pyobo 0.12.10__py3-none-any.whl → 0.12.12__py3-none-any.whl

pyobo/cli/database.py

@@ -5,29 +5,11 @@ import warnings
 from collections.abc import Iterable
 from pathlib import Path
 
-import bioregistry
-import bioversions
 import click
 from more_click import verbose_option
 from tqdm.contrib.logging import logging_redirect_tqdm
 from typing_extensions import Unpack
-from zenodo_client import update_zenodo
-
-from .database_utils import (
-    IterHelperHelperDict,
-    _iter_alts,
-    _iter_definitions,
-    _iter_edges,
-    _iter_mappings,
-    _iter_names,
-    _iter_properties,
-    _iter_relations,
-    _iter_species,
-    _iter_synonyms,
-    _iter_typedefs,
-    _iter_xrefs,
-    iter_helper_helper,
-)
+
 from .utils import (
     Clickable,
     directory_option,
@@ -48,7 +30,6 @@ from ..constants import (
     TYPEDEFS_RECORD,
     DatabaseKwargs,
 )
-from ..getters import db_output_helper, get_ontology
 
 __all__ = [
     "main",
@@ -107,6 +88,8 @@ def build(ctx: click.Context, eager_versions: bool, **kwargs: Unpack[DatabaseKwa
     #    sys.exit(1)
 
     if eager_versions:
+        import bioversions
+
         bioversions.get_rows(use_tqdm=True)
 
     with logging_redirect_tqdm():
@@ -143,6 +126,9 @@ def build(ctx: click.Context, eager_versions: bool, **kwargs: Unpack[DatabaseKwa
 @database_annotate
 def cache(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Cache all things."""
+    from .database_utils import iter_helper_helper
+    from ..getters import get_ontology
+
     if zenodo:
         click.echo("no zenodo for caching")
 
@@ -156,9 +142,13 @@ def cache(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
 @database_annotate
 def metadata(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-metadata dump."""
+    import bioregistry
+
+    from .database_utils import IterHelperHelperDict, iter_helper_helper
     from ..api import get_metadata
+    from ..getters import db_output_helper
 
-    def _iter_metadata(
+    def _iter_metadata_internal(
         **kwargs: Unpack[IterHelperHelperDict],
     ) -> Iterable[tuple[str, str, str, bool]]:
         for prefix, data in iter_helper_helper(get_metadata, **kwargs):
@@ -166,7 +156,7 @@ def metadata(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
             logger.debug(f"[{prefix}] using version {version}")
             yield prefix, version, data["date"], bioregistry.is_deprecated(prefix)
 
-    it = _iter_metadata(**kwargs)
+    it = _iter_metadata_internal(**kwargs)
     db_output_helper(
         it,
         "metadata",
@@ -181,6 +171,9 @@ def metadata(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
 @database_annotate
 def names(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-name dump."""
+    from .database_utils import _iter_names
+    from ..getters import db_output_helper
+
     it = _iter_names(**kwargs)
     with logging_redirect_tqdm():
         paths = db_output_helper(
@@ -190,6 +183,8 @@ def names(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4020486
         update_zenodo(OOH_NA_NA_RECORD, paths)
 
@@ -197,6 +192,9 @@ def names(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
 @database_annotate
 def species(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-species dump."""
+    from .database_utils import _iter_species
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         it = _iter_species(**kwargs)
         paths = db_output_helper(
@@ -206,6 +204,8 @@ def species(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/5334738
         update_zenodo(SPECIES_RECORD, paths)
 
@@ -221,6 +221,9 @@ def _extend_skip_set(kwargs: DatabaseKwargs, skip_set: set[str]) -> None:
 @database_annotate
 def definitions(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-definition dump."""
+    from .database_utils import _iter_definitions
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         _extend_skip_set(kwargs, {"kegg.pathway", "kegg.genes", "kegg.genome", "umls"})
         it = _iter_definitions(**kwargs)
@@ -231,6 +234,8 @@ def definitions(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs])
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4637061
         update_zenodo(DEFINITIONS_RECORD, paths)
 
@@ -238,6 +243,9 @@ def definitions(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs])
 @database_annotate
 def typedefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the typedef prefix-identifier-name dump."""
+    from .database_utils import _iter_typedefs
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         _extend_skip_set(kwargs, {"ncbigene", "kegg.pathway", "kegg.genes", "kegg.genome"})
         it = _iter_typedefs(**kwargs)
@@ -249,6 +257,8 @@ def typedefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4644013
         update_zenodo(TYPEDEFS_RECORD, paths)
 
