This is a combination of 2 commits.

Validate that uns values are all > 0 in length

cellxgene_schema_cli/cellxgene_schema/validate.py

@@ -746,7 +746,7 @@ def _validate_dataframe(self, df_name: str):
                         self.warnings.append(column_def["warning_message"])
                     self._validate_column(column, column_name, df_name, column_def)
 
-    def _validate_colors_in_uns_dict(self, uns_dict: dict) -> None:
+    def _validate_uns_dict(self, uns_dict: dict) -> None:
         df = getattr_anndata(self.adata, "obs")
 
         # Mapping from obs column name to number of unique categorical values
@@ -759,6 +759,8 @@ def _validate_colors_in_uns_dict(self, uns_dict: dict) -> None:
                 category_mapping[column_name] = column.nunique()
 
         for key, value in uns_dict.items():
+            if len(value) == 0:
+                self.errors.append(f"uns['{key}'] cannot be an empty value.")
             if key.endswith("_colors"):
                 # 1. Verify that the corresponding categorical field exists in obs
                 column_name = key.replace("_colors", "")
@@ -1284,7 +1286,7 @@ def _deep_check(self):
             elif component_def["type"] == "dict":
                 self._validate_dict(component, component_name, component_def)
                 if component_name == "uns":
-                    self._validate_colors_in_uns_dict(component)
+                    self._validate_uns_dict(component)
             elif component_def["type"] == "annotation_mapping":
                 self._validate_annotation_mapping(component_name, component)
                 if component_name == "obsm":

cellxgene_schema_cli/tests/test_schema_compliance.py

@@ -1631,6 +1631,30 @@ def test_colors_happy_path_no_column_def(self, validator_with_adata):
         validator.adata.obs["test_column"] = validator.adata.obs["test_column"].astype("category")
         validator.adata.uns["test_column_colors"] = numpy.array(["#000000", "#ffffff"])
         assert validator.validate_adata()
+
+    def test_uns_empty_numpy_array(self, validator_with_adata):
+        validator = validator_with_adata
+        validator.adata.uns["log1p"] = numpy.array([])
+        validator.validate_adata()
+        assert validator.errors == ["ERROR: uns['log1p'] cannot be an empty value, found []"]
+
+    def test_uns_empty_python_array(self, validator_with_adata):
+        validator = validator_with_adata
+        validator.adata.uns["log1p"] = []
+        validator.validate_adata()
+        assert validator.errors == ["ERROR: uns['log1p'] cannot be an empty value, found []"]
+
+    def test_uns_empty_string(self, validator_with_adata):
+        validator = validator_with_adata
+        validator.adata.uns["log1p"] = ""
+        validator.validate_adata()
+        assert validator.errors == ["ERROR: uns['log1p'] cannot be an empty value, found """]
+
+    def test_uns_empty_dictionary(self, validator_with_adata):
+        validator = validator_with_adata
+        validator.adata.uns["log1p"] = {}
+        validator.validate_adata()
+        assert validator.errors == ["ERROR: uns['log1p'] cannot be an empty value."]
 
     def test_colors_happy_path_duplicates(self, validator_with_adata):
         validator = validator_with_adata
@@ -1676,6 +1700,7 @@ def test_empty_color_array(self, validator_with_adata):
         validator.adata.uns["suspension_type_colors"] = numpy.array([])
         validator.validate_adata()
         assert validator.errors == [
+            "ERROR: uns['suspension_type_colors'] cannot be an empty value, found []",
             "ERROR: Annotated categorical field suspension_type must have at least 2 color options in uns[suspension_type_colors]. Found: []"
         ]