pyobo 0.10.10__py3-none-any.whl → 0.10.12__py3-none-any.whl

pyobo/api/alts.py

@@ -28,12 +28,15 @@ NO_ALTS = {
 
 @lru_cache()
 @wrap_norm_prefix
-def get_id_to_alts(prefix: str, force: bool = False) -> Mapping[str, List[str]]:
+def get_id_to_alts(
+    prefix: str, *, force: bool = False, version: Optional[str] = None
+) -> Mapping[str, List[str]]:
     """Get alternate identifiers."""
     if prefix in NO_ALTS:
         return {}
 
-    version = get_version(prefix)
+    if version is None:
+        version = get_version(prefix)
     path = prefix_cache_join(prefix, name="alt_ids.tsv", version=version)
     header = [f"{prefix}_id", "alt_id"]
 
@@ -51,26 +54,28 @@ def get_id_to_alts(prefix: str, force: bool = False) -> Mapping[str, List[str]]:
 
 @lru_cache()
 @wrap_norm_prefix
-def get_alts_to_id(prefix: str, force: bool = False) -> Mapping[str, str]:
+def get_alts_to_id(
+    prefix: str, *, force: bool = False, version: Optional[str] = None
+) -> Mapping[str, str]:
     """Get alternative id to primary id mapping."""
     return {
         alt: primary
-        for primary, alts in get_id_to_alts(prefix, force=force).items()
+        for primary, alts in get_id_to_alts(prefix, force=force, version=version).items()
         for alt in alts
     }
 
 
-def get_primary_curie(curie: str) -> Optional[str]:
+def get_primary_curie(curie: str, *, version: Optional[str] = None) -> Optional[str]:
     """Get the primary curie for an entity."""
     prefix, identifier = normalize_curie(curie)
-    primary_identifier = get_primary_identifier(prefix, identifier)
+    primary_identifier = get_primary_identifier(prefix, identifier, version=version)
     if primary_identifier is not None:
         return f"{prefix}:{primary_identifier}"
     return None
 
 
 @wrap_norm_prefix
-def get_primary_identifier(prefix: str, identifier: str) -> str:
+def get_primary_identifier(prefix: str, identifier: str, *, version: Optional[str] = None) -> str:
     """Get the primary identifier for an entity.
 
     :param prefix: The name of the resource
@@ -82,7 +87,7 @@ def get_primary_identifier(prefix: str, identifier: str) -> str:
     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)
+    alts_to_id = get_alts_to_id(prefix, version=version)
     if alts_to_id and identifier in alts_to_id:
         return alts_to_id[identifier]
     return identifier

pyobo/api/hierarchy.py

@@ -13,6 +13,7 @@ from .properties import get_filtered_properties_mapping
 from .relations import get_filtered_relations_df
 from ..identifier_utils import wrap_norm_prefix
 from ..struct import TypeDef, has_member, is_a, part_of
+from ..struct.reference import Reference
 
 __all__ = [
     "get_hierarchy",
@@ -24,7 +25,6 @@ __all__ = [
     "get_children",
 ]
 
-from ..struct.reference import Reference
 
 logger = logging.getLogger(__name__)
 
@@ -154,14 +154,16 @@ def _get_hierarchy_helper(
     return rv
 
 
-def is_descendent(prefix, identifier, ancestor_prefix, ancestor_identifier) -> bool:
+def is_descendent(
+    prefix, identifier, ancestor_prefix, ancestor_identifier, *, version: Optional[str] = None
+) -> bool:
     """Check that the first identifier has the second as a descendent.
 
