Updating origin_sample to be a list called origin_samples

sennetconsortium · Oct 2, 2024 · e86f2fa · e86f2fa
1 parent a1a6858
commit e86f2fa
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Showing 3 changed files with 17 additions and 16 deletions.
diff --git a/src/schema/provenance_schema.yaml b/src/schema/provenance_schema.yaml
@@ -597,10 +597,10 @@ ENTITIES:
         type: string
         description: 'The timestamp of when this entity was last modified or published.'
         on_index_trigger: get_last_touch
-      origin_sample:
+      origin_samples:
         type: json_string
-        description: 'The Sample ancestor that has the sample_category of "Organ".'
-        on_index_trigger: get_origin_sample
+        description: 'The Sample ancestors that has the sample_category of "Organ".'
+        on_index_trigger: get_origin_samples
       assigned_to_group_name:
         type: string
         description: The group who is responsible for the next step in the ingest process

diff --git a/src/schema/schema_neo4j_queries.py b/src/schema/schema_neo4j_queries.py
@@ -126,12 +126,12 @@ def get_dataset_direct_descendants(neo4j_driver, uuid, property_key=None, match_
 """
 
 
-def get_origin_sample(neo4j_driver, uuid):
+def get_origin_samples(neo4j_driver, uuid):
     result = {}
 
     query = (f"MATCH (e:Entity)-[:WAS_GENERATED_BY|USED*]->(s:Sample) "
              f"WHERE e.uuid='{uuid}' and s.sample_category='Organ' "
-             f"return s AS {record_field_name}")
+             f"return apoc.coll.toSet(COLLECT(s)) AS {record_field_name}")
 
     logger.info("======get_origin_sample() query======")
     logger.info(query)
@@ -140,7 +140,7 @@ def get_origin_sample(neo4j_driver, uuid):
         record = session.read_transaction(_execute_readonly_tx, query)
         if record and record[record_field_name]:
             # Convert the entity node to dict
-            result = _node_to_dict(record[record_field_name])
+            result = _nodes_to_dicts(record[record_field_name])
 
     return result
 

diff --git a/src/schema/schema_triggers.py b/src/schema/schema_triggers.py
@@ -1734,7 +1734,7 @@ def get_last_touch(property_key, normalized_type, user_token, existing_data_dict
     return property_key, last_touch
 
 
-def get_origin_sample(property_key, normalized_type, user_token, existing_data_dict, new_data_dict):
+def get_origin_samples(property_key, normalized_type, user_token, existing_data_dict, new_data_dict):
     """Trigger event method to grab the ancestor of this entity where entity type is Sample and the sample_category is Organ.
 
     Parameters
@@ -1763,19 +1763,20 @@ def get_origin_sample(property_key, normalized_type, user_token, existing_data_d
             # Return the organ if this is an organ
             return property_key, existing_data_dict
 
-        origin_sample = None
+        origin_samples = None
         if normalized_type in ["Sample", "Dataset", "Publication"]:
-            origin_sample = schema_neo4j_queries.get_origin_sample(schema_manager.get_neo4j_driver_instance(),
+            origin_samples = schema_neo4j_queries.get_origin_samples(schema_manager.get_neo4j_driver_instance(),
                                                                    existing_data_dict['uuid'])
 
-            organ_hierarchy_key, organ_hierarchy_value = get_organ_hierarchy(property_key='organ_hierarchy',
-                                                                             normalized_type=Ontology.ops().entities().SAMPLE,
-                                                                             user_token=user_token,
-                                                                             existing_data_dict=origin_sample,
-                                                                             new_data_dict=new_data_dict)
-            origin_sample[organ_hierarchy_key] = organ_hierarchy_value
+            for origin_sample in origin_samples:
+                organ_hierarchy_key, organ_hierarchy_value = get_organ_hierarchy(property_key='organ_hierarchy',
+                                                                                 normalized_type=Ontology.ops().entities().SAMPLE,
+                                                                                 user_token=user_token,
+                                                                                 existing_data_dict=origin_sample,
+                                                                                 new_data_dict=new_data_dict)
+                origin_sample[organ_hierarchy_key] = organ_hierarchy_value
 
-        return property_key, origin_sample
+        return property_key, origin_samples
     except Exception:
         logger.error(f"No origin sample found for {normalized_type} with UUID: {existing_data_dict['uuid']}")
         return property_key, None