Merge pull request #21 from geneontology/fix-node-deduplication

Reuse `Activity.enabled_by` nodes for input/output nodes when available
geneontology · Oct 9, 2024 · 89ae295 · 89ae295
2 parents ca17860 + ccadf3f
commit 89ae295
Showing 1 changed file with 19 additions and 11 deletions.
diff --git a/src/gocam/translation/cx2/main.py b/src/gocam/translation/cx2/main.py
@@ -66,7 +66,8 @@ def _get_context():
 def model_to_cx2(gocam: Model) -> list:
     # Internal state
     input_output_nodes: Dict[str, int] = {}
-    activity_nodes: Dict[str, int] = {}
+    activity_nodes_by_activity_id: Dict[str, int] = {}
+    activity_nodes_by_enabled_by_id: Dict[str, int] = {}
 
     # Internal helper functions that access internal state
     def _get_object_label(object_id: str) -> str:
@@ -82,7 +83,11 @@ def _add_input_output_nodes(
         if not isinstance(associations, list):
             associations = [associations]
         for association in associations:
-            if association.term not in input_output_nodes:
+            if association.term in activity_nodes_by_enabled_by_id:
+                target = activity_nodes_by_enabled_by_id[association.term]
+            elif association.term in input_output_nodes:
+                target = input_output_nodes[association.term]
+            else:
                 node_attributes = {
                     "name": _get_object_label(association.term),
                     "represents": association.term,
@@ -94,13 +99,12 @@ def _add_input_output_nodes(
                         p.contributor for p in association.provenances
                     ]
 
-                input_output_nodes[association.term] = cx2_network.add_node(
-                    attributes=node_attributes
-                )
+                target = cx2_network.add_node(attributes=node_attributes)
+                input_output_nodes[association.term] = target
 
             cx2_network.add_edge(
-                source=activity_nodes[activity.id],
-                target=input_output_nodes[association.term],
+                source=activity_nodes_by_activity_id[activity.id],
+                target=target,
                 attributes=edge_attributes,
             )
 
@@ -174,7 +178,9 @@ def _add_input_output_nodes(
                 p.contributor for p in activity.provenances
             ]
 
-        activity_nodes[activity.id] = cx2_network.add_node(attributes=node_attributes)
+        node = cx2_network.add_node(attributes=node_attributes)
+        activity_nodes_by_activity_id[activity.id] = node
+        activity_nodes_by_enabled_by_id[activity.enabled_by.term] = node
 
     # Add nodes for input/output molecules and create edges to activity nodes
     for activity in gocam.activities:
@@ -196,7 +202,7 @@ def _add_input_output_nodes(
     # Add edges for causal associations between activity nodes
     for activity in gocam.activities:
         for association in activity.causal_associations:
-            if association.downstream_activity in activity_nodes:
+            if association.downstream_activity in activity_nodes_by_activity_id:
                 relation_style = RELATIONS.get(association.predicate, None)
                 if relation_style is None:
                     logger.warning(
@@ -221,8 +227,10 @@ def _add_input_output_nodes(
                     ]
 
                 cx2_network.add_edge(
-                    source=activity_nodes[activity.id],
-                    target=activity_nodes[association.downstream_activity],
+                    source=activity_nodes_by_activity_id[activity.id],
+                    target=activity_nodes_by_activity_id[
+                        association.downstream_activity
+                    ],
                     attributes=edge_attributes,
                 )