     Check that go:0070246 ! natural killer cell apoptotic process is a
     descendant of go:0006915 ! apoptotic process::
     >>> assert is_descendent('go', '0070246', 'go', '0006915')
     """
-    descendants = get_descendants(ancestor_prefix, ancestor_identifier)
+    descendants = get_descendants(ancestor_prefix, ancestor_identifier, version=version)
     return descendants is not None and f"{prefix}:{identifier}" in descendants
 
 
@@ -224,13 +226,15 @@ def get_children(
     return set(hierarchy.predecessors(curie))
 
 
-def has_ancestor(prefix, identifier, ancestor_prefix, ancestor_identifier) -> bool:
+def has_ancestor(
+    prefix, identifier, ancestor_prefix, ancestor_identifier, *, version: Optional[str] = None
+) -> bool:
     """Check that the first identifier has the second as an ancestor.
 
     Check that go:0008219 ! cell death is an ancestor of go:0006915 ! apoptotic process::
     >>> assert has_ancestor('go', '0006915', 'go', '0008219')
     """
-    ancestors = get_ancestors(prefix, identifier)
+    ancestors = get_ancestors(prefix, identifier, version=version)
     return ancestors is not None and f"{ancestor_prefix}:{ancestor_identifier}" in ancestors
 
 

pyobo/api/metadata.py

@@ -4,7 +4,7 @@
 
 import logging
 from functools import lru_cache
-from typing import Mapping
+from typing import Mapping, Optional
 
 from .utils import get_version
 from ..getters import get_ontology
@@ -21,9 +21,12 @@ logger = logging.getLogger(__name__)
 
 @lru_cache()
 @wrap_norm_prefix
-def get_metadata(prefix: str, force: bool = False) -> Mapping[str, str]:
+def get_metadata(
+    prefix: str, *, force: bool = False, version: Optional[str] = None
+) -> Mapping[str, str]:
     """Get metadata for the ontology."""
-    version = get_version(prefix)
+    if version is None:
+        version = get_version(prefix)
     path = prefix_cache_join(prefix, name="metadata.json", version=version)
 
     @cached_json(path=path, force=force)

pyobo/api/names.py

@@ -2,11 +2,15 @@
 
 """High-level API for nomenclature."""
 
+from __future__ import annotations
+
 import logging
 import subprocess
 from functools import lru_cache
 from typing import Callable, List, Mapping, Optional, Set, TypeVar
 
+from curies import Reference, ReferenceTuple
+
 from .alts import get_primary_identifier
 from .utils import get_version
 from ..getters import NoBuild, get_ontology
@@ -32,6 +36,8 @@ logger = logging.getLogger(__name__)
 
 def get_name_by_curie(curie: str, *, version: Optional[str] = None) -> Optional[str]:
     """Get the name for a CURIE, if possible."""
+    if version is None:
+        version = get_version(curie.split(":")[0])
     prefix, identifier = normalize_curie(curie)
     if prefix and identifier:
         return get_name(prefix, identifier, version=version)
@@ -40,7 +46,8 @@ def get_name_by_curie(curie: str, *, version: Optional[str] = None) -> Optional[
 
 X = TypeVar("X")
 
-NO_BUILD_PREFIXES = set()
+NO_BUILD_PREFIXES: Set[str] = set()
+NO_BUILD_LOGGED: Set = set()
 
 
 def _help_get(
@@ -59,8 +66,10 @@ def _help_get(
             logger.warning("[%s] unable to look up results with %s", prefix, f)
             NO_BUILD_PREFIXES.add(prefix)
         return None
-    except ValueError:
-        logger.warning("[%s] unable to look up results with %s", prefix, f)
+    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)
         return None
 
     if not mapping:
@@ -69,20 +78,28 @@ def _help_get(
             NO_BUILD_PREFIXES.add(prefix)
         return None
 
-    primary_id = get_primary_identifier(prefix, identifier)
+    primary_id = get_primary_identifier(prefix, identifier, version=version)
     return mapping.get(primary_id)
 
 
 @wrap_norm_prefix
-def get_name(prefix: str, identifier: str, *, version: Optional[str] = None) -> Optional[str]:
+def get_name(
+    prefix: str | Reference | ReferenceTuple,
+    identifier: Optional[str] = None,
+    /,
+    *,
+    version: Optional[str] = None,
+) -> Optional[str]:
     """Get the name for an entity."""
-    return _help_get(get_id_name_mapping, prefix, identifier, version=version)
+    if isinstance(prefix, (ReferenceTuple, Reference)):
+        prefix, identifier = prefix.prefix, prefix.identifier
+    return _help_get(get_id_name_mapping, prefix, identifier, version=version)  # type:ignore
 
