Rename function

src/pyobo/api/alts.py

@@ -63,7 +63,7 @@ def get_primary_curie(
     **kwargs: Unpack[GetOntologyKwargs],
 ) -> str | None:
     """Get the primary curie for an entity."""
-    reference = Reference.from_curie(curie, strict=kwargs.get("strict", True))
+    reference = Reference.from_curie_or_uri(curie, strict=kwargs.get("strict", True))
     if reference is None:
         return None
     primary_identifier = get_primary_identifier(reference, **kwargs)

src/pyobo/cli/lookup.py

@@ -213,7 +213,7 @@ def relations(
         else:
             echo_df(relations_df)
     else:
-        relation_reference = Reference.from_curie(relation, strict=False)
+        relation_reference = Reference.from_curie_or_uri(relation, strict=False)
         if relation_reference is None:
             click.secho(f"not a valid curie: {relation}", fg="red")
             raise sys.exit(1)

src/pyobo/reader.py

@@ -156,7 +156,11 @@ def from_obonet(graph: nx.MultiDiGraph, *, strict: bool = True) -> Obo:
 
         node_xrefs = list(
             iterate_node_xrefs(
-                prefix=prefix, data=data, strict=strict, ontology_prefix=ontology_prefix
+                prefix=prefix,
+                data=data,
+                strict=strict,
+                ontology_prefix=ontology_prefix,
+                node=reference,
             )
         )
         xrefs, provenance = [], []
@@ -322,7 +326,7 @@ def iterate_graph_synonym_typedefs(
             # assume it's a default reference
             yield SynonymTypeDef(reference=default_reference(ontology_prefix, sid, name=name))
         else:
-            reference = Reference.from_curie(
+            reference = Reference.from_curie_or_uri(
                 sid, name=name, strict=strict, ontology_prefix=ontology_prefix
             )
             if reference is not None:
@@ -350,7 +354,7 @@ def iterate_graph_typedefs(
             logger.debug("[%s] typedef %s is missing a name", graph.graph["ontology"], curie)
 
         if ":" in curie:
-            reference = Reference.from_curie(
+            reference = Reference.from_curie_or_uri(
                 curie, name=name, strict=strict, ontology_prefix=ontology_prefix
             )
         else:
@@ -361,7 +365,9 @@ def iterate_graph_typedefs(
 
         xrefs = []
         for curie in typedef.get("xref", []):
-            _xref = Reference.from_curie(curie, strict=strict, ontology_prefix=ontology_prefix)
+            _xref = Reference.from_curie_or_uri(
+                curie, strict=strict, ontology_prefix=ontology_prefix
+            )
             if _xref:
                 xrefs.append(_xref)
         yield TypeDef(reference=reference, xrefs=xrefs)
@@ -498,7 +504,7 @@ def _parse_trailing_ref_list(
 ):
     rest = rest.lstrip("[").rstrip("]")
     return [
-        Reference.from_curie(
+        Reference.from_curie_or_uri(
             curie.strip(), strict=strict, node=node, ontology_prefix=ontology_prefix
         )
         for curie in rest.split(",")
@@ -564,7 +570,7 @@ def _handle_prop(
     # if the value doesn't start with a quote, we're going to
     # assume that it's a reference
     if not value_type.startswith('"'):
-        obj_reference = Reference.from_curie(
+        obj_reference = Reference.from_curie_or_uri(
             value_type, strict=strict, ontology_prefix=ontology_prefix, node=node
         )
         if obj_reference is None:
@@ -589,7 +595,7 @@ def _handle_prop(
     if not datatype:
         return LiteralProperty(prop_reference, value, Reference(prefix="xsd", identifier="string"))
 
-    datatype_reference = Reference.from_curie(
+    datatype_reference = Reference.from_curie_or_uri(
         datatype, strict=strict, ontology_prefix=ontology_prefix, node=node
     )
     if datatype_reference is None:
@@ -617,7 +623,9 @@ def _get_prop(
     elif ":" not in prop:
         return default_reference(ontology_prefix, prop)
     else:
-        return Reference.from_curie(prop, strict=strict, node=node, ontology_prefix=ontology_prefix)
+        return Reference.from_curie_or_uri(
+            prop, strict=strict, node=node, ontology_prefix=ontology_prefix
+        )
 
