def test_setup_fail():
with patch.object(SetupAMR, "__init__", lambda x: None):
amr_obj = SetupAMR()
amr_obj.contigs = f"{test_folder / 'batch_fail.txt'}"
amr_obj.prefix = ''
amr_obj.jobs = 16
amr_obj.species = ''
amr_obj.logger = logging.getLogger(__name__)
T = collections.namedtuple(
'T', ['run_type', 'input', 'prefix', 'jobs', 'organism'])
input_data = T('batch', amr_obj.contigs, amr_obj.prefix, amr_obj.jobs,
amr_obj.species)
with pytest.raises(SystemExit):
amr_obj.setup()
def run_pipeline(args):
P = SetupAMR(args)
input_data = P.setup()
A = RunFinder(input_data)
amr_data = A.run()
C = Collate(amr_data)
collated_data = C.run()
def test_setup_contigs():
with patch.object(SetupAMR, "__init__", lambda x: None):
amr_obj = SetupAMR()
amr_obj.contigs = f"{test_folder / 'contigs.fa'}"
amr_obj.prefix = 'somename'
amr_obj.jobs = 16
amr_obj.species = ''
amr_obj.identity = ''
amr_obj.logger = logging.getLogger(__name__)
T = collections.namedtuple(
'T',
['run_type', 'input', 'prefix', 'jobs', 'organism', 'identity'])
input_data = T('assembly', amr_obj.contigs, amr_obj.prefix,
amr_obj.jobs, amr_obj.species, amr_obj.identity)
assert amr_obj.setup() == input_data