def test_is_cram_compression_done_no_cram(crunchy_config_dict, bam_path):
"""test cram_compression_done without created CRAM file"""
# GIVEN a crunchy-api, and a bam_path
crunchy_api = CrunchyAPI(crunchy_config_dict)
# WHEN checking if cram compression is done
result = crunchy_api.is_cram_compression_done(bam_path=bam_path)
# THEN result should be false
assert not result
def test_is_cram_compression_done(crunchy_config_dict, compressed_bam):
"""Test cram_compression_done with created CRAM, CRAI, and flag files"""
# GIVEN a crunchy-api, and a bam_path, cram_path, crai_path, and flag_path
crunchy_api = CrunchyAPI(crunchy_config_dict)
bam_path = compressed_bam
# WHEN checking if cram compression is done
result = crunchy_api.is_cram_compression_done(bam_path=bam_path)
# THEN result should be True
assert result
def test_is_cram_compression_done_no_flag(crunchy_config_dict,
compressed_bam_without_flag):
"""test cram_compression_done without created flag file"""
# GIVEN a crunchy-api, and a bam_path, cram_path, crai_path
crunchy_api = CrunchyAPI(crunchy_config_dict)
bam_path = compressed_bam_without_flag
# WHEN checking if cram compression is done
result = crunchy_api.is_cram_compression_done(bam_path=bam_path)
# THEN result should be False
assert not result
def test_cram_compression_before_after(crunchy_config_dict, crunchy_test_dir,
mock_bam_to_cram, mocker):
"""Test cram_compression_done without before and after creating files"""
# GIVEN a crunchy-api, and a bam_path
bam_path = Path(crunchy_test_dir / "file.bam")
mocker.patch.object(CrunchyAPI,
"bam_to_cram",
side_effect=mock_bam_to_cram)
crunchy_api = CrunchyAPI(crunchy_config_dict)
# WHEN calling cram_compression_done on bam_path
result = crunchy_api.is_cram_compression_done(bam_path=bam_path)
# Cram compression is not done
assert not result
# GIVEN created cram, crai, and flag paths
crunchy_api.bam_to_cram(bam_path=bam_path, dry_run=False, ntasks=1, mem=2)
# WHEN calling cram_compression_done on bam_path
result = crunchy_api.is_cram_compression_done(bam_path=bam_path)
# THEN compression is marked as done
assert result