Merge pull request #831 from hubmapconsortium/karlburke/addSampleCategoryCaseValidation

Add case-check to sample_category validator, and use validators durin…

Author: yuanzhou

entity-api-spec.yaml

@@ -434,7 +434,7 @@ components:
             - block
             - section
             - suspension
-          description: 'A code representing the type of specimen. Must be an organ, block, section, or suspension'
+          description: 'A code representing the type of specimen. Must be an organ, block, section, or suspension, in all lower case.'
         protocol_url:
           type: string
           description: 'The protocols.io doi url pointing the protocol under wich the sample was obtained and/or prepared.'
@@ -482,7 +482,7 @@ components:
             - TR
             - UR
             - UT
-          description: 'Organ code specifier, only set if sample_category == organ.  Valid values found in: [organ types](https://github.com/hubmapconsortium/search-api/blob/main/src/search-schema/data/definitions/enums/organ_types.yaml)'
+          description: 'Organ code specifier, only set if sample_category == organ.  Valid values found in: [organ types](https://ontology.api.hubmapconsortium.org/organs/by-code?application_context=HUBMAP)'
         organ_other:
           type: string
           description: The organ type provided by the user if "other" organ type is selected

src/app.py

@@ -1272,7 +1272,15 @@ def create_multiple_samples(count):
         # No need to log the validation errors
         bad_request_error(str(e))
 
-    # `direct_ancestor_uuid` is required on create
+    try:
+        schema_manager.execute_property_level_validators('before_property_create_validators', normalized_entity_type, request, {}, json_data_dict)
+    # Currently only ValueError
+    except ValueError as e:
+        bad_request_error(e)
+    except schema_errors.UnimplementedValidatorException as uve:
+        internal_server_error(uve)
+
+    # `direct_ancestor_uuid` is required on create for a Sample.
     # Check existence of the direct ancestor (either another Sample or Donor)
     direct_ancestor_dict = query_target_entity(json_data_dict['direct_ancestor_uuid'], user_token)
 
@@ -1288,7 +1296,7 @@ def create_multiple_samples(count):
         if ('organ' not in json_data_dict) or (not json_data_dict['organ']):
             bad_request_error("A valid organ code is required since the direct ancestor is a Donor")
 
-    # Generate 'before_create_triiger' data and create the entity details in Neo4j
+    # Generate 'before_create_trigger' data and create the entity details in Neo4j
     generated_ids_dict_list = create_multiple_samples_details(request, normalized_entity_type, user_token, json_data_dict, count)
 
     # Also index the each new Sample node in elasticsearch via search-api

src/schema/schema_validators.py

@@ -564,8 +564,14 @@ def validate_sample_category(property_key, normalized_entity_type, request, exis
     sample_category = new_data_dict[property_key].lower()
 
     if sample_category not in defined_tissue_types:
-        raise ValueError(f"Invalid sample_category: {sample_category}")
-
+        raise ValueError(f"Invalid sample_category: {sample_category}."
+                         f" Should be one of {', '.join(defined_tissue_types)}.")
+
+    # Given the sample_category is a defined_tissue_types element, assure the request has
+    # the proper case for storage
+    if new_data_dict[property_key] != sample_category:
+        raise ValueError(f"The case of sample_category '{new_data_dict[property_key]}'"
+                         f" must be specified as '{sample_category}'.")
 
 """
 Validate the provided value of Publication.publication_date is in the correct format against ISO 8601 Format: