class DefaultArgsParser:
def __init__(self, description):
self.parser = ArgumentParser(description=description)
self.parser.add_argument('-u', '--url', dest='fc_url', action='store', required=False,
help='If set, this will override which api is used (default is https://api.firecloud.org/api)')
def __getattr__(self, attr):
return self.parser.__getattribute__(attr)
def parse_args(self):
args = self.parser.parse_args()
if args.fc_url:
set_fc_url(args.fc_url)
return args
def parse_args():
r""" Parse the command line arguments """
args = ArgumentParser()
args.add_argument("train",
help="Path from where to read the training file")
args.add_argument("test", help="Path from where to read the test file")
args.add_argument("out", help="Path write the generated labels")
args.add_argument("--smooth",
help="Perform add-1 smoothing",
action="store_true")
args = args.parse_args()
for fld in ["train", "test"]:
path = Path(args.__getattribute__(fld))
if not path.is_file(): raise ValueError(f"Unknown {fld} file {path}")
args.__setattr__(fld, path)
args.out = Path(args.out)
if args.out.exists() and not args.out.is_file():
raise ValueError(
f"Out file \"{args.out}\" appears not to be a file. Cannot overwrite"
)
return args