def test_validation_failure_for_empty_input_file(self):
with temp_dir.TempDir() as tempdir:
filename = tempdir.create_temp_file(lines=[])
with self.assertRaisesRegexp(ValueError,
'Input file .* is empty.'):
pipeline_common._get_all_patterns(input_pattern=None,
input_file=filename)
def test_validation_failure_for_wrong_pattern_in_input_file(self):
lines = [
'./gcp_variant_transforms/testing/data/vcf/valid-4.0.vcf\n',
'non_existent.vcf\n',
'./gcp_variant_transforms/testing/data/vcf/valid-4.0.vcf\n'
]
with temp_dir.TempDir() as tempdir:
filename = tempdir.create_temp_file(lines=lines)
with self.assertRaisesRegex(
ValueError,
'Input pattern .* from .* did not match any files.'):
pipeline_common._get_all_patterns(input_pattern=None,
input_file=filename)
def test_validation_failure_for_invalid_input_pattern(self):
with self.assertRaisesRegex(
ValueError, 'Input pattern .* did not match any files.'):
pipeline_common._get_all_patterns(
input_pattern='nonexistent_file.vcf', input_file=None)
def _get_pipeline_mode(self, args):
all_patterns = pipeline_common._get_all_patterns(
args.input_pattern, args.input_file)
return pipeline_common.get_pipeline_mode(all_patterns,
args.pipeline_mode)
def test_validation_failure_for_invalid_input_file(self):
with self.assertRaisesRegex(ValueError,
'Input file .* doesn\'t exist'):
pipeline_common._get_all_patterns(
input_pattern=None, input_file='nonexistent_file.vcf')
def _get_pipeline_mode(self, args):
all_patterns = pipeline_common._get_all_patterns(
args.input_pattern, args.input_file)
return pipeline_common.get_pipeline_mode(
all_patterns, args.optimize_for_large_inputs)
