def test_is_compression_done_spring_new_files(
crunchy_config_dict: dict,
compression_object: CompressionData,
spring_metadata_file: Path,
caplog,
):
"""Test if compression is done when FASTQ files have been unpacked
This test should fail since the FASTQ files are new
"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api, and FASTQ paths
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN a existing SPRING file
compression_object.spring_path.touch()
assert compression_object.spring_path.exists()
# GIVEN a existing flag file
metadata_file = compression_object.spring_metadata_path
assert spring_metadata_file == compression_object.spring_metadata_path
assert metadata_file.exists()
# GIVEN that the files where updated less than three weeks ago
update_metadata_date(metadata_file)
with open(metadata_file, "r") as infile:
content: List[Dict[str, str]] = json.load(infile)
for file_info in content:
assert "updated" in file_info
# WHEN checking if SPRING compression is done
result = crunchy_api.is_fastq_compression_done(compression_object)
# THEN result should be False since the updated date < 3 weeks
assert result is False
# THEN assert that correct information is logged
assert "FASTQ files are not old enough" in caplog.text
def test_is_compression_done_no_spring(crunchy_config_dict: dict,
compression_object: CompressionData,
caplog):
"""Test if compression is done when no SPRING archive"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api, and FASTQ paths
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN no SPRING file exists
spring_file = compression_object.spring_path
assert not spring_file.exists()
# WHEN checking if SPRING compression is done
result = crunchy_api.is_fastq_compression_done(compression_object)
# THEN result should be false
assert not result
# THEN assert that the correct message was communicated
assert f"No SPRING file for {compression_object.run_name}" in caplog.text
def test_is_compression_done_no_flag_spring(
crunchy_config_dict: dict, compression_object: CompressionData,
caplog):
"""Test if SPRING compression is done when no metadata file"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api, and FASTQ paths
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN a existing SPRING file
compression_object.spring_path.touch()
assert compression_object.spring_path.exists()
# GIVEN a non existing flag file
assert not compression_object.spring_metadata_path.exists()
# WHEN checking if SPRING compression is done
result = crunchy_api.is_fastq_compression_done(compression_object)
# THEN result should be false
assert not result
# THEN assert that the correct message was communicated
assert "No metadata file found" in caplog.text
def test_is_compression_done(
crunchy_config_dict: dict,
spring_metadata_file: Path,
compression_object: CompressionData,
caplog,
):
"""Test if compression is done when everything is correct"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api, and FASTQ paths
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN no SPRING file exists
compression_object.spring_path.touch()
assert spring_metadata_file == compression_object.spring_metadata_path
assert spring_metadata_file.exists()
# WHEN checking if SPRING compression is done
result = crunchy_api.is_fastq_compression_done(compression_object)
# THEN result should be True
assert result is True
# THEN assert that the correct message was communicated
assert "FASTQ compression is done" in caplog.text
def test_is_compression_done_spring_old_files(
crunchy_config_dict: dict,
compression_object: CompressionData,
spring_metadata_file: Path,
caplog,
):
"""Test if compression is done when FASTQ files are updated a long time ago
The function should return True since files are old
"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api, and FASTQ paths
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN a existing SPRING file
compression_object.spring_path.touch()
assert compression_object.spring_path.exists()
# GIVEN a existing flag file
metadata_file = compression_object.spring_metadata_path
assert spring_metadata_file == compression_object.spring_metadata_path
assert metadata_file.exists()
# GIVEN that the files where updated less than three weeks ago
update_metadata_date(metadata_file)
with open(metadata_file, "r") as infile:
content = json.load(infile)
for file_info in content:
file_info["updated"] = "2019-01-01"
with open(metadata_file, "w") as outfile:
outfile.write(json.dumps(content))
# WHEN checking if SPRING compression is done
result = crunchy_api.is_fastq_compression_done(compression_object)
# THEN result should be True since the updated date > 3 weeks
assert result is True
# THEN assert that correct information is logged
assert "FASTQ compression is done" in caplog.text
def test_is_compression_done_spring(
crunchy_config_dict: dict,
compression_object: CompressionData,
spring_metadata_file: Path,
caplog,
):
"""Test if compression is done when SPRING files exists"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api, and FASTQ paths
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN a existing SPRING file
compression_object.spring_path.touch()
assert compression_object.spring_path.exists()
# GIVEN a existing flag file
assert spring_metadata_file == compression_object.spring_metadata_path
assert compression_object.spring_metadata_path.exists()
# WHEN checking if SPRING compression is done
result = crunchy_api.is_fastq_compression_done(compression_object)
# THEN result should be True
assert result
# THEN assert that the correct message was communicated
assert f"FASTQ compression is done for {compression_object.run_name}" in caplog.text