fix(schema 5.1.0): throw error if obsm is not type np.ndarray #859
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Bento007
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| "WARNING: All embeddings have to be of 'numpy.ndarray' type, 'adata.obsm['harmony']' is <class 'pandas.core.frame.DataFrame'>').", | ||
| ] | ||
| assert validator.errors == [ | ||
| "WARNING: All embeddings have to be of 'numpy.ndarray' type, 'adata.obsm['harmony']' is <class 'pandas.core.frame.DataFrame'>')." |
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we should be consistent and append errors with ERROR (blocks validation) rather than WARNING (doesn't)
Bento007
requested review from
nayib-jose-gloria and
MillenniumFalconMechanic
and removed request for
danieljhegeman
Bento007
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Bento007
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Change looks good for ndarray check, but I think we're missing validation for the rest of this rule:
The value for each str key MUST be a numpy.ndarray of shape (n_obs, m), where n_obs is the number of rows in X and m >= 1.
We throw a warning if a non-spatial, non-X-prefix embedding value has a row count != n_obs--that should become an error as well. And I don't think we check for column count >= 1 at all; we warn on column count < 2 (and error for spatial / X-prefix embedding keys)
# Conflicts: # cellxgene_schema_cli/tests/test_schema_compliance.py
| f" 'adata.obsm['{key}']' has shape of '{value.shape}'." | ||
| if len(value.shape) < 2: | ||
| self.errors.append( | ||
| f"All embeddings must at least two dimensions. 'adata.obsm['{key}']' has a shape length of '{len(value.shape)}'." |
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EDIT: nvm previous statment was incorrect
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| if unknown_key and value.shape[1] < 1: | ||
| self.errors.append( | ||
| f"All other embeddings must have at least one column. 'adata.obsm['{key}']' has columns='{value.shape[1]}'." |
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nit: in this context, I don't think the curator reading would know what "other embeddings" mean. Maybe "any embeddings not specified in the schema reference"?
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@brian-mott ready for review! |
Reason for Change
Changes
_validate_obsmto make it clear why an error occured.Testing