 
 def iterate_node_parents(
@@ -629,7 +637,7 @@ def iterate_node_parents(
 ) -> Iterable[Reference]:
     """Extract parents from a :mod:`obonet` node's data."""
     for parent_curie in data.get("is_a", []):
-        reference = Reference.from_curie(
+        reference = Reference.from_curie_or_uri(
             parent_curie, strict=strict, ontology_prefix=ontology_prefix, node=node
         )
         if reference is None:
@@ -643,7 +651,7 @@ def iterate_node_alt_ids(
 ) -> Iterable[Reference]:
     """Extract alternate identifiers from a :mod:`obonet` node's data."""
     for curie in data.get("alt_id", []):
-        reference = Reference.from_curie(
+        reference = Reference.from_curie_or_uri(
             curie, strict=strict, node=node, ontology_prefix=ontology_prefix
         )
         if reference is not None:
@@ -678,7 +686,7 @@ def iterate_node_relationships(
                 relation.curie,
             )
 
-        target = Reference.from_curie(
+        target = Reference.from_curie_or_uri(
             target_curie, strict=strict, ontology_prefix=ontology_prefix, node=node
         )
         if target is None:
@@ -689,7 +697,12 @@ def iterate_node_relationships(
 
 
 def iterate_node_xrefs(
-    *, prefix: str, data: Mapping[str, Any], strict: bool = True, ontology_prefix: str | None
+    *,
+    prefix: str,
+    data: Mapping[str, Any],
+    strict: bool = True,
+    ontology_prefix: str | None,
+    node: Reference,
 ) -> Iterable[Reference]:
     """Extract xrefs from a :mod:`obonet` node's data."""
     for xref in data.get("xref", []):
@@ -708,6 +721,8 @@ def iterate_node_xrefs(
                 continue
             xref = _xref_split[0]
 
-        yv = Reference.from_curie(xref, strict=strict, ontology_prefix=ontology_prefix)
+        yv = Reference.from_curie_or_uri(
+            xref, strict=strict, ontology_prefix=ontology_prefix, node=node
+        )
         if yv is not None:
             yield yv

src/pyobo/sources/complexportal.py

@@ -125,7 +125,7 @@ def _parse_xrefs(s) -> list[tuple[Reference, str]]:
             xref_curie = _clean_intenz(xref_curie)
 
         try:
-            reference = Reference.from_curie(xref_curie)
+            reference = Reference.from_curie_or_uri(xref_curie)
         except ValueError:
             logger.warning("can not parse CURIE: %s", xref_curie)
             continue

src/pyobo/sources/conso.py

@@ -42,7 +42,7 @@ def iter_terms() -> Iterable[Term]:
 
     synonyms_df = ensure_df(PREFIX, url=SYNONYMS_URL)
     synonyms_df["reference"] = synonyms_df["reference"].map(
-        lambda s: [Reference.from_curie(s)] if pd.notna(s) and s != "?" else [],
+        lambda s: [Reference.from_curie_or_uri(s)] if pd.notna(s) and s != "?" else [],
     )
     synonyms_df["specificity"] = synonyms_df["specificity"].map(
         lambda s: "EXACT" if pd.isna(s) or s == "?" else s
@@ -71,7 +71,7 @@ def iter_terms() -> Iterable[Term]:
             curie = curie.strip()
             if not curie:
                 continue
-            reference = Reference.from_curie(curie)
+            reference = Reference.from_curie_or_uri(curie)
             if reference is not None:
                 provenance.append(reference)
         identifier = row["Identifier"]

src/pyobo/sources/famplex.py

@@ -107,7 +107,7 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]:
         reference = Reference(prefix=PREFIX, identifier=entity, name=entity)
         definition, provenance = id_to_definition.get(entity, (None, None))
         provenance_reference = (
-            Reference.from_curie(provenance) if isinstance(provenance, str) else None
+            Reference.from_curie_or_uri(provenance) if isinstance(provenance, str) else None
         )
         term = Term(
             reference=reference,

src/pyobo/sources/flybase.py

@@ -154,7 +154,7 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]:
         for hgnc_curie in human_orthologs.get(identifier, []):
             if not hgnc_curie or pd.isna(hgnc_curie):
                 continue
-            hgnc_ortholog = Reference.from_curie(hgnc_curie)
+            hgnc_ortholog = Reference.from_curie_or_uri(hgnc_curie)
             if hgnc_ortholog is None:
                 tqdm.write(f"[{PREFIX}] {identifier} had invalid ortholog: {hgnc_curie}")
             else:

