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)