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import unittest
import re
from createSampleSheet_bcl2fastq import *
class test_sanitize_string(unittest.TestCase):
def testDefault(self):
self.assertEqual(sanitize_string('abc#a$v%c^D&P-'), 'abc_a_v_c_D_P_')
def testOnlySpecialChars(self):
self.assertEqual(sanitize_string('@#$%^&*('), '_')
class test_get_model(unittest.TestCase):
def test_HiseqX(self):
self.assertEqual(get_model('141121_ST-E00107_0356_AH00C3CCXX'), Sequencers.HISEQ_X)
def test_expectError(self):
self.assertNotEqual(get_model('150724_J00121_0017_AH2VYMBBXX'), Sequencers.NEXTSEQ_500)
class test_get_reverse_complement(unittest.TestCase):
def test_happyCase(self):
self.assertEqual(get_reverse_complement('ACTGAATTTT'), 'AAAATTCAGT', 'Reverse complement is faulty')
def test_failingCase(self):
self.assertNotEqual(get_reverse_complement('ACTG'), 'CAGA')
class test_get_flowCell(unittest.TestCase):
def setUp(self):
self.myCode = 'C7GMNANXX'
self.logger = setUpLogger('log/')
configDict = readConfig(self.logger)
self.service = OpenbisServiceFacadeFactory.tryCreate(configDict['openbisUserName'],
configDict['openbisPassword'],
configDict['openbisServer'],
configDict['connectionTimeout'])
self.flowcell, self.containedSamples = get_flowcell('ILLUMINA_FLOW_CELL',
self.myCode, self.service, self.logger)
def test_get_flowCell (self):
self.assertEqual(self.flowcell.getCode(), self.myCode)
self.assertEqual(self.containedSamples.size(), 8)
fcProp = self.flowcell.getProperties()
self.assertEqual(fcProp['SEQUENCER'], 'D00535')
self.flowCellDict = transform_sample_to_dict(self.flowcell)
self.assertEqual(self.flowCellDict['FLOWCELLTYPE'], 'HiSeq Flow Cell v4')
def test_get_contained_sample_properties(self):
self.parentDict, self.samplesPerLaneDict = get_contained_sample_properties(
self.containedSamples, self.service)
self.assertEqual(self.parentDict['BSSE_QGF_34778_C7GMNANXX_1']['BARCODE'], 'GTCCGC')
self.assertEqual(self.parentDict['BSSE_QGF_32285_C7GMNANXX_7']['CONTACT_PERSON_EMAIL'], 'yann.bourgeois@unibas.ch')
self.assertEqual(self.samplesPerLaneDict['2'], 23)
def tearDown(self):
self.service.logout()
self.logger.info('Logged out')
# class test_get_contained_sample_properties(unittest.TestCase):
# def setUp(self):
# self.flowcell = test_get_flowCell.setUp(self)
#
# class test_verify_index_length(test_get_flowCell):
#
# def setUp(self):
# foundFlowCell, containedSamples = test_get_flowCell()
#
#
# def test_verify_index_length(self):
# foundFlowCell
def main():
unittest.main()
if __name__ == '__main__':
main()