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Remove print statements in init() method. Remove support for filterin…
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…g requested entity dictionary to a single property.
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@kburke
kburke committed Jan 16, 2025
1 parent 07f9c09 commit 476bce8
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Showing 2 changed files with 29 additions and 66 deletions.
13 changes: 4 additions & 9 deletions src/app.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -259,13 +259,12 @@ def http_internal_server_error(e):
, schema_mgr = schema_manager
, memcached_client_instance = memcached_client_instance
, neo4j_driver_instance = neo4j_driver_instance)
if not isinstance(entity_worker, EntityWorker):
raise Exception("Error instantiating a EntityWorker during startup.")
logger.info("EntityWorker instantiated using app.cfg setting.")
except Exception as e:
logger.critical(f"Unable to instantiate a EntityWorker during startup.")
print("Error instantiating a EntityWorker during startup.")
print(str(e))
logger.error(e, exc_info=True)
print("Check the log file for further information.")

####################################################################################################
## REFERENCE DOI Redirection
Expand Down Expand Up @@ -640,14 +639,11 @@ def _get_entity_visibility(normalized_entity_type, entity_dict):
This endpoint as publicly accessible. Without presenting a token, only data for
published Datasets may be requested.
Result filtering is supported based on query string
For example: /prov-metadata/<id>?property=data_access_level
When a valid token is presented, a member of the HuBMAP-Read Globus group is authorized to
access any Dataset. Otherwise, only access to published Datasets is authorized.
An HTTP 400 Response is returned for reasons described in the error message, such as
requesting data for a non-Dataset, filtering by an unsupported key, etc.
requesting data for a non-Dataset.
An HTTP 401 Response is returned when a token is presented that is not valid.
Expand Down Expand Up @@ -682,8 +678,7 @@ def get_provenance_metadata_by_id_for_auth_level(id:Annotated[str, 32]) -> str:
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
, request_property_key=req_property_key)
, user_info=user_info)
return jsonify(expanded_entity_metadata)
except entityEx.EntityBadRequestException as e_400:
return jsonify({'error': e_400.message}), 400
Expand Down
82 changes: 25 additions & 57 deletions src/entity_worker.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -260,8 +260,7 @@ def _query_target_entity(self, entity_id):
return entity_dict

''''
Retrieve the metadata information for an entity by id. Results can also be
filtered to a single property for the entity, if in the supported list for filtering.
Retrieve the metadata information for an entity by id.
Get target entity dict based upon the user's authorization. The full dictionary may be
filtered down if credentials were not presented for full access.
Expand All @@ -274,17 +273,14 @@ def _query_target_entity(self, entity_id):
Either the valid current token for an authenticated user or None.
user_info : dict
Information for the logged-in user to be used for authorization accessing non-public entities.
property_key : str
An entity property to be returned as the sole entry in the dictionary rather than
the complete entity dictionary. Must from the valid values supported by this method.
Returns
-------
dict
A dictionary containing all the properties the target entity or just the filtered property.
A dictionary containing all the properties the target entity.
'''
def _get_entity_by_id_for_auth_level(self, entity_id:Annotated[str, 32], valid_user_token:Annotated[str, 32]
, user_info:dict, property_key:str=None) -> dict:
, user_info:dict) -> dict:

# Use the internal token to query the target entity to assure it is returned. This way public
# entities can be accessed even if valid_user_token is None.
Expand Down Expand Up @@ -326,47 +322,23 @@ def _get_entity_by_id_for_auth_level(self, entity_id:Annotated[str, 32], valid_u
# Also normalize the result based on schema
final_result = self.schemaMgr.normalize_entity_result_for_response(complete_dict)

# Result filtering based on query string
# The `data_access_level` property is available in all entities Donor/Sample/Dataset
# and this filter is being used by gateway to check the data_access_level for file assets
# The `status` property is only available in Dataset and being used by search-api for revision
result_filtering_accepted_property_keys = ['data_access_level', 'status']