 
 @lru_cache()
 @wrap_norm_prefix
 def get_ids(
-    prefix: str, force: bool = False, strict: bool = False, version: Optional[str] = None
+    prefix: str, *, force: bool = False, strict: bool = False, version: Optional[str] = None
 ) -> Set[str]:
     """Get the set of identifiers for this prefix."""
     if prefix == "ncbigene":
@@ -150,16 +167,22 @@ def get_id_name_mapping(
 
 @lru_cache()
 @wrap_norm_prefix
-def get_name_id_mapping(prefix: str, force: bool = False) -> Mapping[str, str]:
+def get_name_id_mapping(
+    prefix: str, *, force: bool = False, version: Optional[str] = None
+) -> Mapping[str, str]:
     """Get a name to identifier mapping for the OBO file."""
-    id_name = get_id_name_mapping(prefix=prefix, force=force)
+    id_name = get_id_name_mapping(prefix=prefix, force=force, version=version)
     return {v: k for k, v in id_name.items()}
 
 
 @wrap_norm_prefix
-def get_definition(prefix: str, identifier: str) -> Optional[str]:
+def get_definition(
+    prefix: str, identifier: str | None = None, *, version: Optional[str] = None
+) -> Optional[str]:
     """Get the definition for an entity."""
-    return _help_get(get_id_definition_mapping, prefix, identifier)
+    if identifier is None:
+        prefix, _, identifier = prefix.rpartition(":")
+    return _help_get(get_id_definition_mapping, prefix, identifier, version=version)
 
 
 def get_id_definition_mapping(

pyobo/api/relations.py

@@ -48,9 +48,11 @@ def get_relations_df(
     force: bool = False,
     wide: bool = False,
     strict: bool = True,
+    version: Optional[str] = None,
 ) -> pd.DataFrame:
     """Get all relations from the OBO."""
-    version = get_version(prefix)
+    if version is None:
+        version = get_version(prefix)
     path = prefix_cache_join(prefix, name="relations.tsv", version=version)
 
     @cached_df(path=path, dtype=str, force=force)
@@ -118,9 +120,11 @@ def get_id_multirelations_mapping(
     *,
     use_tqdm: bool = False,
     force: bool = False,
+    version: Optional[str] = None,
 ) -> Mapping[str, List[Reference]]:
     """Get the OBO file and output a synonym dictionary."""
-    version = get_version(prefix)
+    if version is None:
+        version = get_version(prefix)
     ontology = get_ontology(prefix, force=force, version=version)
     return ontology.get_id_multirelations_mapping(typedef=typedef, use_tqdm=use_tqdm)
 
@@ -134,6 +138,7 @@ def get_relation_mapping(
     *,
     use_tqdm: bool = False,
     force: bool = False,
+    version: Optional[str] = None,
 ) -> Mapping[str, str]:
     """Get relations from identifiers in the source prefix to target prefix with the given relation.
 
@@ -147,7 +152,8 @@ def get_relation_mapping(
     >>> hgnc_mgi_orthology_mapping = pyobo.get_relation_mapping('hgnc', 'ro:HOM0000017', 'mgi')
     >>> assert mouse_mapt_mgi_id == hgnc_mgi_orthology_mapping[human_mapt_hgnc_id]
     """
-    version = get_version(prefix)
+    if version is None:
+        version = get_version(prefix)
     ontology = get_ontology(prefix, force=force, version=version)
     return ontology.get_relation_mapping(
         relation=relation, target_prefix=target_prefix, use_tqdm=use_tqdm
@@ -163,6 +169,7 @@ def get_relation(
     *,
     use_tqdm: bool = False,
     force: bool = False,
+    **kwargs,
 ) -> Optional[str]:
     """Get the target identifier corresponding to the given relationship from the source prefix/identifier pair.
 
