Simplify node iteration

src/pyobo/reader.py

@@ -113,22 +113,6 @@ def from_obonet(graph: nx.MultiDiGraph, *, strict: bool = True) -> Obo:
             f"[{ontology_prefix}] will not accept slash in data version: {data_version}"
         )
 
-    #: Parsed CURIEs to references (even external ones)
-    reference_it = (
-        Reference(
-            prefix=prefix,
-            identifier=bioregistry.standardize_identifier(prefix, identifier),
-            # if name isn't available, it means its external to this ontology
-            name=data.get("name"),
-        )
-        for prefix, identifier, data in _iter_obo_graph(
-            graph=graph, strict=strict, ontology_prefix=ontology_prefix
-        )
-    )
-    references: Mapping[ReferenceTuple, Reference] = {
-        reference.pair: reference for reference in reference_it
-    }
-
     #: CURIEs to typedefs
     typedefs: Mapping[ReferenceTuple, TypeDef] = {
         typedef.pair: typedef
@@ -145,18 +129,16 @@ def from_obonet(graph: nx.MultiDiGraph, *, strict: bool = True) -> Obo:
     missing_typedefs: set[ReferenceTuple] = set()
     terms = []
     n_alt_ids, n_parents, n_synonyms, n_relations, n_properties, n_xrefs = 0, 0, 0, 0, 0, 0
-    for prefix, identifier, data in _iter_obo_graph(
+    n_references = 0
+    for reference, data in _iter_obo_graph(
         graph=graph, strict=strict, ontology_prefix=ontology_prefix
     ):
-        if prefix != ontology_prefix or not data:
+        if reference.prefix != ontology_prefix or not data:
             continue
-
-        identifier = bioregistry.standardize_identifier(prefix, identifier)
-        reference = references[ReferenceTuple(ontology_prefix, identifier)]
+        n_references += 1
 
         node_xrefs = list(
             iterate_node_xrefs(
-                prefix=prefix,
                 data=data,
                 strict=strict,
                 ontology_prefix=ontology_prefix,
@@ -245,7 +227,7 @@ def from_obonet(graph: nx.MultiDiGraph, *, strict: bool = True) -> Obo:
         terms.append(term)
 
     logger.info(
-        f"[{ontology_prefix}] got {len(references):,} references, {len(typedefs):,} typedefs, {len(terms):,} terms,"
+        f"[{ontology_prefix}] got {n_references:,} references, {len(typedefs):,} typedefs, {len(terms):,} terms,"
         f" {n_alt_ids:,} alt ids, {n_parents:,} parents, {n_synonyms:,} synonyms, {n_xrefs:,} xrefs,"
         f" {n_relations:,} relations, and {n_properties:,} properties",
     )
@@ -282,13 +264,14 @@ def _iter_obo_graph(
     *,
     strict: bool = True,
     ontology_prefix: str | None = None,
-) -> Iterable[tuple[str, str, Mapping[str, Any]]]:
+) -> Iterable[tuple[Reference, Mapping[str, Any]]]:
     """Iterate over the nodes in the graph with the prefix stripped (if it's there)."""
     for node, data in graph.nodes(data=True):
-        prefix, identifier = normalize_curie(node, strict=strict, ontology_prefix=ontology_prefix)
-        if prefix is None or identifier is None:
-            continue
-        yield prefix, identifier, data
+        node = Reference.from_curie_or_uri(
+            node, strict=strict, ontology_prefix=ontology_prefix, name=data.get("name")
+        )
+        if node:
+            yield node, data
 
 
 def _get_date(graph, ontology_prefix: str) -> datetime | None:
@@ -698,7 +681,6 @@ def iterate_node_relationships(
 
 def iterate_node_xrefs(
     *,
-    prefix: str,
     data: Mapping[str, Any],
     strict: bool = True,
     ontology_prefix: str | None,
@@ -717,7 +699,7 @@ def iterate_node_xrefs(
         if split_space:
             _xref_split = xref.split(" ", 1)
             if _xref_split[1][0] not in {'"', "("}:
-                logger.debug("[%s] Problem with space in xref %s", prefix, xref)
+                logger.debug("[%s] Problem with space in xref %s", node.curie, xref)
                 continue
             xref = _xref_split[0]
 

src/pyobo/struct/reference.py

@@ -95,6 +95,9 @@ def from_curie_or_uri(
         )
         if prefix is None or identifier is None:
             return None
+
+        identifier = bioregistry.standardize_identifier(prefix, identifier)
+
         if name is None and auto:
             from ..api import get_name
 

tests/test_get.py

@@ -85,7 +85,7 @@ def test_extract_definition(self):
         ]:
             with self.subTest(s=s):
                 actual_text, actual_references = _extract_definition(
-                    s, node=Reference(prefix="chebi", identifier="XXX")
+                    s, node=Reference(prefix="chebi", identifier="XXX"), ontology_prefix="chebi"
                 )
                 self.assertEqual(expected_text, actual_text)
                 self.assertEqual(expected_references, actual_references)
@@ -95,7 +95,10 @@ def test_extract_definition_with_escapes(self):
         expected_text = """The canonical 3' splice site has the sequence "AG"."""
         s = """"The canonical 3' splice site has the sequence \\"AG\\"." [PMID:1234]"""
         actual_text, actual_references = _extract_definition(
-            s, strict=True, node=Reference(prefix="chebi", identifier="XXX")
+            s,
+            strict=True,
+            node=Reference(prefix="chebi", identifier="XXX"),
+            ontology_prefix="chebi",
         )
         self.assertEqual(expected_text, actual_text)
         self.assertEqual([Reference(prefix="pubmed", identifier="1234")], actual_references)
@@ -159,7 +162,10 @@ def test_extract_synonym(self):
         ]:
             with self.subTest(s=text):
                 actual_synonym = _extract_synonym(
-                    text, synoynym_typedefs, node=Reference(prefix="chebi", identifier="XXX")
+                    text,
+                    synoynym_typedefs,
+                    node=Reference(prefix="chebi", identifier="XXX"),
+                    ontology_prefix="chebi",
                 )
                 self.assertIsInstance(actual_synonym, Synonym)
                 self.assertEqual(expected_synonym, actual_synonym)
@@ -175,7 +181,10 @@ def test_get_node_synonyms(self):
         data = self.graph.nodes["CHEBI:51990"]
         synonyms = list(
             iterate_node_synonyms(
-                data, synoynym_typedefs, node=Reference(prefix="chebi", identifier="XXX")
+                data,
+                synoynym_typedefs,
+                node=Reference(prefix="chebi", identifier="XXX"),
+                ontology_prefix="chebi",
             )
         )
         self.assertEqual(1, len(synonyms))
@@ -215,7 +224,13 @@ def test_get_node_parents(self):
     def test_get_node_xrefs(self):
         """Test getting parents from a node in a :mod:`obonet` graph."""
         data = self.graph.nodes["CHEBI:51990"]
-        xrefs = list(iterate_node_xrefs(prefix="chebi", data=data))
+        xrefs = list(
+            iterate_node_xrefs(
+                data=data,
+                ontology_prefix="chebi",
+                node=Reference(prefix="chebi", identifier="51990"),
+            )
+        )
         self.assertEqual(7, len(xrefs))
         # NOTE the prefixes are remapped by Bioregistry
         self.assertEqual({"pubmed", "cas", "reaxys"}, {xref.prefix for xref in xrefs})