def test_runparameters():
path = os.path.dirname(os.path.abspath(__file__))
k = classes.RunParametersParser(
os.path.join(
path,
'../test_data/150424_ST-E00214_0031_BH2WY7CCXX/runParameters.xml'))
assert (k.data is not None)
def test_run_parameters_file_missing(self):
path = os.path.dirname(os.path.abspath(__file__))
with self.assertRaises(OSError):
parsed_run_parameters = classes.RunParametersParser(
os.path.join(
path, '../test_data/191018_ST-E00214_0031_BH2WY7CCXX/',
'missing_runParameters.xml'))
def test_lane_barcode_file_missing(self):
path = os.path.dirname(os.path.abspath(__file__))
with self.assertRaises(OSError):
parsed_run_parameters = classes.RunParametersParser(os.path.join(
path,
'../test_data/191018_ST-E00214_0031_BH2WY7CCXX/Demultiplexing/',
'Reports/html/H2WY7CCXX/all/all/all/missing_file.html'))
def test_run_parameters_valid_case(self):
path = os.path.dirname(os.path.abspath(__file__))
parsed_run_parameters = classes.RunParametersParser(
os.path.join(path,
'../test_data/150424_ST-E00214_0031_BH2WY7CCXX/',
'runParameters.xml'))
expected_data = {
'RunParameters': {
'Setup': {
'ScannerID': 'ST-E00214',
'FPGADynamicFocusSettings': {
'MaxInitialZJumpHalfUm': '3'
},
'Reads': {
'Read': [{
'IsIndexedRead': 'N',
'NumCycles': '151',
'Number': '1'
}, {
'IsIndexedRead': 'Y',
'NumCycles': '8',
'Number': '2'
}, {
'IsIndexedRead': 'N',
'NumCycles': '151',
'Number': '3'
}]
},
'ReagentKits': {
'Sbs': {
'SbsReagentKit': {
'Prime': 'false',
'IsNew200Cycle': 'true',
'ID': 'Y'
}
},
'Pe': {
'ReagentKit': {
'ID': 'Y'
}
}
},
'TileWidth': '3200',
'TempFolder': 'O:\\Illumina\\HiSeqTemp\\' +
'150424_ST-E00214_0031_BH2WY7CCXX',
'BaseSpaceSettings': {
'Username': None
},
'SelectedSections': {
'Section': {
'Name': 'A_1'
}
},
'ExperimentName': 'H2WY7CCXX'
}
}
}
assert parsed_run_parameters.data == expected_data
def test_run_parameters_file_missing(self):
path = os.path.dirname(os.path.abspath(__file__))
with self.assertRaises(OSError):
parsed_run_parameters = classes.RunParametersParser(
os.path.join(
path, '../test_data/191018_ST-E00214_0031_BH2WY7CCXX/',
'missing_runParameters.xml'))