "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 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 @@
 {
     "manifest": [
-        {
-            "content-type": "application/json;",
-            "crc32c": "00000000",
-            "indexed": true,
-            "name": "project_0.json",
-            "s3_etag": null,
-            "sha1": null,
-            "sha256": "0000000000000000000000000000000000000000000000000000000000000000",
-            "size": 4353,
-            "uuid": "90bf705c-d891-5ce2-aa54-094488b445c6",
-            "version": "2021-01-01T00:00:00.000000Z"
-        },
-        {
-            "content-type": "application/json;",
-            "crc32c": "00000000",
-            "indexed": true,
-            "name": "process_0.json",
-            "s3_etag": null,
-            "sha1": null,
-            "sha256": "0000000000000000000000000000000000000000000000000000000000000000",
-            "size": 388,
-            "uuid": "1ed68210-eaba-531d-ba9e-db80164d65ef",
-            "version": "2021-01-01T00:00:00.000000Z"
-        },
-        {
-            "content-type": "application/json;",
-            "crc32c": "00000000",
-            "indexed": true,
-            "name": "process_1.json",
-            "s3_etag": null,
-            "sha1": null,
-            "sha256": "0000000000000000000000000000000000000000000000000000000000000000",
-            "size": 388,
-            "uuid": "37e91a9f-b04e-5313-bbc0-4c394406247e",
-            "version": "2021-01-01T00:00:00.000000Z"
-        },
-        {
-            "content-type": "application/json;",
-            "crc32c": "00000000",
-            "indexed": true,
-            "name": "process_2.json",
-            "s3_etag": null,
-            "sha1": null,
-            "sha256": "0000000000000000000000000000000000000000000000000000000000000000",
-            "size": 388,
-            "uuid": "b0092a47-b19d-5b34-b004-cb8edd8c625b",
-            "version": "2021-01-01T00:00:00.000000Z"
-        },
-        {
-            "content-type": "application/json;",
-            "crc32c": "00000000",
-            "indexed": true,
-            "name": "process_3.json",
-            "s3_etag": null,
-            "sha1": null,
-            "sha256": "0000000000000000000000000000000000000000000000000000000000000000",
-            "size": 388,
-            "uuid": "bd6a4a38-c44b-5d17-b2b1-d0d4c4531bf0",
-            "version": "2021-01-01T00:00:00.000000Z"
-        },
-        {
-            "content-type": "application/json;",
-            "crc32c": "00000000",
-            "indexed": true,
-            "name": "cell_suspension_0.json",
-            "s3_etag": null,
-            "sha1": null,
-            "sha256": "0000000000000000000000000000000000000000000000000000000000000000",
-            "size": 728,
-            "uuid": "119c4135-7b77-5003-a150-f052e22c6834",
-            "version": "2021-01-01T00:00:00.000000Z"
-        },
-        {
-            "content-type": "application/json;",
-            "crc32c": "00000000",
-            "indexed": true,
-            "name": "cell_suspension_1.json",
-            "s3_etag": null,
-            "sha1": null,
-            "sha256": "0000000000000000000000000000000000000000000000000000000000000000",
-            "size": 724,
-            "uuid": "6ff38054-9296-5d4c-b238-6a3b01a15175",
-            "version": "2021-01-01T00:00:00.000000Z"
-        },
-        {
-            "content-type": "application/json;",
-            "crc32c": "00000000",
-            "indexed": true,
-            "name": "sequence_file_0.json",
-            "s3_etag": null,
-            "sha1": null,
-            "sha256": "0000000000000000000000000000000000000000000000000000000000000000",
-            "size": 444,
-            "uuid": "8da4bdb9-ab64-5a90-8bce-f0ed5106ea41",
-            "version": "2021-01-01T00:00:00.000000Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "9d9e936d",
@@ -108,18 +12,6 @@
             "uuid": "c88f5811-6b23-5f9c-951f-29b4a80e6b4b",
             "version": "2021-01-01T00:00:00.000000Z"
         },
-        {
-            "content-type": "application/json;",
-            "crc32c": "00000000",
-            "indexed": true,
-            "name": "sequence_file_1.json",
-            "s3_etag": null,
-            "sha1": null,
-            "sha256": "0000000000000000000000000000000000000000000000000000000000000000",
-            "size": 444,
-            "uuid": "de17aa7d-be28-53c1-b7a3-1f4b3989e3e6",
-            "version": "2021-01-01T00:00:00.000000Z"
-        },
         {
             "content-type": "application/gzip; dcp-type=data",
             "crc32c": "e30fa683",
@@ -131,78 +23,6 @@
             "size": 275,
             "uuid": "14c05ce3-f946-5936-893c-ee0ddd7407fb",
             "version": "2021-01-01T00:00:00.000000Z"
-        },
-        {
