def main():
"""run cptools.job.Job on a yaml file containing arguments"""
# check arguments
if len(sys.argv) < 2:
msg = "missing argument: need to pass a config file as an argument"
raise ValueError(msg)
config_file = sys.argv[1]
if os.path.isfile(config_file) is False:
msg = "'{}' is not a file".format(config_file)
raise ValueError(msg)
# parse yaml file into a dictionary
yaml_dict = parse_yaml.open_yaml(config_file)
# check the arguments in the yaml file are recognised
parse_yaml.check_yaml_args(yaml_dict)
# parse all possible commands
experiment_args = parse_yaml.experiment(yaml_dict)
chunk_args = parse_yaml.chunk(yaml_dict)
remove_plate_args = parse_yaml.remove_plate(yaml_dict)
add_plate_args = parse_yaml.add_plate(yaml_dict)
create_command_args = parse_yaml.create_commands(yaml_dict)
# some of the optional arguments might be none, in which case don't
# pass them as arguments to the methods
jobber = job.Job()
if experiment_args is not None:
jobber.add_experiment(**experiment_args)
if remove_plate_args is not None:
jobber.remove_plate(**remove_plate_args)
if add_plate_args is not None:
jobber.add_plate(**add_plate_args)
if chunk_args is not None:
jobber.chunk(**chunk_args)
jobber.create_commands(**create_command_args)
def test_add_plate():
"""cptools2.parse_yaml.add_plate(yaml_dict)"""
yaml_dict = parse_yaml.open_yaml(TEST_PATH)
output = parse_yaml.add_plate(yaml_dict)
assert output == {
"exp_dir": "/path/to/new/experiment",
"plates": ["plate_3", "plate_4"]
}
def test_create_commands():
"""cptools2.parse_yaml.create_commands(yaml_dict)"""
yaml_dict = parse_yaml.open_yaml(TEST_PATH)
output = parse_yaml.create_commands(yaml_dict)
assert output == {
"pipeline": "/path/to/example_pipeline.cppipe",
"location": "/example/location",
"commands_location": "/home/user"
}
def test_open_yaml():
"""cptools2.parse_yaml.open_yaml(path_to_yaml)"""
yaml_dict = parse_yaml.open_yaml(TEST_PATH)
assert isinstance(yaml_dict, dict)
def test_remove_plate():
"""cptools2.parse_yaml.remove_plate(yaml_dict):"""
yaml_dict = parse_yaml.open_yaml(TEST_PATH)
output = parse_yaml.remove_plate(yaml_dict)
assert output == {"plates": ["plate_1", "plate_2"]}
def test_chunk():
"""cptools2.parse_yaml.chunk(yaml_dict)"""
yaml_dict = parse_yaml.open_yaml(TEST_PATH)
output = parse_yaml.chunk(yaml_dict)
assert output == {"job_size": 46}
def test_experiment():
"""cptools2.parse_yaml.experiment(yaml_dict)"""
yaml_dict = parse_yaml.open_yaml(TEST_PATH)
output = parse_yaml.experiment(yaml_dict)
assert output == {"exp_dir": "/path/to/experiment"}
def test_check_yaml_args():
"""cptools2.parse_yaml.check_yaml_args(yaml_dict)"""
yaml_dict = parse_yaml.open_yaml(TEST_BROKEN)
with pytest.raises(ValueError):
parse_yaml.check_yaml_args(yaml_dict)