@@ -256,6 +266,9 @@ def typedefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
 @database_annotate
 def alts(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-alt-id dump."""
+    from .database_utils import _iter_alts
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         _extend_skip_set(kwargs, {"kegg.pathway", "kegg.genes", "kegg.genome", "umls"})
         it = _iter_alts(**kwargs)
@@ -266,6 +279,8 @@ def alts(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> Non
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4021476
         update_zenodo(ALTS_DATA_RECORD, paths)
 
@@ -273,6 +288,9 @@ def alts(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> Non
 @database_annotate
 def synonyms(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-synonym dump."""
+    from .database_utils import _iter_synonyms
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         _extend_skip_set(kwargs, {"kegg.pathway", "kegg.genes", "kegg.genome"})
         it = _iter_synonyms(**kwargs)
@@ -283,6 +301,8 @@ def synonyms(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4021482
         update_zenodo(SYNONYMS_RECORD, paths)
 
@@ -290,6 +310,9 @@ def synonyms(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) ->
 @database_annotate
 def relations(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the relation dump."""
+    from .database_utils import _iter_relations
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         it = _iter_relations(**kwargs)
         paths = db_output_helper(
@@ -307,6 +330,8 @@ def relations(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4625167
         update_zenodo(RELATIONS_RECORD, paths)
 
@@ -314,6 +339,9 @@ def relations(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -
 @database_annotate
 def edges(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the edges dump."""
+    from .database_utils import _iter_edges
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         it = _iter_edges(**kwargs)
         db_output_helper(
@@ -334,6 +362,9 @@ def edges(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
 @database_annotate
 def properties(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the properties dump."""
+    from .database_utils import _iter_properties
+    from ..getters import db_output_helper
+
     with logging_redirect_tqdm():
         it = _iter_properties(**kwargs)
         paths = db_output_helper(
@@ -344,6 +375,8 @@ def properties(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs])
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4625172
         update_zenodo(PROPERTIES_RECORD, paths)
 
@@ -351,6 +384,9 @@ def properties(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs])
 @database_annotate
 def xrefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the prefix-identifier-xref dump."""
+    from .database_utils import _iter_xrefs
+    from ..getters import db_output_helper
+
     warnings.warn("Use pyobo.database.mappings instead", DeprecationWarning, stacklevel=2)
     with logging_redirect_tqdm():
         it = _iter_xrefs(**kwargs)
@@ -362,6 +398,8 @@ def xrefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
             directory=directory,
         )
     if zenodo:
+        from zenodo_client import update_zenodo
+
         # see https://zenodo.org/record/4021477
         update_zenodo(JAVERT_RECORD, paths)
 
@@ -369,6 +407,9 @@ def xrefs(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> No
 @database_annotate
 def mappings(zenodo: bool, directory: Path, **kwargs: Unpack[DatabaseKwargs]) -> None:
     """Make the SSSOM dump."""
+    from .database_utils import _iter_mappings
+    from ..getters import db_output_helper
+
     columns = [
         "subject_id",
         "object_id",

pyobo/cli/lookup.py

@@ -4,7 +4,6 @@ import json
 import sys
 from collections.abc import Mapping
 
-import bioregistry
 import click
 from more_click import verbose_option
 from typing_extensions import Unpack
@@ -18,30 +17,7 @@ from .utils import (
     strict_option,
     version_option,
 )
-from ..api import (
-    get_ancestors,
-    get_descendants,
-    get_filtered_properties_df,
-    get_filtered_relations_df,
-    get_filtered_xrefs,
-    get_hierarchy,
-    get_id_definition_mapping,
-    get_id_name_mapping,
-    get_id_species_mapping,
-    get_id_synonyms_mapping,
-    get_id_to_alts,
-    get_ids,
-    get_mappings_df,
-    get_metadata,
-    get_name,
-    get_properties_df,
-    get_relations_df,
-    get_typedef_df,
-    get_xrefs_df,
-)
 from ..constants import LookupKwargs
-from ..getters import get_ontology
-from ..struct.reference import _parse_str_or_curie_or_uri
 