-            "content-type": "application/json;",
-            "crc32c": "00000000",
-            "indexed": true,
-            "name": "library_preparation_protocol_0.json",
-            "s3_etag": null,
-            "sha1": null,
-            "sha256": "0000000000000000000000000000000000000000000000000000000000000000",
-            "size": 2557,
-            "uuid": "767282b2-2fc1-5559-b020-29686b810206",
-            "version": "2021-01-01T00:00:00.000000Z"
-        },
-        {
-            "content-type": "application/json;",
-            "crc32c": "00000000",
-            "indexed": true,
-            "name": "sequencing_protocol_0.json",
-            "s3_etag": null,
-            "sha1": null,
-            "sha256": "0000000000000000000000000000000000000000000000000000000000000000",
-            "size": 945,
-            "uuid": "1b8dfafd-178f-5826-a661-8a022334aaeb",
-            "version": "2021-01-01T00:00:00.000000Z"
-        },
-        {
-            "content-type": "application/json;",
-            "crc32c": "00000000",
-            "indexed": true,
-            "name": "specimen_from_organism_0.json",
-            "s3_etag": null,
-            "sha1": null,
-            "sha256": "0000000000000000000000000000000000000000000000000000000000000000",
-            "size": 770,
-            "uuid": "3bee0c9a-aced-52f2-b97f-89518f826b36",
-            "version": "2021-01-01T00:00:00.000000Z"
-        },
-        {
-            "content-type": "application/json;",
-            "crc32c": "00000000",
-            "indexed": true,
-            "name": "enrichment_protocol_0.json",
-            "s3_etag": null,
-            "sha1": null,
-            "sha256": "0000000000000000000000000000000000000000000000000000000000000000",
-            "size": 1836,
-            "uuid": "46435803-7ee8-5157-8569-8a61ad50c315",
-            "version": "2021-01-01T00:00:00.000000Z"
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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
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+++ b/test/indexer/data/1f6afb64-fa14-5c6f-a474-a742540108a3.dss.hca.json
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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
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index 3859c59bc..1bdfee488 100644
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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 0b94b5ece..261e65119 100644
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+++ b/test/indexer/data/3ac62c33-93e1-56b4-b857-59497f5d942d.dss.hca.json
@@ -1,77 +1,5 @@
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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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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
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+++ 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
--- a/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
+++ b/test/indexer/data/4426adc5-b3c5-5aab-ab86-51d8ce44dfbe.tdr.hca.json
@@ -1,45 +1,5 @@
 {
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@@ -177,16 +37,6 @@
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@@ -211,26 +61,6 @@
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@@ -244,26 +74,6 @@
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@@ -276,16 +86,6 @@
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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
--- a/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
+++ b/test/indexer/data/4b03c1ce-9df1-5cd5-a8e4-48a2fe095081.dss.hca.json
@@ -1,15 +1,5 @@
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@@ -21,17 +11,6 @@
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index 190412c61..2328e97fd 100644
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             "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 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 @@
 {
     "manifest": [
-        {
-            "name": "cell_suspension_0.json",
-            "uuid": "00ccb65c-2134-4309-9199-bea00ea1d5de",
-            "version": "2019-10-22T17:46:02.113000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 704,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "analysis_file_0.json",
-            "uuid": "0115dbfc-99f2-59b4-8430-75cd79e3c04d",
-            "version": "2020-02-03T10:30:00.000000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 327,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "process_0.json",
-            "uuid": "01f7c3d0-d4be-432d-aa25-8c7fbce20b49",
-            "version": "2019-10-22T17:46:06.177000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 320,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "process_1.json",
-            "uuid": "03c1159c-1a7a-4ede-bac4-d2093b260c65",
