[r] Use DCP2 schema name for HCA replica_type (#6453)

DataBiosphere · Jul 31, 2024 · f7f5f27 · f7f5f27
1 parent d4dac36
commit f7f5f27
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Showing 3 changed files with 8 additions and 8 deletions.
diff --git a/src/azul/plugins/metadata/hca/indexer/transform.py b/src/azul/plugins/metadata/hca/indexer/transform.py
@@ -462,8 +462,8 @@ class BaseTransformer(Transformer, metaclass=ABCMeta):
     api_bundle: api.Bundle
 
     def replica_type(self, entity: EntityReference) -> str:
-        assert entity.entity_type == self.entity_type(), entity
-        return entity.entity_type.removesuffix('s')
+        api_entity = self.api_bundle.entities[UUID(entity.entity_id)]
+        return api_entity.schema_name
 
     @classmethod
     def aggregator(cls, entity_type: EntityType) -> Optional[EntityAggregator]:

diff --git a/...ndexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.results.json b/...ndexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T11:33:44.698028Z.results.json
diff --git a/test/service/test_manifest.py b/test/service/test_manifest.py
@@ -1309,9 +1309,9 @@ def test_verbatim_jsonl_manifest(self):
                 ('links', 'links.json'),
                 ('cell_suspension', 'cell_suspension_0.json'),
                 ('project', 'project_0.json'),
-                ('file', 'sequence_file_0.json'),
-                ('file', 'sequence_file_1.json'),
-                ('sample', 'specimen_from_organism_0.json')
+                ('sequence_file', 'sequence_file_0.json'),
+                ('sequence_file', 'sequence_file_1.json'),
+                ('specimen_from_organism', 'specimen_from_organism_0.json')
             ]
         ]
         response = self._get_manifest(ManifestFormat.verbatim_jsonl, {})