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)
