Minor refactors before implementing SKOS reader (#515)

Author: cthoyt

src/pyobo/constants.py

@@ -218,7 +218,12 @@ class IterHelperHelperDict(SlimGetOntologyKwargs):
 
 
 #: The ontology format
-OntologyFormat: TypeAlias = Literal["obo", "owl", "json", "rdf"]
+OntologyFormat: TypeAlias = Literal[
+    "obo",
+    "owl",
+    "json",
+    "rdf",
+]
 
 #: from table 2 of the Functional OWL syntax definition
 #: at https://www.w3.org/TR/owl2-syntax/#IRIs

src/pyobo/struct/reference.py

@@ -284,7 +284,7 @@ def _parse_reference_or_uri_literal(
         case BlocklistError():
             return None
         case UnparsableIRIError():
-            # this means that it's defininitely a URI,
+            # this means that it's definitely a URI,
             # but it couldn't be parsed with Bioregistry
             return OBOLiteral.uri(str_or_curie_or_uri)
         case NotCURIEError() as exc:

src/pyobo/struct/struct.py

@@ -376,6 +376,60 @@ def append_exact_match(
         self.annotate_object(v.exact_match, reference, annotations=axioms)
         return self
 
+    def append_broad_match(
+        self,
+        reference: ReferenceHint,
+        *,
+        mapping_justification: Reference | None = None,
+        confidence: float | None = None,
+        contributor: Reference | None = None,
+    ) -> Self:
+        """Append a broad match, also adding an xref."""
+        reference = _ensure_ref(reference)
+        axioms = self._prepare_mapping_annotations(
+            mapping_justification=mapping_justification,
+            confidence=confidence,
+            contributor=contributor,
+        )
+        self.annotate_object(v.broad_match, reference, annotations=axioms)
+        return self
+
+    def append_narrow_match(
+        self,
+        reference: ReferenceHint,
+        *,
+        mapping_justification: Reference | None = None,
+        confidence: float | None = None,
+        contributor: Reference | None = None,
+    ) -> Self:
+        """Append a narrow match, also adding an xref."""
+        reference = _ensure_ref(reference)
+        axioms = self._prepare_mapping_annotations(
+            mapping_justification=mapping_justification,
+            confidence=confidence,
+            contributor=contributor,
+        )
+        self.annotate_object(v.narrow_match, reference, annotations=axioms)
+        return self
+
+    def append_related_match(
+        self,
+        reference: ReferenceHint,
+        *,
+        mapping_justification: Reference | None = None,
+        confidence: float | None = None,
+        contributor: Reference | None = None,
+    ) -> Self:
+        """Append a related match, also adding an xref."""
+        reference = _ensure_ref(reference)
+        axioms = self._prepare_mapping_annotations(
+            mapping_justification=mapping_justification,
+            confidence=confidence,
+            contributor=contributor,
+        )
+        self.annotate_object(v.related_match, reference, annotations=axioms)
+        return self
+
     def set_species(self, identifier: str, name: str | None = None) -> Self:
         """Append the from_species relation."""
         if name is None:

src/pyobo/utils/misc.py

@@ -5,10 +5,11 @@
 import logging
 from collections.abc import Callable, Iterable
 from datetime import datetime
+from typing import TypeAlias
 
 import bioversions.utils
 
-from pyobo.constants import ONTOLOGY_GETTERS, OntologyFormat
+from ..constants import ONTOLOGY_GETTERS, OntologyFormat
 
 __all__ = [
     "VERSION_GETTERS",
@@ -137,8 +138,10 @@ def _get_obograph_json_version(prefix: str, url: str) -> str | None:
     return cleanup_version(rv, prefix)
 
 
+VersionGetter: TypeAlias = Callable[[str, str], str | None]
+
 #: A mapping from data type to gersion getter function
-VERSION_GETTERS: dict[OntologyFormat, Callable[[str, str], str | None]] = {
+VERSION_GETTERS: dict[OntologyFormat, VersionGetter] = {
     "obo": _get_obo_version,
     "owl": _get_owl_version,
     "json": _get_obograph_json_version,