map legacy is_primary boolean to categorical process_state in legacy assaytype and assayname endpoints

src/hs_ontology_api/routes/assayname/assayname_controller.py

@@ -72,7 +72,9 @@ def assayname_post():
         assaytype = {}
         val = r.get('value')
         assaytype['name'] = val.get('assaytype')
-        assaytype['primary'] = val.get('primary')
+        # July 2024 - Process states have changed from a simple binary for primary/derived to a categorical
+        # value of 'primary', 'derived', or 'epic'. The legacy model will observe the binary model.
+        assaytype['primary'] = val.get('process_state')=='primary'
         assaytype['description'] = val.get('description')
         assaytype['vitessce-hints'] = val.get('vitessce_hints')
         # The vis-only and contains-pii properties have been deprecated.

src/hs_ontology_api/routes/assaytype/assaytype_controller.py

@@ -30,7 +30,7 @@ def assaytype_get(name=None):
     # Validate parameters.
 
     # Check for invalid parameter names.
-    err = validate_query_parameter_names(parameter_name_list=['application_context', 'is_primary'])
+    err = validate_query_parameter_names(parameter_name_list=['application_context', 'primary'])
     if err != 'ok':
         return make_response(err, 400)
 
@@ -48,17 +48,24 @@ def assaytype_get(name=None):
         return make_response(err, 400)
 
     # Check for valid parameter values.
-    is_primary = request.args.get('is_primary')
+    # Map the legacy is_primary parameter to new process_state parameter.
+    is_primary = request.args.get('primary')
     if is_primary is not None:
         is_primary = is_primary.lower()
         val_enum = ['true', 'false']
-        err = validate_parameter_value_in_enum(param_name='is_primary', param_value=is_primary, enum_list=val_enum)
+        err = validate_parameter_value_in_enum(param_name='primary', param_value=is_primary, enum_list=val_enum)
         if err != 'ok':
             return make_response(err, 400)
+        if is_primary == 'true':
+            process_state = 'primary'
+        else:
+            process_state = 'derived'
+    else:
+        process_state = None
 
     neo4j_instance = current_app.neo4jConnectionHelper.instance()
     result = assayclasses_get_logic(
-        neo4j_instance, assaytype=name, context=application_context)
+        neo4j_instance, assaytype=name, process_state=process_state, context=application_context)
 
     if (result is None or result == []):
         # Empty result
@@ -72,7 +79,10 @@ def assaytype_get(name=None):
         assaytype = {}
         val = r.get('value')
         assaytype['name'] = val.get('assaytype')
-        assaytype['primary'] = val.get('primary')
+        # July 2024 - Process states have changed from a simple binary for primary/derived to a categorical
+        # value of 'primary', 'derived', or 'epic'. The legacy model will observe the binary model.
+        assaytype['primary'] = val.get('process_state') == 'primary'
+        #assaytype['primary'] = val.get('primary')
         assaytype['description'] = val.get('description')
         assaytype['vitessce-hints'] = val.get('vitessce_hints')
         # The vis-only and contains-pii properties have been deprecated.