fix: prevent unwanted phenopacket dataset update in ingestion

chord_metadata_service/chord/ingest/phenopackets.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import uuid
 from humps import decamelize
 
 from dateutil.parser import isoparse
@@ -320,7 +319,12 @@ def ingest_phenopacket(phenopacket_data: dict[str, Any],
     if phenopacket_data.get("files", []):
         logger.warning("Found files in phenopacket.files are not ingested by Katsu.")
 
-    new_phenopacket_id = phenopacket_data.get("id", str(uuid.uuid4()))
+    # Abort the ingestion if the phenopacket's ID exists in the DB
+    phenopacket_id = phenopacket_data.get("id")
+    if pm.Phenopacket.objects.filter(id=phenopacket_id).exists():
+        error_msg = f"Cannot ingest Phenopacket with ID {phenopacket_id}, ID already exists in the database."
+        logger.error(error_msg)
+        raise IngestError(error_msg)
 
     subject = phenopacket_data.get("subject")
 
@@ -377,25 +381,25 @@ def ingest_phenopacket(phenopacket_data: dict[str, Any],
     meta_data_obj.resources.set(resources_db)
 
     # Create the phenopacket object...
-    new_phenopacket = pm.Phenopacket(
-        id=new_phenopacket_id,
+    phenopacket = pm.Phenopacket(
+        id=phenopacket_id,
         subject=subject_obj,
         measurements=measurements,
         medical_actions=medical_actions,
         meta_data=meta_data_obj,
         dataset=Dataset.objects.get(identifier=dataset_id),
     )
 
-    # ... save it to the database...
-    new_phenopacket.save()
+    #  ... save it to the database...
+    phenopacket.save()
 
     # ... and attach all the other objects to it.
-    new_phenopacket.phenotypic_features.set(phenotypic_features_db)
-    new_phenopacket.interpretations.set(interpretations_db)
-    new_phenopacket.biosamples.set(biosamples_db)
-    new_phenopacket.diseases.set(diseases_db)
+    phenopacket.phenotypic_features.set(phenotypic_features_db)
+    phenopacket.interpretations.set(interpretations_db)
+    phenopacket.biosamples.set(biosamples_db)
+    phenopacket.diseases.set(diseases_db)
 
-    return new_phenopacket
+    return phenopacket
 
 
 def ingest_phenopacket_workflow(json_data, dataset_id) -> Union[list[pm.Phenopacket], pm.Phenopacket]: