def main():
global syn
parser = argparse.ArgumentParser()
parser.add_argument("-u", "--user", help="UserName", default=None)
parser.add_argument("-p", "--password", help="Password", default=None)
parser.add_argument("--notifications", help="Send error notifications to challenge admins", action="store_true", default=False)
parser.add_argument("--send-messages", help="Send error confirmation and validation errors to participants", action="store_true", default=False)
parser.add_argument("--dry-run", help="Perform the requested command without updating anything in Synapse", action="store_true", default=False)
parser.add_argument("--debug", help="Show verbose error output from Synapse API calls", action="store_true", default=False)
subparsers = parser.add_subparsers(title="subcommand")
parser_list = subparsers.add_parser('list', help="List submissions to an evaluation or list evaluations")
parser_list.add_argument("evaluation", metavar="EVALUATION-ID", nargs='?', default=None)
parser_list.add_argument("--challenge-project", "--challenge", "--project", metavar="SYNAPSE-ID", default=None)
parser_list.add_argument("-s", "--status", default=None)
parser_list.add_argument("--all", action="store_true", default=False)
parser_list.set_defaults(func=command_list)
parser_status = subparsers.add_parser('status', help="Check the status of a submission")
parser_status.add_argument("submission")
parser_status.set_defaults(func=command_check_status)
parser_reset = subparsers.add_parser('reset', help="Reset a submission to RECEIVED for re-scoring (or set to some other status)")
parser_reset.add_argument("submission", metavar="SUBMISSION-ID", type=int, nargs='*', help="One or more submission IDs, or omit if using --rescore-all")
parser_reset.add_argument("-s", "--status", default='RECEIVED')
parser_reset.add_argument("--rescore-all", action="store_true", default=False)
parser_reset.set_defaults(func=command_reset)
parser_validate = subparsers.add_parser('validate', help="Validate all RECEIVED submissions to an evaluation")
parser_validate.add_argument("evaluation", metavar="EVALUATION-ID", nargs='?', default=None, )
parser_validate.add_argument("--all", action="store_true", default=False)
parser_validate.add_argument("--send-validation-passed-message", help="Send confirmation email to participants when a submission passes validation", action="store_true", default=False)
parser_validate.set_defaults(func=command_validate)
parser_score = subparsers.add_parser('score', help="Score all VALIDATED submissions to an evaluation")
parser_score.add_argument("evaluation", metavar="EVALUATION-ID", nargs='?', default=None)
parser_score.add_argument("--all", action="store_true", default=False)
parser_score.set_defaults(func=command_score)
parser_rank = subparsers.add_parser('rank', help="Rank all SCORED submissions to an evaluation")
parser_rank.add_argument("evaluation", metavar="EVALUATION-ID", default=None)
parser_rank.set_defaults(func=command_rank)
parser_leaderboard = subparsers.add_parser('leaderboard', help="Print the leaderboard for an evaluation")
parser_leaderboard.add_argument("evaluation", metavar="EVALUATION-ID", default=None)
parser_leaderboard.add_argument("--out", default=None)
parser_leaderboard.set_defaults(func=command_leaderboard)
args = parser.parse_args()
print "\n" * 2, "=" * 75
print datetime.utcnow().isoformat()
## Acquire lock, don't run two scoring scripts at once
try:
update_lock = lock.acquire_lock_or_fail('challenge', max_age=timedelta(hours=4))
except lock.LockedException:
print u"Is the scoring script already running? Can't acquire lock."
# can't acquire lock, so return error code 75 which is a
# temporary error according to /usr/include/sysexits.h
return 75
try:
syn = synapseclient.Synapse(debug=args.debug)
if not args.user:
args.user = os.environ.get('SYNAPSE_USER', None)
if not args.password:
args.password = os.environ.get('SYNAPSE_PASSWORD', None)
syn.login(email=args.user, password=args.password)
args.func(args)
except Exception as ex1:
sys.stderr.write('Error in scoring script:\n')
st = StringIO()
traceback.print_exc(file=st)
sys.stderr.write(st.getvalue())
sys.stderr.write('\n')
if args.notifications:
message = error_notification_template.format(message=st.getvalue())
if args.dry_run:
print "Dry Run: error notification:", "Exception while scoring " + ismb_akes_challenge.CHALLENGE_NAME
print message
else:
response = syn.sendMessage(
userIds=ismb_akes_challenge.ADMIN_USER_IDS,
messageSubject="Exception while scoring " + ismb_akes_challenge.CHALLENGE_NAME,
messageBody=message)
print "sent notification: ", unicode(response).encode('utf-8')
finally:
update_lock.release()
print "\ndone: ", datetime.utcnow().isoformat()
print "=" * 75, "\n" * 2
def main():
if conf.CHALLENGE_SYN_ID == "":
sys.stderr.write("Please configure your challenge. See sample_challenge.py for an example.")