src/pyobo/sources/uniprot/uniprot.py

@@ -126,7 +126,7 @@ def iter_terms(version: str | None = None) -> Iterable[Term]:
                         # FIXME this needs a different relation than enables
                         #  see https://github.com/biopragmatics/pyobo/pull/168#issuecomment-1918680152
                         enables,
-                        cast(Reference, Reference.from_curie(rhea_curie, strict=True)),
+                        cast(Reference, Reference.from_curie_or_uri(rhea_curie, strict=True)),
                     )
 
             if bindings:
@@ -136,7 +136,7 @@ def iter_terms(version: str | None = None) -> Iterable[Term]:
                     if part.startswith("/ligand_id"):
                         curie = part.removeprefix('/ligand_id="').rstrip('"')
                         binding_references.add(
-                            cast(Reference, Reference.from_curie(curie, strict=True))
+                            cast(Reference, Reference.from_curie_or_uri(curie, strict=True))
                         )
                 for binding_reference in sorted(binding_references):
                     term.annotate_object(molecularly_interacts_with, binding_reference)

src/pyobo/sources/uniprot/uniprot_ptm.py

@@ -96,7 +96,7 @@ def _parse(i, lines: Iterable[tuple[str, str]]) -> Term | None:
             if line.startswith(y):
                 line = x + line[len(y) :]
 
-        ref = Reference.from_curie(line.replace("; ", ":"))
+        ref = Reference.from_curie_or_uri(line.replace("; ", ":"))
         if ref:
             term.append_xref(ref)
         else:

src/pyobo/sources/zfin.py

@@ -150,7 +150,7 @@ def get_terms(force: bool = False, version: str | None = None) -> Iterable[Term]
         for hgnc_id in human_orthologs.get(identifier, []):
             term.append_relationship(orthologous, Reference(prefix="hgnc", identifier=hgnc_id))
         for mgi_curie in mouse_orthologs.get(identifier, []):
-            mouse_ortholog = Reference.from_curie(mgi_curie)
+            mouse_ortholog = Reference.from_curie_or_uri(mgi_curie)
             if mouse_ortholog:
                 term.append_relationship(orthologous, mouse_ortholog)
         for flybase_id in fly_orthologs.get(identifier, []):

src/pyobo/struct/reference.py

@@ -73,7 +73,7 @@ def bioregistry_link(self) -> str:
         return f"https://bioregistry.io/{self.curie}"
 
     @classmethod
-    def from_curie(  # type:ignore[override]
+    def from_curie_or_uri(
         cls,
         curie: str,
         name: str | None = None,

src/pyobo/struct/struct.py

@@ -190,7 +190,7 @@ def _ensure_ref(
         if not ontology_prefix:
             raise ValueError(f"can't parse reference: {reference}")
         return default_reference(ontology_prefix, reference)
-    _rv = Reference.from_curie(reference, strict=True, ontology_prefix=ontology_prefix)
+    _rv = Reference.from_curie_or_uri(reference, strict=True, ontology_prefix=ontology_prefix)
     if _rv is None:
         raise ValueError(f"[{ontology_prefix}] unable to parse {reference}")
     return _rv

tests/test_get.py

@@ -290,7 +290,9 @@ def test_typedefs(self):
 
     def test_iter_filtered_relations(self):
         """Test getting filtered relations w/ upgrade."""
+        term_reference = Reference(prefix="chebi", identifier="17051")
         reference = default_reference("chebi", "is_conjugate_base_of")
+        object_reference = Reference(prefix="chebi", identifier="29228")
         for inp in [
             reference.curie,
             reference,
@@ -303,6 +305,5 @@ def test_iter_filtered_relations(self):
                     for term, target in self.ontology.iterate_filtered_relations(inp)
                 )
                 self.assertNotEqual(0, len(rr))
-                term = Reference.from_curie("chebi:17051")
-                self.assertIn(term, rr)
-                self.assertIn(Reference.from_curie("chebi:29228"), rr[term])
+                self.assertIn(term_reference, rr)
+                self.assertIn(object_reference, rr[term_reference])

tests/test_struct.py

@@ -12,7 +12,7 @@
 LYSINE_DEHYDROGENASE_ACT = Reference(
     prefix="GO", identifier="0050069", name="lysine dehydrogenase activity"
 )
-RO_DUMMY = TypeDef(reference=Reference.from_curie("RO:1234567"))
+RO_DUMMY = TypeDef(reference=Reference(prefix="RO", identifier="1234567"))
 CHARLIE = Reference(prefix="orcid", identifier="0000-0003-4423-4370")