node_info_by_name

nxontology/imports.py

@@ -11,6 +11,8 @@
 from nxontology.exceptions import NodeNotFound
 from nxontology.node import Node
 
+logger = logging.getLogger(__name__)
+
 
 def pronto_to_nxontology(onto: Prontology) -> NXOntology[str]:
  """
@@ -38,7 +40,7 @@ def pronto_to_nxontology(onto: Prontology) -> NXOntology[str]:
  try:
  nxo.add_edge(term.id, child.id)
  except NodeNotFound as e:
- logging.warning(
+ logger.warning(
  f"Cannot add edge: {term.id} --> {child.id} "
  f"({term.name} --> {child.name}): {e}"
  )
@@ -114,7 +116,7 @@ def pronto_to_multidigraph(
  # https://github.com/althonos/pronto/issues/122
  continue
  if term.id in graph:
- logging.warning(f"Skipping node already in graph: {term}")
+ logger.warning(f"Skipping node already in graph: {term}")
  continue
  graph.add_node(
  term.id,
@@ -128,16 +130,16 @@ def pronto_to_multidigraph(
  ):
  for node in source, target:
  if node not in graph:
- logging.warning(
+ logger.warning(
  f"Skipping edge: node does not exist in graph: {node}"
  )
  if graph.has_edge(source, target, key):
- logging.warning(
+ logger.warning(
  f"Skipping edge already in graph: {source} --> {target} (key={key!r})"
  )
  graph.add_edge(source, target, key=key)
  rel_counts = Counter(key for _, _, key in graph.edges(keys=True))
- logging.info(f"MultiDiGraph relationship counts:\n{rel_counts}")
+ logger.info(f"MultiDiGraph relationship counts:\n{rel_counts}")
  return graph
 
 
@@ -161,7 +163,7 @@ def multidigraph_to_digraph(
  — i.e. those that are already captured by a more specific ancestral path.
  The default is reduce=False since the reduction can be a computationally expensive step.
  """
- logging.info(f"Received MultiDiGraph with {graph.number_of_edges():,} edges.")
+ logger.info(f"Received MultiDiGraph with {graph.number_of_edges():,} edges.")
  if rel_types is not None:
  graph = graph.copy()
  graph.remove_edges_from(
@@ -171,7 +173,7 @@ def multidigraph_to_digraph(
  if key not in rel_types
  ]
  )
- logging.info(
+ logger.info(
  f"Filtered MultiDiGraph to {graph.number_of_edges():,} edges of the following types: {rel_types}."
  )
  if reverse:
@@ -187,12 +189,12 @@ def multidigraph_to_digraph(
  )
  no_data_digraph.graph.update(digraph.graph)
  digraph = no_data_digraph
- logging.info(
+ logger.info(
  f"Reduced DiGraph by removing {n_edges_before - digraph.number_of_edges():,} redundant edges."
  )
  for source, target in digraph.edges(data=False):
  digraph[source][target]["rel_types"] = sorted(graph[source][target])
- logging.info(
+ logger.info(
  f"Converted MultiDiGraph to DiGraph with {digraph.number_of_nodes():,} nodes and {digraph.number_of_edges():,} edges."
  )
  return digraph
@@ -228,7 +230,7 @@ def read_gene_ontology(
  else:
  date.fromisoformat(release) # check that release is a valid date
  url = f"http:https://release.geneontology.org/{release}/ontology/{source_file}"
- logging.info(f"Loading Gene Ontology into Pronto from <{url}>.")
+ logger.info(f"Loading Gene Ontology into Pronto from <{url}>.")
  go_pronto = Prontology(handle=url)
  go_multidigraph = pronto_to_multidigraph(go_pronto, default_rel_type="is a")
  go_digraph = multidigraph_to_digraph(

nxontology/ontology.py

@@ -2,6 +2,7 @@
 
 import itertools
 import json
+import logging
 from typing import Any, Dict, Generic, Iterable, List, Optional, Set, cast
 
 import fsspec
@@ -17,6 +18,8 @@
 from .similarity import SimilarityIC
 from .utils import Freezable, cache_on_frozen
 
+logger = logging.getLogger(__name__)
+
 
 class NXOntology(Freezable, Generic[Node]):
  """
@@ -205,6 +208,30 @@ def node_info(self, node: Node) -> Node_Info[Node]:
  self._node_info_cache[node] = Node_Info(self, node)
  return self._node_info_cache[node]
 
+ @cache_on_frozen
+ def _get_name_to_node_info(self) -> dict[str, Node_Info[Node]]:
+ name_to_node_info: dict[str, Node_Info[Node]] = dict()
+ for node in self.graph:
+ info = self.node_info(node)
+ name = info.label
+ if not name:
+ continue
+ if name in name_to_node_info:
+ logger.warning(
+ f"Node name duplicated for nodes {name_to_node_info[name].node!r} & {node!r}: {name!r}"
+ )
+ name_to_node_info[name] = info
+ return name_to_node_info
+
+ def node_info_by_name(self, name: str) -> Node_Info[Node]:
+ """
+ Return Node_Info instance using a lookup by name.
+ """
+ name_to_node_info = self._get_name_to_node_info()
+ if name not in name_to_node_info:
+ raise NodeNotFound(f"No node found named {name!r}.")
+ return name_to_node_info[name]
+
  @property
  def n_nodes(self) -> int:
  """

nxontology/tests/ontology_test.py

@@ -121,6 +121,18 @@ def test_set_graph_attributes(metal_nxo: NXOntology[str]) -> None:
  assert silver_info.url is None
 
 
+def test_node_info_by_name() -> None:
+ nxo: NXOntology[str] = NXOntology()
+ nxo.set_graph_attributes(node_label_attribute="name")
+ nxo.add_node("a", name="a_name")
+ nxo.add_node("b", name="b_name")
+ nxo.add_node("c")
+ assert nxo.node_info_by_name("a_name").node == "a"
+ assert nxo.node_info_by_name("b_name").node == "b"
+ with pytest.raises(NodeNotFound, match="No node found named"):
+ nxo.node_info_by_name("missing_name")
+
+
 def test_node_info_not_found(metal_nxo_frozen: NXOntology[str]) -> None:
  with pytest.raises(NodeNotFound, match="not-a-metal not in graph"):
  metal_nxo_frozen.node_info("not-a-metal")