Consolidate AnVIL and HCA boilerplate (partial #5358)

src/azul/indexer/transform.py

@@ -9,20 +9,31 @@
     Optional,
 )
 
+import attr
+
 from azul.indexer import (
+    Bundle,
     BundlePartition,
 )
 from azul.indexer.aggregate import (
     EntityAggregator,
 )
 from azul.indexer.document import (
     Contribution,
+    ContributionCoordinates,
+    EntityReference,
     EntityType,
     FieldTypes,
 )
+from azul.types import (
+    MutableJSON,
+)
 
 
+@attr.s(frozen=True, kw_only=True, auto_attribs=True)
 class Transformer(metaclass=ABCMeta):
+    bundle: Bundle
+    deleted: bool
 
     @classmethod
     @abstractmethod
@@ -75,3 +86,15 @@ def get_aggregator(cls, entity_type: EntityType) -> Optional[EntityAggregator]:
         entities of types other than X.
         """
         raise NotImplementedError
+
+    def _contribution(self,
+                      contents: MutableJSON,
+                      entity: EntityReference
+                      ) -> Contribution:
+        coordinates = ContributionCoordinates(entity=entity,
+                                              bundle=self.bundle.fqid.upcast(),
+                                              deleted=self.deleted)
+        return Contribution(coordinates=coordinates,
+                            version=None,
+                            source=self.bundle.fqid.source,
+                            contents=contents)

src/azul/plugins/metadata/anvil/indexer/transform.py

@@ -39,7 +39,6 @@
 )
 from azul.indexer.document import (
     Contribution,
-    ContributionCoordinates,
     EntityReference,
     EntityType,
     FieldTypes,
@@ -120,7 +119,6 @@ def _search(cls,
 @attr.s(frozen=True, kw_only=True, auto_attribs=True)
 class BaseTransformer(Transformer, metaclass=ABCMeta):
     bundle: AnvilBundle
-    deleted: bool
 
     @classmethod
     def field_types(cls) -> FieldTypes:
@@ -307,8 +305,8 @@ def get_bound(field_name: str) -> Optional[float]:
         }
 
     def _contribution(self,
-                      entity: EntityReference,
                       contents: MutableJSON,
+                      entity: EntityReference,
                       ) -> Contribution:
         # The entity type is used to determine the index name.
         # All activities go into the same index, regardless of their polymorphic type.
@@ -317,13 +315,7 @@ def _contribution(self,
                                 if entity.entity_type.endswith('activity') else
                                 entity.entity_type)
         entity = attr.evolve(entity, entity_type=entity_type)
-        coordinates = ContributionCoordinates(entity=entity,
-                                              bundle=self.bundle.fqid.upcast(),
-                                              deleted=self.deleted)
-        return Contribution(coordinates=coordinates,
-                            version=None,
-                            source=self.bundle.fqid.source,
-                            contents=contents)
+        return super()._contribution(contents, entity)
 
     def _entity(self,
                 entity: EntityReference,
@@ -422,7 +414,7 @@ def _transform(self, entity: EntityReference) -> Contribution:
             donors=self._entities(self._donor, linked['donor']),
             files=self._entities(self._file, linked['file']),
         )
-        return self._contribution(entity, contents)
+        return self._contribution(contents, entity)
 
 
 class BiosampleTransformer(BaseTransformer):
@@ -444,7 +436,7 @@ def _transform(self, entity: EntityReference) -> Contribution:
             donors=self._entities(self._donor, linked['donor']),
             files=self._entities(self._file, linked['file']),
         )
-        return self._contribution(entity, contents)
+        return self._contribution(contents, entity)
 
 
 class DatasetTransformer(BaseTransformer):
@@ -465,7 +457,7 @@ def _transform(self, entity: EntityReference) -> Contribution:
             donors=self._entities(self._donor, self._entities_by_type['donor']),
             files=self._entities(self._file, self._entities_by_type['file']),
         )
-        return self._contribution(entity, contents)
+        return self._contribution(contents, entity)
 
 
 class DonorTransformer(BaseTransformer):
@@ -487,7 +479,7 @@ def _transform(self, entity: EntityReference) -> Contribution:
             donors=[self._donor(entity)],
             files=self._entities(self._file, linked['file']),
         )
-        return self._contribution(entity, contents)
+        return self._contribution(contents, entity)
 
 
 class FileTransformer(BaseTransformer):
@@ -509,4 +501,4 @@ def _transform(self, entity: EntityReference) -> Contribution:
             donors=self._entities(self._donor, linked['donor']),
             files=[self._file(entity)],
         )
-        return self._contribution(entity, contents)
+        return self._contribution(contents, entity)

src/azul/plugins/metadata/hca/indexer/transform.py

@@ -63,7 +63,6 @@
 from azul.indexer.document import (
     ClosedRange,
     Contribution,
-    ContributionCoordinates,
     EntityReference,
     EntityType,
     FieldType,
@@ -455,7 +454,6 @@ class DatedEntity(Entity, Protocol):
 class BaseTransformer(Transformer, metaclass=ABCMeta):
     bundle: HCABundle
     api_bundle: api.Bundle
-    deleted: bool
 
     # This stub is only needed to aid PyCharm's type inference. Without this,
     # a constructor invocation that doesn't refer to the class explicitly, but
@@ -1206,19 +1204,8 @@ def _build_strata_string(self, file):
                 point_strings.append(dimension + '=' + ','.join(sorted(values)))
         return ';'.join(point_strings)
 
-    def _contribution(self,
-                      contents: MutableJSON,
-                      entity_id: api.UUID4
-                      ) -> Contribution:
-        entity = EntityReference(entity_type=self.entity_type(),
-                                 entity_id=str(entity_id))
-        coordinates = ContributionCoordinates(entity=entity,
-                                              bundle=self.bundle.fqid.upcast(),
-                                              deleted=self.deleted)
-        return Contribution(coordinates=coordinates,
-                            version=None,
-                            source=self.bundle.fqid.source,
-                            contents=contents)
+    def _entity_ref(self, entity_id: api.UUID4) -> EntityReference:
+        return EntityReference(entity_id=str(entity_id), entity_type=self.entity_type())
 
     @classmethod
     def field_types(cls) -> FieldTypes:
@@ -1436,7 +1423,7 @@ def _transform(self, files: Iterable[api.File]) -> Iterable[Contribution]:
                         additional_contents = self.matrix_stratification_values(file)
                         for entity_type, values in additional_contents.items():
                             contents[entity_type].extend(values)
-                yield self._contribution(contents, file.document_id)
+                yield self._contribution(contents, self._entity_ref(file.document_id))
 
     def matrix_stratification_values(self, file: api.File) -> JSON:
         """
@@ -1531,7 +1518,7 @@ def _transform(self,
                             ),
                             dates=[self._date(cell_suspension)],
                             projects=[self._project(self._api_project)])
-            yield self._contribution(contents, cell_suspension.document_id)
+            yield self._contribution(contents, self._entity_ref(cell_suspension.document_id))
 
 
 class SampleTransformer(PartitionedTransformer):
@@ -1578,7 +1565,7 @@ def _transform(self, samples: Iterable[Sample]) -> Iterable[Contribution]:
                             ),
                             dates=[self._date(sample)],
                             projects=[self._project(self._api_project)])
-            yield self._contribution(contents, sample.document_id)
+            yield self._contribution(contents, self._entity_ref(sample.document_id))
 
 
 class BundleAsEntity(DatedEntity):
@@ -1678,8 +1665,7 @@ def _transform(self) -> Contribution:
                         contributed_analyses=contributed_analyses,
                         dates=[self._date(self._singleton_entity())],
                         projects=[self._project(self._api_project)])
-
-        return self._contribution(contents, self._singleton_id)
+        return self._contribution(contents, self._entity_ref(self._singleton_id))
 
 
 class ProjectTransformer(SingletonTransformer):