Push down HCA specifics to a Bundle subclass (#4940)

scripts/can_bundle.py

@@ -38,6 +38,9 @@
 from azul.plugins import (
     RepositoryPlugin,
 )
+from azul.plugins.anvil import (
+    AnvilBundle,
+)
 from azul.types import (
     AnyJSON,
     AnyMutableJSON,
@@ -117,10 +120,12 @@ def save_bundle(bundle: Bundle, output_dir: str) -> None:
 
 
 def redact_bundle(bundle: Bundle, key: bytes) -> None:
-    for name in bundle.metadata_files.keys():
-        entity_type = name.split('_')[0]
-        if entity_type in redacted_entity_types:
-            bundle.metadata_files[name] = redact_json(bundle.metadata_files[name], key)
+    if isinstance(bundle, AnvilBundle):
+        for entity_ref, entity_metadata in bundle.entities.items():
+            if entity_ref.entity_type in redacted_entity_types:
+                bundle.entities[entity_ref] = redact_json(entity_metadata, key)
+    else:
+        raise RuntimeError('HCA bundles do not support redaction', type(bundle))
 
 
 def redact_json(o: AnyJSON, key: bytes) -> AnyMutableJSON:

src/azul/indexer/__init__.py

@@ -33,7 +33,6 @@
     AnyJSON,
     JSON,
     MutableJSON,
-    MutableJSONs,
     SupportsLessThan,
     get_generic_type_params,
 )
@@ -399,23 +398,6 @@ def to_json(self) -> SourcedBundleFQIDJSON:
 @attr.s(auto_attribs=True, kw_only=True)
 class Bundle(Generic[BUNDLE_FQID], metaclass=ABCMeta):
     fqid: BUNDLE_FQID
-    manifest: MutableJSONs
-    """
-    Each item of the `manifest` attribute's value has this shape:
-    {
-        'content-type': 'application/json; dcp-type="metadata/biomaterial"',
-        'crc32c': 'fd239631',
-        'indexed': True,
-        'name': 'cell_suspension_0.json',
-        's3_etag': 'aa31c093cc816edb1f3a42e577872ec6',
-        'sha1': 'f413a9a7923dee616309e4f40752859195798a5d',
-        'sha256': 'ea4c9ed9e53a3aa2ca4b7dffcacb6bbe9108a460e8e15d2b3d5e8e5261fb043e',
-        'size': 1366,
-        'uuid': '0136ebb4-1317-42a0-8826-502fae25c29f',
-        'version': '2019-05-16T162155.020000Z'
-    }
-    """
-    metadata_files: MutableJSON
 
     @property
     def uuid(self) -> BundleUUID:
@@ -453,26 +435,19 @@ def reject_joiner(self):
         """
         Raise a requirement error if the given string is found in the bundle
         """
-        self._reject_joiner(self.manifest)
-        self._reject_joiner(self.metadata_files)
+        self._reject_joiner(self.to_json())
 
     @classmethod
     def extension(cls) -> str:
         return ''
 
-    def to_json(self) -> MutableJSON:
-        return {
-            'manifest': self.manifest,
-            'metadata': self.metadata_files
-        }
-
     @classmethod
     def from_json(cls, fqid: BUNDLE_FQID, json_: JSON) -> 'Bundle':
-        manifest = json_['manifest']
-        metadata = json_['metadata']
-        assert isinstance(manifest, list), manifest
-        assert isinstance(metadata, dict), metadata
-        return cls(fqid=fqid, manifest=manifest, metadata_files=metadata)
+        raise NotImplementedError
+
+    @abstractmethod
+    def to_json(self) -> MutableJSON:
+        raise NotImplementedError
 
 
 BUNDLE = TypeVar('BUNDLE', bound=Bundle)

src/azul/plugins/__init__.py

@@ -499,6 +499,11 @@ def _bundle_fqid_cls(self) -> Type[BUNDLE_FQID]:
         bundle_cls, spec_cls, ref_cls, fqid_cls = self._generic_params
         return fqid_cls
 
+    @property
+    def _bundle_cls(self) -> Type[BUNDLE]:
+        bundle_cls, spec_cls, ref_cls, fqid_cls = self._generic_params
+        return bundle_cls
+
     def resolve_source(self, spec: str) -> SOURCE_REF:
         """
         Return an instance of :class:`SourceRef` for the repository source

