def test_is_spring_decompression_done_all_files_exist_not_updated(
crunchy_config_dict, compression_object, spring_metadata_file, caplog):
"""Test if SPRING decompression is done when FASTQ files are not unarchived
The function should return False since the files has not been updated in the metadata file
"""
caplog.set_level(logging.DEBUG)
# 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 are missing the updated tag
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:
assert "updated" not in file_info
# WHEN checking if SPRING decompression is done
result = crunchy_api.is_spring_decompression_done(compression_object)
# THEN result should be False since all files exists but miss the updated tag
assert result is False
# THEN assert that it was communicated that files have not been updated
assert "Files have not been unarchived" in caplog.text
def test_is_spring_decompression_done_missing_fastq_files(
crunchy_config_dict, compression_object, spring_metadata_file, caplog):
"""Test if SPRING decompression is done when FASTQ files are missing
The function should return False since FASTQ files are missing
"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN that the FASTQ paths 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()
# GIVEN a existing SPRING file
compression_object.spring_path.touch()
# WHEN checking if SPRING decompression is done
result = crunchy_api.is_spring_decompression_done(compression_object)
# THEN result should be False since FASTQ files are missing
assert result is False
# THEN assert that it was communicated that decompression is done
assert "does not exist" in caplog.text
def test_is_spring_decompression_done_empty_metadata_file(
crunchy_config_dict, compression_object, caplog):
"""Test if SPRING decompression is done when SPRING metadata file has no content
The function should return False since the metadata file has no content
"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN that the SPRING metadata file has no content
compression_object.spring_metadata_path.touch()
# WHEN checking if SPRING decompression is done
with pytest.raises(SyntaxError):
# THEN assert that an exception should be raised since the file is malformed
crunchy_api.is_spring_decompression_done(compression_object)
# THEN assert that it was communicated that the content is malformed
assert "Malformed metadata content" in caplog.text
def test_is_spring_decompression_done_missing_metadata_file(
crunchy_config_dict, compression_object, caplog):
"""Test if SPRING decompression is done when SPRING metadata file is missing
The function should return False since no metadata file is found
"""
caplog.set_level(logging.DEBUG)
# GIVEN a crunchy-api
crunchy_api = CrunchyAPI(crunchy_config_dict)
# GIVEN that the SPRING metadata file is missing
assert not compression_object.spring_metadata_path.exists()
# WHEN checking if SPRING decompression is done
result = crunchy_api.is_spring_decompression_done(compression_object)
# THEN result should be False since the metadata file is missing
assert result is False
# THEN assert that it was communicated that files have not been updated
assert "No SPRING metadata file found" in caplog.text
def test_is_spring_decompression_done_all_files_exist(crunchy_config_dict,
compression_object,
spring_metadata_file,
caplog):
"""Test if SPRING decompression is done when FASTQ files are unarchived
The function should return true since both FASTQ files and SPRING files exists and there is an
updated field in the SPRING metadata config.
"""
caplog.set_level(logging.DEBUG)
# 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_done(compression_object)
# THEN result should be True since all files exists and has been updated
assert result is True
# THEN assert that it was communicated that decompression is done
assert f"SPRING decompression is done for run {compression_object.run_name}" in caplog.text