class TestUploadVcfToSamples(TestEPP): def setUp(self): self.epp = UploadVcfToSamples( 'http://server:8080/a_step_uri', 'a_user', 'a_password', self.log_file, 'igmm', file=self.genotype_csv ) self.epp._lims = Mock() self.epp._process = Mock(all_inputs=fake_all_inputs) def test_upload(self): patched_log = patch('EPPs.convert_and_dispatch_genotypes.UploadVcfToSamples.info') patched_generate_vcf = patch('EPPs.convert_and_dispatch_genotypes.GenotypeConversion.generate_vcf') patched_remove = patch('EPPs.convert_and_dispatch_genotypes.remove') exp_log_msgs = ( ('Matching against %s artifacts', 1), ('Matching %s against user sample name %s', 'this', '9504430'), ('Matched and uploaded %s artifacts against %s genotype results', 1, 1), ('%s artifacts did not match', 0), ('%s genotyping results were not used', 0) ) with patched_log as p, patched_generate_vcf, patched_remove: self.epp._run() for m in exp_log_msgs: p.assert_any_call(*m)
def setUp(self): self.epp = UploadVcfToSamples( 'http://server:8080/a_step_uri', 'a_user', 'a_password', self.log_file, 'igmm', file=self.genotype_csv ) self.epp._lims = Mock() self.epp._process = Mock(all_inputs=fake_all_inputs)