def test_get_splittable_bgzf(self):
non_gs_metadata_list = [
filesystem.FileMetadata(path, size)
for (path, size) in [('1.vcf', 100), ('2.vcf', 100)]
]
with mock.patch.object(FileSystems,
'match',
return_value=[
filesystem.MatchResult(
'non_gs', non_gs_metadata_list)
]):
self.assertEqual(pipeline_common._get_splittable_bgzf(['non_gs']),
[])
gs_metadata_list = [
filesystem.FileMetadata(path, size)
for (path, size) in [('gs://1.vcf.bgz',
100), ('gs://2.vcf.bgz', 100)]
]
with mock.patch.object(
FileSystems,
'match',
return_value=[filesystem.MatchResult('gs', gs_metadata_list)]):
with mock.patch.object(FileSystems, 'exists', return_value=True):
self.assertEqual(
pipeline_common._get_splittable_bgzf(['index file exists'
]),
['gs://1.vcf.bgz', 'gs://2.vcf.bgz'])
with mock.patch.object(FileSystems, 'exists', return_value=False):
self.assertEqual(
pipeline_common._get_splittable_bgzf(['no index file']),
[])
def test_get_compression_type(self):
vcf_metadata_list = [
filesystem.FileMetadata(path, size)
for (path, size) in [('gs://1.vcf', 100), ('2.vcf', 100)]
]
with mock.patch.object(FileSystems,
'match',
return_value=[
filesystem.MatchResult(
'vcf', vcf_metadata_list)
]):
self.assertEqual(pipeline_common.get_compression_type(['vcf']),
filesystem.CompressionTypes.AUTO)
gzip_metadata_list = [
filesystem.FileMetadata(path, size)
for (path, size) in [('gs://1.vcf.gz', 100), ('2.vcf.gz', 100)]
]
with mock.patch.object(FileSystems,
'match',
return_value=[
filesystem.MatchResult(
'gzip', gzip_metadata_list)
]):
self.assertEqual(pipeline_common.get_compression_type('gzip'),
filesystem.CompressionTypes.GZIP)
mixed_metadata_list = [
filesystem.FileMetadata(path, size)
for (path, size) in [('gs://1.vcf.gz', 100), ('2.vcf', 100)]
]
with mock.patch.object(FileSystems,
'match',
return_value=[
filesystem.MatchResult(
'mixed', mixed_metadata_list)
]):
with self.assertRaises(ValueError):
pipeline_common.get_compression_type('mixed')