global syn
parser = argparse.ArgumentParser()
parser.add_argument("-u", "--user", help="UserName", default=None)
parser.add_argument("-p", "--password", help="Password", default=None)
parser.add_argument("--notifications", help="Send error notifications to challenge admins", action="store_true", default=False)
parser.add_argument("--send-messages", help="Send validation and scoring messages to participants", action="store_true", default=False)
parser.add_argument("--acknowledge-receipt", help="Send confirmation message on passing validation to participants", action="store_true", default=False)
parser.add_argument("--dry-run", help="Perform the requested command without updating anything in Synapse", action="store_true", default=False)
parser.add_argument("--debug", help="Show verbose error output from Synapse API calls", action="store_true", default=False)
parser.add_argument("--threads", help="Number of parallel processes to use for validation and scoring", type=int, default=1)
subparsers = parser.add_subparsers(title="subcommand")
parser_list = subparsers.add_parser('list', help="List submissions to an evaluation or list evaluations")
parser_list.add_argument("evaluation", metavar="EVALUATION-ID", nargs='?', default=None)
parser_list.add_argument("--challenge-project", "--challenge", "--project", metavar="SYNAPSE-ID", default=None)
parser_list.add_argument("-s", "--status", default=None)
parser_list.add_argument("--all", action="store_true", default=False)
parser_list.set_defaults(func=command_list)
parser_status = subparsers.add_parser('status', help="Check the status of a submission")
parser_status.add_argument("submission")
parser_status.set_defaults(func=command_check_status)
parser_reset = subparsers.add_parser('reset', help="Reset a submission to RECEIVED for re-scoring (or set to some other status)")
parser_reset.add_argument("submission", metavar="SUBMISSION-ID", type=int, nargs='*', help="One or more submission IDs, or omit if using --rescore-all")
parser_reset.add_argument("-s", "--status", default='RECEIVED')
parser_reset.add_argument("--rescore-all", action="store_true", default=False)
parser_reset.add_argument("--rescore", metavar="EVALUATION-ID", type=int, nargs='*', help="One or more evaluation IDs to rescore")
parser_reset.set_defaults(func=command_reset)
parser_validate = subparsers.add_parser('validate', help="Validate all RECEIVED submissions to an evaluation")
parser_validate.add_argument("evaluation", metavar="EVALUATION-ID", nargs='?', default=None)
parser_validate.add_argument("--all", action="store_true", default=False)
parser_validate.add_argument("--canCancel", action="store_true", default=False)
parser_validate.set_defaults(func=command_validate)
parser_score = subparsers.add_parser('score', help="Score all VALIDATED submissions to an evaluation")
parser_score.add_argument("evaluation", metavar="EVALUATION-ID", nargs='?', default=None)
parser_score.add_argument("--all", action="store_true", default=False)
parser_score.add_argument("--canCancel", action="store_true", default=False)
parser_score.set_defaults(func=command_score)
parser_rank = subparsers.add_parser('rank', help="Rank all SCORED submissions to an evaluation")
parser_rank.add_argument("evaluation", metavar="EVALUATION-ID", default=None)
parser_rank.set_defaults(func=command_rank)
parser_archive = subparsers.add_parser('archive', help="Archive submissions to a challenge")
parser_archive.add_argument("evaluation", metavar="EVALUATION-ID", default=None)
parser_archive.add_argument("archiveType",metavar="TYPE", choices=["submission","writeup"])
parser_archive.add_argument("destination", metavar="FOLDER-ID", default=None)
parser_archive.add_argument("-q", "--query", default=None)
parser_archive.add_argument("-n", "--name", default=None)
parser_archive.set_defaults(func=command_archive)
parser_leaderboard = subparsers.add_parser('leaderboard', help="Print the leaderboard for an evaluation")
parser_leaderboard.add_argument("evaluation", metavar="EVALUATION-ID", default=None)
parser_leaderboard.add_argument("--out", default=None)
parser_leaderboard.set_defaults(func=command_leaderboard)
args = parser.parse_args()
print "\n" * 2, "=" * 75
print datetime.utcnow().isoformat()
## Acquire lock, don't run two scoring scripts at once
try:
update_lock = lock.acquire_lock_or_fail('challenge', max_age=timedelta(hours=4))
except lock.LockedException:
print u"Is the scoring script already running? Can't acquire lock."
