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revisions from initial test in Dev #794

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Jan 23, 2025
Merged

revisions from initial test in Dev #794

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95806ca
Limit provenance metadata support to only Datasets. Error immediatel…
kburke Jan 23, 2025
dcc4b1b
Replace usage of shadowed id variable with the local entity_id of the…
kburke Jan 23, 2025
9e4ee8c
Remove remnant of property support.
kburke Jan 23, 2025
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9 changes: 4 additions & 5 deletions src/app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -675,10 +675,9 @@ def get_provenance_metadata_by_id_for_auth_level(id:Annotated[str, 32]) -> str:

# Retrieve the expanded metadata for the entity. If authorization of token or group membership
# does not allow access to the entity, exceptions will be raised describing the problem.
req_property_key = request.args.get('property') if request.args else None
expanded_entity_metadata = entity_worker.get_expanded_entity_metadata(entity_id=id
, valid_user_token=user_token
, user_info=user_info)
expanded_entity_metadata = entity_worker.get_expanded_dataset_metadata( dataset_id=id
, valid_user_token=user_token
, user_info=user_info)
return jsonify(expanded_entity_metadata)
except entityEx.EntityBadRequestException as e_400:
return jsonify({'error': e_400.message}), 400
Expand Down Expand Up @@ -5765,7 +5764,7 @@ def _get_metadata_by_id(entity_id:str=None, metadata_scope:MetadataScopeEnum=Met
# Without token, the user can only access public collections, modify the collection result
# by only returning public datasets attached to this collection
if isinstance(user_token, Response):
forbidden_error(f"{normalized_entity_type} for {id} is not accessible without presenting a token.")
forbidden_error(f"{normalized_entity_type} for {entity_id} is not accessible without presenting a token.")
else:
# When the groups token is valid, but the user doesn't belong to HuBMAP-READ group
# Or the token is valid but doesn't contain group information (auth token or transfer token)
Expand Down
34 changes: 20 additions & 14 deletions src/dev_entity_worker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -540,44 +540,50 @@ def get_request_user_info_with_groups(self, request):
dict
A dictionary containing all the properties the target entity.
'''
def get_expanded_entity_metadata(self, entity_id:Annotated[str, 32], valid_user_token:Annotated[str, 32]
def get_expanded_dataset_metadata(self, dataset_id:Annotated[str, 32], valid_user_token:Annotated[str, 32]
, user_info:dict) -> dict:
# Retrieve the metadata dictionary for the entity, which will be expanded later to hold entries for the
# Retrieve the metadata dictionary for the Dataset, which will be expanded later to hold entries for the
# associated data.
expanded_entity_dict = self._get_entity_by_id_for_auth_level(entity_id=entity_id
expanded_dataset_dict = self._get_entity_by_id_for_auth_level(entity_id=dataset_id
, valid_user_token=valid_user_token
, user_info=user_info)
# Confirm the dataset_id passed in is for a Dataset entity.
if expanded_dataset_dict['entity_type'] not in ['Dataset','Publication']:
raise entityEx.EntityBadRequestException( f"Only Dataset provenance metadata can be retrieved."
f" An entity of type '{expanded_dataset_dict['entity_type']}'"
f" for uuid={expanded_dataset_dict['uuid']} is not supported.")

# Determine if the entity is publicly visible base on its data, only.
# To verify if a Collection is public, it is necessary to have its Datasets, which
# are populated as triggered data. So pull back the complete entity for
# _get_entity_visibility() to check.
entity_scope = self._get_entity_visibility(entity_dict=expanded_entity_dict)
dataset_scope = self._get_entity_visibility(entity_dict=expanded_dataset_dict)

# Retrieve the associated data for the entity, and add it to the expanded dictionary.
associated_organ_list = self._get_dataset_associated_data( dataset_dict=expanded_entity_dict
, dataset_visibility=entity_scope
associated_organ_list = self._get_dataset_associated_data( dataset_dict=expanded_dataset_dict
, dataset_visibility=dataset_scope
, valid_user_token=valid_user_token
, user_info=user_info
, associated_data='Organs')
expanded_entity_dict['organs'] = associated_organ_list
expanded_dataset_dict['organs'] = associated_organ_list

associated_sample_list = self._get_dataset_associated_data( dataset_dict=expanded_entity_dict
, dataset_visibility=entity_scope
associated_sample_list = self._get_dataset_associated_data( dataset_dict=expanded_dataset_dict
, dataset_visibility=dataset_scope
, valid_user_token=valid_user_token
, user_info=user_info
, associated_data='Samples')
expanded_entity_dict['samples'] = associated_sample_list
expanded_dataset_dict['samples'] = associated_sample_list

associated_donor_list = self._get_dataset_associated_data( dataset_dict=expanded_entity_dict
, dataset_visibility=entity_scope
associated_donor_list = self._get_dataset_associated_data( dataset_dict=expanded_dataset_dict
, dataset_visibility=dataset_scope
, valid_user_token=valid_user_token
, user_info=user_info
, associated_data='Donors')

expanded_entity_dict['donors'] = associated_donor_list
expanded_dataset_dict['donors'] = associated_donor_list

# Return the dictionary containing the entity metadata as well as metadata for the associated data.
return expanded_entity_dict
return expanded_dataset_dict

# KBKBKB @TODO for future use of /datasets/<id>/organs endpoint of app.py needs.
def get_organs_associated_with_dataset(self, dataset_id: Annotated[str, 32], valid_user_token: Annotated[str, 32]
Expand Down
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