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removed 2 outdated comments about linking to ancestors #936

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Merged
yuanzhou merged 2 commits into from
Oct 3, 2025
Merged

removed 2 outdated comments about linking to ancestors #936

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194033a
removed 2 outdated comments about linking to ancestors
DerekFurstPitt Oct 2, 2025
f447d7d
added additional logging to the link to direct ancestor triggers to s…
DerekFurstPitt Oct 3, 2025
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2 changes: 0 additions & 2 deletions src/schema/provenance_schema.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -462,7 +462,6 @@ ENTITIES:
exposed: false
indexed: false
description: "The uuids of source entities from which this new entity is derived. Used to pass source entity ids in on POST or PUT calls used to create the linkages."
# Note: link_dataset_to_direct_ancestors() will always delete all the old linkages first
after_create_trigger: link_dataset_to_direct_ancestors
after_update_trigger: link_dataset_to_direct_ancestors
direct_ancestors:
Expand Down Expand Up @@ -1034,7 +1033,6 @@ ENTITIES:
exposed: false
indexed: false
description: "The uuid of source entity from which this new entity is derived from. Used on creation or edit to create an action and relationship to the ancestor. The direct ancestor must be a Donor or Sample. If the direct ancestor is a Donor, the sample must be of type organ."
# Note: link_sample_to_direct_ancestor() will always delete all the old linkages first
after_create_trigger: link_sample_to_direct_ancestor
after_update_trigger: link_sample_to_direct_ancestor
before_property_update_validators:
Expand Down
31 changes: 23 additions & 8 deletions src/schema/schema_triggers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -907,18 +907,22 @@ def link_dataset_to_direct_ancestors(property_key, normalized_type, request, use
activity_uuid = activity_data_dict['uuid']
create_activity = True

if new_ancestors:

if new_ancestors:
logger.info(f"Linking the following new ancestors: {', '.join(new_ancestors)}")
try:
schema_neo4j_queries.add_new_ancestors_to_existing_activity(schema_manager.get_neo4j_driver_instance(), list(new_ancestors), activity_uuid, create_activity, activity_data_dict, dataset_uuid)
except TransactionError:
raise

if ancestors_to_unlink:
logger.info(f"Unlinking the following ancestors: {', '.join(ancestors_to_unlink)}")
try:
schema_neo4j_queries.delete_ancestor_linkages_tx(schema_manager.get_neo4j_driver_instance(), dataset_uuid, list(ancestors_to_unlink))
except TransactionError:
raise

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


"""
Expand Down Expand Up @@ -1921,13 +1925,19 @@ def link_sample_to_direct_ancestor(property_key, normalized_type, request, user_
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")
new_ancestors = set(direct_ancestor_uuids)-set(existing_sample_ancestor_uuids)
ancestors_to_unlink = set(existing_sample_ancestor_uuids)-set(direct_ancestor_uuids)
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
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)

if not activity_uuid:
Expand All @@ -1936,17 +1946,22 @@ def link_sample_to_direct_ancestor(property_key, normalized_type, request, user_
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(), list(new_ancestors), activity_uuid, create_activity, activity_data_dict, sample_uuid)
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

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, list(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
Expand Down