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()