def test_samplesheet_missing(self):
path = os.path.dirname(os.path.abspath(__file__))
with self.assertRaises(OSError):
parsed_sample_sheet = classes.SampleSheetParser(
os.path.join(path,
'../test_data/191018_ST-E00214_0031_BH2WY7CCXX/',
'missing_SampleSheet.csv'))
def test_sample_sheet_header_issue(self):
path = os.path.dirname(os.path.abspath(__file__))
with self.assertRaises(RuntimeError):
parsed_sample_sheet = classes.SampleSheetParser(
os.path.join(path,
'../test_data/191018_ST-E00214_0031_BH2WY7CCXX/',
'SampleSheet_with_bad_header.csv'))
def test_sample_sheet_valid_case(self):
path = os.path.dirname(os.path.abspath(__file__))
parsed_sample_sheet = classes.SampleSheetParser(
os.path.join(
path,
'../test_data/150424_ST-E00214_0031_BH2WY7CCXX/',
'SampleSheet.csv'))
expected_header = {
'Investigator Name': 'Christian Natanaelsson',
'Date': '2015-04-23',
'Experiment Name': 'H2WY7CCXX'
}
expected_first_row_data = {
'Lane': '1',
'Project': 'J_Lundeberg_14_24',
'SampleID': 'Sample_P1775_147',
'SampleName': 'P1775_147',
'SamplePlate': 'FCB_150423',
'SampleWell': '1:1',
'index': 'GAATTCGT'
}
self.assertEqual(parsed_sample_sheet.header, expected_header)
self.assertEqual(parsed_sample_sheet.settings, {})
self.assertEqual(parsed_sample_sheet.reads, [])
self.assertEqual(parsed_sample_sheet.data[0], expected_first_row_data)
def test_samplesheet():
path = os.path.dirname(os.path.abspath(__file__))
k = classes.SampleSheetParser(
os.path.join(
path,
'../test_data/150424_ST-E00214_0031_BH2WY7CCXX/SampleSheet.csv'))
assert (k.header is not None)
assert (k.settings is not None)
assert (k.reads is not None)
def test_sample_sheet_valid_case(self):
path = os.path.dirname(os.path.abspath(__file__))
parsed_sample_sheet = classes.SampleSheetParser(
os.path.join(path,
'../test_data/150424_ST-E00214_0031_BH2WY7CCXX/',
'SampleSheet.csv'))
expected_header = {
'Investigator Name': 'Christian Natanaelsson',
'Date': '2015-04-23',
'Experiment Name': 'H2WY7CCXX'
}
assert parsed_sample_sheet.header == expected_header
assert parsed_sample_sheet.settings == []
assert parsed_sample_sheet.reads == []