src/azul/plugins/anvil.py

@@ -0,0 +1,104 @@
+from abc import (
+    ABC,
+)
+from typing import (
+    AbstractSet,
+    Generic,
+    Iterable,
+    Optional,
+    TypeVar,
+    Union,
+)
+
+import attr
+from more_itertools import (
+    one,
+)
+
+from azul.indexer import (
+    BUNDLE_FQID,
+    Bundle,
+)
+from azul.indexer.document import (
+    EntityReference,
+    EntityType,
+)
+from azul.types import (
+    JSON,
+    MutableJSON,
+)
+
+# AnVIL snapshots do not use UUIDs for primary/foreign keys.
+# This type alias helps us distinguish these keys from the document UUIDs,
+# which are drawn from the `datarepo_row_id` column.
+# Note that entities from different tables may have the same key, so
+# `KeyReference` should be used when mixing keys from different entity types.
+Key = str
+
+
+@attr.s(frozen=True, auto_attribs=True, kw_only=True, slots=True)
+class KeyReference:
+    key: Key
+    entity_type: EntityType
+
+
+ENTITY_REF = TypeVar(name='ENTITY_REF', bound=Union[EntityReference, KeyReference])
+
+
+@attr.s(auto_attribs=True, frozen=True, kw_only=True, order=False)
+class Link(Generic[ENTITY_REF]):
+    inputs: AbstractSet[ENTITY_REF] = attr.ib(factory=frozenset, converter=frozenset)
+    activity: Optional[ENTITY_REF] = attr.ib(default=None)
+    outputs: AbstractSet[ENTITY_REF] = attr.ib(factory=frozenset, converter=frozenset)
+
+    @property
+    def all_entities(self) -> AbstractSet[ENTITY_REF]:
+        return self.inputs | self.outputs | (set() if self.activity is None else {self.activity})
+
+    @classmethod
+    def from_json(cls, link: JSON) -> 'Link':
+        return cls(inputs=set(map(EntityReference.parse, link['inputs'])),
+                   activity=None if link['activity'] is None else EntityReference.parse(link['activity']),
+                   outputs=set(map(EntityReference.parse, link['outputs'])))
+
+    def to_json(self) -> MutableJSON:
+        return {
+            'inputs': sorted(map(str, self.inputs)),
+            'activity': None if self.activity is None else str(self.activity),
+            'outputs': sorted(map(str, self.outputs))
+        }
+
+    @classmethod
+    def merge(cls, links: Iterable['Link']) -> 'Link':
+        return cls(inputs=frozenset.union(*[link.inputs for link in links]),
+                   activity=one({link.activity for link in links}),
+                   outputs=frozenset.union(*[link.outputs for link in links]))
+
+    def __lt__(self, other: 'Link') -> bool:
+        return min(self.inputs) < min(other.inputs)
+
+
+@attr.s(auto_attribs=True, kw_only=True)
+class AnvilBundle(Bundle[BUNDLE_FQID], ABC):
+    entities: dict[EntityReference, MutableJSON] = attr.ib(factory=dict)
+    links: set[Link[EntityReference]] = attr.ib(factory=set)
+
+    def to_json(self) -> MutableJSON:
+        return {
+            'entities': {
+                str(entity_ref): entity
+                for entity_ref, entity in sorted(self.entities.items())
+            },
+            'links': [link.to_json() for link in sorted(self.links)]
+        }
+
+    @classmethod
+    def from_json(cls, fqid: BUNDLE_FQID, json_: JSON) -> 'AnvilBundle':
+        return cls(
+            fqid=fqid,
+            entities={
+                EntityReference.parse(entity_ref): entity
+                for entity_ref, entity in json_['entities'].items()
+            },
+            links=set(map(Link.from_json, json_['links']))
+        )

src/azul/plugins/hca.py

@@ -0,0 +1,53 @@
+from abc import (
+    ABC,
+)
+import logging
+
+import attr
+
+from azul.indexer import (
+    BUNDLE_FQID,
+    Bundle,
+)
+from azul.types import (
+    JSON,
+    MutableJSON,
+    MutableJSONs,
+)
+
+log = logging.getLogger(__name__)
+
+
+@attr.s(auto_attribs=True, kw_only=True)
+class HCABundle(Bundle[BUNDLE_FQID], ABC):
+    manifest: MutableJSONs
+    """
+    Each item of the `manifest` attribute's value has this shape:
+    {
+        'content-type': 'application/json; dcp-type="metadata/biomaterial"',
+        'crc32c': 'fd239631',
+        'indexed': True,
+        'name': 'cell_suspension_0.json',
+        's3_etag': 'aa31c093cc816edb1f3a42e577872ec6',
+        'sha1': 'f413a9a7923dee616309e4f40752859195798a5d',
+        'sha256': 'ea4c9ed9e53a3aa2ca4b7dffcacb6bbe9108a460e8e15d2b3d5e8e5261fb043e',
+        'size': 1366,
+        'uuid': '0136ebb4-1317-42a0-8826-502fae25c29f',
+        'version': '2019-05-16T162155.020000Z'
+    }
+    """
+    metadata_files: MutableJSON
+
+    def to_json(self) -> MutableJSON:
+        return {
+            'manifest': self.manifest,
+            'metadata': self.metadata_files
+        }
+
+    @classmethod
+    def from_json(cls, fqid: BUNDLE_FQID, json_: JSON) -> 'Bundle':
+        manifest = json_['manifest']
+        metadata = json_['metadata']
+        assert isinstance(manifest, list), manifest
+        assert isinstance(metadata, dict), metadata
+        return cls(fqid=fqid, manifest=manifest, metadata_files=metadata)

src/azul/plugins/metadata/anvil/__init__.py

@@ -6,15 +6,15 @@
     Type,
 )
 
-from azul.indexer import (
-    Bundle,
-)
 from azul.plugins import (
     DocumentSlice,
     ManifestConfig,
     MetadataPlugin,
     Sorting,
 )
+from azul.plugins.anvil import (
+    AnvilBundle,
+)
 from azul.plugins.metadata.anvil.indexer.transform import (
     ActivityTransformer,
     BaseTransformer,
@@ -42,7 +42,7 @@
 )
 
 
-class Plugin(MetadataPlugin[Bundle]):
+class Plugin(MetadataPlugin[AnvilBundle]):
 
     @classmethod
     def atlas(cls) -> str:
@@ -71,7 +71,7 @@ def transformer_types(self) -> Iterable[Type[BaseTransformer]]:
             FileTransformer,
         )
 
-    def transformers(self, bundle: Bundle, *, delete: bool) -> Iterable[BaseTransformer]:
+    def transformers(self, bundle: AnvilBundle, *, delete: bool) -> Iterable[BaseTransformer]:
         return [
             transformer_cls(bundle=bundle, deleted=delete)
             for transformer_cls in self.transformer_types()