feat: update validation for uns['spatial']

cellxgene_schema_cli/cellxgene_schema/validate.py

@@ -28,14 +28,14 @@
 
 VISIUM_AND_IS_SINGLE_TRUE_MATRIX_SIZE = 4992
 SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE = 2000
-SPATIAL_HIRES_IMAGE_MAX_DIEMSNION_SIZE_VISIUM_11MM = 4000
+SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE_VISIUM_11MM = 4000
 
 CONDITION_IS_VISIUM = "a descendant of 'EFO:0010961' (Visium Spatial Gene Expression)"
 CONDITION_IS_SEQV2 = f"'{ASSAY_SLIDE_SEQV2}' (Slide-seqV2)"
 
 
-ERROR_SUFFIX_VISIUM = f"obs['assay_ontology_term_id'] is either {CONDITION_IS_VISIUM} or {CONDITION_IS_SEQV2}"
-ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE = f"{ERROR_SUFFIX_VISIUM} and uns['spatial']['is_single'] is True"
+ERROR_SUFFIX_SPATIAL = f"obs['assay_ontology_term_id'] is either {CONDITION_IS_VISIUM} or {CONDITION_IS_SEQV2}"
+ERROR_SUFFIX_VISIUM_AND_IS_SINGLE_TRUE = f"{ERROR_SUFFIX_SPATIAL} and uns['spatial']['is_single'] is True"
 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"
@@ -1474,7 +1474,7 @@ def _validate_spatial_assay_ontology_term_id(self):
         # Validate assay ontology term ids are identical.
         term_count = obs["assay_ontology_term_id"].nunique()
         if term_count > 1:
-            self.errors.append(f"When {ERROR_SUFFIX_VISIUM}" ", all observations must contain the same value.")
+            self.errors.append(f"When {ERROR_SUFFIX_SPATIAL}" ", all observations must contain the same value.")
 
     def _validate_spatial_cell_type_ontology_term_id(self):
         """
@@ -1604,7 +1604,7 @@ def _check_spatial_uns(self):
         uns_spatial = self.adata.uns.get("spatial")
         is_supported_spatial_assay = self._is_supported_spatial_assay()
         if uns_spatial is not None and not is_supported_spatial_assay:
-            self.errors.append(f"uns['spatial'] is only allowed when {ERROR_SUFFIX_VISIUM}")
+            self.errors.append(f"uns['spatial'] is only allowed when {ERROR_SUFFIX_SPATIAL}")
             return
 
         # Exit if we aren't dealing with a supported spatial assay as no further checks are necessary.
@@ -1613,7 +1613,7 @@ def _check_spatial_uns(self):
 
         # spatial is required for supported spatial assays.
         if not isinstance(uns_spatial, dict):
-            self.errors.append("A dict in uns['spatial'] is required when " f"{ERROR_SUFFIX_VISIUM}.")
+            self.errors.append("A dict in uns['spatial'] is required when " f"{ERROR_SUFFIX_SPATIAL}.")
             return
 
         # is_single is required.
@@ -1695,7 +1695,7 @@ def _check_spatial_uns(self):
                 _assay_term = self.adata.obs["assay_ontology_term_id"].values[0]
                 _max_size = SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE
                 if is_ontological_descendant_of(ONTOLOGY_PARSER, _assay_term, "EFO:0022860", True):
-                    _max_size = SPATIAL_HIRES_IMAGE_MAX_DIEMSNION_SIZE_VISIUM_11MM
+                    _max_size = SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE_VISIUM_11MM
                 self._validate_spatial_image_shape("hires", uns_images["hires"], _max_size)
 
             # fullres is optional.

cellxgene_schema_cli/tests/test_validate.py

@@ -15,8 +15,8 @@
     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,
-    SPATIAL_HIRES_IMAGE_MAX_DIEMSNION_SIZE_VISIUM_11MM,
     SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE,
+    SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE_VISIUM_11MM,
     Validator,
     validate,
 )
@@ -781,7 +781,7 @@ def test__validate_images_image_is_shape_error(self, image_name):
         "assay_ontology_term_id, hi_res_size, image_max",
         [
             ("EFO:0022858", 2001, SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE),
-            ("EFO:0022860", 4001, SPATIAL_HIRES_IMAGE_MAX_DIEMSNION_SIZE_VISIUM_11MM),
+            ("EFO:0022860", 4001, SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE_VISIUM_11MM),
         ],
     )
     def test__validate_images_hires_max_dimension_greater_than_error(
@@ -801,11 +801,43 @@ def test__validate_images_hires_max_dimension_greater_than_error(
             f"The largest dimension of uns['spatial'][library_id]['images']['hires'] must be {image_max} pixels, it has a largest dimension of {hi_res_size} pixels."
         ]
 
+    @pytest.mark.parametrize(
+        "assay_ontology_term_id, hi_res_size, size_requirement",
+        [
+            ("EFO:0022858", SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE, SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE),
+            ("EFO:0022858", SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE_VISIUM_11MM, SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE),
+            ("EFO:0022860", SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE, SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE_VISIUM_11MM),
+            (
+                "EFO:0022860",
+                SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE_VISIUM_11MM,
+                SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE_VISIUM_11MM,
+            ),
+        ],
+    )
+    def test__validate_images_hires_max_dimension(self, assay_ontology_term_id, hi_res_size, size_requirement):
+        validator: Validator = Validator()
+        validator._set_schema_def()
+        validator.adata = adata_visium.copy()
+        validator.adata.obs["assay_ontology_term_id"] = assay_ontology_term_id
+        validator.adata.uns["spatial"][visium_library_id]["images"]["hires"] = np.zeros(
+            (1, hi_res_size, 3), dtype=np.uint8
+        )
+
+        # Confirm hires is identified as invalid.
+        validator.reset()
+        validator._check_spatial_uns()
+        if hi_res_size == size_requirement:
+            assert validator.errors == []
+        else:
+            assert validator.errors == [
+                f"The largest dimension of uns['spatial'][library_id]['images']['hires'] must be {size_requirement} pixels, it has a largest dimension of {hi_res_size} pixels."
+            ]
+
     @pytest.mark.parametrize(
         "assay_ontology_term_id, hi_res_size, image_max",
         [
             ("EFO:0022858", 1999, SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE),
-            ("EFO:0022860", 3999, SPATIAL_HIRES_IMAGE_MAX_DIEMSNION_SIZE_VISIUM_11MM),
+            ("EFO:0022860", 3999, SPATIAL_HIRES_IMAGE_MAX_DIMENSION_SIZE_VISIUM_11MM),
         ],
     )
     def test__validate_images_hires_max_dimension_less_than_error(self, assay_ontology_term_id, hi_res_size, image_max):