def do_rm(args):
wids = args.wid
for wid in wids:
try:
ConfigManager.get_from_path_or_submission_lazy(
wid, readonly=True).remove_task(wid, keep_output=args.keep)
except Exception as e:
Logger.critical(f"Can't remove {wid}: " + str(e))
def abort_wids(sids: List[str], wait=True):
cm = ConfigManager(db_path=None)
for sid in sids:
try:
row = cm.get_row_for_submission_id_or_path(sid)
WorkflowManager.mark_aborted(row.execution_dir, row.submission_id)
except Exception as e:
Logger.critical(f"Couldn't abort '{sid}': " + str(e))
raise e
if wait:
Logger.info(
"Waiting until completely aborted. This can take up to a few minutes to complete."
)
for sid in sids:
try:
wm = ConfigManager.get_from_path_or_submission_lazy(
sid, readonly=True)
check_attempts = 0
while not wm.database.get_uncached_status().is_in_final_state(
):
time.sleep(1)
check_attempts += 1
if check_attempts % 5 == 0:
Logger.info(
f"Still waiting for '{sid}' to move to final state"
)
except Exception as e:
Logger.critical(
f"Couldn't watch '{sid}' until aborted: {str(e)}")
Logger.info(f"Jobs {' '.join(sids)} should be completely aborted now")
def do_watch(args):
wid = args.wid
refresh = args.refresh
if args.once:
# --once overrides --refresh
refresh = -1
brief = args.brief
monochrome = args.monochrome
wm = ConfigManager.get_from_path_or_submission_lazy(wid, readonly=False)
wm.watch(seconds=refresh, brief=brief, monochrome=monochrome)
def do_resume(args):
# if args.job:
# from os import getcwd
#
# # parse and load the job file
# Logger.info("Specified job file, ignoring all other parameters")
# d = parse_dict(get_file_from_searchname(args.job, getcwd()))
# job = PreparedJob(**d)
# wm = ConfigManager.get_from_path_or_submission_lazy(
# job.execution_dir, readonly=False
# )
#
# else:
wm = ConfigManager.get_from_path_or_submission_lazy(args.wid,
readonly=False)
run_in_background = False
if args.foreground:
run_in_background = False
elif wm.database.workflowmetadata.configuration.run_in_background:
run_in_background = True
wm.start_or_submit(run_in_background=run_in_background)
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 do_pause(args):
wm = ConfigManager.get_from_path_or_submission_lazy(args.wid,
readonly=True)
wm.mark_paused(wm.execution_dir)
def do_rawquery(args):
wid = args.wid
wm = ConfigManager.get_from_path_or_submission_lazy(wid, readonly=True)
with wm.database.with_cursor() as cursor:
result = cursor.execute(args.query).fetchall()
return print(tabulate.tabulate(result))