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modified the schema trigger for updating sample direct ancestors. It … #940

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Merged
yuanzhou merged 1 commit into from
Oct 6, 2025
Merged

modified the schema trigger for updating sample direct ancestors. It … #940

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29 changes: 13 additions & 16 deletions src/schema/schema_triggers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1919,50 +1919,47 @@ def delete_metadata_files(property_key, normalized_type, request, user_token, ex
def link_sample_to_direct_ancestor(property_key, normalized_type, request, user_token, existing_data_dict, new_data_dict):
if 'uuid' not in existing_data_dict:
raise KeyError("Missing 'uuid' key in 'existing_data_dict' during calling 'link_sample_to_direct_ancestor()' trigger method.")

if 'direct_ancestor_uuid' not in new_data_dict:
raise KeyError("Missing 'direct_ancestor_uuid' key in 'new_data_dict' during calling 'link_sample_to_direct_ancestor()' trigger method.")

create_activity = False
activity_data_dict = {}
sample_uuid = existing_data_dict['uuid']
new_ancestors = None
ancestors_to_unlink = None

# Build a list of direct ancestor uuids
# Only one uuid in the list in this case
direct_ancestor_uuids = [new_data_dict['direct_ancestor_uuid']]
existing_sample_ancestor_uuids = schema_neo4j_queries.get_sample_direct_ancestor(schema_manager.get_neo4j_driver_instance(), sample_uuid, "uuid")
if isinstance(existing_sample_ancestor_uuids, list):
existing_sample_ancestor_uuids = existing_sample_ancestor_uuids[0]
if existing_sample_ancestor_uuids and existing_sample_ancestor_uuids != direct_ancestor_uuids:
new_ancestors = direct_ancestor_uuids
direct_ancestor_uuids = new_data_dict['direct_ancestor_uuid']
existing_sample_ancestor_uuids = schema_neo4j_queries.get_parents(schema_manager.get_neo4j_driver_instance(), sample_uuid, "uuid")
if direct_ancestor_uuids not in existing_sample_ancestor_uuids:
new_ancestors = [direct_ancestor_uuids]
if not existing_sample_ancestor_uuids:
new_ancestors = direct_ancestor_uuids
activity_uuid = schema_neo4j_queries.get_parent_activity_uuid_from_entity(schema_manager.get_neo4j_driver_instance(), sample_uuid)
new_ancestors = [direct_ancestor_uuids]

activity_uuid = schema_neo4j_queries.get_parent_activity_uuid_from_entity(schema_manager.get_neo4j_driver_instance(), sample_uuid)
if not activity_uuid:
activity_data_dict = schema_manager.generate_activity_data(normalized_type, request, user_token, existing_data_dict)
activity_uuid = activity_data_dict['uuid']
create_activity = True

if new_ancestors:
ancestors_to_unlink = existing_sample_ancestor_uuids
logger.info(f"Linking the following new ancestors: {new_ancestors}")
try:
schema_neo4j_queries.add_new_ancestors_to_existing_activity(schema_manager.get_neo4j_driver_instance(), new_ancestors, activity_uuid, create_activity, activity_data_dict, sample_uuid)
except TransactionError:
raise

ancestors_to_unlink = existing_sample_ancestor_uuids
else:
ancestors_to_unlink = existing_sample_ancestor_uuids
ancestors_to_unlink.remove(direct_ancestor_uuids)
if ancestors_to_unlink:
logger.info(f"Unlinking the following ancestor: {ancestors_to_unlink}")
try:
schema_neo4j_queries.delete_ancestor_linkages_tx(schema_manager.get_neo4j_driver_instance(), sample_uuid, [ancestors_to_unlink])
schema_neo4j_queries.delete_ancestor_linkages_tx(schema_manager.get_neo4j_driver_instance(), sample_uuid, ancestors_to_unlink)
except TransactionError:
raise

if not(ancestors_to_unlink or new_ancestors):
logger.info("No new ancestors linked, nor old ancestors unlinked")


"""
TriggerTypeEnum.BEFORE_CREATE and TriggerTypeEnum.BEFORE_UPDATE

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