Refactor reference passing (#316)

More consistently use the prefix/identifier handler function

src/pyobo/api/alts.py

@@ -7,11 +7,10 @@
 import curies
 from typing_extensions import Unpack
 
-from .utils import get_version_from_kwargs
+from .utils import _get_pi, get_version_from_kwargs
 from ..constants import GetOntologyKwargs, check_should_cache, check_should_force
 from ..getters import get_ontology
 from ..identifier_utils import wrap_norm_prefix
-from ..struct.reference import Reference
 from ..utils.cache import cached_multidict
 from ..utils.path import prefix_cache_join
 
@@ -62,18 +61,23 @@ def get_alts_to_id(prefix: str, **kwargs: Unpack[GetOntologyKwargs]) -> Mapping[
 
 
 def get_primary_curie(
-    curie: str,
+    prefix: str | curies.Reference | curies.ReferenceTuple,
+    identifier: str | None = None,
+    /,
     **kwargs: Unpack[GetOntologyKwargs],
 ) -> str | None:
     """Get the primary curie for an entity."""
-    reference = Reference.from_curie_or_uri(curie, strict=kwargs.get("strict", True))
-    if reference is None:
+    reference = _get_pi(prefix, identifier)
+    try:
+        primary_identifier = get_primary_identifier(reference, **kwargs)
+    except ValueError:
+        if kwargs.get("strict"):
+            raise
+        # this happens on invalid prefix. maybe revise?
         return None
-    primary_identifier = get_primary_identifier(reference, **kwargs)
     return f"{reference.prefix}:{primary_identifier}"
 
 
-@wrap_norm_prefix
 def get_primary_identifier(
     prefix: str | curies.Reference | curies.ReferenceTuple,
     identifier: str | None = None,
@@ -88,14 +92,8 @@ def get_primary_identifier(
 
     Returns the original identifier if there are no alts available or if there's no mapping.
     """
-    if isinstance(prefix, curies.ReferenceTuple | curies.Reference):
-        identifier = prefix.identifier
-        prefix = prefix.prefix
-    elif identifier is None:
-        raise ValueError("passed a prefix but no local unique identifier")
-
-    if prefix in NO_ALTS:  # TODO later expand list to other namespaces with no alts
-        return identifier
-
-    alts_to_id = get_alts_to_id(prefix, **kwargs)
-    return alts_to_id.get(identifier, identifier)
+    t = _get_pi(prefix, identifier)
+    if t.prefix in NO_ALTS:  # TODO later expand list to other namespaces with no alts
+        return t.identifier
+    alts_to_id = get_alts_to_id(t.prefix, **kwargs)
+    return alts_to_id.get(t.identifier, t.identifier)

src/pyobo/api/names.py

@@ -6,13 +6,13 @@
 import subprocess
 from collections.abc import Callable, Mapping
 from functools import lru_cache
-from typing import TypeVar
+from typing import Any, TypeVar
 
 from curies import Reference, ReferenceTuple
 from typing_extensions import Unpack
 
 from .alts import get_primary_identifier
-from .utils import _get_pi, get_version, get_version_from_kwargs
+from .utils import _get_pi, get_version_from_kwargs
 from ..constants import GetOntologyKwargs, check_should_cache, check_should_force
 from ..getters import NoBuildError, get_ontology
 from ..identifier_utils import wrap_norm_prefix
@@ -35,12 +35,9 @@
 logger = logging.getLogger(__name__)
 
 
-def get_name_by_curie(curie: str, *, version: str | None = None) -> str | None:
+def get_name_by_curie(curie: str, **kwargs: Any) -> str | None:
     """Get the name for a CURIE, if possible."""
-    reference = Reference.from_curie(curie)
-    if version is None:
-        version = get_version(reference.prefix)
-    return get_name(reference, version=version)
+    return get_name(curie, **kwargs)
 
