def test_analyze_one(self, mock_parse, L):
fake_isamp = self.gen_fake_isamp()
fake_series = Series('GSE0')
sample_list = [Sample('GSM10', fake_series)]
for __ in sample_list :
__.organism = 'H**o Sapiens'
fake_series.add_passed_sample(__)
mock_parse.return_value = fake_series
self.assertEqual(ppr.analyze_one('GSE0_family.soft.subset', fake_isamp, ['H**o sapiens']),
sample_list)
L.check(('rsempipeline.utils.pre_pipeline_run', 'ERROR',
'Discrepancy for GSE0: 1 GSMs in soft, 2 GSMs in isamp, and only 1 left after intersection.'),)
def test_analyze_one_soft_series_name_not_in_isamp_series_names_list(self, mock_parse, L):
fake_isamp = self.gen_fake_isamp()
fake_series = Series('GSE9999')
mock_parse.return_value = fake_series
self.assertIsNone(ppr.analyze_one('GSE9999_family.soft.subset', fake_isamp, []))
def test_analyze_one_invalid_filename(self):
self.assertIsNone(
ppr.analyze_one('invalid_soft_filename', 'some_fake_isamp', ['']))