Merge pull request #647 from chanzuckerberg/joyce/fix-colors

fix: only validate colors if the key is specified
chanzuckerberg · Sep 26, 2023 · 518d7e6 · 518d7e6
2 parents 40d56c8 + 1aa127d
commit 518d7e6
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Showing 2 changed files with 16 additions and 10 deletions.
diff --git a/cellxgene_schema_cli/cellxgene_schema/validate.py b/cellxgene_schema_cli/cellxgene_schema/validate.py
@@ -695,18 +695,20 @@ def _validate_colors_in_uns_dict(self, uns_dict: dict) -> None:
                     category_mapping[column_name] = df[column_name].nunique()
 
         for column_name, num_unique_vals in category_mapping.items():
-            colors_options = uns_dict.get(f"{column_name}_colors", [])
-            if len(colors_options) < num_unique_vals:
-                self.errors.append(
-                    f"Annotated categorical field {column_name} must have at least {num_unique_vals} color options "
-                    f"in uns[{column_name}_colors]. Found: {colors_options}"
-                )
-            for color in colors_options:
-                if not self._validate_color(color):
+            colors_options = uns_dict.get(f"{column_name}_colors")
+            # If there are no colors specified, that's fine. We only want to validate this field if it's set
+            if colors_options is not None:
+                if len(colors_options) < num_unique_vals:
                     self.errors.append(
-                        f"Color {color} in uns[{column_name}_colors] is not valid. Colors must be a valid hex "
-                        f"code (#08c0ff) or a CSS4 named color"
+                        f"Annotated categorical field {column_name} must have at least {num_unique_vals} color options "
+                        f"in uns[{column_name}_colors]. Found: {colors_options}"
                     )
+                for color in colors_options:
+                    if not self._validate_color(color):
+                        self.errors.append(
+                            f"Color {color} in uns[{column_name}_colors] is not valid. Colors must be a valid hex "
+                            f"code (#08c0ff) or a CSS4 named color"
+                        )
 
     def _validate_color(self, color: str) -> bool:
         css4_named_colors = [

diff --git a/cellxgene_schema_cli/tests/test_schema_compliance.py b/cellxgene_schema_cli/tests/test_schema_compliance.py
@@ -1360,6 +1360,10 @@ def test_deprecated_fields(self):
             ],
         )
 
+    def test_no_colors_should_pass(self):
+        del self.validator.adata.uns["suspension_type_colors"]
+        self.assertTrue(self.validator.validate_adata())
+
     def test_not_enough_color_options(self):
         self.validator.adata.uns["suspension_type_colors"] = ["green"]
         self.validator.validate_adata()