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",)
