update raw values error to include requirement

chanzuckerberg · Dec 2, 2024 · b97cc18 · b97cc18
1 parent 8aeced2
commit b97cc18
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Showing 2 changed files with 9 additions and 11 deletions.
diff --git a/cellxgene_schema_cli/cellxgene_schema/validate.py b/cellxgene_schema_cli/cellxgene_schema/validate.py
@@ -36,15 +36,12 @@
 CONDITION_IS_VISIUM_11M = f"'{ASSAY_VISIUM_11M} (Visium CytAssist Spatial Gene Expression, 11mm)"
 CONDITION_IS_SEQV2 = f"'{ASSAY_SLIDE_SEQV2}' (Slide-seqV2)"
 
-CONDITION_IS_VISIUM = "a descendant of 'EFO:0010961' (Visium Spatial Gene Expression)"
-CONDITION_IS_SEQV2 = f"'{ASSAY_SLIDE_SEQV2}' (Slide-seqV2)"
-
-
 ERROR_SUFFIX_SPATIAL = f"obs['assay_ontology_term_id'] is either {CONDITION_IS_VISIUM} or {CONDITION_IS_SEQV2}"
 ERROR_SUFFIX_VISIUM = f"obs['assay_ontology_term_id'] is {CONDITION_IS_VISIUM}"
 ERROR_SUFFIX_VISIUM_11M = f"obs['assay_ontology_term_id'] is {CONDITION_IS_VISIUM_11M}"
 
-ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE = f"{ERROR_SUFFIX_VISIUM} and uns['spatial']['is_single'] is True"
+ERROR_SUFFIX_IS_SINGLE = "uns['spatial']['is_single'] is True"
+ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE = f"{ERROR_SUFFIX_VISIUM} and {ERROR_SUFFIX_IS_SINGLE}"
 ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_FORBIDDEN = f"is only allowed for {ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE}"
 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"
@@ -99,10 +96,10 @@ def visium_and_is_single_true_matrix_size(self) -> Optional[int]:
                 .apply(lambda t: is_ontological_descendant_of(ONTOLOGY_PARSER, t, ASSAY_VISIUM_11M, True))
                 .any()
             ):
-                self._visium_error_suffix = ERROR_SUFFIX_VISIUM_11M
+                self._visium_error_suffix = f"{ERROR_SUFFIX_VISIUM_11M} and {ERROR_SUFFIX_IS_SINGLE}"
                 self._visium_and_is_single_true_matrix_size = VISIUM_11MM_AND_IS_SINGLE_TRUE_MATRIX_SIZE
             elif self._is_visium_including_descendants():
-                self._visium_error_suffix = ERROR_SUFFIX_VISIUM
+                self._visium_error_suffix = f"{ERROR_SUFFIX_VISIUM} and {ERROR_SUFFIX_IS_SINGLE}"
                 self._visium_and_is_single_true_matrix_size = VISIUM_AND_IS_SINGLE_TRUE_MATRIX_SIZE
         return self._visium_and_is_single_true_matrix_size
 

diff --git a/cellxgene_schema_cli/tests/test_schema_compliance.py b/cellxgene_schema_cli/tests/test_schema_compliance.py
@@ -19,6 +19,7 @@
     ERROR_SUFFIX_VISIUM,
     ERROR_SUFFIX_VISIUM_11M,
     ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE,
+    ERROR_SUFFIX_IS_SINGLE,
     SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE,
     SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE_VISIUM_11MM,
     VISIUM_11MM_AND_IS_SINGLE_TRUE_MATRIX_SIZE,
@@ -336,14 +337,14 @@ def test_raw_values__invalid_visium_and_is_single_true_row_length(
         validator.validate_adata()
         if assay_ontology_term_id == ASSAY_VISIUM_11M:
             _errors = [
-                f"ERROR: When {ERROR_SUFFIX_VISIUM_11M}, the raw matrix must be the "
+                f"ERROR: When {ERROR_SUFFIX_VISIUM_11M} and {ERROR_SUFFIX_IS_SINGLE}, the raw matrix must be the "
                 "unfiltered feature-barcode matrix 'raw_feature_bc_matrix'. It must have exactly "
                 f"{validator.visium_and_is_single_true_matrix_size} rows. Raw matrix row count is 2.",
                 "ERROR: Raw data may be missing: data in 'raw.X' does not meet schema requirements.",
             ]
         else:
             _errors = [
-                f"ERROR: When {ERROR_SUFFIX_VISIUM}, the raw matrix must be the "
+                f"ERROR: When {ERROR_SUFFIX_VISIUM} and {ERROR_SUFFIX_IS_SINGLE}, the raw matrix must be the "
                 "unfiltered feature-barcode matrix 'raw_feature_bc_matrix'. It must have exactly "
                 f"{validator.visium_and_is_single_true_matrix_size} rows. Raw matrix row count is 2.",
                 "ERROR: Raw data may be missing: data in 'raw.X' does not meet schema requirements.",
@@ -387,13 +388,13 @@ def test_raw_values__multiple_invalid_in_tissue_errors(
         validator.validate_adata()
         if assay_ontology_term_id == ASSAY_VISIUM_11M:
             assert (
-                validator.errors[0] == f"ERROR: When {ERROR_SUFFIX_VISIUM_11M}, the raw matrix must be the "
+                validator.errors[0] == f"ERROR: When {ERROR_SUFFIX_VISIUM_11M} and {ERROR_SUFFIX_IS_SINGLE}, the raw matrix must be the "
                 "unfiltered feature-barcode matrix 'raw_feature_bc_matrix'. It must have exactly "
                 f"{validator.visium_and_is_single_true_matrix_size} rows. Raw matrix row count is 2."
             )
         else:
             assert (
-                validator.errors[0] == f"ERROR: When {ERROR_SUFFIX_VISIUM}, the raw matrix must be the "
+                validator.errors[0] == f"ERROR: When {ERROR_SUFFIX_VISIUM} and {ERROR_SUFFIX_IS_SINGLE}, the raw matrix must be the "
                 "unfiltered feature-barcode matrix 'raw_feature_bc_matrix'. It must have exactly "
                 f"{validator.visium_and_is_single_true_matrix_size} rows. Raw matrix row count is 2."
             )