@@ -181,6 +188,7 @@ def get_relation(
         target_prefix=target_prefix,
         use_tqdm=use_tqdm,
         force=force,
+        **kwargs,
     )
     return relation_mapping.get(source_identifier)
 

pyobo/api/species.py

@@ -22,13 +22,13 @@ logger = logging.getLogger(__name__)
 
 
 @wrap_norm_prefix
-def get_species(prefix: str, identifier: str) -> Optional[str]:
+def get_species(prefix: str, identifier: str, *, version: Optional[str] = None) -> Optional[str]:
     """Get the species."""
     if prefix == "uniprot":
         raise NotImplementedError
 
     try:
-        id_species = get_id_species_mapping(prefix)
+        id_species = get_id_species_mapping(prefix, version=version)
     except NoBuild:
         logger.warning("unable to look up species for prefix %s", prefix)
         return None
@@ -37,7 +37,7 @@ def get_species(prefix: str, identifier: str) -> Optional[str]:
         logger.warning("no results produced for prefix %s", prefix)
         return None
 
-    primary_id = get_primary_identifier(prefix, identifier)
+    primary_id = get_primary_identifier(prefix, identifier, version=version)
     return id_species.get(primary_id)
 
 

pyobo/api/typedefs.py

@@ -4,6 +4,7 @@
 
 import logging
 from functools import lru_cache
+from typing import Optional
 
 import pandas as pd
 
@@ -22,9 +23,12 @@ logger = logging.getLogger(__name__)
 
 @lru_cache()
 @wrap_norm_prefix
-def get_typedef_df(prefix: str, force: bool = False) -> pd.DataFrame:
+def get_typedef_df(
+    prefix: str, *, force: bool = False, version: Optional[str] = None
+) -> pd.DataFrame:
     """Get an identifier to name mapping for the typedefs in an OBO file."""
-    version = get_version(prefix)
+    if version is None:
+        version = get_version(prefix)
     path = prefix_cache_join(prefix, name="typedefs.tsv", version=version)
 
     @cached_df(path=path, dtype=str, force=force)

pyobo/api/utils.py

@@ -7,6 +7,7 @@ from typing import Optional
 
 import bioversions
 
+from ..constants import VERSION_PINS
 from ..utils.path import prefix_directory_join
 
 __all__ = [
@@ -25,6 +26,10 @@ def get_version(prefix: str) -> Optional[str]:
     :param prefix: the resource name
     :return: The version if available else None
     """
+    # Prioritize loaded environmental variable VERSION_PINS dictionary
+    version = VERSION_PINS.get(prefix)
+    if version:
+        return version
     try:
         version = bioversions.get_version(prefix)
     except KeyError:

pyobo/api/xrefs.py

@@ -30,9 +30,16 @@ logger = logging.getLogger(__name__)
 
 
 @wrap_norm_prefix
-def get_xref(prefix: str, identifier: str, new_prefix: str, flip: bool = False) -> Optional[str]:
+def get_xref(
+    prefix: str,
+    identifier: str,
+    new_prefix: str,
+    *,
+    flip: bool = False,
+    version: Optional[str] = None,
+) -> Optional[str]:
     """Get the xref with the new prefix if a direct path exists."""
-    filtered_xrefs = get_filtered_xrefs(prefix, new_prefix, flip=flip)
+    filtered_xrefs = get_filtered_xrefs(prefix, new_prefix, flip=flip, version=version)
     return filtered_xrefs.get(identifier)
 
 
@@ -41,8 +48,8 @@ def get_xref(prefix: str, identifier: str, new_prefix: str, flip: bool = False)
 def get_filtered_xrefs(
     prefix: str,
     xref_prefix: str,
-    flip: bool = False,
     *,
+    flip: bool = False,
     use_tqdm: bool = False,
     force: bool = False,
     strict: bool = False,

pyobo/aws.py

@@ -77,14 +77,19 @@ def upload_artifacts(
         upload_artifacts_for_prefix(prefix=prefix, bucket=bucket, s3_client=s3_client)
 
