[a r] Index supplementary files for AnVIL (#5000)

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

@@ -180,6 +180,7 @@ def _field_mapping(self) -> MetadataPlugin._FieldMapping:
                             'file_md5sum',
                             'reference_assembly',
                             'file_name',
+                            'is_supplementary',
                             # Not in schema
                             'crc32',
                             'sha256',
@@ -223,6 +224,7 @@ def facets(self) -> Sequence[str]:
             'files.data_modality',
             'files.file_format',
             'files.reference_assembly',
+            'files.is_supplementary',
         ]
 
     @property

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

@@ -42,6 +42,7 @@
     EntityReference,
     EntityType,
     FieldTypes,
+    null_bool,
     null_datetime,
     null_int,
     null_str,
@@ -275,6 +276,7 @@ def _file_types(cls) -> FieldTypes:
             'file_md5sum': null_str,
             'reference_assembly': [null_str],
             'file_name': null_str,
+            'is_supplementary': null_bool,
             # Not in schema
             'version': null_str,
             'uuid': null_str,

src/azul/plugins/metadata/anvil/service/response.py

@@ -230,6 +230,7 @@ def _non_pivotal_fields_by_entity_type(self) -> dict[str, set[str]]:
                 'count',
                 'data_modality',
                 'file_format',
+                'is_supplementary',
                 'reference_assembly'
             }
         }

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

@@ -116,6 +116,7 @@ def merge(cls, links: Iterable['Link']) -> 'Link':
 
 class BundleEntityType(Enum):
     primary: EntityType = 'biosample'
+    supplementary: EntityType = 'file'
 
 
 @attr.s(auto_attribs=True, frozen=True, kw_only=True)
@@ -225,10 +226,15 @@ def _list_bundles(self,
         partition_prefix = spec.prefix.common + prefix
         validate_uuid_prefix(partition_prefix)
         primary = BundleEntityType.primary.value
+        supplementary = BundleEntityType.supplementary.value
         rows = self._run_sql(f'''
             SELECT datarepo_row_id, {primary!r} AS entity_type
             FROM {backtick(self._full_table_name(spec, primary))}
             WHERE STARTS_WITH(datarepo_row_id, '{partition_prefix}')
+            UNION ALL
+            SELECT datarepo_row_id, {supplementary!r} AS entity_type
+            FROM {backtick(self._full_table_name(spec, supplementary))} AS supp
+            WHERE STARTS_WITH(datarepo_row_id, '{partition_prefix}') AND supp.is_supplementary
         ''')
         return [
             AnvilBundleFQID(source=source,
@@ -264,6 +270,8 @@ def list_partitions(self,
     def _emulate_bundle(self, bundle_fqid: AnvilBundleFQID) -> TDRAnvilBundle:
         if bundle_fqid.entity_type is BundleEntityType.primary:
             return self._primary_bundle(bundle_fqid)
+        elif bundle_fqid.entity_type is BundleEntityType.supplementary:
+            return self._supplementary_bundle(bundle_fqid)
         else:
             assert False, bundle_fqid.entity_type
 
@@ -308,6 +316,40 @@ def _primary_bundle(self, bundle_fqid: AnvilBundleFQID) -> TDRAnvilBundle:
 
         return result
 
+    def _supplementary_bundle(self, bundle_fqid: AnvilBundleFQID) -> TDRAnvilBundle:
+        entity_id = uuids.change_version(bundle_fqid.uuid,
+                                         self.bundle_uuid_version,
+                                         self.datarepo_row_uuid_version)
+        source = bundle_fqid.source.spec
+        bundle_entity_type = bundle_fqid.entity_type.value
+        result = TDRAnvilBundle(fqid=bundle_fqid, manifest=[], metadata_files={})
+        columns = self._columns(bundle_entity_type)
+        bundle_entity = one(self._run_sql(f'''
+            SELECT {', '.join(sorted(columns))}
+            FROM {backtick(self._full_table_name(source, bundle_entity_type))}
+            WHERE datarepo_row_id = '{entity_id}'
+        '''))
+        linked_entity_type = 'dataset'
+        columns = self._columns(linked_entity_type)
+        linked_entity = one(self._run_sql(f'''
+            SELECT {', '.join(sorted(columns))}
+            FROM {backtick(self._full_table_name(source, linked_entity_type))}
+            LIMIT 2
+        '''))
+        entities_by_key = {}
+        link_args = {}
+        for entity_type, row, arg in [
+            (bundle_entity_type, bundle_entity, 'outputs'),
+            (linked_entity_type, linked_entity, 'inputs')
+        ]:
+            entity_ref = EntityReference(entity_type=entity_type, entity_id=row['datarepo_row_id'])
+            key_ref = KeyReference(key=row[entity_type + '_id'], entity_type=entity_type)
+            entities_by_key[key_ref] = entity_ref
+            result.add_entity(entity_ref, self._version, row)
+            link_args[arg] = key_ref
+        result.add_links(bundle_fqid, {Link.create(**link_args)}, entities_by_key)
+        return result
+
     def _bundle_entity(self, bundle_fqid: AnvilBundleFQID) -> KeyReference:
         source = bundle_fqid.source
         bundle_uuid = bundle_fqid.uuid
@@ -696,6 +738,7 @@ def _convert_column(self, value):
             'reference_assembly',
             'file_name',
             'file_ref',
+            'is_supplementary',
         },
         'activity': {
             'activity_id',