-            "version": "2019-10-22T17:46:04.919000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 302,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "donor_organism_0.json",
-            "uuid": "05617ca5-c033-40aa-b865-45b34a14bc27",
-            "version": "2019-10-22T17:46:01.981000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 1110,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "specimen_from_organism_0.json",
-            "uuid": "0635494f-d45d-48a9-81b1-5f1d4ac15835",
-            "version": "2019-10-22T17:46:02.097000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
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-            "indexed": true,
-            "crc32c": "",
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-        {
-            "name": "supplementary_file_0.json",
-            "uuid": "06e90b33-4403-41e8-b783-e65bf7de982a",
-            "version": "2019-10-22T19:46:28.778000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 446,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "CZIKidney7587405_S1_L001_R1_001.fastq.gz",
             "uuid": "075284e4-6a7b-45ba-a990-112beefd1296",
@@ -96,56 +26,6 @@
             "sha256": "f2ec67873c9ac76a4eb94bd8f7aa13aabe877778115b567471a6237d06f3d35f",
             "s3_etag": "2365f210fc1bab590021b2031d893706-522"
         },
-        {
-            "name": "process_2.json",
-            "uuid": "082e87ac-5cf6-4bad-bedb-5f6591b8f566",
-            "version": "2019-10-22T17:46:06.486000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 320,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
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-        {
-            "name": "process_3.json",
-            "uuid": "09cd4cb6-65e3-44eb-b5b1-796ac895013d",
-            "version": "2019-10-22T17:46:02.644000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 301,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
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-        {
-            "name": "analysis_process_0.json",
-            "uuid": "0aa931a7-1850-47ff-86f9-2e3b1260cbb3",
-            "version": "2020-02-03T10:30:00.000000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 14716,
-            "indexed": true,
-            "crc32c": "",
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-        },
-        {
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-            "uuid": "0b52914d-687b-44d1-9a70-a95df55ed502",
-            "version": "2019-10-22T17:46:06.278000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 320,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "sequence_file_0.json",
-            "uuid": "0c8d1b87-0d6e-4e47-8130-1372bfa05c51",
-            "version": "2019-10-22T19:55:25.167000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 382,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "51fb7eb7-a422-482e-a98e-c9e6f9628e97.bam",
             "uuid": "0d2f92fd-72da-53e6-8035-6b9b2b41a2f6",
@@ -157,26 +37,6 @@
             "crc32c": "1747a06c",
             "sha256": "2bb185ee6e44e7bf6a2768dbf4e0509cc79f7ee0f956cbdaf87977b0a1b8ca96"
         },
-        {
-            "name": "cell_suspension_1.json",
-            "uuid": "0d6404e4-f507-4c6d-aa26-4c83c058b623",
-            "version": "2019-10-22T17:46:02.024000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 773,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
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-        {
-            "name": "process_5.json",
-            "uuid": "0de1f04e-aaf3-4dc7-9869-248e87207d93",
-            "version": "2019-10-22T17:46:04.924000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 302,
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-            "crc32c": "",
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         {
             "name": "0f14c412-5014-4ac0-9a71-858b2f047777.bam",
             "uuid": "0df377a4-119b-5600-a3e6-e7c1bc94033f",
@@ -201,16 +61,6 @@
             "sha256": "dfeed362194feb9731fb01ddb194b5d32bef27aa71be1ac96145e99d89321092",
             "s3_etag": "aaab19ef6c64720286e392b72168b0a0-230"
         },
-        {
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-            "uuid": "0f14c412-5014-4ac0-9a71-858b2f047777",
-            "version": "2019-10-22T17:46:05.065000Z",
-            "content-type": "application/json; dcp-type=\"metadata/process\"",
-            "size": 320,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "3a20b6a5-6652-4486-86bc-842c7c31c343.loom",
             "uuid": "0f2bdf51-97c6-5892-b9e7-ad826dbf1321",
@@ -222,16 +72,6 @@
             "crc32c": "c3003233",
             "sha256": "b4c9abbc701054b0b8685c6567566df4f01180dcb83ba6bdb35d250167bb7ca1"
         },
-        {
-            "name": "analysis_file_1.json",
