def setUp(self):
self.analysis_output_1 = SnsWESAnalysisOutput(dir = sns_analysis1_dir, id = 'sns_analysis1', sns_config = configs)
# remove the handlers because they are too verbose here
self.analysis_output_1.logger = log.remove_all_handlers(logger = self.analysis_output_1.logger)
self.sns_analysis1_nosettings = SnsWESAnalysisOutput(dir = sns_analysis1_nosettings_dir, id = 'analysis1_nosettings', sns_config = configs, debug = True)
self.sns_analysis1_nosettings.logger = log.remove_all_handlers(logger = self.sns_analysis1_nosettings.logger)
self.sns_analysis1_qsuberrors = SnsWESAnalysisOutput(dir = sns_analysis1_qsuberrors_dir, id = 'sns_analysis1_qsuberrors', sns_config = configs, debug = True)
self.sns_analysis1_qsuberrors.logger = log.remove_all_handlers(logger = self.sns_analysis1_qsuberrors.logger)
self.sns_analysis1_summaryX = SnsWESAnalysisOutput(dir = sns_analysis1_summaryX_dir, id = 'sns_analysis1_summaryX', sns_config = configs, debug = True)
self.sns_analysis1_summaryX.logger = log.remove_all_handlers(logger = self.sns_analysis1_summaryX.logger)
def test_invalid_NextSeq_run1(self):
'''
Missing RunInfo.xml
'''
run_id = '170809_NB501073_0019_AH5FFYBGX3_broke1'
x = NextSeqRun(id=run_id, config=configs)
x.logger = log.remove_all_handlers(logger=x.logger)
self.assertFalse(x.validate(), 'Invalid run passed validations')
def test_valid_NextSeq_run(self):
'''
Test a NextSeq demo run that should be valid
'''
run_id = '170809_NB501073_0019_AH5FFYBGX3'
x = NextSeqRun(id=run_id, config=configs)
# remove the handlers because they are too verbose here
x.logger = log.remove_all_handlers(logger=x.logger)
self.assertTrue(x.validate(), 'Valid run did not pass validations')
def test_invalid_NextSeq_run1(self):
'''
Missing RunInfo.xml
'''
run_id = '170809_NB501073_0019_AH5FFYBGX3_broke1'
samplesheet = os.path.join(
samplesheet_source_dir,
'170809_NB501073_0019_AH5FFYBGX3_broke1-SampleSheet.csv')
x = NextSeqRun(id=run_id, samplesheet=samplesheet, config=configs)
x.logger = log.remove_all_handlers(logger=x.logger)
self.assertFalse(x.validate(), 'Invalid run passed validations')
def test_valid_NextSeq_run(self):
'''
Test a NextSeq demo run that should be valid
'''
run_id = '170809_NB501073_0019_AH5FFYBGX3_notdemultiplexed'
samplesheet = os.path.join(
samplesheet_source_dir,
'170809_NB501073_0019_AH5FFYBGX3_notdemultiplexed-SampleSheet.csv')
x = NextSeqRun(id=run_id, samplesheet=samplesheet, config=configs)
# remove the handlers because they are too verbose here
x.logger = log.remove_all_handlers(logger=x.logger)
self.assertTrue(x.validate(), 'Valid run did not pass validations')
def setUp(self):
self.analysis_item1 = AnalysisItem(id = 'foo')
# remove the handlers because they are too verbose here
self.analysis_item1.logger = log.remove_all_handlers(logger = self.analysis_item1.logger)