def test_check_init_should_raise_unexpected_library_strategy_exception(
self, mock_dir, accession, experiment_type, version,
result_folder):
mock_dir.return_value = "test"
with pytest.raises(UnexpectedLibraryStrategyException):
sanity_check.SanityCheck(accession, result_folder, experiment_type,
version)
def test_check_qc_not_passed_do_not_raise_exception(
self, accession, experiment_type, version, result_folder):
root_dir = os.path.join(os.path.dirname(__file__), "test_data")
result_dir = os.path.join(root_dir, result_folder)
test_instance = sanity_check.SanityCheck(accession, result_dir,
experiment_type, version)
test_instance.run_quality_control_check()
assert True
def test_coverage_check_succeeds(self, accession, experiment_type, version,
result_folder, result_status):
root_dir = os.path.join(os.path.dirname(__file__), "test_data")
result_dir = os.path.join(root_dir, result_folder)
test_instance = sanity_check.SanityCheck(accession, result_dir,
experiment_type, version,
result_status)
test_instance.run_coverage_check()
assert True
def test_check_file_existence_wgs_v4_v5_results_succeeds(
self, accession, experiment_type, version, result_folder,
result_status):
root_dir = os.path.join(os.path.dirname(__file__), "test_data")
result_dir = os.path.join(root_dir, result_folder)
test_instance = sanity_check.SanityCheck(accession, result_dir,
experiment_type, version,
result_status)
test_instance.check_file_existence()
def test_check_amplicon_v4_results_raise_exception(self, accession,
experiment_type,
version, result_folder):
root_dir = os.path.join(os.path.dirname(__file__), "test_data")
result_dir = os.path.join(root_dir, result_folder)
test_instance = sanity_check.SanityCheck(accession, result_dir,
experiment_type, version)
with pytest.raises(FileNotFoundError):
test_instance.check_file_existence()
def test_coverage_check_should_raise_coverage_check_exception(
self, accession, experiment_type, version, result_folder,
result_status):
root_dir = os.path.join(os.path.dirname(__file__), "test_data")
result_dir = os.path.join(root_dir, result_folder)
test_instance = sanity_check.SanityCheck(accession, result_dir,
experiment_type, version,
result_status)
with pytest.raises(CoverageCheckException):
test_instance.run_coverage_check()
def test_check_file_existence_should_raise_file_not_found_error(
self, accession, experiment_type, version, result_folder,
result_status):
root_dir = os.path.join(os.path.dirname(__file__), "test_data")
result_dir = os.path.join(root_dir, result_folder)
test_instance = sanity_check.SanityCheck(accession, result_dir,
experiment_type, version,
result_status)
with pytest.raises(FileNotFoundError):
test_instance.check_file_existence()
def test_v5_check_qc_not_passed_select_no_qc_config(
self, accession, experiment_type, version, result_folder, caplog):
root_dir = os.path.join(os.path.dirname(__file__), "test_data")
result_dir = os.path.join(root_dir, result_folder)
test_instance = sanity_check.SanityCheck(accession,
result_dir,
experiment_type,
version,
result_status='no_qc')
caplog.set_level(logging.INFO)
assert 'no_qc' in caplog.text
def test_check_amplicon_ssu_v5_results_succeeds(self):
accession = "ERR2237853"
experiment_type = "amplicon"
version = "5.0"
root_dir = os.path.join(os.path.dirname(__file__), "test_data")
result_dir = os.path.join(
root_dir,
"results/2018/01/ERP106131/version_{}/ERR223/003/{}_MERGED_FASTQ".
format(version, accession))
test_instance = sanity_check.SanityCheck(accession,
result_dir,
experiment_type,
version,
result_status='full')
test_instance.check_file_existence()