-            "uuid": "0f9e435b-dbd3-5fd6-9b4e-347433de69b0",
-            "version": "2020-02-03T10:30:00.000000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 327,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
         {
             "name": "CZIKidney7632802_S1_L001_R2_001.fastq.gz",
             "uuid": "0fadf81a-30b4-4e70-ba6f-028950d06ec4",
@@ -245,16 +85,6 @@
             "sha256": "f2743a5243764eb59f04f88f673abc500d0a4c5538ae03b2fb81634155eba960",
             "s3_etag": "afe7816bac5b09b8496366eda4bb52cd-197"
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-        {
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-            "uuid": "10439c86-98bb-5009-8374-577a41575424",
-            "version": "2020-02-03T10:30:00.000000Z",
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-            "crc32c": "",
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-        },
         {
             "name": "CZIKidney7632803_S1_L001_R2_001.fastq.gz",
             "uuid": "10e05576-100a-48cc-aa83-a30f09514384",
@@ -268,66 +98,6 @@
             "sha256": "c85efb39f331adeb34c937226e6661a4a575259ec6e36e6e3d353d606cdbdfaf",
             "s3_etag": "dcfb4f63603f7909ea8f5f1b6e8f86e0-212"
         },
-        {
-            "name": "analysis_process_1.json",
-            "uuid": "119ebaa3-a3b6-4cfe-8978-46d93796b9aa",
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-            "size": 14716,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "sequence_file_1.json",
-            "uuid": "121b6c9b-3b12-4fb8-8d98-fba4f1005770",
-            "version": "2019-10-22T20:00:22.379000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 379,
-            "indexed": true,
-            "crc32c": "",
-            "sha256": ""
-        },
-        {
-            "name": "donor_organism_1.json",
-            "uuid": "125a0c93-3187-463f-990b-1166aeb26e84",
-            "version": "2019-10-22T17:46:02.061000Z",
-            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
-            "size": 1108,
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-            "sha256": ""
-        },
-        {
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-            "uuid": "12995713-3c1b-4e13-a7b9-26d242e9ad71",
-            "version": "2019-10-22T17:46:04.915000Z",
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-        {
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-            "version": "2019-10-22T19:56:54.931000Z",
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-            "size": 381,
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-            "crc32c": "",
-            "sha256": ""
-        },
-        {
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-            "uuid": "13a062ba-2b8e-43a1-bc2a-bc17f650b37d",
-            "version": "2019-10-22T17:46:06.071000Z",
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         {
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             "uuid": "1456adad-9a4b-4a80-b115-9813f7a6b93c",
@@ -341,66 +111,6 @@
             "sha256": "ff538f40e72691b1c6f581d401144cf11b885622428985b216d97c3e43e62ef3",
             "s3_etag": "fe9271acb1ebea16f8f12e1327310298-31"
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-            "version": "2019-10-22T20:52:15.350000Z",
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-            "version": "2019-10-22T17:46:05.371000Z",
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-            "version": "2019-10-22T17:46:02.077000Z",
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-            "version": "2019-10-22T20:00:50.357000Z",
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-        {
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-            "uuid": "17aea4fd-cd72-4c36-8ded-d686162804b4",
-            "version": "2019-10-22T17:46:02.024000Z",
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-        {
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-            "version": "2019-10-22T19:46:28.764000Z",
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         {
             "name": "CZIKidney7587404_S1_L001_R2_001.fastq.gz",
             "uuid": "1841191a-cad6-4bb8-b174-f41d94bee738",
@@ -464,36 +174,6 @@
             "sha256": "4c559dba0abed8f728e89eb48325dce81263d818812f3c9fa5a0e5b807e8d0e9",
             "s3_etag": "dce00c3dcdf1725d7ae0fbc365c8dbcc-126"
         },
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-            "version": "2019-10-22T17:46:04.931000Z",
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-            "version": "2020-02-03T10:30:00.000000Z",
-            "content-type": "application/json; dcp-type=\"metadata/file\"",
-            "size": 327,
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-        {
