lint

Author: rxu17

genie_registry/bed.py

@@ -715,4 +715,4 @@ def _validate(self, beddf):
             total_error += error
             warning += warn
 
-        return (total_error, warning)
+        return (total_error, warning)

genie_registry/clinical.py

@@ -1336,4 +1336,4 @@ def _cross_validate(self, clinicaldf) -> tuple:
 
         errors = errors_assay + errors_bed
         warnings = warnings_assay + warnings_bed
-        return errors, warnings
+        return errors, warnings

genie_registry/cna.py

@@ -243,4 +243,4 @@ def _validate(self, cnvDF, nosymbol_check):
                             ",".join(cnvDF["remapped"][duplicated]),
                         )
                     )
-        return (total_error, warning)
+        return (total_error, warning)

genie_registry/mutationsInCis.py

@@ -115,4 +115,4 @@ def _validate(self, mutationInCisDf):
             )
             total_error += error
 
-        return total_error, warning
+        return total_error, warning

tests/test_load.py

@@ -221,7 +221,7 @@ def test_store_database_with_rows_to_update_and_delete(syn):
     ):
         load.store_database(syn, database_synid, all_updates, to_delete_rows)
         patch_get.assert_called_once_with(database_synid)
-        patch_store_rows.assert_called_once_with(values =all_updates)
+        patch_store_rows.assert_called_once_with(values=all_updates)
         patch_delete_rows.assert_called_once_with(df=to_delete_rows)
         patch_info.assert_has_calls(
             [
@@ -253,7 +253,7 @@ def test_store_database_only_rows_to_update(syn):
     ):
         load.store_database(syn, database_synid, all_updates, to_delete_rows)
         patch_get.assert_called_once_with(database_synid)
-        patch_store_rows.assert_called_once_with(values =all_updates)
+        patch_store_rows.assert_called_once_with(values=all_updates)
         patch_delete_rows.assert_not_called()
         patch_info.assert_called_once_with(
             f"Upserting {len(all_updates)} rows from {mock_database_ent.name} table"
@@ -323,16 +323,32 @@ def test_that_update_table_has_expected_calls(
     syn, cols_subset, to_delete, subsetted_data
 ):
     test_table_synid = "synZZZ"
-    test_data = pd.DataFrame({"ROW_ID": ["1"], "ROW_VERSION": ["1"], "CENTER": ["test-center"], "data": [123]})
-    test_new_data = pd.DataFrame({"ROW_ID": ["1"], "ROW_VERSION": ["1"], "CENTER": ["test-center"], "data": [123]})
+    test_data = pd.DataFrame(
+        {
+            "ROW_ID": ["1"],
+            "ROW_VERSION": ["1"],
+            "CENTER": ["test-center"],
+            "data": [123],
+        }
+    )
+    test_new_data = pd.DataFrame(
+        {
+            "ROW_ID": ["1"],
+            "ROW_VERSION": ["1"],
+            "CENTER": ["test-center"],
+            "data": [123],
+        }
+    )
 
     mock_database_ent = Mock()
     mock_database_ent.primaryKey = "PRIMARY_KEY"
     mock_database = Mock()
 
     with (
         patch.object(syn, "get", return_value=mock_database_ent),
-        patch("synapseclient.models.mixins.table_components.QueryMixin.query_async", return_value=test_data
+        patch(
+            "synapseclient.models.mixins.table_components.QueryMixin.query_async",
+            return_value=test_data,
         ) as patch_table_query,
         patch.object(load, "_update_table") as patch__update_table,
     ):