diff --git a/tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/validate_soma.py b/tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/validate_soma.py index a098212d2..d6ec847d1 100644 --- a/tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/validate_soma.py +++ b/tools/cellxgene_census_builder/src/cellxgene_census_builder/build_soma/validate_soma.py @@ -9,7 +9,7 @@ from collections.abc import Iterable, Sequence from dataclasses import dataclass from datetime import datetime -from typing import Any, Self, TypeVar +from typing import Any, Self, TypeVar, cast import dask import numpy as np @@ -543,13 +543,14 @@ def validate_X_layers_presence( 3. Presence mask per dataset is correct for each dataset """ - def _read_var_names(path: str) -> npt.NDArray[object]: + def _read_var_names(path: str) -> npt.NDArray[np.object_]: import h5py from anndata.io import read_elem with h5py.File(path) as f: index_key = f["var"].attrs["_index"] - return read_elem(f["var"][index_key]) + var_names = read_elem(f["var"][index_key]) + return cast(npt.NDArray[np.object_], var_names) @logit(logger) def _validate_X_layers_presence_general(experiment_specifications: list[ExperimentSpecification]) -> bool: