Merge pull request #638 from hubmapconsortium/upload_and_dataset_status_add_incomplete

Added incomplete to schema_validators for dataset and upload status

Author: yuanzhou

src/schema/provenance_schema.yaml

@@ -312,7 +312,7 @@ ENTITIES:
           - validate_dataset_status_value
           - validate_status_changed
         generated: true
-        description: "One of: New|Processing|QA|Published|Error|Hold|Invalid|Submitted"
+        description: "One of: New|Processing|Published|QA|Error|Hold|Invalid|Submitted|Incomplete"
         before_create_trigger: set_dataset_status_new
         after_create_trigger: set_status_history
         after_update_trigger: set_status_history
@@ -931,7 +931,7 @@ ENTITIES:
           - validate_status_changed
         type: string
         generated: true
-        description: "One of: New|Valid|Invalid|Error|Reorganized|Processing"
+        description: "One of: New|Valid|Invalid|Error|Reorganized|Processing|Submitted|Incomplete"
         # Trigger method will set the status to "New" on create
         before_create_trigger: set_upload_status_new
         after_create_trigger: set_status_history

src/schema/schema_validators.py

@@ -280,7 +280,9 @@ def validate_application_header_before_property_update(property_key, normalized_
 """
 def validate_dataset_status_value(property_key, normalized_entity_type, request, existing_data_dict, new_data_dict):
     # Use lowercase for comparison
-    accepted_status_values = ['new', 'processing', 'published', 'qa', 'error', 'hold', 'invalid', 'submitted']
+    accepted_status_values = [
+        'new', 'processing', 'published', 'qa', 'error', 'hold', 'invalid', 'submitted', 'incomplete'
+    ]
     new_status = new_data_dict[property_key].lower()
 
     if new_status not in accepted_status_values:
@@ -456,7 +458,9 @@ def validate_retracted_dataset_sub_status_value(property_key, normalized_entity_
 """
 def validate_upload_status_value(property_key, normalized_entity_type, request, existing_data_dict, new_data_dict):
     # Use lowercase for comparison
-    accepted_status_values = ['new', 'valid', 'invalid', 'error', 'reorganized', 'processing', 'submitted']
+    accepted_status_values = [
+        'new', 'valid', 'invalid', 'error', 'reorganized', 'processing', 'submitted', 'incomplete'
+    ]
     new_status = new_data_dict[property_key].lower()
 
     if new_status not in accepted_status_values:
@@ -481,7 +485,7 @@ def validate_upload_status_value(property_key, normalized_entity_type, request,
 """
 def validate_sample_category(property_key, normalized_entity_type, request, existing_data_dict, new_data_dict):
     defined_tissue_types = ["organ", "block", "section", "suspension"]
-    sample_category = new_data_dict[property_key]
+    sample_category = new_data_dict[property_key].lower()
 
     if sample_category not in defined_tissue_types:
         raise ValueError(f"Invalid sample_category: {sample_category}")