 
-def upload_artifacts_for_prefix(*, prefix: str, bucket: str, s3_client=None):
+def upload_artifacts_for_prefix(
+    *, prefix: str, bucket: str, s3_client=None, version: Optional[str] = None
+):
     """Upload compiled parts for the given prefix to AWS."""
     if s3_client is None:
         s3_client = boto3.client("s3")
 
+    if version is None:
+        version = get_version(prefix)
+
     logger.info("[%s] getting id->name mapping", prefix)
     get_id_name_mapping(prefix)
-    id_name_path = prefix_cache_join(prefix, name="names.tsv", version=get_version(prefix))
+    id_name_path = prefix_cache_join(prefix, name="names.tsv", version=version)
     if not id_name_path.exists():
         raise FileNotFoundError
     id_name_key = os.path.join(prefix, "cache", "names.tsv")
@@ -93,7 +98,7 @@ def upload_artifacts_for_prefix(*, prefix: str, bucket: str, s3_client=None):
 
     logger.info("[%s] getting id->synonyms mapping", prefix)
     get_id_synonyms_mapping(prefix)
-    id_synonyms_path = prefix_cache_join(prefix, name="synonyms.tsv", version=get_version(prefix))
+    id_synonyms_path = prefix_cache_join(prefix, name="synonyms.tsv", version=version)
     if not id_synonyms_path.exists():
         raise FileNotFoundError
     id_synonyms_key = os.path.join(prefix, "cache", "synonyms.tsv")
@@ -102,7 +107,7 @@ def upload_artifacts_for_prefix(*, prefix: str, bucket: str, s3_client=None):
 
     logger.info("[%s] getting xrefs", prefix)
     get_xrefs_df(prefix)
-    xrefs_path = prefix_cache_join(prefix, name="xrefs.tsv", version=get_version(prefix))
+    xrefs_path = prefix_cache_join(prefix, name="xrefs.tsv", version=version)
     if not xrefs_path.exists():
         raise FileNotFoundError
     xrefs_key = os.path.join(prefix, "cache", "xrefs.tsv")
@@ -111,7 +116,7 @@ def upload_artifacts_for_prefix(*, prefix: str, bucket: str, s3_client=None):
 
     logger.info("[%s] getting relations", prefix)
     get_relations_df(prefix)
-    relations_path = prefix_cache_join(prefix, name="relations.tsv", version=get_version(prefix))
+    relations_path = prefix_cache_join(prefix, name="relations.tsv", version=version)
     if not relations_path.exists():
         raise FileNotFoundError
     relations_key = os.path.join(prefix, "cache", "relations.tsv")
@@ -120,7 +125,7 @@ def upload_artifacts_for_prefix(*, prefix: str, bucket: str, s3_client=None):
 
     logger.info("[%s] getting properties", prefix)
     get_properties_df(prefix)
-    properties_path = prefix_cache_join(prefix, name="properties.tsv", version=get_version(prefix))
+    properties_path = prefix_cache_join(prefix, name="properties.tsv", version=version)
     if not properties_path.exists():
         raise FileNotFoundError
     properties_key = os.path.join(prefix, "cache", "properties.tsv")
@@ -129,7 +134,7 @@ def upload_artifacts_for_prefix(*, prefix: str, bucket: str, s3_client=None):
 
     logger.info("[%s] getting alternative identifiers", prefix)
     get_id_to_alts(prefix)
-    alts_path = prefix_cache_join(prefix, name="alt_ids.tsv", version=get_version(prefix))
+    alts_path = prefix_cache_join(prefix, name="alt_ids.tsv", version=version)
     if not alts_path.exists():
         raise FileNotFoundError
     alts_key = os.path.join(prefix, "cache", "alt_ids.tsv")

pyobo/cli/lookup.py

@@ -76,9 +76,10 @@ def xrefs(prefix: str, target: str, force: bool, no_strict: bool, version: Optio
 @prefix_argument
 @verbose_option
 @force_option
-def metadata(prefix: str, force: bool):
+@version_option
+def metadata(prefix: str, force: bool, version: Optional[str]):
     """Print the metadata for the given namespace."""
-    metadata = get_metadata(prefix, force=force)
+    metadata = get_metadata(prefix, force=force, version=version)
     click.echo(json.dumps(metadata, indent=2))
 
