[r] Fix: Verbatim JSONL manifest issues (#6453, PR #6459)

DataBiosphere · Aug 14, 2024 · e1bb690 · e1bb690
2 parents f4f4375 + 7766c1d
commit e1bb690
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Showing 6 changed files with 129 additions and 129 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/src/azul/service/manifest_service.py b/src/azul/service/manifest_service.py
@@ -2081,7 +2081,7 @@ def create_file(self) -> tuple[str, Optional[str]]:
         with open(path, 'w') as f:
             for replica in self._all_replicas():
                 entry = {
-                    'contents': replica['contents'],
+                    'value': replica['contents'],
                     'type': replica['replica_type']
                 }
                 json.dump(entry, f)

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/data/verbatim/hca/pfb_entities.json b/test/service/data/verbatim/hca/pfb_entities.json
@@ -14,28 +14,28 @@
                 },
                 {
                     "links": [],
-                    "name": "file",
+                    "name": "links",
                     "ontology_reference": "",
                     "properties": [],
                     "values": {}
                 },
                 {
                     "links": [],
-                    "name": "links",
+                    "name": "project",
                     "ontology_reference": "",
                     "properties": [],
                     "values": {}
                 },
                 {
                     "links": [],
-                    "name": "project",
+                    "name": "sequence_file",
                     "ontology_reference": "",
                     "properties": [],
                     "values": {}
                 },
                 {
                     "links": [],
-                    "name": "sample",
+                    "name": "specimen_from_organism",
                     "ontology_reference": "",
                     "properties": [],
                     "values": {}
@@ -46,7 +46,7 @@
     },
     {
         "id": "70d1af4a-82c8-478a-8960-e9028b3616ca",
-        "name": "file",
+        "name": "sequence_file",
         "object": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.5.2/sequence_file",
             "file_core": {
@@ -69,7 +69,7 @@
     },
     {
         "id": "0c5ac7c0-817e-40d4-b1b1-34c3d5cfecdb",
-        "name": "file",
+        "name": "sequence_file",
         "object": {
             "describedBy": "https://schema.humancellatlas.org/type/file/6.5.2/sequence_file",
             "file_core": {
@@ -122,7 +122,7 @@
     },
     {
         "id": "a21dc760-a500-4236-bcff-da34a0e873d2",
-        "name": "sample",
+        "name": "specimen_from_organism",
         "object": {
             "biomaterial_core": {
                 "biomaterial_id": "DID_scRSq06_pancreas",