Fix E722 and do not ignore globally

setup.cfg

@@ -1,9 +1,8 @@
 # flake8 configuration
 [flake8]
 
-# E722: do not use bare 'except'
 # W605: invalid escape sequence '\*'
 # E121: continuation line under-indented for hanging indent
 # E126: continuation line over-indented for hanging indent
 # W503: line break before binary operator
-ignore = E722, W605, E121, E126, W503
+ignore = W605, E121, E126, W503

xena_gdc_etl/gdc.py

@@ -413,16 +413,16 @@ def gdc_check_new(new_file_uuids):
  lambda c: ', '.join({p['project']['project_id']
  for p in c})
  )
- except:
+ except: # noqa: E722
  pass
  df_list.append(df)
  df = pd.concat(df_list, axis=0)
  try:
  df = df.drop('id', axis=1)
- except:
+ except KeyError:
  pass
  try:
  df = df.drop_duplicates()
- except:
+ except: # noqa: E722
  pass
  df.to_csv(sys.stdout, sep='\t', index=False)

xena_gdc_etl/main.py

@@ -32,7 +32,8 @@ def main():
  try:
  assert_frame_equal(df1, df2)
  print('Equal.')
- except: # appeantly AssertionError doesn't catch all
+ # apparently AssertionError doesn't catch all
+ except: # noqa: E722
  print('Not equal.')
  # handle gdc_check_new
  elif options.subcomm == "gdc-check-new":