def _create_test_instance(self, pipeline_args=None):
# type: (List[str]) -> vep_runner.VepRunner
test_object = vep_runner.VepRunner(
self._mock_service, _ASSEMBLY, _SPECIES, _INPUT_PATTERN,
_OUTPUT_DIR, _VEP_INFO_FIELD, _IMAGE, _CACHE, _NUM_FORK,
pipeline_args or self._get_pipeline_args())
return test_object
def test_make_vep_cache_path(self):
test_instance = self._create_test_instance()
self.assertEqual(test_instance._vep_cache_path, _CACHE)
test_instance = vep_runner.VepRunner(
self._mock_service, _SPECIES, _ASSEMBLY, _INPUT_PATTERN, _OUTPUT_DIR,
_VEP_INFO_FIELD, _IMAGE, '', _NUM_FORK, self._get_pipeline_args(),
None, 30)
self.assertEqual(test_instance._vep_cache_path,
('gs://cloud-lifesciences/vep/'
'vep_cache_homo_sapiens_GRCh38_91.tar.gz'))
test_instance = vep_runner.VepRunner(
self._mock_service, 'mouse', 'mm9', _INPUT_PATTERN, _OUTPUT_DIR,
_VEP_INFO_FIELD, _IMAGE, '', _NUM_FORK, self._get_pipeline_args(),
None, 30)
self.assertEqual(test_instance._vep_cache_path,
('gs://cloud-lifesciences/vep/'
'vep_cache_mouse_mm9_91.tar.gz'))