feat: update X matrix validation to validate Visium assays #876
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# Conflicts: # cellxgene_schema_cli/tests/test_schema_compliance.py
| is_sparse_matrix = matrix_format in SPARSE_MATRIX_TYPES | ||
| for matrix_chunk, _, _ in self._chunk_matrix(x): |
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moved to _validate_raw_data
| has_row_of_zeros = True | ||
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| if not has_invalid_nonzero_value: | ||
| data = matrix_chunk if isinstance(matrix_chunk, np.ndarray) else matrix_chunk.data |
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moved to _matrix_has_invalid_nonzero_values for re-use
Bento007
approved these changes
May 3, 2024
| @@ -38,6 +41,7 @@ def __init__(self, ignore_labels=False): | |||
| self.schema_def = dict() | |||
| self.schema_version: str = None | |||
| self.ignore_labels = ignore_labels | |||
| self.visium_and_is_single_true_matrix_size = VISIUM_AND_IS_SINGLE_TRUE_MATRIX_SIZE | |||
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nit: in the future you can patch VISIUM_AND_IS_SINGLE_TRUE_MATRIX_SIZE in the tests to avoid having this class variable. Just one less duplicated variable.
MillenniumFalconMechanic
approved these changes
May 6, 2024
brian-mott
approved these changes
May 6, 2024
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Reason for Change
Changes
obs['in_tissue'] == 0rows CAN be all zeros--as long as there is at least ONE non-zero value among the group of in_tissue == 0 rows)- this includes datasets where visium + is_single + in_tissue is 1 for all cases because that pathway has the same value ruleset as the other assays we validate for. The only diff is validating 4992 rows for visium + is_single datasets, so that check is done outside of this helper function.