def process_run(args: Namespace) -> None:
"""
CLI command for running a study.
:param [Namespace] `args`: parsed CLI arguments
"""
print(banner_small)
filepath: str = verify_filepath(args.specification)
variables_dict: str = parse_override_vars(args.variables)
samples_file: Optional[str] = None
if args.samples_file:
samples_file = verify_filepath(args.samples_file)
# pgen checks
if args.pargs and not args.pgen_file:
raise ValueError(
"Cannot use the 'pargs' parameter without specifying a 'pgen'!")
if args.pgen_file:
verify_filepath(args.pgen_file)
study: MerlinStudy = MerlinStudy(
filepath,
override_vars=variables_dict,
samples_file=samples_file,
dry_run=args.dry,
no_errors=args.no_errors,
pgen_file=args.pgen_file,
pargs=args.pargs,
)
router.run_task_server(study, args.run_mode)
def process_run(args):
"""
CLI command for running a study.
:param `args`: parsed CLI arguments
"""
print(banner_small)
filepath = verify_filepath(args.specification)
variables_dict = parse_override_vars(args.variables)
samples_file = None
if args.samples_file:
samples_file = verify_filepath(args.samples_file)
study = MerlinStudy(
filepath,
override_vars=variables_dict,
samples_file=samples_file,
dry_run=args.dry,
no_errors=args.no_errors,
)
router.run_task_server(study, args.run_mode)
def process_restart(args):
"""
CLI command for restarting a study.
:param `args`: parsed CLI arguments
"""
print(banner_small)
restart_dir = verify_dirpath(args.restart_dir)
filepath = os.path.join(args.restart_dir, "merlin_info", "*.expanded.yaml")
possible_specs = glob.glob(filepath)
if len(possible_specs) == 0:
raise ValueError(
f"'{filepath}' does not match any provenance spec file to restart from."
)
elif len(possible_specs) > 1:
raise ValueError(
f"'{filepath}' matches more than one provenance spec file to restart from."
)
filepath = verify_filepath(possible_specs[0])
LOG.info(f"Restarting workflow at '{restart_dir}'")
study = MerlinStudy(filepath, restart_dir=restart_dir)
router.run_task_server(study, args.run_mode)
