def parse_standard_calls(cls, parentid, name, calls) -> List[RunJobModel]:
jobs = []
parents: Dict[str, RunJobModel] = {}
for c in calls:
job = cls.parse_standard_call(parentid, name, c)
if job.shard is None:
jobs.append(job)
else:
if job.parent in parents:
parents[job.parent].jobs.append(job)
else:
parents[job.parent] = RunJobModel(
submission_id=job.submission_id,
run_id=job.run_id,
id_=job.parent,
parent=parentid,
jobs=[job],
name=job.name,
status=TaskStatus.PROCESSING,
)
for parent in parents.values():
parent.start = min(j.start for j in parent.jobs)
finishes = [j.finish for j in parent.jobs]
if all(f is not None for f in finishes):
parent.finish = max(finishes)
parent.status = TaskStatus.collapse_states([j.status for j in parent.jobs])
return [*parents.values(), *jobs]
def do_query(args):
status = None
if args.status:
status = TaskStatus(args.status.lower())
name = args.name
tasks = ConfigManager.manager().query_tasks(status=status, name=name)
prepared = [(
wid,
t.status,
t.name,
t.start,
(", ".join(t.labels) if t.labels else ""),
t.outdir,
) for wid, t in tasks.items()]
prepared.sort(key=lambda p: p[3] if p[3] else DateUtil.max())
print(
tabulate.tabulate(
prepared,
headers=[
"TaskID", "status", "name", "start date", "labels", "path"
],
),
file=sys.stdout,
)
def __init__(self, submission_id: str, run_id: str, status: TaskStatus,
date: datetime):
self.submission_id = submission_id
self.run_id = run_id
self.status = status if isinstance(status,
TaskStatus) else TaskStatus(status)
if not isinstance(date, datetime):
date = DateUtil.parse_iso(date)
self.date = date
def __init__(
self,
jid: str,
parentjid: Optional[str],
name: str,
batchid: Optional[str],
shard: Optional[int],
attempt: Optional[int],
container: Optional[str],
status: TaskStatus,
start: Union[str, datetime],
finish: Optional[Union[str, datetime]],
backend: Optional[str],
cached: bool,
stdout: Optional[str],
stderr: Optional[str],
jobs: Optional[list] = None,
):
self.jid = jid
self.parentjid = parentjid
self.status = status if isinstance(status,
TaskStatus) else TaskStatus(status)
self.name = name
self.batchid = batchid
self.shard = None
if shard is not None:
if isinstance(shard, str) and shard.isdigit:
shard = int(shard)
if shard >= 0:
self.shard = shard
self.attempt = None
if attempt is not None:
if isinstance(attempt, str) and attempt.isdigit():
attempt = int(attempt)
if attempt > 1:
self.attempt = attempt
self.container = container
self.backend = backend
self.cached = cached
self.stderr = stderr
self.stdout = stdout
self.start = start
self.finish = finish
if start and isinstance(start, str):
self.start = DateUtil.parse_iso(start)
if finish and isinstance(finish, str):
self.finish = DateUtil.parse_iso(finish)
self.jobs = jobs or None
self.events = None
def do_wait(args):
wids = args.wid
statuses = {}
for wid in wids:
wm = ConfigManager.get_from_path_or_submission_lazy(wid, readonly=True)
Logger.info(f"Waiting for '{wid}' to finish")
status = wm.database.get_uncached_status()
while not status.is_in_final_state():
sleep(2)
status = wm.database.get_uncached_status()
statuses[wid] = (wm.submission_id, status)
Logger.info(
f"Workflow {wid} finished with status: {status.to_string()}")
collapsed_status = TaskStatus.collapse_states(
[s[1] for s in statuses.values()])
rc = collapsed_status.get_exit_code()
Logger.info(
f"All workflows finished with collapsed status {collapsed_status.to_string()}, exiting with rc={rc}"
)
sys.exit(rc)
def add_query_args(parser):
statuses = [v.value for v in TaskStatus.all()]
parser.add_argument("--status", help="workflow status", choices=statuses)
parser.add_argument("--name", help="workflow name")
return parser
def __init__(
self,
id_: str,
submission_id: str,
run_id: str,
parent: Optional[str],
name: str,
batchid: Optional[str] = None,
shard: Optional[int] = None,
attempt: Optional[int] = None,
container: Optional[str] = None,
status: TaskStatus = None,
start: Union[str, datetime] = None,
finish: Optional[Union[str, datetime]] = None,
backend: Optional[str] = None,
cached: bool = None,
stdout: Optional[str] = None,
stderr: Optional[str] = None,
script: Optional[str] = None,
error: Optional[str] = None,
returncode: Optional[str] = None,
memory: Optional[str] = None,
cpu: Optional[str] = None,
analysis: Optional[str] = None,
# Optional
jobs: Optional[list] = None,
lastupdated: Union[str, datetime] = None,
workdir: Optional[str] = None,
):
self.id_ = id_
self.submission_id = submission_id
self.run_id = run_id
self.parent = parent
self.status = status if isinstance(status, TaskStatus) else TaskStatus(status)
self.name = name
self.batchid = batchid
self.shard = None
if shard is not None:
if isinstance(shard, str) and shard.isdigit:
shard = int(shard)
if shard >= 0:
self.shard = shard
self.attempt = None
if attempt is not None:
if isinstance(attempt, str) and attempt.isdigit():
attempt = int(attempt)
if attempt > 1:
self.attempt = attempt
self.container = container
self.backend = backend
self.cached = cached
self.stderr = stderr
self.stdout = stdout
self.error = error
self.returncode = returncode
self.workdir = workdir
self.lastupdated = lastupdated or DateUtil.now()
if isinstance(lastupdated, str):
self.lastupdated = DateUtil.parse_iso(lastupdated)
self.start = start
self.finish = finish
if start and isinstance(start, str):
self.start = DateUtil.parse_iso(start)
if finish and isinstance(finish, str):
self.finish = DateUtil.parse_iso(finish)
self.script = script
self.memory = memory
self.cpu = cpu
self.analysis = analysis
self.jobs: Optional[List[RunJobModel]] = jobs or None
self.events = None