[r] Fix: AnVIL indexer doesn't follow downstream links from files to …

…files (#4761)

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

@@ -229,7 +229,7 @@ def _bundle_entity(self, bundle_fqid: SourcedBundleFQID) -> KeyReference:
         return bundle_entity
 
     def _consolidate_by_type(self, entities: Keys) -> MutableKeysByType:
-        result = defaultdict(set)
+        result = {entity_type: set() for entity_type in self.indexed_columns_by_entity_type}
         for e in entities:
             result[e.entity_type].add(e.key)
         return result
@@ -259,7 +259,7 @@ def _follow_downstream(self,
                            ) -> Links:
         return set.union(
             self._downstream_from_biosamples(source, entities['biosample']),
-            self._downstream_from_files(source, entities['files'])
+            self._downstream_from_files(source, entities['file'])
         )
 
     def _upstream_from_biosamples(self,
@@ -407,8 +407,8 @@ def _downstream_from_files(self,
         rows = self._run_sql(f'''
             WITH activities AS (
                 SELECT
-                    ala.alignmentactivity_id,
-                    'alignmentactivity',
+                    ala.alignmentactivity_id AS activity_id,
+                    'alignmentactivity' AS activity_table,
                     ala.used_file_id,
                     ala.generated_file_id
                 FROM {backtick(self._full_table_name(source, 'alignmentactivity'))} AS ala
@@ -433,7 +433,7 @@ def _downstream_from_files(self,
                             KeyReference(key=file_id, entity_type='file')
                             for file_id in row['generated_file_id']
                         ],
-                        activity=KeyReference(key=row['actvity_id'], entity_type=row['activity_table']))
+                        activity=KeyReference(key=row['activity_id'], entity_type=row['activity_table']))
             for row in rows
         }
 
@@ -442,6 +442,8 @@ def _retrieve_entities(self,
                            entity_type: EntityType,
                            keys: AbstractSet[Key],
                            ) -> MutableJSONs:
+        if not keys:
+            return []
         table_name = self._full_table_name(source, entity_type)
         columns = set.union(
             self.common_indexed_columns,