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fix str column showing object dtype #489

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merged 1 commit into from
Mar 15, 2024
Merged

fix str column showing object dtype #489

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5 changes: 4 additions & 1 deletion src/spatialdata/models/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -794,7 +794,10 @@ def _validate_table_annotation_metadata(self, data: AnnData) -> None:
raise ValueError(f"`{attr[self.REGION_KEY_KEY]}` not found in `adata.obs`.")
if attr[self.INSTANCE_KEY] not in data.obs:
raise ValueError(f"`{attr[self.INSTANCE_KEY]}` not found in `adata.obs`.")
if (dtype := data.obs[attr[self.INSTANCE_KEY]].dtype) not in [np.int16, np.int32, np.int64, str]:
if (dtype := data.obs[attr[self.INSTANCE_KEY]].dtype) not in [np.int16, np.int32, np.int64, "O"] or (
dtype == "O" and (val_dtype := type(data.obs[attr[self.INSTANCE_KEY]][0])) != str
):
dtype = dtype if dtype != "O" else val_dtype
raise TypeError(
f"Only np.int16, np.int32, np.int64 or string allowed as dtype for "
f"instance_key column in obs. Dtype found to be {dtype}"
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