Merge branch 'main' into Derek-Furst/multiple-components-datasets

src/app.py

@@ -4294,7 +4294,6 @@ def create_entity_details(request, normalized_entity_type, user_token, json_data
     # Meaning the returned target property key is different from the original key
     # in the trigger method, e.g., Donor.image_files_to_add
     filtered_merged_dict = schema_manager.remove_transient_and_none_values(merged_dict, normalized_entity_type)
-
     # Create new entity
     try:
         # Check if the optional `superclass` property is defined, None otherwise

src/schema/provenance_schema.yaml

@@ -88,8 +88,6 @@ ACTIVITIES:
       <<: *shared_properties
       creation_action:
         type: string
-        generated: true
-        immutable: true
         description: "The activity that was performed."
         before_create_trigger: set_activity_creation_action
 
@@ -279,6 +277,13 @@ ENTITIES:
       antibodies:
         type: list
         description: "A list of antibodies used in the assay that created the dataset"
+      creation_action:
+        type: string
+        transient: true
+        immutable: true
+        description: "The activity that was performed."
+        before_property_create_validators:
+          - validate_creation_action
       description:
         type: string
         description: "Free text description of the dataset"
@@ -508,6 +513,13 @@ ENTITIES:
         type: string
         description: "Additional information about the dataset, which can be used to find this dataset, including lab specific (non-PHI) identifiers."
       # The Dataset.data_access_level is based on Dataset.status and Dataset.contains_human_genetic_sequences
+      creation_action:
+        type: string
+        transient: true
+        immutable: true
+        description: "The activity that was performed."
+        before_property_create_validators:
+          - validate_creation_action
       data_access_level:
         type: string
         generated: true

src/schema/schema_triggers.py

@@ -1907,7 +1907,8 @@ def get_upload_datasets(property_key, normalized_type, user_token, existing_data
 def set_activity_creation_action(property_key, normalized_type, user_token, existing_data_dict, new_data_dict):
     if 'normalized_entity_type' not in new_data_dict:
         raise KeyError("Missing 'normalized_entity_type' key in 'existing_data_dict' during calling 'set_activity_creation_action()' trigger method.")
-
+    if new_data_dict and new_data_dict.get('creation_action'):
+        return property_key, new_data_dict['creation_action'].title()
     return property_key, f"Create {new_data_dict['normalized_entity_type']} Activity"
 
 

src/schema/schema_validators.py

@@ -509,6 +509,30 @@ def validate_publication_date(property_key, normalized_entity_type, request, exi
     except ValueError:
         raise ValueError(f"Invalid {property_key} format, must be YYYY-MM-DD")
 
+"""
+Validate the provided value of the activity creation action. Only very specific
+values are allowed.
+Parameters
+----------
+property_key : str
+    The target property key
+normalized_type : str
+    Submission
+request: Flask request object
+    The instance of Flask request passed in from application request
+existing_data_dict : dict
+    A dictionary that contains all existing entity properties
+new_data_dict : dict
+    The json data in request body, already after the regular validations
+"""
+def validate_creation_action(property_key, normalized_entity_type, request, existing_data_dict, new_data_dict):
+    accepted_creation_action_values = ["central process", "lab process"]
+    creation_action = new_data_dict[property_key].lower()
+    if creation_action and creation_action not in accepted_creation_action_values:
+        raise ValueError("Invalid {} value. Accepted values are: {}".format(property_key, ", ".join(accepted_creation_action_values)))
+    if creation_action == '':
+        raise ValueError(f"The property {property_key} cannot be empty, when specified.")
+
 
 ####################################################################################################
 ## Internal Functions