 __all__ = [
     "lookup",
@@ -75,6 +51,10 @@ identifier_option = click.option("-i", "--identifier")
 @click.option("-t", "--target")
 def xrefs(target: str, **kwargs: Unpack[LookupKwargs]) -> None:
     """Page through xrefs for the given namespace to the second given namespace."""
+    import bioregistry
+
+    from ..api import get_filtered_xrefs, get_xrefs_df
+
     if target:
         target_norm = bioregistry.normalize_prefix(target)
         filtered_xrefs = get_filtered_xrefs(xref_prefix=target_norm, **kwargs)
@@ -91,6 +71,10 @@ def xrefs(target: str, **kwargs: Unpack[LookupKwargs]) -> None:
 @click.option("-t", "--target")
 def mappings(include_names: bool, target: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
     """Page through mappings for the given namespace."""
+    import bioregistry
+
+    from ..api import get_mappings_df
+
     mappings_df = get_mappings_df(names=include_names, **kwargs)
     if target:
         target_norm = bioregistry.normalize_prefix(target)
@@ -106,6 +90,8 @@ def mappings(include_names: bool, target: str | None, **kwargs: Unpack[LookupKwa
 @lookup_annotate
 def metadata(**kwargs: Unpack[LookupKwargs]) -> None:
     """Print the metadata for the given namespace."""
+    from ..api import get_metadata
+
     metadata = get_metadata(**kwargs)
     click.echo(json.dumps(metadata, indent=2))
 
@@ -113,6 +99,8 @@ def metadata(**kwargs: Unpack[LookupKwargs]) -> None:
 @lookup_annotate
 def ids(**kwargs: Unpack[LookupKwargs]) -> None:
     """Page through the identifiers of entities in the given namespace."""
+    from ..api import get_ids
+
     id_list = get_ids(**kwargs)
     if not id_list:
         click.secho("no data", fg="red")
@@ -124,6 +112,8 @@ def ids(**kwargs: Unpack[LookupKwargs]) -> None:
 @identifier_option
 def names(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
     """Page through the identifiers and names of entities in the given namespace."""
+    from ..api import get_id_name_mapping
+
     id_to_name = get_id_name_mapping(**kwargs)
     _help_page_mapping(id_to_name, identifier=identifier)
 
@@ -132,6 +122,8 @@ def names(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
 @identifier_option
 def species(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
     """Page through the identifiers and species of entities in the given namespace."""
+    from ..api import get_id_species_mapping
+
     id_to_species = get_id_species_mapping(**kwargs)
     _help_page_mapping(id_to_species, identifier=identifier)
 
@@ -140,6 +132,8 @@ def species(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
 @identifier_option
 def definitions(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
     """Page through the identifiers and definitions of entities in the given namespace."""
+    from ..api import get_id_definition_mapping
+
     id_to_definition = get_id_definition_mapping(**kwargs)
     _help_page_mapping(id_to_definition, identifier=identifier)
 
@@ -147,6 +141,8 @@ def definitions(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
 @lookup_annotate
 def typedefs(**kwargs: Unpack[LookupKwargs]) -> None:
     """Page through the identifiers and names of typedefs in the given namespace."""
+    from ..api import get_typedef_df
+
     df = get_typedef_df(**kwargs)
     echo_df(df)
 
@@ -168,6 +164,8 @@ def _help_page_mapping(id_to_name: Mapping[str, str], *, identifier: str | None
 @identifier_option
 def synonyms(identifier: str | None, **kwargs: Unpack[LookupKwargs]) -> None:
     """Page through the synonyms for entities in the given namespace."""
+    from ..api import get_id_synonyms_mapping
+
     id_to_synonyms = get_id_synonyms_mapping(**kwargs)
     if identifier is None:
         click.echo_via_pager(
@@ -198,6 +196,11 @@ def relations(
     **kwargs: Unpack[LookupKwargs],
 ) -> None:
     """Page through the relations for entities in the given namespace."""
+    import bioregistry
+
+    from ..api import get_filtered_relations_df, get_relations_df
+    from ..struct.reference import _parse_str_or_curie_or_uri
+
     if relation is None:
         relations_df = get_relations_df(**kwargs)
         if summarize:
@@ -232,6 +235,8 @@ def hierarchy(
     **kwargs: Unpack[LookupKwargs],
 ) -> None:
     """Page through the hierarchy for entities in the namespace."""
+    from ..api import get_hierarchy
+
     h = get_hierarchy(
         include_part_of=include_part_of,
         include_has_member=include_has_member,
@@ -250,6 +255,8 @@ def ancestors(
     **kwargs: Unpack[LookupKwargs],
 ) -> None:
     """Look up ancestors."""
+    from ..api import get_ancestors, get_name
+
     # note, prefix is passed via kwargs
     ancestors = get_ancestors(identifier=identifier, **kwargs)
     for ancestor in sorted(ancestors or []):
@@ -263,6 +270,8 @@ def descendants(
     **kwargs: Unpack[LookupKwargs],
 ) -> None:
     """Look up descendants."""
+    from ..api import get_descendants, get_name
+
     # note, prefix is passed via kwargs
     descendants = get_descendants(identifier=identifier, **kwargs)
     for descendant in sorted(descendants or []):
@@ -276,6 +285,8 @@ def properties(
     **kwargs: Unpack[LookupKwargs],
 ) -> None:
     """Page through the properties for entities in the given namespace."""
+    from ..api import get_filtered_properties_df, get_properties_df
+
     if key is None:
         properties_df = get_properties_df(**kwargs)
     else:
@@ -290,6 +301,8 @@ def alts(
     **kwargs: Unpack[LookupKwargs],
 ) -> None:
     """Page through alt ids in a namespace."""
+    from ..api import get_id_to_alts
+
     id_to_alts = get_id_to_alts(**kwargs)
     _help_page_mapping(id_to_alts, identifier=identifier)
 
@@ -297,6 +310,8 @@ def alts(
 @lookup_annotate
 def prefixes(**kwargs: Unpack[LookupKwargs]) -> None:
     """Page through prefixes appearing in an ontology."""
+    from ..getters import get_ontology
+
     ontology = get_ontology(**kwargs)
     for prefix in sorted(ontology._get_prefixes(), key=str.casefold):
         click.echo(prefix)

pyobo/cli/utils.py

@@ -1,15 +1,19 @@
 """Utilities for the CLI."""
 
+from __future__ import annotations
+
 import datetime
 import pathlib
 from collections.abc import Callable
-from typing import TypeVar
+from typing import TYPE_CHECKING, TypeVar
 
 import click
-import pandas as pd
 
 from ..constants import DATABASE_DIRECTORY
 
+if TYPE_CHECKING:
+    import pandas as pd
+
 __all__ = [
     "Clickable",
     "directory_option",

pyobo/constants.py

@@ -8,14 +8,26 @@ from collections.abc import Callable
 from pathlib import Path
 from typing import Literal, NamedTuple, TypeAlias
 
-import bioregistry
 import pystow
 from typing_extensions import NotRequired, TypedDict
 
 __all__ = [
     "DATABASE_DIRECTORY",
+    "DEFAULT_PREFIX_MAP",
+    "ONTOLOGY_GETTERS",
+    "PROVENANCE_PREFIXES",
     "RAW_DIRECTORY",
     "SPECIES_REMAPPING",
+    "DatabaseKwargs",
+    "GetOntologyKwargs",
+    "IterHelperHelperDict",
+    "LookupKwargs",
+    "OntologyFormat",
+    "OntologyPathPack",
+    "SlimGetOntologyKwargs",
+    "check_should_cache",
+    "check_should_force",
+    "check_should_use_tqdm",
 ]
 
 logger = logging.getLogger(__name__)
@@ -96,6 +108,8 @@ SPECIES_FILE = "species.tsv.gz"
 
 NCBITAXON_PREFIX = "ncbitaxon"
 DATE_FORMAT = "%d:%m:%Y %H:%M"
+
+#: Prefixes for resources that are considered as provenance
 PROVENANCE_PREFIXES = {
     "pubmed",
     "pmc",
@@ -117,13 +131,21 @@ PROVENANCE_PREFIXES = {
 class DatabaseKwargs(TypedDict):
     """Keyword arguments for database CLI functions."""
 
+    #: Should strict identifier parsing be enabled?
     strict: bool
+    #: Should re-download and re-processing be forced?
     force: bool
+    #: Should re-processing be forced?
     force_process: bool
-    skip_pyobo: bool
+
+    #: Should a progress bar be used?
+    use_tqdm: bool
+    #: Skip all prefixes lexicographically sorted below the given prefix
     skip_below: str | None
+    #: If true, skips prefixes that are ontologized as sources in PyOBO
+    skip_pyobo: bool
+    #: An enumerated set of prefixes to skip
     skip_set: set[str] | None
-    use_tqdm: bool
 
 
 class SlimGetOntologyKwargs(TypedDict):
@@ -134,8 +156,11 @@ class SlimGetOntologyKwargs(TypedDict):
     only a single ontology is requested.
     """
 
+    #: Should strict identifier parsing be enabled?
     strict: NotRequired[bool]
+    #: Should re-download and re-processing be forced?
     force: NotRequired[bool]
+    #: Should re-processing be forced?
     force_process: NotRequired[bool]
 
 
@@ -145,8 +170,11 @@ class GetOntologyKwargs(SlimGetOntologyKwargs):
     This dictionary doesn't contain ``prefix`` since this is always explicitly handled.
     """
 
+    #: The version of the ontology to get
     version: NotRequired[str | None]
+    #: Should the cache be used?
     cache: NotRequired[bool]
+    #: Should a progress bar be used?
     use_tqdm: NotRequired[bool]
 
 
@@ -186,12 +214,17 @@ class IterHelperHelperDict(SlimGetOntologyKwargs):
     :func:`pyobo.get_ontology` in each iteration.
     """
 
+    #: Should a progress bar be used?
     use_tqdm: bool
+    #: Skip all prefixes lexicographically sorted below the given prefix
     skip_below: str | None
+    #: If true, skips prefixes that are ontologized as sources in PyOBO
     skip_pyobo: bool
+    #: An enumerated set of prefixes to skip
     skip_set: set[str] | None
 
 
+#: The ontology format
 OntologyFormat: TypeAlias = Literal["obo", "owl", "json", "rdf"]
 
 #: from table 2 of the Functional OWL syntax definition
@@ -207,15 +240,41 @@ DEFAULT_PREFIX_MAP = {
 class OntologyPathPack(NamedTuple):
     """A format and path tuple."""
 
+    #: The ontology format
     format: OntologyFormat
+    #: The path to the ontology file
     path: Path
 
 
+def _get_obo_download(prefix: str) -> str | None:
+    import bioregistry
+
+    return bioregistry.get_obo_download(prefix)
+
+
+def _get_owl_download(prefix: str) -> str | None:
+    import bioregistry
+
+    return bioregistry.get_owl_download(prefix)
+
+
+def _get_json_download(prefix: str) -> str | None:
+    import bioregistry
+
+    return bioregistry.get_json_download(prefix)
+
+
+def _get_rdf_download(prefix: str) -> str | None:
+    import bioregistry
+
+    return bioregistry.get_rdf_download(prefix)
+
+
 #: Functions that get ontology files. Order matters in this list,
 #: since order implicitly defines priority
 ONTOLOGY_GETTERS: list[tuple[OntologyFormat, Callable[[str], str | None]]] = [
-    ("obo", bioregistry.get_obo_download),
-    ("owl", bioregistry.get_owl_download),
-    ("json", bioregistry.get_json_download),
-    ("rdf", bioregistry.get_rdf_download),
+    ("obo", _get_obo_download),
+    ("owl", _get_owl_download),
+    ("json", _get_json_download),
+    ("rdf", _get_rdf_download),
 ]

pyobo/getters.py

@@ -45,8 +45,14 @@ from .utils.path import ensure_path, prefix_directory_join
 from .version import get_git_hash, get_version
 
 __all__ = [
+    "REQUIRES_NO_ROBOT_CHECK",
+    "SKIP",
     "NoBuildError",
+    "UnhandledFormatError",
+    "db_output_helper",
     "get_ontology",
+    "iter_helper",
+    "iter_helper_helper",
 ]
 
 logger = logging.getLogger(__name__)
@@ -112,8 +118,6 @@ def get_ontology(
 
     :returns: An OBO object
 
-    :raises OnlyOWLError: If the OBO foundry only has an OWL document for this resource.
-
     Alternate usage if you have a custom url
 
     .. code-block:: python
@@ -220,7 +224,8 @@ def _ensure_ontology_path(
     return None
 
 
-SKIP = {
+#: A dictioanry of prefixes to skip during full build with reasons as values
+SKIP: dict[str, str] = {
     "ncbigene": "too big, refs acquired from other dbs",
     "pubchem.compound": "top big, can't deal with this now",
     "gaz": "Gazetteer is irrelevant for biology",