fixup! Refactor transformer method

src/azul/indexer/transform.py

@@ -54,15 +54,18 @@ def entity_type(cls) -> EntityType:
         """
         raise NotImplementedError
 
-    @abstractmethod
-    def _replicate(self, entity: EntityReference) -> tuple[str, JSON]:
+    def _replica_type(self, entity: EntityReference) -> str:
         """
-        A tuple consisting of:
-
-            1. The name of the type of replica emitted by this transformer for a
-               given entity. See :py:attr:`Replica.replica_type`.
+        The name of the type of replica emitted by this transformer for a given
+        entity. See :py:attr:`Replica.replica_type`.
+        """
+        return entity.entity_type
 
-            2. The contents of the replica for that entity.
+    @abstractmethod
+    def _replica_contents(self, entity: EntityReference) -> JSON:
+        """
+        The contents of the replica emitted by this transformer for a given
+        entity.
         """
         raise NotImplementedError
 
@@ -136,7 +139,8 @@ def _replica(self,
                  root_hub: EntityID,
                  file_hub: EntityID | None,
                  ) -> Replica:
-        replica_type, contents = self._replicate(entity)
+        replica_type = self._replica_type(entity)
+        contents = self._replica_contents(entity)
         coordinates = ReplicaCoordinates(content_hash=json_hash(contents).hexdigest(),
                                          entity=entity)
         return Replica(coordinates=coordinates,

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

@@ -192,9 +192,8 @@ def _transform(self,
                    ) -> Iterable[Contribution | Replica]:
         raise NotImplementedError
 
-    def _replicate(self, entity: EntityReference) -> tuple[str, JSON]:
-        content = ChainMap(self.bundle.entities, self.bundle.orphans)[entity]
-        return entity.entity_type, content
+    def _replica_contents(self, entity: EntityReference) -> JSON:
+        return ChainMap(self.bundle.entities, self.bundle.orphans)[entity]
 
     def _convert_entity_type(self, entity_type: str) -> str:
         assert entity_type == 'bundle' or entity_type.startswith('anvil_'), entity_type
@@ -428,9 +427,6 @@ def _activity_polymorphic_types(self) -> AbstractSet[str]:
             if table['name'].endswith('activity')
         }
 
-    def _is_duos(self, dataset: JSON) -> bool:
-        return 'duos_id' in dataset
-
     @classmethod
     def inner_entity_id(cls, entity_type: EntityType, entity: JSON) -> EntityID:
         return entity['document_id']
@@ -509,8 +505,11 @@ def _duos_types(cls) -> FieldTypes:
     def _duos(self, dataset: EntityReference) -> MutableJSON:
         return self._entity(dataset, self._duos_types())
 
+    def _is_duos(self, dataset: EntityReference) -> bool:
+        return 'duos_id' in self.bundle.entities[dataset]
+
     def _dataset(self, dataset: EntityReference) -> MutableJSON:
-        if self._is_duos(self.bundle.entities[dataset]):
+        if self._is_duos(dataset):
             return self._duos(dataset)
         else:
             return super()._dataset(dataset)

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

@@ -497,13 +497,12 @@ def aggregator(cls, entity_type: EntityType) -> EntityAggregator | None:
             agg_cls = SimpleAggregator
         return agg_cls(entity_type)
 
-    def _replicate(self, entity: EntityReference) -> tuple[str, JSON]:
+    def _replica_contents(self, entity: EntityReference) -> JSON:
         if entity == self.api_bundle.ref:
-            content = self.bundle.links
+            return self.bundle.links
         else:
             api_entity = self.api_bundle.entities[UUID(entity.entity_id)]
-            content = api_entity.json
-        return entity.entity_type, content
+            return api_entity.json
 
     def _find_ancestor_samples(self,
                                entity: api.LinkedEntity,