Track orphans in AnVIL bundles

src/azul/indexer/index_service.py

@@ -212,7 +212,8 @@ def index(self, catalog: CatalogName, bundle: Bundle) -> None:
         for contributions, replicas in transforms:
             tallies.update(self.contribute(catalog, contributions))
             self.replicate(catalog, replicas)
-        self.aggregate(tallies)
+        if tallies:
+            self.aggregate(tallies)
 
     def delete(self, catalog: CatalogName, bundle: Bundle) -> None:
         """

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

@@ -118,28 +118,37 @@ def to_entity_link(self,
 class AnvilBundle(Bundle[BUNDLE_FQID], ABC):
     entities: dict[EntityReference, MutableJSON] = attrs.field(factory=dict)
     links: set[EntityLink] = attrs.field(factory=set)
+    orphans: dict[EntityReference, MutableJSON] = attrs.field(factory=dict)
 
     def reject_joiner(self, catalog: CatalogName):
         # FIXME: Optimize joiner rejection and re-enable it for AnVIL
         #        https://github.com/DataBiosphere/azul/issues/5256
         pass
 
     def to_json(self) -> MutableJSON:
-        return {
-            'entities': {
+        def serialize_entities(entities):
+            return {
                 str(entity_ref): entity
-                for entity_ref, entity in sorted(self.entities.items())
-            },
+                for entity_ref, entity in sorted(entities.items())
+            }
+
+        return {
+            'entities': serialize_entities(self.entities),
+            'orphans': serialize_entities(self.orphans),
             'links': [link.to_json() for link in sorted(self.links)]
         }
 
     @classmethod
     def from_json(cls, fqid: BUNDLE_FQID, json_: JSON) -> Self:
+        def deserialize_entities(json_entities):
+            return {
+                EntityReference.parse(entity_ref): entity
+                for entity_ref, entity in json_entities.items()
+            }
+
         return cls(
             fqid=fqid,
-            entities={
-                EntityReference.parse(entity_ref): entity
-                for entity_ref, entity in json_['entities'].items()
-            },
-            links=set(map(EntityLink.from_json, json_['links']))
+            entities=deserialize_entities(json_['entities']),
+            links=set(map(EntityLink.from_json, json_['links'])),
+            orphans=deserialize_entities(json_['orphans'])
         )

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

@@ -169,6 +169,9 @@ def aggregator(cls, entity_type) -> EntityAggregator:
             assert False, entity_type
 
     def estimate(self, partition: BundlePartition) -> int:
+        # Orphans are not considered when deciding whether to partition the
+        # bundle, but if the bundle is partitioned then each orphan will be
+        # replicated in a single partition
         return sum(map(partial(self._contains, partition), self.bundle.entities))
 
     def transform(self,
@@ -188,7 +191,9 @@ def _transform(self,
         raise NotImplementedError
 
     def _replicate(self, entity: EntityReference) -> tuple[str, JSON]:
-        return f'anvil_{entity.entity_type}', self.bundle.entities[entity]
+        replica_type = f'anvil_{entity.entity_type}'
+        content = ChainMap(self.bundle.entities, self.bundle.orphans)[entity]
+        return replica_type, content
 
     def _pluralize(self, entity_type: str) -> str:
         if entity_type == 'diagnosis':
@@ -400,7 +405,10 @@ def _file(self, file: EntityReference) -> MutableJSON:
                             uuid=file.entity_id)
 
     def _only_dataset(self) -> EntityReference:
-        return one(self._entities_by_type['dataset'])
+        try:
+            return one(self._entities_by_type['dataset'])
+        except ValueError:
+            return one(o for o in self.bundle.orphans if o.entity_type == 'dataset')
 
     _activity_polymorphic_types = {
         'activity',
@@ -497,7 +505,9 @@ def _dataset(self, dataset: EntityReference) -> MutableJSON:
             return super()._dataset(dataset)
 
     def _list_entities(self) -> Iterable[EntityReference]:
-        yield self._singleton()
+        # Suppress contributions for bundles that only contain orphans
+        if self.bundle.entities:
+            yield self._singleton()
 
     @abstractmethod
     def _singleton(self) -> EntityReference:
@@ -555,6 +565,15 @@ def _singleton(self) -> EntityReference:
         return EntityReference(entity_type='bundle',
                                entity_id=self.bundle.uuid)
 
+    def transform(self,
+                  partition: BundlePartition
+                  ) -> Iterable[Contribution | Replica]:
+        yield from super().transform(partition)
+        dataset_id = self._only_dataset().entity_id
+        for orphan in self.bundle.orphans:
+            if partition.contains(UUID(orphan.entity_id)):
+                yield self._replica(orphan, file_hub=None)
+
 
 class DatasetTransformer(SingletonTransformer):
 

src/azul/plugins/repository/tdr_anvil/__init__.py

@@ -137,9 +137,14 @@ def canning_qualifier(cls) -> str:
     def add_entity(self,
                    entity: EntityReference,
                    version: str,
-                   row: MutableJSON
+                   row: MutableJSON,
+                   *,
+                   is_orphan: bool = False
                    ) -> None:
-        assert entity not in self.entities, entity
+        dst = self.orphans if is_orphan else self.entities
+        # In DUOS bundles, the dataset is represented as both as entity and an
+        # orphan
+        assert entity not in dst, entity
         metadata = dict(row,
                         version=version)
         if entity.entity_type == 'file':
@@ -149,7 +154,7 @@ def add_entity(self,
             metadata.update(drs_uri=drs_uri,
                             sha256='',
                             crc32='')
-        self.entities[entity] = metadata
+        dst[entity] = metadata
 
     def add_links(self, links: Iterable[EntityLink]):
         self.links.update(links)