Avoid filtering graph again when getting root node ids

Ontobio function generates a filtered grap before getting root node ids. Since the GD code used ontobio get_roots() function in multiple places, this was taking up extra time. Now the code directly extracts root nodes one time only without generating a subgraph to save time.

genedescriptions/data_manager.py

@@ -203,10 +203,13 @@ def set_ontology(self, ontology_type: DataType, ontology: Ontology, config: Gene
         terms_replacement_regex = config.get_module_property(module=module, prop=ConfigModuleProperty.RENAME_TERMS)
         if terms_replacement_regex:
             self.rename_ontology_terms(ontology=ontology, terms_replacement_regex=terms_replacement_regex)
-        set_all_depths(ontology=ontology, relations=self.get_relations(ontology_type))
+        root_nodes = [n for n in ontology.nodes() if len(
+            list(g.predecessors(n))) == 0 and len(list(ontology.successors(n))) > 0]
+        set_all_depths(ontology=ontology, root_node_ids=root_nodes, relations=self.get_relations(ontology_type))
         if config.get_module_property(module=module,
                                       prop=ConfigModuleProperty.TRIMMING_ALGORITHM) == "ic":
-            set_ic_ontology_struct(ontology=ontology, relations=self.get_relations(ontology_type))
+            set_ic_ontology_struct(ontology=ontology, relations=self.get_relations(ontology_type),
+                                   root_node_ids=root_nodes)
         if slim_cache_path:
             slim_url = config.get_module_property(module=module, prop=ConfigModuleProperty.SLIM_URL)
             self.load_slim(module=module, slim_url=slim_url, slim_cache_path=slim_cache_path)

genedescriptions/ontology_tools.py

@@ -72,10 +72,10 @@ def get_all_common_ancestors(node_ids: List[str], ontology: Ontology, min_distan
             ancestors.items() if len(covered_nodes) > 1 or ancestor == covered_nodes[0]]
 
 
-def set_all_depths(ontology: Ontology, relations: List[str] = None, comparison_func=max):
+def set_all_depths(ontology: Ontology, root_node_ids: List[str], relations: List[str] = None, comparison_func=max):
     logger.info("Setting depth for all nodes")
     start_time = time.time()
-    for root_id in ontology.get_roots():
+    for root_id in root_node_ids:
         if "type" not in ontology.node(root_id) or ontology.node_type(root_id) == "CLASS":
             set_all_depths_in_subgraph(ontology=ontology, root_id=root_id, relations=relations,
                                        comparison_func=comparison_func)
@@ -111,31 +111,30 @@ def set_all_depths_in_subgraph(ontology: Ontology, root_id: str, relations: List
         stack.extend([(child_id, current_depth + 1) for child_id in children])
 
 
-def set_ic_ontology_struct(ontology: Ontology, relations: List[str] = None):
+def set_ic_ontology_struct(ontology: Ontology, root_node_ids: List[str], relations: List[str] = None):
     logger.info("Setting information content values based on ontology structure")
     start_time = time.time()
-    roots = ontology.get_roots(relations=relations)
-    for root_id in roots:
+    for root_id in root_node_ids:
         if "num_subsumers" not in ontology.node(root_id) and ("type" not in ontology.node(root_id) or
                                                               ontology.node_type(root_id) == "CLASS"):
             set_num_subsumers(ontology=ontology, root_id=root_id, relations=relations)
-    for root_id in roots:
+    for root_id in root_node_ids:
         if "num_leaves" not in ontology.node(root_id) and ("type" not in ontology.node(root_id) or
                                                            ontology.node_type(root_id) == "CLASS"):
             set_leaf_sets(ontology=ontology, root_id=root_id, relations=relations)
             set_num_leaves(ontology=ontology, root_id=root_id, relations=relations)
-    for root_id in roots:
+    for root_id in root_node_ids:
         if "depth" not in ontology.node(root_id) and ("type" not in ontology.node(root_id) or
                                                       ontology.node_type(root_id) == "CLASS"):
             set_all_depths_in_subgraph(ontology=ontology, root_id=root_id, relations=relations)
-    for root_id in roots:
+    for root_id in root_node_ids:
         if "type" not in ontology.node(root_id) or ontology.node_type(root_id) == "CLASS":
             set_information_content_in_subgraph(ontology=ontology, root_id=root_id,
                                                 maxleaves=ontology.node(root_id)["num_leaves"], relations=relations)
     logger.info(f"setting information content values based on ic took {time.time() - start_time} seconds")
 
 
-def set_ic_annot_freq(ontology: Ontology, annotations: AssociationSet):
+def set_ic_annot_freq(ontology: Ontology, annotations: AssociationSet, root_node_ids: List[str]):
     logger.info("Setting information content values based on annotation frequency")
     for node_id in ontology.nodes():
         node_prop = ontology.node(node_id)
@@ -145,7 +144,7 @@ def set_ic_annot_freq(ontology: Ontology, annotations: AssociationSet):
             del node_prop["tot_annot_genes"]
         if "IC" in node_prop:
             del node_prop["IC"]
-    for root_id in ontology.get_roots():
+    for root_id in root_node_ids:
         if "depth" not in ontology.node(root_id) and ("type" not in ontology.node(root_id) or
                                                       ontology.node_type(root_id) == "CLASS"):
             set_all_depths_in_subgraph(ontology=ontology, root_id=root_id)