From bbb75b80744cc73832ce06612513870afc62fe09 Mon Sep 17 00:00:00 2001
From: yuanzhou <zhy19@pitt.edu>
Date: Mon, 11 Aug 2025 15:09:31 -0400
Subject: [PATCH] Remove unnecessary warning log on superclass

---
 src/app.py                         |  4 +-
 src/schema/schema_manager.py       | 71 ++++++++++++++++++------------
 src/schema/schema_neo4j_queries.py |  4 +-
 3 files changed, 47 insertions(+), 32 deletions(-)

diff --git a/src/app.py b/src/app.py
index 99ef704e..36bff7ab 100644
--- a/src/app.py
+++ b/src/app.py
@@ -4538,7 +4538,7 @@ def _get_entity_visibility(normalized_entity_type, entity_dict):
     return entity_visibility
 
 
-'''
+"""
 Retrieve the organ, donor, or sample metadata information associated with a Dataset, based
 up the user's authorization to access the Dataset.
 
@@ -4561,7 +4561,7 @@ def _get_entity_visibility(normalized_entity_type, entity_dict):
 -------
 list
     A dictionary containing the metadata properties the Dataset associated data.
-'''
+"""
 def _get_dataset_associated_metadata(dataset_dict, dataset_visibility, valid_user_token, request, associated_data: str):
 
     # Confirm the associated data requested is supported by this method.
diff --git a/src/schema/schema_manager.py b/src/schema/schema_manager.py
index 10ffa360..faa583d2 100644
--- a/src/schema/schema_manager.py
+++ b/src/schema/schema_manager.py
@@ -192,7 +192,7 @@ def get_all_entity_types():
 
 
 """
-Get the superclass (if defined) of the given entity class
+Get the optional superclass (if defined) of the given entity class
 
 Parameters
 ----------
@@ -209,32 +209,40 @@ def get_entity_superclass(normalized_entity_class):
 
     all_entity_types = get_all_entity_types()
 
-    if normalized_entity_class in all_entity_types:
-        if 'superclass' in _schema['ENTITIES'][normalized_entity_class]:
-            normalized_superclass = normalize_entity_type(_schema['ENTITIES'][normalized_entity_class]['superclass'])
+    if normalized_entity_class not in all_entity_types:
+        msg = f"Unrecognized value of 'normalized_entity_class': {normalized_entity_class}"
+        logger.error(msg)
+        raise ValueError(msg)
 
-            if normalized_superclass not in all_entity_types:
-                msg = f"Invalid 'superclass' value defined for {normalized_entity_class}: {normalized_superclass}"
-                logger.error(msg)
-                raise ValueError(msg)
-        else:
-            # Since the 'superclass' property is optional, we just log the warning message, no need to bubble up
-            msg = f"The 'superclass' property is not defined for entity class: {normalized_entity_class}"
-            logger.warning(msg)
+    if 'superclass' in _schema['ENTITIES'][normalized_entity_class]:
+        normalized_superclass = normalize_entity_type(_schema['ENTITIES'][normalized_entity_class]['superclass'])
+
+        # Additional check to ensure no schema yaml mistake
+        if normalized_superclass not in all_entity_types:
+            msg = f"Invalid 'superclass' value defined for {normalized_entity_class}: {normalized_superclass}"
+            logger.error(msg)
+            raise ValueError(msg)
 
     return normalized_superclass
 
 
-def entity_type_instanceof(entity_type: str, entity_class: str) -> bool:
-    """
-    Determine if the Entity type with 'entity_type' is an instance of 'entity_class'.
-    Use this function if you already have the Entity type. Use entity_instanceof(uuid, class)
-    if you just have the Entity uuid.
+"""
+Determine if the Entity type with 'entity_type' is an instance of 'entity_class'.
+Use this function if you already have the Entity type. Use `entity_instanceof(uuid, class)` 
+if you just have the Entity uuid.
 
-    :param entity_type: from Entity
-    :param entity_class: found in .yaml file
-    :return:  True or False
-    """
+Parameters
+----------
+entity_type : str
+    The superclass
+entity_class : str
+    The subclass
+
+Returns
+-------
+bool
+"""
+def entity_type_instanceof(entity_type: str, entity_class: str) -> bool:
     if entity_type is None:
         return False
 
@@ -247,14 +255,21 @@ def entity_type_instanceof(entity_type: str, entity_class: str) -> bool:
     return False
 
 
-def entity_instanceof(entity_uuid: str, entity_class: str) -> bool:
-    """
-    Determine if the Entity with 'entity_uuid' is an instance of 'entity_class'.
+"""
+Determine if the Entity with 'entity_uuid' is an instance of 'entity_class'.
 
-    :param entity_uuid: from Entity
-    :param entity_class: found in .yaml file
-    :return: True or False
-    """
+Parameters
+----------
+entity_uuid : str
+    The uuid of the given entity
+entity_class : str
+    The superclass
+
+Returns
+-------
+bool
+"""
+def entity_instanceof(entity_uuid: str, entity_class: str) -> bool:
     entity_type: str =\
         schema_neo4j_queries.get_entity_type(get_neo4j_driver_instance(), entity_uuid.strip())
     return entity_type_instanceof(entity_type, entity_class)
diff --git a/src/schema/schema_neo4j_queries.py b/src/schema/schema_neo4j_queries.py
index bbff230e..9d6e28d4 100644
--- a/src/schema/schema_neo4j_queries.py
+++ b/src/schema/schema_neo4j_queries.py
@@ -21,10 +21,10 @@
     The neo4j database connection pool
 entity_type : str
     One of the normalized entity types: Dataset, Collection, Sample, Donor
-superclass : str
-    The normalized entity superclass type if defined, None by default
 entity_data_dict : dict
     The target Entity node to be created
+superclass : str
+    The normalized entity superclass type if defined, None by default
 
 Returns
 -------