multidigraph_to_digraph: preserve data (#18)

merges #18
refs networkx/networkx#3392

nxontology/imports.py

@@ -163,6 +163,7 @@ def multidigraph_to_digraph(
  """
  logging.info(f"Received MultiDiGraph with {graph.number_of_edges():,} edges.")
  if rel_types is not None:
+ graph = graph.copy()
  graph.remove_edges_from(
  [
  (u, v, key)
@@ -178,7 +179,14 @@ def multidigraph_to_digraph(
  digraph = nx.DiGraph(graph)
  if reduce:
  n_edges_before = digraph.number_of_edges()
- digraph = nx.transitive_reduction(digraph)
+ no_data_digraph = nx.transitive_reduction(digraph)
+ # restore data https://github.com/networkx/networkx/issues/3392
+ no_data_digraph.add_nodes_from(digraph.nodes.items())
+ no_data_digraph.add_edges_from(
+ (u, v, digraph[u][v]) for (u, v) in no_data_digraph.edges()
+ )
+ no_data_digraph.update(digraph.graph)
+ digraph = no_data_digraph
  logging.info(
  f"Reduced DiGraph by removing {n_edges_before - digraph.number_of_edges():,} redundant edges."
  )

nxontology/tests/imports_test.py

@@ -69,18 +69,24 @@ def test_multigraph_to_digraph():
  mdg.add_edge("a", "b", key="rel_type 1")
  mdg.add_edge("a", "b", key="rel_type 2")
  mdg.add_edge("b", "c", key="rel_type 1")
+ mdg.nodes["a"]["attribute"] = "preserve me"
  dg = multidigraph_to_digraph(mdg)
  assert dg.number_of_nodes() == 3
  assert dg.number_of_edges() == 2
  assert dg["b"]["a"]["rel_types"] == ["rel_type 1", "rel_type 2"]
  assert dg["c"]["b"]["rel_types"] == ["rel_type 1"]
+ # make sure node data is preserved
+ # https://github.com/networkx/networkx/issues/3392
+ assert dg.nodes["a"]["attribute"] == "preserve me"
  dg = multidigraph_to_digraph(mdg, reverse=False)
  assert dg.has_edge("a", "b")
  assert not dg.has_edge("b", "a")
+ assert dg.nodes["a"]["attribute"] == "preserve me"
  dg = multidigraph_to_digraph(mdg, rel_types=["rel_type 2"])
  assert dg.number_of_nodes() == 3
  assert dg.number_of_edges() == 1
  assert dg.has_edge("b", "a")
+ assert dg.nodes["a"]["attribute"] == "preserve me"
 
 
 def test_read_gene_ontology():
@@ -89,6 +95,9 @@ def test_read_gene_ontology():
  nxo.graph.graph["source_url"]
  == "http://release.geneontology.org/2021-02-01/ontology/go-basic.json.gz"
  )
+ bp_info = nxo.node_info("GO:0008150")
+ assert bp_info.label == "biological_process"
+ assert bp_info.data["namespace"] == "biological_process"
  assert "regulates" in nxo.graph["GO:0006310"]["GO:0000018"]["rel_types"]
  # Transitive reduction should remove this edge
  # from "defense response to insect" to "negative regulation of defense response to insect"