# can't acquire lock, so return error code 75 which is a
# temporary error according to /usr/include/sysexits.h
return 75
try:
syn = synapseclient.Synapse(debug=args.debug)
if not args.user:
args.user = os.environ.get('SYNAPSE_USER', None)
if not args.password:
args.password = os.environ.get('SYNAPSE_PASSWORD', None)
syn.login(email=args.user, password=args.password)
## initialize messages
messages.syn = syn
messages.dry_run = args.dry_run
messages.send_messages = args.send_messages
messages.send_notifications = args.notifications
messages.acknowledge_receipt = args.acknowledge_receipt
args.func(args)
except Exception as ex1:
sys.stderr.write('Error in scoring script:\n')
st = StringIO()
traceback.print_exc(file=st)
sys.stderr.write(st.getvalue())
sys.stderr.write('\n')
if conf.ADMIN_USER_IDS:
messages.error_notification(userIds=conf.ADMIN_USER_IDS, message=st.getvalue(), queue_name=conf.CHALLENGE_NAME)
finally:
update_lock.release()
print "\ndone: ", datetime.utcnow().isoformat()
print "=" * 75, "\n" * 2
def main():
if conf.CHALLENGE_SYN_ID == "":
sys.stderr.write("Please configure your challenge. See sample_challenge.py for an example.")
global syn
parser = argparse.ArgumentParser()
parser.add_argument("-u", "--user", help="UserName", default=None)
parser.add_argument("-p", "--password", help="Password", default=None)
parser.add_argument("--notifications", help="Send error notifications to challenge admins", action="store_true", default=False)
parser.add_argument("--send-messages", help="Send validation and scoring messages to participants", action="store_true", default=False)
parser.add_argument("--acknowledge-receipt", help="Send confirmation message on passing validation to participants", action="store_true", default=False)
parser.add_argument("--dry-run", help="Perform the requested command without updating anything in Synapse", action="store_true", default=False)
parser.add_argument("--debug", help="Show verbose error output from Synapse API calls", action="store_true", default=False)
subparsers = parser.add_subparsers(title="subcommand")
parser_list = subparsers.add_parser('list', help="List submissions to an evaluation or list evaluations")
parser_list.add_argument("evaluation", metavar="EVALUATION-ID", nargs='?', default=None)
parser_list.add_argument("--challenge-project", "--challenge", "--project", metavar="SYNAPSE-ID", default=None)
parser_list.add_argument("-s", "--status", default=None)
parser_list.add_argument("--all", action="store_true", default=False)
parser_list.set_defaults(func=command_list)
parser_status = subparsers.add_parser('status', help="Check the status of a submission")
parser_status.add_argument("submission")
parser_status.set_defaults(func=command_check_status)
parser_reset = subparsers.add_parser('reset', help="Reset a submission to RECEIVED for re-scoring (or set to some other status)")
parser_reset.add_argument("submission", metavar="SUBMISSION-ID", type=int, nargs='*', help="One or more submission IDs, or omit if using --rescore-all")
parser_reset.add_argument("-s", "--status", default='RECEIVED')
parser_reset.add_argument("--rescore-all", action="store_true", default=False)
parser_reset.add_argument("--rescore", metavar="EVALUATION-ID", type=int, nargs='*', help="One or more evaluation IDs to rescore")
parser_reset.set_defaults(func=command_reset)
parser_validate = subparsers.add_parser('validate', help="Validate all RECEIVED submissions to an evaluation")
parser_validate.add_argument("evaluation", metavar="EVALUATION-ID", nargs='?', default=None, )
parser_validate.add_argument("--all", action="store_true", default=False)
parser_validate.set_defaults(func=command_validate)
parser_score = subparsers.add_parser('score', help="Score all VALIDATED submissions to an evaluation")
parser_score.add_argument("evaluation", metavar="EVALUATION-ID", nargs='?', default=None)
parser_score.add_argument("--all", action="store_true", default=False)
parser_score.set_defaults(func=command_score)
parser_rank = subparsers.add_parser('rank', help="Rank all SCORED submissions to an evaluation")
parser_rank.add_argument("evaluation", metavar="EVALUATION-ID", default=None)
parser_rank.set_defaults(func=command_rank)
parser_archive = subparsers.add_parser('archive', help="Archive submissions to a challenge")
parser_archive.add_argument("evaluation", metavar="EVALUATION-ID", default=None)
parser_archive.add_argument("destination", metavar="FOLDER-ID", default=None)
parser_archive.add_argument("-q", "--query", default=None)
parser_archive.add_argument("-n", "--name", default=None)
parser_archive.set_defaults(func=command_archive)
parser_leaderboard = subparsers.add_parser('leaderboard', help="Print the leaderboard for an evaluation")
parser_leaderboard.add_argument("evaluation", metavar="EVALUATION-ID", default=None)
parser_leaderboard.add_argument("--out", default=None)
parser_leaderboard.set_defaults(func=command_leaderboard)
args = parser.parse_args()
print "\n" * 2, "=" * 75
print datetime.utcnow().isoformat()
## Acquire lock, don't run two scoring scripts at once
try:
update_lock = lock.acquire_lock_or_fail('challenge', max_age=timedelta(hours=4))
except lock.LockedException:
print u"Is the scoring script already running? Can't acquire lock."
# can't acquire lock, so return error code 75 which is a
# temporary error according to /usr/include/sysexits.h
return 75
try:
syn = synapseclient.Synapse(debug=args.debug)
if not args.user:
args.user = os.environ.get('SYNAPSE_USER', None)
if not args.password:
args.password = os.environ.get('SYNAPSE_PASSWORD', None)
syn.login(email=args.user, password=args.password)
## initialize messages
messages.syn = syn
messages.dry_run = args.dry_run
messages.send_messages = args.send_messages
messages.send_notifications = args.notifications
messages.acknowledge_receipt = args.acknowledge_receipt
args.func(args)
except Exception as ex1:
sys.stderr.write('Error in scoring script:\n')
st = StringIO()
traceback.print_exc(file=st)
sys.stderr.write(st.getvalue())
sys.stderr.write('\n')
if conf.ADMIN_USER_IDS:
messages.error_notification(userIds=conf.ADMIN_USER_IDS, message=st.getvalue(), queue_name=conf.CHALLENGE_NAME)
finally:
update_lock.release()
print "\ndone: ", datetime.utcnow().isoformat()
print "=" * 75, "\n" * 2
def main():
global syn
parser = argparse.ArgumentParser()
parser.add_argument("-u", "--user", help="UserName", default=None)
parser.add_argument("-p", "--password", help="Password", default=None)
parser.add_argument("--challengeName", help="Challenge Name", required=True)
parser.add_argument("--notifications", help="Send error notifications to challenge admins", action="store_true", default=False)
parser.add_argument("--send-messages", help="Send validation and scoring messages to participants", action="store_true", default=False)
parser.add_argument("--acknowledge-receipt", help="Send confirmation message on passing validation to participants", action="store_true", default=False)
parser.add_argument("--dry-run", help="Perform the requested command without updating anything in Synapse", action="store_true", default=False)
parser.add_argument("--debug", help="Show verbose error output from Synapse API calls", action="store_true", default=False)
subparsers = parser.add_subparsers(title="subcommand")
parser_validate = subparsers.add_parser('validate', help="Validate all RECEIVED submissions to an evaluation")
parser_validate.add_argument("evaluation", metavar="EVALUATION-IDs", nargs='*', default=None)
parser_validate.add_argument("--admin", metavar="ADMIN", default=None)
parser_validate.add_argument("--public", action="store_true", default=False)
parser_validate.set_defaults(func=command_validate)
parser_archive = subparsers.add_parser('archive', help="Archive submissions to a challenge")
parser_archive.add_argument("evaluation", metavar="EVALUATION-ID", default=None)
parser_archive.add_argument("--status",metavar="STATUS", default="VALIDATED")
parser_archive.add_argument("--reArchive", action="store_true", default=False)
parser_archive.set_defaults(func=command_archive)
args = parser.parse_args()
print("\n" * 2, "=" * 75)
print(datetime.utcnow().isoformat())
## Acquire lock, don't run two scoring scripts at once
try:
update_lock = lock.acquire_lock_or_fail('challenge', max_age=timedelta(hours=4))
except lock.LockedException:
print("Is the scoring script already running? Can't acquire lock.")
