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', ['']))