Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix for prov-metadata generation to filter entity exclusions regardle… #802

Merged
merged 1 commit into from
Feb 4, 2025
Merged

Fix for prov-metadata generation to filter entity exclusions regardle… #802

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
67 changes: 32 additions & 35 deletions src/app.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -699,30 +699,30 @@ def get_provenance_metadata_by_id_for_auth_level(id):
# Identify fields to exclude from non-authorized responses for the entity type.
fields_to_exclude = schema_manager.get_fields_to_exclude(normalized_entity_type)

# Response with the dict
if public_entity and not user_authorized:
final_result = schema_manager.exclude_properties_from_response(fields_to_exclude, final_result)
# Remove fields which do not belong in provenance metadata, regardless of
# entity scope or user authorization.
final_result = schema_manager.exclude_properties_from_response(fields_to_exclude, final_result)

# Retrieve the associated data for the entity, and add it to the expanded dictionary.
associated_organ_list = _get_dataset_associated_data( dataset_dict=final_result
, dataset_visibility=entity_scope
, valid_user_token=user_token
, request=request
, associated_data='Organs')
associated_organ_list = _get_dataset_associated_metadata( dataset_dict=final_result
, dataset_visibility=entity_scope
, valid_user_token=user_token
, request=request
, associated_data='Organs')
final_result['organs'] = associated_organ_list

associated_sample_list = _get_dataset_associated_data( dataset_dict=final_result
, dataset_visibility=entity_scope
, valid_user_token=user_token
, request=request
, associated_data='Samples')
associated_sample_list = _get_dataset_associated_metadata( dataset_dict=final_result
, dataset_visibility=entity_scope
, valid_user_token=user_token
, request=request
, associated_data='Samples')
final_result['samples'] = associated_sample_list

associated_donor_list = _get_dataset_associated_data( dataset_dict=final_result
, dataset_visibility=entity_scope
, valid_user_token=user_token
, request=request
, associated_data='Donors')
associated_donor_list = _get_dataset_associated_metadata( dataset_dict=final_result
, dataset_visibility=entity_scope
, valid_user_token=user_token
, request=request
, associated_data='Donors')

final_result['donors'] = associated_donor_list

Expand Down Expand Up @@ -5019,12 +5019,9 @@ def _get_entity_visibility(normalized_entity_type, entity_dict):
return entity_visibility


"""
Retrieve the metadata information for certain data associated with entity. This method supports
Dataset entities, and can get the associated data for organs, samples, or donors.

Get associated data dict based upon the user's authorization. The associated data may be
filtered down if credentials were not presented for full access.
'''
Retrieve the organ, donor, or sample metadata information associated with a Dataset, based
up the user's authorization to access the Dataset.

Parameters
----------
Expand All @@ -5044,9 +5041,9 @@ def _get_entity_visibility(normalized_entity_type, entity_dict):
Returns
-------
list
A dictionary containing all the properties the target entity.
"""
def _get_dataset_associated_data(dataset_dict, dataset_visibility, valid_user_token, request, associated_data: str):
A dictionary containing the metadata properties the Dataset associated data.
'''
def _get_dataset_associated_metadata(dataset_dict, dataset_visibility, valid_user_token, request, associated_data: str):

# Confirm the associated data requested is supported by this method.
retrievable_associations = ['organs', 'samples', 'donors']
Expand Down Expand Up @@ -5115,17 +5112,17 @@ def _get_dataset_associated_data(dataset_dict, dataset_visibility, valid_user_to

# For public entities, limit the fields in the response unless the authorization presented in the
# Request allows the user to see all properties.
if public_entity and not user_authorized:
filtered_entities_list = []
for entity in final_result:
final_entity_dict = schema_manager.exclude_properties_from_response(excluded_fields=fields_to_exclude
, output_dict=entity)
filtered_entities_list.append(final_entity_dict)
final_result = filtered_entities_list
# Remove fields which do not belong in provenance metadata, regardless of
# entity scope or user authorization.
filtered_entities_list = []
for entity in final_result:
final_entity_dict = schema_manager.exclude_properties_from_response(excluded_fields=fields_to_exclude
, output_dict=entity)
filtered_entities_list.append(final_entity_dict)
final_result = filtered_entities_list

return final_result


"""
Generate 'before_create_triiger' data and create the entity details in Neo4j

Expand Down