 
 X = TypeVar("X")
@@ -51,44 +48,42 @@ def get_name_by_curie(curie: str, *, version: str | None = None) -> str | None:
 
 def _help_get(
     f: Callable[[str, Unpack[GetOntologyKwargs]], Mapping[str, X]],
-    prefix: str,
-    identifier: str,
+    reference: ReferenceTuple,
     **kwargs: Unpack[GetOntologyKwargs],
 ) -> X | None:
     """Get the result for an entity based on a mapping maker function ``f``."""
     try:
-        mapping = f(prefix, **kwargs)  # type:ignore
+        mapping = f(reference.prefix, **kwargs)  # type:ignore
     except NoBuildError:
-        if prefix not in NO_BUILD_PREFIXES:
-            logger.warning("[%s] unable to look up results with %s", prefix, f)
-            NO_BUILD_PREFIXES.add(prefix)
+        if reference.prefix not in NO_BUILD_PREFIXES:
+            logger.warning("[%s] unable to look up results with %s", reference, f)
+            NO_BUILD_PREFIXES.add(reference.prefix)
         return None
     except ValueError as e:
-        if prefix not in NO_BUILD_PREFIXES:
-            logger.warning("[%s] value error while looking up results with %s: %s", prefix, f, e)
-            NO_BUILD_PREFIXES.add(prefix)
+        if reference.prefix not in NO_BUILD_PREFIXES:
+            logger.warning("[%s] value error while looking up results with %s: %s", reference, f, e)
+            NO_BUILD_PREFIXES.add(reference.prefix)
         return None
 
     if not mapping:
-        if prefix not in NO_BUILD_PREFIXES:
-            logger.warning("[%s] no results produced with %s", prefix, f)
-            NO_BUILD_PREFIXES.add(prefix)
+        if reference.prefix not in NO_BUILD_PREFIXES:
+            logger.warning("[%s] no results produced with %s", reference, f)
+            NO_BUILD_PREFIXES.add(reference.prefix)
         return None
 
-    primary_id = get_primary_identifier(prefix, identifier, **kwargs)
+    primary_id = get_primary_identifier(reference, **kwargs)
     return mapping.get(primary_id)
 
 
-@wrap_norm_prefix
 def get_name(
     prefix: str | Reference | ReferenceTuple,
     identifier: str | None = None,
     /,
     **kwargs: Unpack[GetOntologyKwargs],
 ) -> str | None:
     """Get the name for an entity."""
-    t = _get_pi(prefix, identifier)
-    return _help_get(get_id_name_mapping, prefix=t.prefix, identifier=t.identifier, **kwargs)
+    reference = _get_pi(prefix, identifier)
+    return _help_get(get_id_name_mapping, reference, **kwargs)
 
 
 @lru_cache
@@ -167,16 +162,15 @@ def get_name_id_mapping(
     return {v: k for k, v in id_name.items()}
 
 
-@wrap_norm_prefix
 def get_definition(
-    prefix: str, identifier: str | None = None, **kwargs: Unpack[GetOntologyKwargs]
+    prefix: str | Reference | ReferenceTuple,
+    identifier: str | None = None,
+    /,
+    **kwargs: Unpack[GetOntologyKwargs],
 ) -> str | None:
     """Get the definition for an entity."""
-    if identifier is None:
-        prefix, _, identifier = prefix.rpartition(":")
-    if identifier is None:
-        raise ValueError
-    return _help_get(get_id_definition_mapping, prefix=prefix, identifier=identifier, **kwargs)
+    reference = _get_pi(prefix, identifier)
+    return _help_get(get_id_definition_mapping, reference, **kwargs)
 
 
 def get_id_definition_mapping(
@@ -219,12 +213,15 @@ def _get_obsolete() -> list[str]:
     return set(_get_obsolete())
 
 
-@wrap_norm_prefix
 def get_synonyms(
-    prefix: str, identifier: str, **kwargs: Unpack[GetOntologyKwargs]
+    prefix: str | Reference | ReferenceTuple,
+    identifier: str | None = None,
+    /,
+    **kwargs: Unpack[GetOntologyKwargs],
 ) -> list[str] | None:
     """Get the synonyms for an entity."""
-    return _help_get(get_id_synonyms_mapping, prefix=prefix, identifier=identifier, **kwargs)
+    reference = _get_pi(prefix, identifier)
+    return _help_get(get_id_synonyms_mapping, reference, **kwargs)
 
 
 @wrap_norm_prefix

src/pyobo/api/species.py

@@ -4,10 +4,11 @@
 from collections.abc import Mapping
 from functools import lru_cache
 
+import curies
 from typing_extensions import Unpack
 
 from .alts import get_primary_identifier
-from .utils import get_version_from_kwargs
+from .utils import _get_pi, get_version_from_kwargs
 from ..constants import GetOntologyKwargs, check_should_force
 from ..getters import NoBuildError, get_ontology
 from ..identifier_utils import wrap_norm_prefix
@@ -22,23 +23,29 @@
 logger = logging.getLogger(__name__)
 
 
-@wrap_norm_prefix
-def get_species(prefix: str, identifier: str, **kwargs: Unpack[GetOntologyKwargs]) -> str | None:
+def get_species(
+    prefix: str | curies.Reference | curies.ReferenceTuple,
+    identifier: str | None = None,
+    /,
+    **kwargs: Unpack[GetOntologyKwargs],
+) -> str | None:
     """Get the species."""
-    if prefix == "uniprot":
+    t = _get_pi(prefix, identifier)
+
+    if t.prefix == "uniprot":
         raise NotImplementedError
 
     try:
-        id_species = get_id_species_mapping(prefix, **kwargs)
+        id_species = get_id_species_mapping(t.prefix, **kwargs)
     except NoBuildError:
-        logger.warning("unable to look up species for prefix %s", prefix)
+        logger.warning("unable to look up species for prefix %s", t.prefix)
         return None
 
     if not id_species:
-        logger.warning("no results produced for prefix %s", prefix)
+        logger.warning("no results produced for prefix %s", t.prefix)
         return None
 
-    primary_id = get_primary_identifier(prefix, identifier, **kwargs)
+    primary_id = get_primary_identifier(t, **kwargs)
     return id_species.get(primary_id)
 
 

src/pyobo/api/utils.py

@@ -145,6 +145,8 @@ def _get_pi(
         if identifier is not None:
             raise ValueError("unexpected non-none value passed as second positional argument")
         return prefix.pair
+    if isinstance(prefix, str) and identifier is None:
+        return ReferenceTuple.from_curie(prefix)
     if identifier is None:
         raise ValueError(
             "prefix was given as a string, so an identifier was expected to be passed as a string as well"

src/pyobo/struct/struct_utils.py

@@ -675,9 +675,11 @@ def _ensure_ref(
         return Reference(prefix=reference[0], identifier=reference[1])
     if isinstance(reference, Reference):
         return reference
+    if isinstance(reference, curies.Reference):
+        return Reference(prefix=reference.prefix, identifier=reference.identifier)
     if ":" not in reference:
         if not ontology_prefix:
-            raise ValueError(f"can't parse reference: {reference}")
+            raise ValueError(f"can't parse reference of type {type(reference)}: {reference}")
         return default_reference(ontology_prefix, reference)
     _rv = Reference.from_curie_or_uri(reference, strict=True, ontology_prefix=ontology_prefix)
     if _rv is None:

tests/test_api.py

@@ -77,7 +77,7 @@ def test_get_primary(self, _, __):
         primary_id = get_primary_identifier("go", "0001071")
         self.assertIsNotNone(primary_id)
         self.assertEqual("0003700", primary_id)
-        name = get_name("go", "0001071")
+        name = get_name(ReferenceTuple("go", "0001071"))
         self.assertIsNotNone(name)
         self.assertEqual("DNA-binding transcription factor activity", name)
 
@@ -96,10 +96,10 @@ def test_get_primary_by_curie(self, _, __):
     @mock_id_names_mapping
     def test_already_primary(self, _, __):
         """Test when you give a primary id."""
-        primary_id = get_primary_identifier("go", "0003700")
+        primary_id = get_primary_identifier(ReferenceTuple("go", "0003700"))
         self.assertIsNotNone(primary_id)
         self.assertEqual("0003700", primary_id)
-        name = get_name("go", "0003700")
+        name = get_name(ReferenceTuple("go", "0003700"))
         self.assertIsNotNone(name)
         self.assertEqual("DNA-binding transcription factor activity", name)
 
@@ -134,9 +134,9 @@ def test_already_primary_by_curie(self, _, __):
     @mock_id_names_mapping
     def test_no_alts(self, _, __):
         """Test alternate behavior for nomenclature source with no alts."""
-        primary_id = get_primary_identifier("ncbitaxon", "52818")
+        primary_id = get_primary_identifier(ReferenceTuple("ncbitaxon", "52818"))
         self.assertEqual("52818", primary_id)
-        self.assertEqual("Allamanda cathartica", get_name("ncbitaxon", "52818"))
+        self.assertEqual("Allamanda cathartica", get_name(ReferenceTuple("ncbitaxon", "52818")))
 
     def test_api(self) -> None:
         """Test getting the hierarchy."""