# can't acquire lock, so return error code 75 which is a
# temporary error according to /usr/include/sysexits.h
return 75
try:
syn = synapseclient.Synapse(debug=args.debug)
if not args.user:
args.user = os.environ.get('SYNAPSE_USER', None)
if not args.password:
args.password = os.environ.get('SYNAPSE_PASSWORD', None)
syn.login(email=args.user, password=args.password)
## initialize messages
messages.syn = syn
messages.dry_run = args.dry_run
messages.send_messages = args.send_messages
messages.send_notifications = args.notifications
messages.acknowledge_receipt = args.acknowledge_receipt
args.func(args)
except Exception as ex1:
sys.stderr.write('Error in scoring script:\n')
st = StringIO()
traceback.print_exc(file=st)
sys.stderr.write(st.getvalue())
sys.stderr.write('\n')
if conf.ADMIN_USER_IDS:
messages.error_notification(userIds=conf.ADMIN_USER_IDS, message=st.getvalue(), queue_name=args.challengeName)
finally:
update_lock.release()
print("\ndone: ", datetime.utcnow().isoformat())
print("=" * 75, "\n" * 2)
def main():
global syn
parser = argparse.ArgumentParser()
parser.add_argument("-u", "--user", help="UserName", default=None)
parser.add_argument("-p", "--password", help="Password", default=None)
parser.add_argument("--notifications",
help="Send error notifications to challenge admins",
action="store_true",
default=False)
parser.add_argument(
"--send-messages",
help="Send error confirmation and validation errors to participants",
action="store_true",
default=False)
parser.add_argument(
"--dry-run",
help=
"Perform the requested command without updating anything in Synapse",
action="store_true",
default=False)
parser.add_argument(
"--debug",
help="Show verbose error output from Synapse API calls",
action="store_true",
default=False)
subparsers = parser.add_subparsers(title="subcommand")
parser_list = subparsers.add_parser(
'list', help="List submissions to an evaluation or list evaluations")
parser_list.add_argument("evaluation",
metavar="EVALUATION-ID",
nargs='?',
default=None)
parser_list.add_argument("--challenge-project",
"--challenge",
"--project",
metavar="SYNAPSE-ID",
default=None)
parser_list.add_argument("-s", "--status", default=None)
parser_list.add_argument("--all", action="store_true", default=False)
parser_list.set_defaults(func=command_list)
parser_status = subparsers.add_parser(
'status', help="Check the status of a submission")
parser_status.add_argument("submission")
parser_status.set_defaults(func=command_check_status)
parser_reset = subparsers.add_parser(
'reset',
help=
"Reset a submission to RECEIVED for re-scoring (or set to some other status)"
)
parser_reset.add_argument(
"submission",
metavar="SUBMISSION-ID",
type=int,
nargs='*',
help="One or more submission IDs, or omit if using --rescore-all")
parser_reset.add_argument("-s", "--status", default='RECEIVED')
parser_reset.add_argument("--rescore-all",
action="store_true",
default=False)
parser_reset.set_defaults(func=command_reset)
parser_validate = subparsers.add_parser(
'validate', help="Validate all RECEIVED submissions to an evaluation")
parser_validate.add_argument(
"evaluation",
metavar="EVALUATION-ID",
nargs='?',
default=None,
)
parser_validate.add_argument("--all", action="store_true", default=False)
parser_validate.add_argument(
"--send-validation-passed-message",
help=
"Send confirmation email to participants when a submission passes validation",
action="store_true",
default=False)
parser_validate.set_defaults(func=command_validate)
parser_score = subparsers.add_parser(
'score', help="Score all VALIDATED submissions to an evaluation")
parser_score.add_argument("evaluation",
