fixup: appease pylint

data_pipeline/data_pipeline/config.py

@@ -18,5 +18,6 @@
     for section, option in REQUIRED_CONFIGURATION:
         value = pipeline_config.get(section, option)
         assert value
+# pylint: disable=broad-exception-raised
 except (configparser.NoOptionError, AssertionError) as exc:
     raise Exception(f"Missing required configuration '{section}.{option}'") from exc

data_pipeline/data_pipeline/datasets/ibd/ibd_variant_results.py

@@ -16,10 +16,12 @@ def prepare_variant_results():
         an_case=results.ac_case[0],
         an_ctrl=results.ac_control[0],
     )
-
+
+    # pylint: disable=fixme
     # TODO: I also should do some renaming and filtering here:
     # the three sub-things I have coming in are lowercase, and end in -control
-
+
+    # pylint: disable=broad-exception-raised
     # TODO: also, in gene results I should figure out what is going on with all the
     # bajillion fields I'm returning (0_001_03, etc)
     # need to check the input schema of something like Epi25 vs IBD

data_pipeline/write_results_files.py

@@ -73,6 +73,7 @@ def split_data(row):
 
 def write_data_files(table_path, output_directory, genes=None):
     if output_directory.startswith("gs://"):
+        # pylint: disable=broad-exception-raised
         raise Exception("Cannot write output to Google Storage")
 
     ds = hl.read_table(table_path)