lint checks

chanzuckerberg · Jan 30, 2025 · 9c2c812 · 9c2c812
1 parent ff7727c
commit 9c2c812
Show file tree

Hide file tree

Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/cellxgene_schema_cli/cellxgene_schema/validate.py b/cellxgene_schema_cli/cellxgene_schema/validate.py
@@ -56,7 +56,9 @@
 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_NOTNULL = f"cannot have missing or NaN values when {ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE}"
+ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_NOTNULL = (
+    f"cannot have missing or NaN values when {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)})"
@@ -1787,12 +1789,14 @@ def _validate_spatial_tissue_position(self, tissue_position_name: str, min: int,
             # report column is required
             self.errors.append(f"obs['{tissue_position_name}'] {ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_REQUIRED}.")
             return
-        elif ((
+        elif (
+            (
                 self.adata.obs["assay_ontology_term_id"]
                 .apply(lambda t: is_ontological_descendant_of(ONTOLOGY_PARSER, t, ASSAY_VISIUM, False))
                 .astype(bool)
             )
-            & (self.adata.obs[tissue_position_name].isnull())).any():
+            & (self.adata.obs[tissue_position_name].isnull())
+        ).any():
             # report column has bad values
             self.errors.append(f"obs['{tissue_position_name}'] {ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_NOTNULL}.")
             return

diff --git a/cellxgene_schema_cli/tests/test_validate.py b/cellxgene_schema_cli/tests/test_validate.py
@@ -16,8 +16,8 @@
     ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE,
     ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_FORBIDDEN,
     ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_IN_TISSUE_0,
-    ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_REQUIRED,
     ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_NOTNULL,
+    ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE_REQUIRED,
     SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE,
     SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE_VISIUM_11MM,
     Validator,