Merge pull request #867 from hubmapconsortium/Derek-Furst/priority-project-list

Added new property priority_project_list and accompanying validator

Author: yuanzhou

entity-api-spec.yaml

@@ -542,6 +542,9 @@ components:
             type: string
             format: uuid
           description: 'List of image files previously uploaded to delete. Provide as a json array of the file_uuids of the file like: ["232934234234234234234270c0ea6c51d604a850558ef2247d0b4", "230948203482234234234a57bfe9c056d08a0f8e6cd612baa3bfa"]'
+        rui_exemption:
+          type: boolean
+          description: 'Identifies Sample Blocks that are exempt from spatial registration via RUI.'
     Dataset:
       type: object
       properties:
@@ -809,6 +812,9 @@ components:
         intended_organ:
           type: string
           description: 'The organ code representing the organ type that the data contained in the upload will be registered/associated with.'
+        priority_project_list:
+          type: array
+          description: 'The list of priority projects that this Dataset data will be used For'
     Upload:
       type: object
       properties:
@@ -909,6 +915,9 @@ components:
         anticipated_dataset_count:
           type: integer
           description: 'The total number of datasets that this Upload will eventually contain.'
+        priority_project_list:
+          type: array
+          description: 'The list of priority projects that this Upload data will be used For'
     Collection:
       type: object
       properties:
@@ -1403,6 +1412,7 @@ components:
         group_name: 'University TMC'
         visit: 'abc123'
         rui_location: object
+        rui_exemption: False
     DatasetExample:
       summary: 'An example of a Dataset response'
       value:
@@ -1456,6 +1466,7 @@ components:
         intended_organ: 'AO'
         group_uuid: 'abcd1234-ef56-gh78-ij90-klmnop123456'
         group_name: 'University TMC'
+        priority_project_list: ['SWAT']
     UploadExample:
       summary: 'An example of an upload response'
       value:
@@ -1479,6 +1490,7 @@ components:
         dataset_uuids_to_link: ['abcd1234-ef56-gh78-ij90-klmnop123456']
         dataset_uuids_to_unlink: ['abcd1234-ef56-gh78-ij90-klmnop123456']
         datasets: [dataset objects]
+        priority_project_list: ['SWAT']
     CollectionExample:
       summary: 'An example of a collection response'
       value:
@@ -1633,6 +1645,7 @@ components:
           intended_organ: 'AO'
           group_uuid: 'abcd1234-ef56-gh78-ij90-klmnop123456'
           group_name: 'University TMC'
+          priority_project_list: ['SWAT']
         - created_timestamp: 1710243867000
           created_by_user_displayname: 'JaneDoe1'
           created_by_user_email: '[email protected]'
@@ -1683,6 +1696,7 @@ components:
           intended_organ: 'AO'
           group_uuid: 'abcd1234-ef56-gh78-ij90-klmnop123456'
           group_name: 'University TMC'
+          priority_project_list:: ['SWAT']
     SampleArrayExample:
       summary: 'An example of an array of sample objects'
       value:
@@ -1719,6 +1733,7 @@ components:
           group_name: 'University TMC'
           visit: 'abc123'
           rui_location: object
+          rui_exemption: False
         - created_timestamp: 1710243867000
           created_by_user_displayname: 'JaneDoe1'
           created_by_user_email: '[email protected]'
@@ -1752,6 +1767,7 @@ components:
           group_name: 'University TMC'
           visit: 'abc123'
           rui_location: object
+          rui_exemption: False
     CollectionArrayExample:
       summary: 'An example of an array of collection objects'
       value:
@@ -1814,6 +1830,7 @@ components:
           dataset_uuids_to_link: ['abcd1234-ef56-gh78-ij90-klmnop123456']
           dataset_uuids_to_unlink: ['abcd1234-ef56-gh78-ij90-klmnop123456']
           datasets: [dataset objects]
+          priority_project_list: ['SWAT']
         - created_timestamp: 1710243867000
           created_by_user_displayname: 'JaneDoe1'
           created_by_user_email: '[email protected]'
@@ -1834,6 +1851,7 @@ components:
           dataset_uuids_to_link: ['abcd1234-ef56-gh78-ij90-klmnop123456']
           dataset_uuids_to_unlink: ['abcd1234-ef56-gh78-ij90-klmnop123456']
           datasets: [dataset objects]
+          priority_project_list: ['SWAT']
     DatasetProvMetadata:
       summary: 'An example of a dataset prov metadata response'
       value:

src/schema/provenance_schema.yaml

@@ -677,6 +677,16 @@ ENTITIES:
           - validate_in_admin_group
         before_property_update_validators:
           - validate_in_admin_group
+      priority_project_list:
+        type: list
+        required: false
+        indexted: false
+        description: The list of priority projects that this Dataset data will be used For
+        immutable: false
+        before_property_update_validators:
+          - validate_priority_project
+        before_property_create_validators:
+          - validate_priority_project
 
   ############################################# Publication #############################################
   Publication:
@@ -796,6 +806,7 @@ ENTITIES:
       ingest_task: null # This ingest_task is Dataset specific, Publication doesn't have it
       new_associated_multi_assay_uuid: null # Dataset-only attribute of Multi-Assay Dataset relationships
       superseded_associated_processed_component_uuids: null # Dataset-only attribute of Multi-Assay Dataset relationships
+      priority_project_list: null # Dataset-only attribute 
 
   ############################################# Donor #############################################
   Donor:
@@ -1344,6 +1355,16 @@ ENTITIES:
           - validate_anticipated_dataset_count
         before_property_update_validators:
           - validate_anticipated_dataset_count
+      priority_project_list:
+        type: list
+        required: false
+        indexted: false
+        description: The list of priority projects that this Uploaded data will be used For
+        immutable: false
+        before_property_update_validators:
+          - validate_priority_project
+        before_property_create_validators:
+          - validate_priority_project
 
   ############################################# EPICollection #############################################
   Epicollection:

src/schema/schema_constants.py

@@ -26,6 +26,8 @@ class SchemaConstants(object):
 
     OMITTED_FIELDS = ['ingest_metadata', 'files']
 
+    ALLOWED_PRIORITY_PROJECTS = ['SWAT', 'MOSDAP']
+
 # Define an enumeration to classify an entity's visibility, which can be combined with
 # authorization info when verify operations on a request.
 class DataVisibilityEnum(Enum):

src/schema/schema_validators.py

@@ -887,6 +887,31 @@ def verify_multi_assay_dataset_components(property_key, normalized_type, user_to
     # fall out successfully if no raise() occurred.
     return
 
+
+"""
+Validate the specified value for an Upload's priority_project_list is in a recognized value 
+
+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_priority_project(property_key, normalized_entity_type, request, existing_data_dict, new_data_dict):
+    allowed_priority_projects = SchemaConstants.ALLOWED_PRIORITY_PROJECTS
+    for priority_project in new_data_dict.get('priority_project_list'):
+        if priority_project not in allowed_priority_projects:
+            raise ValueError(f"Provided priority_project_list contains unrecognized value: {priority_project}. Allowed values are {', '.join(allowed_priority_projects)}. These are case-sensitive values.")
+    new_data_dict['priority_project_list'] = [project.upper() for project in new_data_dict['priority_project_list']]
+    
+
 ####################################################################################################
 ## Internal Functions
 ####################################################################################################