Merge pull request #832 from hubmapconsortium/karlburke/AddUploadFields

Karlburke/add upload fields

Author: yuanzhou

entity-api-spec.yaml

@@ -903,6 +903,12 @@ components:
             $ref: '#/components/schemas/Dataset'
           readOnly: true
           description: 'The datasets that are contained in this Upload.'
+        anticipated_complete_upload_month:
+          type: string
+          description: 'The month that the Upload is anticipated to have all required data uploaded, in the format YYYY-MM.'
+        anticipated_dataset_count:
+          type: integer
+          description: 'The total number of datasets that this Upload will eventually contain.'
     Collection:
       type: object
       properties:

src/schema/provenance_schema.yaml

@@ -1241,6 +1241,24 @@ ENTITIES:
         type: string
         indexed: true
         description: The organ code representing the organ type that the data contained in the upload will be registered/associated with.
+      anticipated_complete_upload_month:
+        type: string
+        indexed: true
+        description: The specific month the Upload is anticipated to have all required data uploaded, in the format YYYY-MM.
+        required_on_create: false
+        before_property_create_validators:
+          - validate_anticipated_complete_date
+        before_property_update_validators:
+          - validate_anticipated_complete_date
+      anticipated_dataset_count:
+        type: integer
+        indexed: true
+        description: The total number of datasets that this Upload will eventually contain.
+        required_on_create: false
+        before_property_create_validators:
+          - validate_anticipated_dataset_count
+        before_property_update_validators:
+          - validate_anticipated_dataset_count
 
   ############################################# EPICollection #############################################
   Epicollection:

src/schema/schema_validators.py

@@ -542,6 +542,63 @@ def validate_upload_status_value(property_key, normalized_entity_type, request,
     if new_status not in accepted_status_values:
         raise ValueError(f"Invalid status value: {new_status}")
 
+"""
+Validate the anticipated_complete_data string provided for an Upload
+
+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_anticipated_complete_date(property_key, normalized_entity_type, request, existing_data_dict, new_data_dict):
+    MAX_ANTICIPATED_COMPLETE_DATE = '2026-12'
+    anticipated_complete_date_str = new_data_dict[property_key]
+    if not re.fullmatch(pattern=r'^\d{4}-\d{2}$', string=anticipated_complete_date_str):
+        raise ValueError(f"Format of '{anticipated_complete_date_str}' does not match the format YYYY-MM")
+    anticipated_year, anticipated_month = map(int, anticipated_complete_date_str.split("-"))
+    if anticipated_month < 1 or anticipated_month > 12:
+        raise ValueError(f"Anticipated completion month of '{anticipated_complete_date_str[5:]}' is not valid")
+    now = datetime.now()
+    current_year = now.year
+    current_month = now.month
+    if  anticipated_year < current_year or \
+        (anticipated_year == current_year and anticipated_month < current_month):
+        raise ValueError(   f"Anticipated complete date '{anticipated_complete_date_str}'"
+                            f" cannot be before the current month.")
+    max_anticipated_year, max_anticipated_month = map(int, MAX_ANTICIPATED_COMPLETE_DATE.split("-"))
+    if anticipated_year > max_anticipated_year:
+        raise ValueError(   f"Anticipated complete date '{anticipated_complete_date_str}'"
+                            f" cannot be after '{MAX_ANTICIPATED_COMPLETE_DATE}'.")
+
+"""
+Validate the anticipated_dataset_count integer provided for an Upload
+
+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_anticipated_dataset_count(property_key, normalized_entity_type, request, existing_data_dict, new_data_dict):
+    # anticipated_dataset_count of type int, assured by provenance_schema.yaml "type: integer"
+    anticipated_dataset_count = new_data_dict[property_key]
+    if anticipated_dataset_count <= 0:
+        raise ValueError(f"{property_key} must be positive integer when specified.")
 
 """
 Validate the provided value of Sample.sample_category on create via POST and update via PUT

src/schema_templating/example-yaml-templates/upload-schema.yaml

@@ -81,4 +81,10 @@ Upload:
       items:
         $ref: '#/components/schemas/Dataset'
       readOnly: true
-      description: "The datasets that are contained in this Upload."
+      description: "The datasets that are contained in this Upload."
+    anticipated_complete_upload_month:
+      type: string
+      description: The month that the Upload is anticipated to have all required data uploaded, in the format YYYY-MM.
+    anticipated_dataset_count:
+      type: integer
+      description: The total number of datasets that this Upload will eventually contain.