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 setUp(self):
self.tmpdir = tempfile.mkdtemp()
self.merlin_spec_filepath = os.path.join(self.tmpdir, "basic_ensemble.yaml")
with open(self.merlin_spec_filepath, "w+") as _file:
_file.write(MERLIN_SPEC)
self.study = MerlinStudy(self.merlin_spec_filepath)
def test_column_label_conflict(self):
"""
If there is a common key between Maestro's global.parameters and
Merlin's sample/column_labels, an error should be raised.
"""
merlin_spec_conflict: str = os.path.join(
self.tmpdir, "basic_ensemble_conflict.yaml")
with open(merlin_spec_conflict, "w+") as _file:
_file.write(MERLIN_SPEC_CONFLICT)
# for some reason flake8 doesn't believe variables instantiated inside the try/with context are assigned
with pytest.raises(ValueError):
study_conflict: MerlinStudy = MerlinStudy(merlin_spec_conflict)
assert not study_conflict, "study_conflict completed construction without raising a ValueError."
def test_no_env(self):
"""
A MerlinStudy should be able to support a MerlinSpec that does not contain
the optional `env` section.
"""
merlin_spec_no_env_filepath = os.path.join(
self.tmpdir, "basic_ensemble_no_env.yaml")
with open(merlin_spec_no_env_filepath, "w+") as _file:
_file.write(MERLIN_SPEC_NO_ENV)
try:
study_no_env = MerlinStudy(merlin_spec_no_env_filepath)
except Exception as e:
assert False
def test_column_label_conflict(self):
"""
If there is a common key between Maestro's global.parameters and
Merlin's sample/column_labels, an error should be raised.
"""
merlin_spec_conflict = os.path.join(self.tmpdir, "basic_ensemble_conflict.yaml")
with open(merlin_spec_conflict, "w+") as _file:
_file.write(MERLIN_SPEC_CONFLICT)
try:
study_conflict = MerlinStudy(merlin_spec_conflict)
except ValueError:
pass
else:
assert False
def test_no_env(self):
"""
A MerlinStudy should be able to support a MerlinSpec that does not contain
the optional `env` section.
"""
merlin_spec_no_env_filepath: str = os.path.join(
self.tmpdir, "basic_ensemble_no_env.yaml")
with open(merlin_spec_no_env_filepath, "w+") as _file:
_file.write(MERLIN_SPEC_NO_ENV)
try:
study_no_env: MerlinStudy = MerlinStudy(
merlin_spec_no_env_filepath)
bad_type_err: str = f"study_no_env failed construction, is type {type(study_no_env)}."
assert isinstance(study_no_env, MerlinStudy), bad_type_err
except Exception as e:
assert False, f"Encountered unexpected exception, {e}, for viable MerlinSpec without optional 'env' section."
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)