def main():
"""run cptools.job.Job on a yaml file containing arguments"""
parser = argparse.ArgumentParser()
parser.add_argument("-t", "--template", action="store_true")
args, unknown = parser.parse_known_args()
if args.template:
# print out template and exit
template.print_template()
sys.exit(0)
print(
green(
textwrap.dedent("""\
___ ___ _____ ___ ___ _ ___ ___
/ __| _ \_ _/ _ \ / _ \| | / __|_ )
| (__| _/ | || (_) | (_) | |__\__ \/ /
\___|_| |_| \___/ \___/|____|___/___|
""")))
check_arguments()
# parse yaml file into a dictionary
path_to_config = sys.argv[1]
config = parse_config.Config(path_to_config)
pretty_print("parsing config file {}".format(
colours.yellow(path_to_config)))
configure_job(config)
pretty_print("creating SGE script")
make_scripts(config)
pretty_print("DONE!")
def test_create_commands():
config = parse_config.Config(TEST_PATH)
pipeline_loc = os.path.abspath("./tests/example_pipeline.cppipe")
expected = {
"pipeline": pipeline_loc,
"location": "/example/location",
"commands_location": "/home/user",
"job_size": 46,
"channel_dict": None,
}
assert config.create_command_args() == expected
def test_open_yaml():
config = parse_config.Config(TEST_PATH)
config_dict = config.config_dict
assert isinstance(config_dict, dict)
def test_remove_plate():
config = parse_config.Config(TEST_PATH)
assert config.remove_plate == ["plate_1", "plate_2"]
def test_add_plate():
config = parse_config.Config(TEST_PATH)
assert config.add_plate == {
"exp_dir": "/path/to/new/experiment",
"plates": ["plate_3", "plate_4"]
}
def test_chunk():
config = parse_config.Config(TEST_PATH)
assert config.chunk == 46
def test_experiment():
config = parse_config.Config(TEST_PATH)
assert config.experiment == "/path/to/experiment"
def test_check_yaml_args():
with pytest.raises(ValueError):
config = parse_config.Config(TEST_BROKEN)