 
@@ -281,7 +282,7 @@ def ancestors(prefix: str, identifier: str, force: bool, version: Optional[str])
     """Look up ancestors."""
     curies = get_ancestors(prefix=prefix, identifier=identifier, force=force, version=version)
     for curie in sorted(curies or []):
-        click.echo(f"{curie}\t{get_name_by_curie(curie)}")
+        click.echo(f"{curie}\t{get_name_by_curie(curie, version=version)}")
 
 
 @lookup.command()
@@ -294,7 +295,7 @@ def descendants(prefix: str, identifier: str, force: bool, version: Optional[str
     """Look up descendants."""
     curies = get_descendants(prefix=prefix, identifier=identifier, force=force, version=version)
     for curie in sorted(curies or []):
-        click.echo(f"{curie}\t{get_name_by_curie(curie)}")
+        click.echo(f"{curie}\t{get_name_by_curie(curie, version=version)}")
 
 
 @lookup.command()

pyobo/constants.py

@@ -2,19 +2,18 @@
 
 """Constants for PyOBO."""
 
+import json
 import logging
+import os
 import re
-from functools import partial
-from typing import Callable
 
-import bioversions
 import pystow
 
 __all__ = [
     "RAW_DIRECTORY",
     "DATABASE_DIRECTORY",
     "SPECIES_REMAPPING",
-    "version_getter",
+    "VERSION_PINS",
 ]
 
 logger = logging.getLogger(__name__)
@@ -84,12 +83,6 @@ TYPEDEFS_FILE = "typedefs.tsv.gz"
 SPECIES_RECORD = "5334738"
 SPECIES_FILE = "species.tsv.gz"
 
-
-def version_getter(name: str) -> Callable[[], str]:
-    """Make a function appropriate for getting versions."""
-    return partial(bioversions.get_version, name)
-
-
 NCBITAXON_PREFIX = "NCBITaxon"
 DATE_FORMAT = "%d:%m:%Y %H:%M"
 PROVENANCE_PREFIXES = {
@@ -108,3 +101,31 @@ PROVENANCE_PREFIXES = {
     "isbn",
     "issn",
 }
+
+# Load version pin dictionary from the environmental variable VERSION_PINS
+try:
+    VERSION_PINS_STR = os.getenv("VERSION_PINS")
+    if not VERSION_PINS_STR:
+        VERSION_PINS = {}
+    else:
+        VERSION_PINS = json.loads(VERSION_PINS_STR)
+        for k, v in VERSION_PINS.items():
+            if not isinstance(k, str) or not isinstance(v, str):
+                logger.error("The prefix and version name must both be " "strings")
+            VERSION_PINS = {}
+            break
+except ValueError as e:
+    logger.error(
+        "The value for the environment variable VERSION_PINS must be a valid JSON string: %s" % e
+    )
+    VERSION_PINS = {}
+
+if VERSION_PINS:
+    logger.debug(
+        f"These are the resource versions that are pinned.\n{VERSION_PINS}. "
+        f"\nPyobo will download the latest version of a resource if it's "
+        f"not pinned.\nIf you want to use a specific version of a "
+        f"resource, edit your VERSION_PINS environmental "
+        f"variable which is a JSON string to include a prefix and version "
+        f"name."
+    )

pyobo/gilda_utils.py

@@ -15,6 +15,7 @@ from gilda.term import filter_out_duplicates
 from tqdm.auto import tqdm
 
