def test_is_fastq_compression_possible_compression_pending(
crunchy_config_dict: dict, compression_object: CompressionData,
caplog):
"""Test if FASTQ compression is possible when FASTQ compression is pending
This means that there should exist a FASTQ compression flag
"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api, and existing FASTQ paths
crunchy_api = CrunchyAPI(crunchy_config_dict)
compression_object.fastq_first.touch()
compression_object.fastq_second.touch()
# GIVEN that the pending path exists
compression_object.pending_path.touch()
# 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_possible(compression_object)
# THEN result should be False since the compression flag exists
assert result is False
# THEN assert that the correct message was communicated
assert "Compression/decompression is pending for" in caplog.text
def test_is_fastq_compression_possible_spring_exists(
crunchy_config_dict: dict, compression_object: CompressionData,
caplog):
"""Test if FASTQ compression is possible when FASTQ compression is done
This means that the SPRING file exists
"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api, and existing FASTQ paths
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN that the SPRING path exists
compression_object.spring_path.touch()
spring_file = compression_object.spring_path
assert spring_file.exists()
# WHEN checking if SPRING compression is done
result = crunchy_api.is_fastq_compression_possible(compression_object)
# THEN result should be False since the compression flag exists
assert result is False
# THEN assert that the correct message was communicated
assert "SPRING file found" in caplog.text
def test_is_fastq_compression_possible(crunchy_config_dict: dict,
compression_object: CompressionData,
caplog):
"""Test if FASTQ compression is possible under correct circumstances
This means that there should exist FASTQ files but no SPRING archive
"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api, and existing FASTQ paths
crunchy_api = CrunchyAPI(crunchy_config_dict)
compression_object.fastq_first.touch()
compression_object.fastq_second.touch()
# 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_possible(compression_object)
# THEN result should be True
assert result is True
# THEN assert that the correct message was communicated
assert "FASTQ compression is possible" in caplog.text