def is_runfolder_done(path: typing.Union[str, pathlib.Path]) -> bool: path = pathlib.Path(path) for name in ("RunParameters.xml", "runParameters.xml"): if (path / name).exists(): markers = runparameters_to_marker_file( parse_runparameters_xml(path / name), path / name) return all((path / marker).exists() for marker in markers) return False # pragma: no cover
def test_runparameters_to_marker_files_m060205(): """Test for file from MiSeq M06205.""" path = "tests/data/run_folder/runParameters-M06205.xml" data = parse_runparameters_xml(path) assert runparameters_to_marker_file(data, path) == ( "Basecalling_Netcopy_complete.txt", "ImageAnalysis_Netcopy_complete.txt", )
def _post_runinfoxml_create_or_update(logger, session, meta): """Actually parse the XML files and apply meta data.""" path = meta["path"] if path.lower().endswith("/runinfo.xml"): logger.info("applying RunInfo.xml meta data from %s" % path) apply_runinfo_metadata(session, parse_runinfo_xml(path), meta["target"]) elif path.lower().endswith("/runparameters.xml"): values = parse_runparameters_xml(path) logger.info("applying runParameters.xml meta data from %s (%d)" % (path, len(values))) apply_runparameters_metadata(session, values, meta["target"]) elif "netcopy_complete" in path.lower(): netcopy_info = parse_netcopy_complete_txt(path) if netcopy_info: logger.info("applying Netcopy_complete meta data from %s" % path) apply_netcopy_complete_metadata(session, netcopy_info, meta["target"])
def test_parse_run_parameters_st_k00106(): """Test for file from HiSeq 4000 ST-K00106.""" data = parse_runparameters_xml("tests/data/run_folder/runParameters-ST-K00106.xml") assert data["%s::scan_number" % RUN_PARAMETERS_AVU_KEY_PREFIX] == "95"
def test_parse_run_parameters_nb502131(): """Test for file from NextSeq NB502131.""" data = parse_runparameters_xml("tests/data/run_folder/RunParameters-NB502131.xml") assert data["%s::run_number" % RUN_PARAMETERS_AVU_KEY_PREFIX] == "93"
def test_parse_run_parameters_mn00157(): """Test for file from MiniSeq MN00157.""" data = parse_runparameters_xml("tests/data/run_folder/RunParameters-MN00157.xml") assert data["%s::run_number" % RUN_PARAMETERS_AVU_KEY_PREFIX] == "67"
def test_parse_run_parameters_m060205(): """Test for file from MiSeq M06205.""" data = parse_runparameters_xml("tests/data/run_folder/runParameters-M06205.xml") assert data["%s::run_number" % RUN_PARAMETERS_AVU_KEY_PREFIX] == "9"
def test_parse_run_parameters_a01077(): """Test for file from NovaSeq A01077.""" data = parse_runparameters_xml("tests/data/run_folder/RunParameters-A01077.xml") assert data["%s::run_number" % RUN_PARAMETERS_AVU_KEY_PREFIX] == "48"
def test_runparameters_to_marker_files_st_k00106(): """Test for file from HiSeq 4000 ST-K00106.""" path = "tests/data/run_folder/runParameters-ST-K00106.xml" data = parse_runparameters_xml(path) assert runparameters_to_marker_file(data, path) == ("RTAComplete.txt",)
def test_runparameters_to_marker_files_nb502131(): """Test for file from NextSeq NB502131.""" path = "tests/data/run_folder/RunParameters-NB502131.xml" data = parse_runparameters_xml(path) assert runparameters_to_marker_file(data, path) == ("RTAComplete.txt",)
def test_runparameters_to_marker_files_mn00157(): """Test for file from MiniSeq MN00157.""" path = "tests/data/run_folder/RunParameters-MN00157.xml" data = parse_runparameters_xml(path) assert runparameters_to_marker_file(data, path) == ("RTAComplete.txt",)
def test_runparameters_to_marker_files_a01077(): """Test for file from NovaSeq A01077.""" path = "tests/data/run_folder/RunParameters-A01077.xml" data = parse_runparameters_xml(path) assert runparameters_to_marker_file(data, path) == ("CopyComplete.txt",)