def test_is_spring_decompression_possible_no_fastq(
crunchy_config_dict: dict, compression_object: CompressionData,
caplog):
"""Test if decompression is possible when there are no FASTQ files
The function should return true since there are no FASTQ files
"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN a existing SPRING file
compression_object.spring_path.touch()
assert compression_object.spring_path.exists()
# GIVEN that there are no fastq files
compression_object.fastq_first.unlink()
compression_object.fastq_second.unlink()
assert not compression_object.fastq_first.exists()
assert not compression_object.fastq_second.exists()
# WHEN checking if SPRING compression is done
result = crunchy_api.is_spring_decompression_possible(compression_object)
# THEN result should be True since there are no fastq files
assert result is True
# THEN assert the correct information is communicated
assert "Decompression is possible" in caplog.text
def test_is_spring_decompression_possible(crunchy_config_dict,
compression_object,
spring_metadata_file, caplog):
"""Test if SPRING decompression is possible
The function should return True since there is a SPRING file and no FASTQ files
"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN a existing SPRING file
compression_object.spring_path.touch()
# GIVEN that the FASTQ files does not exist
compression_object.fastq_first.unlink()
compression_object.fastq_second.unlink()
assert not compression_object.fastq_first.exists()
assert not compression_object.fastq_second.exists()
# WHEN checking if SPRING decompression is done
result = crunchy_api.is_spring_decompression_possible(compression_object)
# THEN result should be True since decompression is possible
assert result is True
# THEN assert that it was communicated that compression is pending
assert "Decompression is possible" in caplog.text
def test_is_spring_decompression_possible(crunchy_config_dict,
compression_object,
spring_metadata_file):
"""Test if SPRING decompression is possible when decompression is already done
The function should return False since decompression is already done
"""
# GIVEN a crunchy-api
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN that the FASTQ paths exists
compression_object.fastq_first.touch()
compression_object.fastq_second.touch()
# GIVEN a existing SPRING file
compression_object.spring_path.touch()
# GIVEN a existing flag file
# GIVEN that the files have an updated tag
old_date = "2019-01-01"
with open(spring_metadata_file, "r") as infile:
content = json.load(infile)
# GIVEN that the files where updated more than three weeks ago
for file_info in content:
file_info["updated"] = old_date
with open(spring_metadata_file, "w") as outfile:
outfile.write(json.dumps(content))
# WHEN checking if SPRING decompression is done
result = crunchy_api.is_spring_decompression_possible(compression_object)
# THEN result should be False since decompression is already done
assert result is False
def test_is_spring_decompression_possible_no_spring(
crunchy_config_dict: dict, compression_object: CompressionData,
caplog):
"""Test if decompression is possible when there are no SPRING archive
The function should return False since there is no SPRING archive
"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api, and FASTQ paths
crunchy_api = CrunchyAPI(crunchy_config_dict)
# WHEN checking if SPRING compression is done
result = crunchy_api.is_spring_decompression_possible(compression_object)
# THEN result should be False since there is no SPRING archive
assert result is False
# THEN assert the correct information is communicated
assert "No SPRING file found" in caplog.text
def test_is_spring_decompression_possible_decompression_pending(
crunchy_config_dict, compression_object, spring_metadata_file, caplog):
"""Test if SPRING decompression is possible when decompression is pending
The function should return False since decompression is pending
"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN a existing pending file
compression_object.pending_path.touch()
# WHEN checking if SPRING decompression is done
result = crunchy_api.is_spring_decompression_possible(compression_object)
# THEN result should be False since decompression is pending
assert result is False
# THEN assert that it was communicated that compression is pending
assert "decompression is pending" in caplog.text
def test_is_spring_decompression_possible_fastq(
crunchy_config_dict: dict, compression_object: CompressionData,
caplog):
"""Test if decompression is possible when there are existing FASTQ files
The function should return False since there are decompressed FASTQ files
"""
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()
# GIVEN that the FASTQ files exists
compression_object.fastq_first.touch()
compression_object.fastq_second.touch()
# WHEN checking if SPRING decompression is possible
result = crunchy_api.is_spring_decompression_possible(compression_object)
# THEN result should be False since the FASTQ files already exists
assert result is False
# THEN assert the correct information is communicated
assert "FASTQ files already exists" in caplog.text