def test_is_bam_compression_possible_no_bam(crunchy_config_dict, bam_path):
"""Test bam_compression_possible for non-existing BAM"""
# GIVEN a bam path to non existing file and a crunchy api
crunchy_api = CrunchyAPI(crunchy_config_dict)
# WHEN calling test_bam_compression_possible
result = crunchy_api.is_bam_compression_possible(bam_path=bam_path)
# THEN this should return False
assert not result
def test_is_bam_compression_possible(crunchy_config_dict, crunchy_test_dir):
"""Test bam_compression_possible compressable BAM"""
# GIVEN a bam path to existing file and a crunchy api
crunchy_api = CrunchyAPI(crunchy_config_dict)
bam_path = crunchy_test_dir / "file.bam"
bam_path.touch()
# WHEN calling test_bam_compression_possible
result = crunchy_api.is_bam_compression_possible(bam_path=bam_path)
# THEN this will return True
assert result
def test_is_bam_compression_possible_cram_done(crunchy_config_dict,
crunchy_test_dir,
mock_bam_to_cram, mocker):
"""Test bam_compression_possible for existing compression"""
# GIVEN a bam path to a existing file and a crunchy api
mocker.patch.object(CrunchyAPI,
"bam_to_cram",
side_effect=mock_bam_to_cram)
crunchy_api = CrunchyAPI(crunchy_config_dict)
bam_path = crunchy_test_dir / "file.bam"
bam_path.touch()
# WHEN calling test_bam_compression_possible when cram_compression is done
crunchy_api.bam_to_cram(bam_path=bam_path, dry_run=False, ntasks=1, mem=2)
result = crunchy_api.is_bam_compression_possible(bam_path=bam_path)
# THEN this should return False
assert not result