chore: update logging to log by donor id instead (#1150)

chanzuckerberg · Dec 10, 2024 · a6c9086 · a6c9086
1 parent 6de64f6
commit a6c9086
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Showing 2 changed files with 7 additions and 4 deletions.
diff --git a/cellxgene_schema_cli/cellxgene_schema/validate.py b/cellxgene_schema_cli/cellxgene_schema/validate.py
@@ -554,9 +554,10 @@ def is_valid_row(row):
         invalid_rows = ~self.adata.obs.apply(is_valid_row, axis=1)
 
         if invalid_rows.any():
-            invalid_indices = self.adata.obs.index[invalid_rows].tolist()
+            donor_ids = self.adata.obs[donor_id_column].tolist()
+            unique_donor_ids = list(set(donor_ids))
             self.errors.append(
-                f"obs rows with indices {invalid_indices} have invalid genetic_ancestry_* values. All "
+                f"obs rows with donor ids {unique_donor_ids} have invalid genetic_ancestry_* values. All "
                 f"observations with the same donor_id must contain the same genetic_ancestry_* values. If "
                 f"organism_ontolology_term_id is NOT 'NCBITaxon:9606' for Homo sapiens, then all genetic"
                 f"ancestry values MUST be float('nan'). If organism_ontolology_term_id is 'NCBITaxon:9606' "
@@ -959,7 +960,6 @@ def _validate_dataframe(self, df_name: str):
                                 f"Column '{column_name}' in dataframe '{df_name}' contains a category '{category}' with "
                                 f"zero observations. These categories will be removed when `--add-labels` flag is present."
                             )
-                    self._validate_genetic_ancestry()
                 categorical_types = {type(x) for x in column.dtype.categories.values}
                 # Check for columns that have illegal categories, which are not supported by anndata 0.8.0
                 # TODO: check if this can be removed after upgading to anndata 0.10.0
@@ -2058,6 +2058,9 @@ def _deep_check(self):
         # Checks spatial
         self._check_spatial()
 
+        # Validate genetic ancestry
+        self._validate_genetic_ancestry()
+
         # Checks each component
         for component_name, component_def in self.schema_def["components"].items():
             logger.debug(f"Validating component: {component_name}")

diff --git a/cellxgene_schema_cli/tests/test_schema_compliance.py b/cellxgene_schema_cli/tests/test_schema_compliance.py
@@ -1740,7 +1740,7 @@ def test_genetic_ancestry_same_donor_id(self, validator_with_adata):
         validator.adata.obs["genetic_ancestry_South_Asian"] = [0.0, 0.0]
         validator.reset(None, 2)
         validator.validate_adata()
-        assert len(validator.errors) > 0
+        assert len(validator.errors) == 1
 
         # Change the donor id back to two different donor id's. Now, this should pass validation
         validator.adata.obs["donor_id"] = original_donor_id_column