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-            "uuid": "1c531e83-02f4-4c00-b161-f186a1b5e1fb",
-            "version": "2019-10-22T19:46:28.769000Z",
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         {
             "name": "4834STDY7002881_S1_L001_R2_001.fastq.gz",
             "uuid": "1d428c59-694c-4596-a360-a5e857f90635",
@@ -531,36 +211,6 @@
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-            "version": "2019-10-22T19:57:02.257000Z",
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-            "version": "2019-10-22T19:54:54.409000Z",
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             "uuid": "210c7287-2f6e-4a93-8c63-202fa0b596b7",
@@ -574,26 +224,6 @@
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@@ -620,16 +250,6 @@
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             "uuid": "29a8f5fb-43a8-4f18-9255-f7573e9c4600",
@@ -643,76 +263,6 @@
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-            "version": "2019-10-22T20:07:27.579000Z",
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@@ -3996,16 +1405,6 @@
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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
--- a/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
+++ b/test/indexer/data/7a330531-ec7f-5aee-84d4-2ba24d66e93b.dss.hca.json
@@ -1,101 +1,5 @@
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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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@@ -23,66 +13,6 @@
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@@ -130,127 +60,6 @@
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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
--- a/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
+++ b/test/indexer/data/8338b891-f3fa-5e7b-885f-e4ee5689ee15.dss.hca.json
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index d2c2c780a..3645044d6 100644
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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
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+++ 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
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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
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index a48a0e666..dfc852edc 100644
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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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index bf3b5d476..67955da34 100644
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+++ b/test/indexer/data/d7b8cbff-aee9-5a05-a4a1-d8f4e720aee7.dss.hca.json
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index fe1e5410a..1cc9b3a28 100644
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+++ b/test/indexer/data/dcccb551-4766-4210-966c-f9ee25d19190.dss.hca.json
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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
--- a/test/indexer/data/e0ae8cfa-2b51-4419-9cde-34df44c6458a.dss.hca.json
+++ 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
--- a/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
+++ b/test/indexer/data/e2c3054e-9fba-4d7a-b85b-a2220d16da73.dss.hca.json
@@ -1,581 +1,5 @@
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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
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+++ 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
--- a/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
+++ b/test/indexer/data/f79257a7-dfc6-46d6-ae00-ba4b25313c10.dss.hca.json
@@ -1,209 +1,5 @@
 {
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-            "crc32c": "926a2f8b",
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-            "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": "12c204f0",
-            "indexed": true,
-            "name": "cell_suspension_0.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 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",
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@@ -43,36 +13,6 @@
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-            "version": "2020-08-13T10:24:31.566000Z",
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             "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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             "name": "FCAImmP7316890_S1_L001_R1_001.fastq.gz",
             "uuid": "085e5f88-ab09-4d69-bc14-afa71e1ae17c",
@@ -159,46 +39,6 @@
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-            "version": "2020-08-13T10:24:41.908000Z",
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index 7bdbb3fbd..d3055ed30 100644
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-            "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)