update input to add_edges_from

 - Modified input to add_edges_from to only take the edges which connects the existing nodes, to avoid internal creation of obsolete nodes

Author: aditya0by0

chebai/preprocessing/datasets/chebi.py

@@ -258,7 +258,16 @@ def _extract_class_hierarchy(self, data_path: str) -> nx.DiGraph:
         g = nx.DiGraph()
         for n in elements:
             g.add_node(n["id"], **n)
-        g.add_edges_from([(p, q["id"]) for q in elements for p in q["parents"]])
+
+        # Only take the edges which connects the existing nodes, to avoid internal creation of obsolete nodes
+        g.add_edges_from(
+            [
+                (p, q["id"])
+                for q in elements
+                for p in q["parents"]
+                if g.has_node(p) and g.has_node(q["id"])
+            ]
+        )
 
         print("Compute transitive closure")
         return nx.transitive_closure_dag(g)