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_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'