Don't override categories now that synonymizer is clean

code/ARAX/ARAXQuery/ARAX_expander.py

@@ -353,7 +353,8 @@ def apply(self, response, input_parameters, mode: str = "ARAX"):
                 if inferred_qedge_keys and len(query_graph.edges) == 1:
                     for edge in query_sub_graph.edges.keys():
                         query_sub_graph.edges[edge].knowledge_type = 'lookup'
-            # Expand the query graph edge-by-edge
+
+            # Expand the query graph edge-by-edge (in regular 'lookup' fashion)
             for qedge_key in ordered_qedge_keys_to_expand:
                 log.debug(f"Expanding qedge {qedge_key}")
                 response.update_query_plan(qedge_key, 'edge_properties', 'status', 'Expanding')
@@ -583,9 +584,6 @@ def apply(self, response, input_parameters, mode: str = "ARAX"):
             decorator = ARAXDecorator()
             decorator.decorate_nodes(response)
             decorator.decorate_edges(response, kind="RTX-KG2")
-
-            # Override node types to only include descendants of what was asked for in the QG (where applicable) #1360
-            self._override_node_categories(message.knowledge_graph, message.query_graph, log)
         elif mode == "RTXKG2":
             decorator = ARAXDecorator()
             decorator.decorate_edges(response, kind="SEMMEDDB")
@@ -1400,31 +1398,6 @@ def _load_fda_approved_drug_ids() -> Set[str]:
             fda_approved_drug_ids = pickle.load(fda_pickle)
         return fda_approved_drug_ids
 
-    def _override_node_categories(self, kg: KnowledgeGraph, qg: QueryGraph, log: ARAXResponse):
-        # Clean up what we list as the TRAPI node.categories; list descendants of what was asked for in the QG
-        log.debug(f"Overriding node categories to better align with what's in the QG")
-        qnode_descendant_categories_map = {qnode_key: set(self.bh.get_descendants(qnode.categories))
-                                           for qnode_key, qnode in qg.nodes.items() if qnode.categories}
-        for node_key, node in kg.nodes.items():
-            final_categories = set()
-            for qnode_key in node.qnode_keys:
-                # If qnode has categories specified, use node's all_categories that are descendants of qnode categories
-                if qnode_key in qnode_descendant_categories_map:
-                    all_categories_attributes = [attribute for attribute in eu.convert_to_list(node.attributes)
-                                                 if attribute.attribute_type_id == "biolink:category"]
-                    node_categories = all_categories_attributes[0].value if all_categories_attributes else node.categories
-                    relevant_categories = set(node_categories).intersection(qnode_descendant_categories_map[qnode_key])
-                # Otherwise just use what's already in the node's categories (for KG2 this is the 'preferred' category)
-                else:
-                    relevant_categories = set(node.categories)
-                final_categories = final_categories.union(relevant_categories)
-            if final_categories:
-                node.categories = list(final_categories)
-            else:
-                # Leave categories as they are but issue a warning
-                log.warning(f"None of the categories KPs gave node {node_key} ({node.categories}) are descendants of "
-                            f"those asked for in the QG (for qnode {node.qnode_keys})")
-
     @staticmethod
     def _map_back_to_input_curies(kg: KnowledgeGraph, qg: QueryGraph, log: ARAXResponse):
         """

code/ARAX/ARAXQuery/Expand/kp_selector.py

@@ -42,10 +42,7 @@ def _load_cached_kp_info(self) -> tuple:
                 self.log.error(f"Failed to load KP info caches due to {e}", error_code="LoadKPCachesFailed")
                 return None, None, None, None
 
-            # Record None URLs for our local KPs
-            allowed_kp_urls = smart_api_info["allowed_kp_urls"]
-
-            return (meta_map, allowed_kp_urls, smart_api_info["kps_excluded_by_version"],
+            return (meta_map, smart_api_info["allowed_kp_urls"], smart_api_info["kps_excluded_by_version"],
                     smart_api_info["kps_excluded_by_maturity"])
 
     def get_kps_for_single_hop_qg(self, qg: QueryGraph) -> Optional[Set[str]]: