diff --git a/src/pyobo/cli/lookup.py b/src/pyobo/cli/lookup.py index 06ff62e9..cf2f2b10 100644 --- a/src/pyobo/cli/lookup.py +++ b/src/pyobo/cli/lookup.py @@ -282,7 +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, version)}") + click.echo(f"{curie}\t{get_name_by_curie(curie, version=version)}") @lookup.command() @@ -295,7 +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, version)}") + click.echo(f"{curie}\t{get_name_by_curie(curie, version=version)}") @lookup.command() diff --git a/src/pyobo/sources/mesh.py b/src/pyobo/sources/mesh.py index b7c0ddae..7d5b81a2 100644 --- a/src/pyobo/sources/mesh.py +++ b/src/pyobo/sources/mesh.py @@ -333,6 +333,7 @@ def get_mesh_category_curies( """ if version is None: version = get_version("mesh") + assert version is not None tree_to_mesh = get_tree_to_mesh_id(version=version) rv = [] for i in range(1, 100): diff --git a/src/pyobo/utils/path.py b/src/pyobo/utils/path.py index b5e27971..4fac7643 100644 --- a/src/pyobo/utils/path.py +++ b/src/pyobo/utils/path.py @@ -25,7 +25,7 @@ logger = logging.getLogger(__name__) -VersionHint = Union[None, str, Callable[[], str]] +VersionHint = Union[None, str, Callable[[], Optional[str]]] requests_ftp.monkeypatch_session() @@ -46,6 +46,7 @@ def prefix_directory_join( logger.info("[%s] got version %s", prefix, version) elif not isinstance(version, str): raise TypeError(f"Invalid type: {version} ({type(version)})") + assert version is not None version = cleanup_version(version, prefix=prefix) if version is not None and "/" in version: raise ValueError(f"[{prefix}] Can not have slash in version: {version}") diff --git a/src/pyobo/xrefdb/sources/pubchem.py b/src/pyobo/xrefdb/sources/pubchem.py index 673858c0..09262a48 100644 --- a/src/pyobo/xrefdb/sources/pubchem.py +++ b/src/pyobo/xrefdb/sources/pubchem.py @@ -19,6 +19,7 @@ def get_pubchem_mesh_df(version: Optional[str] = None) -> pd.DataFrame: """Get PubChem Compound-MeSH xrefs.""" if version is None: version = get_version("pubchem") + assert version is not None cid_mesh_url = _get_pubchem_extras_url(version, "CID-MeSH") return pd.DataFrame( [