# if bool(request.args):
# property_key = request.args.get('property')

if property_key is not None:
# Validate the target property
if property_key not in result_filtering_accepted_property_keys:
raise entityEx.EntityBadRequestException( f"Only the following property keys are supported in the query string:"
f" {COMMA_SEPARATOR.join(result_filtering_accepted_property_keys)}")
if property_key == 'status' and \
not self.schemaMgr.entity_type_instanceof(normalized_entity_type, 'Dataset'):
raise entityEx.EntityBadRequestException(f"Only Dataset or Publication supports"
f" 'status' property key in the query string")

# Return a dict containing only the requested property value
return {property_key: complete_dict[property_key]}
# else:
# bad_request_error("The specified query string is not supported. Use '?property=<key>' to filter the result")
else:
# Identify fields in the entity based upon user's authorization
fields_to_exclude = self.schemaMgr.get_fields_to_exclude(normalized_entity_type)

# Response with the dict
#if public_entity and not user_in_hubmap_read_group(request):
if public_entity and not user_authorized:
final_result = self.schemaMgr.exclude_properties_from_response(fields_to_exclude, final_result)
if normalized_entity_type == 'Collection':
for i, dataset in enumerate(final_result.get('datasets', [])):
if self._get_entity_visibility( entity_dict=dataset) != DataVisibilityEnum.PUBLIC \
or user_authorized: # or user_in_hubmap_read_group(request):
# If the dataset is public, or if the user has read-group access, there is
# no need to remove fields, continue to the next dataset
continue
dataset_excluded_fields = self.schemaMgr.get_fields_to_exclude('Dataset')
final_result.get('datasets')[i] = self.schemaMgr.exclude_properties_from_response(dataset_excluded_fields, dataset)
return final_result
# Identify fields in the entity based upon user's authorization
fields_to_exclude = self.schemaMgr.get_fields_to_exclude(normalized_entity_type)

# Response with the dict
#if public_entity and not user_in_hubmap_read_group(request):
if public_entity and not user_authorized:
final_result = self.schemaMgr.exclude_properties_from_response(fields_to_exclude, final_result)
if normalized_entity_type == 'Collection':
for i, dataset in enumerate(final_result.get('datasets', [])):
if self._get_entity_visibility( entity_dict=dataset) != DataVisibilityEnum.PUBLIC \
or user_authorized: # or user_in_hubmap_read_group(request):
# If the dataset is public, or if the user has read-group access, there is
# no need to remove fields, continue to the next dataset
continue
dataset_excluded_fields = self.schemaMgr.get_fields_to_exclude('Dataset')
final_result.get('datasets')[i] = self.schemaMgr.exclude_properties_from_response(dataset_excluded_fields, dataset)
return final_result

'''
Retrieve the metadata information for certain data associated with entity. This method supports
Expand All @@ -393,7 +365,7 @@ def _get_entity_by_id_for_auth_level(self, entity_id:Annotated[str, 32], valid_u
Returns
-------
list
A dictionary containing all the properties the target entity or just the filtered property.
A dictionary containing all the properties the target entity.
'''
def _get_dataset_associated_data( self, dataset_dict:dict, dataset_visibility:DataVisibilityEnum
, valid_user_token:Annotated[str, 32], user_info:dict
Expand Down Expand Up @@ -561,7 +533,7 @@ def get_request_user_info_with_groups(self, request):

''''
Retrieve expanded metadata information for an entity by id, including metadata for
associated data. Results can also be filtered to a supported single property for the entity.
associated data.
Get target entity dict based upon the user's authorization. The full dictionary may be
filtered down if credentials were not presented for full access.
Expand All @@ -574,23 +546,19 @@ def get_request_user_info_with_groups(self, request):
Either the valid current token for an authenticated user or None.
user_info : dict
Information for the logged-in user to be used for authorization accessing non-public entities.
request_property_key : str
An entity property to be returned as the sole entry in the dictionary rather than
the complete entity dictionary. Must from the valid values supported for the entity type.
Returns
-------
dict
A dictionary containing all the properties the target entity or just the filtered property.
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]
, user_info:dict, request_property_key:str) -> dict:
, user_info:dict) -> dict:
# Retrieve the metadata dictionary for the entity, 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
, valid_user_token=valid_user_token
, user_info=user_info
, property_key=request_property_key)
, user_info=user_info)
# 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
Expand Down

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