Merge pull request #122 from c3g/fixes-to-ingest

Fixes to ingest

chord_metadata_service/chord/views_ingest.py

@@ -153,13 +153,13 @@ def ingest(request):
 
 def _query_and_check_nulls(obj: dict, key: str, transform: Callable = lambda x: x):
     value = obj.get(key, None)
-    return {f"{key}__isnull": True} if value is None else {key: transform(value)}
+    return {f"{key}__isnull": True} if value is None or value == "" else {key: transform(value)}
 
 
 def ingest_phenopacket(phenopacket_data, table_id):
     """ Ingests one phenopacket. """
 
-    new_phenopacket_id = str(uuid.uuid4())  # TODO: Is this provided?
+    new_phenopacket_id = phenopacket_data.get("id", str(uuid.uuid4()))
 
     subject = phenopacket_data.get("subject", None)
     phenotypic_features = phenopacket_data.get("phenotypic_features", [])
@@ -222,7 +222,7 @@ def ingest_phenopacket(phenopacket_data, table_id):
             term=disease["term"],
             disease_stage=disease.get("disease_stage", []),
             tnm_finding=disease.get("tnm_finding", []),
-            **_query_and_check_nulls(disease, "onset")
+            onset=disease.get("onset", None)
         )
         diseases_db.append(d_obj.id)