def slurp_braindb(run_dir, brain_alternate=None):
"""
Consume braindump file and return it's content as a `dict`.
:param run_dir: [description]
:type run_dir: [type]
:param brain_alternate: [description], defaults to None
:type brain_alternate: [type], optional
:return: [description]
:rtype: [type]
"""
if not run_dir:
raise ValueError("run_dir is required")
bdump = Path(run_dir) / (
"braindump.yml" if brain_alternate is None else brain_alternate
)
if bdump.exists() is False:
# TODO: Remove this except block one backwards compatibility for
# 4.9 is not needed.
cfg = _slurp_braindb(run_dir, brain_alternate)
else:
if bdump.is_file() is False:
raise TypeError("%s is not a valid file" % bdump.resolve())
with bdump.open("r") as fp:
cfg = braindump.load(fp)
cfg = {
k: str(v) if isinstance(v, Path) else v
for k, v in attr.asdict(cfg).items()
}
return cfg
def test_load(s, obj):
fp = io.StringIO(s)
b = load(fp)
assert isinstance(b, Braindump)
for k, v in obj.items():
assert k in fields
assert isinstance(getattr(b, k), fields[k].type)
assert isinstance(getattr(b, k), fields[k].type)
def _get_braindump(submit_dir: str):
try:
with (Path(submit_dir) / "braindump.yml").open("r") as f:
bd = braindump.load(f)
except FileNotFoundError:
raise WorkflowInstanceError(
"Unable to load braindump file: {}".format(path)
)
return bd
def get_wf_uuid(self):
"Get the workflow UUID from the braindump file"
submitdir = self.find_submitdir()
braindump_file_path = os.path.join(submitdir, "braindump.yml")
if not os.path.isfile(braindump_file_path):
raise EMError("braindump.yml not found")
with open(braindump_file_path) as f:
bd = braindump.load(f)
if bd.wf_uuid is None:
raise EMError("wf_uuid not found in braindump.yml")
return bd.wf_uuid