 from pyobo import (
+    get_descendants,
     get_id_name_mapping,
     get_id_species_mapping,
     get_id_synonyms_mapping,
@@ -247,3 +248,23 @@ def get_gilda_terms(
             )
             if term is not None:
                 yield term
+
+
+def get_gilda_term_subset(
+    source: str, ancestors: Union[str, List[str]], **kwargs
+) -> Iterable[gilda.term.Term]:
+    """Get a subset of terms."""
+    subset = {
+        descendant
+        for parent_curie in _ensure_list(ancestors)
+        for descendant in get_descendants(*parent_curie.split(":")) or []
+    }
+    for term in get_gilda_terms(source, **kwargs):
+        if bioregistry.curie_to_str(term.db, term.id) in subset:
+            yield term
+
+
+def _ensure_list(s: Union[str, List[str]]) -> List[str]:
+    if isinstance(s, str):
+        return [s]
+    return s

pyobo/identifier_utils.py

@@ -2,11 +2,14 @@
 
 """Utilities for handling prefixes."""
 
+from __future__ import annotations
+
 import logging
 from functools import wraps
 from typing import Optional, Tuple, Union
 
 import bioregistry
+from curies import Reference, ReferenceTuple
 
 from .registries import (
     curie_has_blacklisted_prefix,
@@ -108,11 +111,25 @@ def wrap_norm_prefix(f):
     """Decorate a function that take in a prefix to auto-normalize, or return None if it can't be normalized."""
 
     @wraps(f)
-    def _wrapped(prefix, *args, **kwargs):
-        norm_prefix = bioregistry.normalize_prefix(prefix)
-        if norm_prefix is None:
-            raise ValueError(f"Invalid prefix: {prefix}")
-        return f(norm_prefix, *args, **kwargs)
+    def _wrapped(prefix: str | Reference | ReferenceTuple, *args, **kwargs):
+        if isinstance(prefix, str):
+            norm_prefix = bioregistry.normalize_prefix(prefix)
+            if norm_prefix is None:
+                raise ValueError(f"Invalid prefix: {prefix}")
+            prefix = norm_prefix
+        elif isinstance(prefix, Reference):
+            norm_prefix = bioregistry.normalize_prefix(prefix.prefix)
+            if norm_prefix is None:
+                raise ValueError(f"Invalid prefix: {prefix.prefix}")
+            prefix = Reference(prefix=norm_prefix, identifier=prefix.identifier)
+        elif isinstance(prefix, ReferenceTuple):
+            norm_prefix = bioregistry.normalize_prefix(prefix.prefix)
+            if norm_prefix is None:
+                raise ValueError(f"Invalid prefix: {prefix.prefix}")
+            prefix = ReferenceTuple(norm_prefix, prefix.identifier)
+        else:
+            raise TypeError
+        return f(prefix, *args, **kwargs)
 
     return _wrapped
 

pyobo/reader.py

@@ -417,7 +417,7 @@ def _clean_definition(s: str) -> str:
     # if '\t' in s:
     #     logger.warning('has tab')
     return (
-        s.replace('\\"', '"').replace("\n", " ").replace("\t", " ").replace("\d", "")  # noqa:W605
+        s.replace('\\"', '"').replace("\n", " ").replace("\t", " ").replace(r"\d", "")  # noqa:W605
     )
 
 

pyobo/sources/__init__.py

@@ -12,6 +12,7 @@ from .civic_gene import CIVICGeneGetter
 from .complexportal import ComplexPortalGetter
 from .conso import CONSOGetter
 from .cpt import CPTGetter
+from .credit import CreditGetter
 from .cvx import CVXGetter
 from .depmap import DepMapGetter
 from .dictybase_gene import DictybaseGetter
@@ -69,6 +70,7 @@ __all__ = [
     "CVXGetter",
     "ChEMBLCompoundGetter",
     "ComplexPortalGetter",
+    "CreditGetter",
     "DepMapGetter",
     "DictybaseGetter",
     "DrugBankGetter",