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_prefix_string():
"""
assert True when non-empty string is given
"""
with patch.object(SetupAMR, "__init__", lambda x: None):
amr_obj = SetupAMR()
amr_obj.prefix = "some_isolate"
amr_obj.logger = logging.getLogger(__name__)
assert amr_obj._check_prefix()
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 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
def test_check_run_type_wrong_data():
"""
assert true when error raised because input is wrong shape
"""
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.logger = logging.getLogger(__name__)
with pytest.raises(SystemExit):
amr_obj._get_input_shape()
def test_prefix_empty():
"""
assert True when non-empty string is given
"""
with patch.object(SetupAMR, "__init__", lambda x: None):
amr_obj = SetupAMR()
amr_obj.prefix = ""
amr_obj.logger = logging.getLogger(__name__)
with pytest.raises(SystemExit):
amr_obj._check_prefix()
def test_check_run_type_single():
"""
assert true when a contigs file is provided and batch recorded as assembly
"""
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.logger = logging.getLogger(__name__)
assert amr_obj._get_input_shape() == 'assembly'
def test_check_run_type_batch():
"""
assert true when a tab file is provided with two columns
"""
with patch.object(SetupAMR, "__init__", lambda x: None):
amr_obj = SetupAMR()
amr_obj.contigs = f"{test_folder / 'batch.txt'}"
amr_obj.prefix = ''
amr_obj.logger = logging.getLogger(__name__)
assert amr_obj._get_input_shape() == 'batch'