update error message and corresponding tests for invalid matrix encod…

…ings

cellxgene_schema_cli/cellxgene_schema/validate.py

@@ -50,6 +50,7 @@
 ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_REQUIRED = f"is required for {ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE}"
 ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_IN_TISSUE_0 = f"{ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE} and in_tissue is 0"
 
+ERROR_SUFFIX_SPARSE_FORMAT = f"Please ensure it is either a dense array or one of the supported sparse matrix encodings ({','.join(SUPPORTED_SPARSE_MATRIX_TYPES)})"
 
 class Validator:
     """Handles validation of AnnData"""
@@ -936,7 +937,8 @@ def _validate_uns_dict(self, uns_dict: dict) -> None:
                 category_mapping[column_name] = column.nunique()
 
         for key, value in uns_dict.items():
-            if isinstance(value, scipy.sparse.csr_matrix) and value.nnz == 0:
+            if isinstance(value, scipy.sparse.csr_matrix):
+                if value.nnz == 0:
                     self.errors.append(f"uns['{key}'] cannot be an empty value.")
             elif value is not None and not isinstance(value, (np.bool_, bool, numbers.Number)) and len(value) == 0:
                 self.errors.append(f"uns['{key}'] cannot be an empty value.")
@@ -1019,7 +1021,7 @@ def _validate_sparsity(self):
                 self.errors.append(f"Invalid sparse encoding for {x_name} with encoding {matrix_format}. Onle {','.join(SUPPORTED_SPARSE_MATRIX_TYPES)} sparse encodings are supported.")
                 continue
             elif matrix_format == "unknown":
-                self.errors.append(f"Unknown encoding for matrix {x_name}. Please ensure it is either a dense array or one of {','.join(SUPPORTED_SPARSE_MATRIX_TYPES)} sparse encodings.")
+                self.errors.append(f"Unknown encoding for matrix {x_name}. {ERROR_SUFFIX_SPARSE_FORMAT}")
                 continue
 
             # It seems silly to perform this test for 'coo' and 'csc' formats,
@@ -1219,7 +1221,7 @@ def _has_valid_raw(self, force: bool = False) -> bool:
 
             matrix_format = get_matrix_format(x)
             if matrix_format == "unknown":
-                self.errors.append(f"Unknown encoding for matrix {xloc}. Please ensure it is either a dense array or one of {','.join(SUPPORTED_SPARSE_MATRIX_TYPES)} sparse encodings.")
+                self.errors.append(f"Unknown encoding for matrix {xloc}. {ERROR_SUFFIX_SPARSE_FORMAT}")
                 self._raw_layer_exists = False
                 return self._raw_layer_exists
 

cellxgene_schema_cli/tests/test_schema_compliance.py

@@ -2225,7 +2225,7 @@ def test_uns_bool_allowed(self, validator_with_adata):
         assert validator.errors == []
 
     def test_uns_scipy_matrices_cannot_be_empty(self, validator_with_adata):
-        validator = validator_with_adata
+        validator: Validator = validator_with_adata
 
         validator.adata.uns["test"] = scipy.sparse.csr_matrix([[1]], dtype=int)
         validator.validate_adata()

cellxgene_schema_cli/tests/test_validate.py

@@ -18,6 +18,7 @@
     ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_REQUIRED,
     SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE,
     SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE_VISIUM_11MM,
+    ERROR_SUFFIX_SPARSE_FORMAT,
     Validator,
     validate,
 )
@@ -1276,7 +1277,10 @@ def test_has_valid_raw(self, data, matrix_format, expected_result):
 
     @mock.patch("cellxgene_schema.validate.get_matrix_format", return_value="unknown")
     def test_has_valid_raw_with_unknown_format(self, mock_get_matrix_format):
+        # a matrix with unknown format should be invalid
         data = np.array([[1, 2, 3], [4, 5, 6]], dtype=np.float32)
         validator = self.create_validator(data, "unknown")
-        with pytest.raises(AssertionError):
-            validator._has_valid_raw()
+        assert validator._has_valid_raw() is False
+        assert validator.errors == [
+            f'Unknown encoding for matrix X. {ERROR_SUFFIX_SPARSE_FORMAT}'
+        ]