Turn off primary identifier resolution in pyobo.get_name() by default (#440)

Author: cthoyt

src/pyobo/api/names.py

@@ -6,7 +6,7 @@
 import subprocess
 from collections.abc import Callable, Mapping
 from functools import lru_cache
-from typing import Any, TypeVar
+from typing import TypeVar
 
 import curies
 import pandas as pd
@@ -49,9 +49,15 @@
 logger = logging.getLogger(__name__)
 
 
-def get_name_by_curie(curie: str, **kwargs: Any) -> str | None:
+def get_name_by_curie(
+    curie: str,
+    /,
+    *,
+    upgrade_identifier: bool | None = None,
+    **kwargs: Unpack[GetOntologyKwargs],
+) -> str | None:
     """Get the name for a CURIE, if possible."""
-    return get_name(curie, **kwargs)
+    return get_name(curie, upgrade_identifier=upgrade_identifier, **kwargs)
 
 
 X = TypeVar("X")
@@ -63,6 +69,8 @@ def get_name_by_curie(curie: str, **kwargs: Any) -> str | None:
 def _help_get(
     f: Callable[[str, Unpack[GetOntologyKwargs]], Mapping[str, X]],
     reference: Reference,
+    *,
+    upgrade_identifier: bool | None = None,
     **kwargs: Unpack[GetOntologyKwargs],
 ) -> X | None:
     """Get the result for an entity based on a mapping maker function ``f``."""
@@ -87,19 +95,32 @@ def _help_get(
             NO_BUILD_PREFIXES.add(reference.prefix)
         return None
 
-    primary_id = get_primary_identifier(reference, **kwargs)
-    return mapping.get(primary_id)
+    if upgrade_identifier is None:
+        if reference.identifier in mapping:
+            return mapping[reference.identifier]
+        else:
+            primary_id = get_primary_identifier(reference, **kwargs)
+            return mapping.get(primary_id)
+    elif upgrade_identifier is True:
+        primary_id = get_primary_identifier(reference, **kwargs)
+        return mapping.get(primary_id)
+    else:
+        return mapping.get(reference.identifier)
 
 
 def get_name(
     prefix: str | curies.Reference | curies.ReferenceTuple,
     identifier: str | None = None,
     /,
+    *,
+    upgrade_identifier: bool | None = None,
     **kwargs: Unpack[GetOntologyKwargs],
 ) -> str | None:
     """Get the name for an entity."""
     reference = _get_pi(prefix, identifier)
-    return _help_get(get_id_name_mapping, reference, **kwargs)
+    return _help_get(
+        get_id_name_mapping, reference, upgrade_identifier=upgrade_identifier, **kwargs
+    )
 
 
 @lru_cache

tests/test_api.py

@@ -90,7 +90,8 @@ def test_get_primary(self, _, __):
         primary_id = get_primary_identifier("go", "0001071")
         self.assertIsNotNone(primary_id)
         self.assertEqual("0003700", primary_id)
-        name = get_name(ReferenceTuple("go", "0001071"))
+        self.assertIsNone(get_name(ReferenceTuple("go", "0001071"), upgrade_identifier=False))
+        name = get_name(ReferenceTuple("go", "0001071"), upgrade_identifier=True)
         self.assertIsNotNone(name)
         self.assertEqual("DNA-binding transcription factor activity", name)
 
@@ -101,7 +102,16 @@ def test_get_primary_by_curie(self, _, __):
         primary_curie = get_primary_curie("go:0001071")
         self.assertIsNotNone(primary_curie)
         self.assertEqual("go:0003700", primary_curie)
-        name = get_name_by_curie("go:0001071")
+        self.assertIsNone(get_name_by_curie("go:0001071", upgrade_identifier=False))
+
+        # if set explicitly to true, then it will do it eagerly
+        name = get_name_by_curie("go:0001071", upgrade_identifier=True)
+        self.assertIsNotNone(name)
+        self.assertEqual("DNA-binding transcription factor activity", name)
+
+        # if not set, or left as default, then it will do it only if there's no
+        # original name
+        name = get_name_by_curie("go:0001071", upgrade_identifier=None)
         self.assertIsNotNone(name)
         self.assertEqual("DNA-binding transcription factor activity", name)
 
@@ -209,7 +219,8 @@ def test_api(self) -> None:
             self.assertEqual({t1.name: t1.identifier}, name_id)
 
             self.assertEqual(t1.name, pyobo.get_name(r1, cache=False))
-            self.assertEqual(t1.name, pyobo.get_name(r2, cache=False))
+            self.assertEqual(t1.name, pyobo.get_name(r2, cache=False, upgrade_identifier=True))
+            self.assertIsNone(pyobo.get_name(r2, cache=False, upgrade_identifier=False))
 
             # Xrefs
             d = pyobo.get_filtered_xrefs(TEST_P1, TEST_P2, cache=False, use_tqdm=False)