metavar="EVALUATION-ID",
nargs='?',
default=None)
parser_score.add_argument("--all", action="store_true", default=False)
parser_score.set_defaults(func=command_score)
parser_rank = subparsers.add_parser(
'rank', help="Rank all SCORED submissions to an evaluation")
parser_rank.add_argument("evaluation",
metavar="EVALUATION-ID",
default=None)
parser_rank.set_defaults(func=command_rank)
parser_leaderboard = subparsers.add_parser(
'leaderboard', help="Print the leaderboard for an evaluation")
parser_leaderboard.add_argument("evaluation",
metavar="EVALUATION-ID",
default=None)
parser_leaderboard.add_argument("--out", default=None)
parser_leaderboard.set_defaults(func=command_leaderboard)
args = parser.parse_args()
print "\n" * 2, "=" * 75
print datetime.utcnow().isoformat()
## Acquire lock, don't run two scoring scripts at once
try:
update_lock = lock.acquire_lock_or_fail('challenge',
max_age=timedelta(hours=4))
except lock.LockedException:
print u"Is the scoring script already running? Can't acquire lock."
# can't acquire lock, so return error code 75 which is a
# temporary error according to /usr/include/sysexits.h
return 75
try:
syn = synapseclient.Synapse(debug=args.debug)
if not args.user:
args.user = os.environ.get('SYNAPSE_USER', None)
if not args.password:
args.password = os.environ.get('SYNAPSE_PASSWORD', None)
syn.login(email=args.user, password=args.password)
args.func(args)
except Exception as ex1:
sys.stderr.write('Error in scoring script:\n')
st = StringIO()
traceback.print_exc(file=st)
sys.stderr.write(st.getvalue())
sys.stderr.write('\n')
if args.notifications:
message = error_notification_template.format(message=st.getvalue())
if args.dry_run:
print "Dry Run: error notification:", "Exception while scoring " + ismb_akes_challenge.CHALLENGE_NAME
print message
else:
response = syn.sendMessage(
userIds=ismb_akes_challenge.ADMIN_USER_IDS,
messageSubject="Exception while scoring " +
ismb_akes_challenge.CHALLENGE_NAME,
messageBody=message)
print "sent notification: ", unicode(response).encode('utf-8')
finally:
update_lock.release()
print "\ndone: ", datetime.utcnow().isoformat()
print "=" * 75, "\n" * 2
def main():
parser = argparse.ArgumentParser()
parser.add_argument("submissionId", metavar="Submission Id")
parser.add_argument("--challengePredFolder", required=True)
parser.add_argument("--challengeLogFolder", required=True)
parser.add_argument("--outputDir", required=True)
parser.add_argument("--mountedVolumes", nargs="*", required=True)
parser.add_argument("--configFile", required=True)
parser.add_argument("--timeQuota",
help="Time quota in milliseconds",
type=int)
#Has default values
parser.add_argument("-u", "--user", help="UserName", default=None)
parser.add_argument("-p", "--password", help="Password", default=None)
parser.add_argument("--notifications",
help="Send error notifications to challenge admins",
action="store_true",
default=False)
parser.add_argument(
"--send-messages",
help="Send validation and scoring messages to participants",
action="store_true",
default=False)
parser.add_argument(
"--acknowledge-receipt",
help="Send confirmation message on passing validation to participants",
action="store_true",
default=False)
parser.add_argument(
"--dry-run",
help=
"Perform the requested command without updating anything in Synapse",
action="store_true",
default=False)
parser.add_argument(
"--debug",
help="Show verbose error output from Synapse API calls",
action="store_true",
default=False)
parser.add_argument("--canCancel", action="store_true", default=False)
#Test run
#python runDockerSubmission.py 9636069 --challengePredFolder syn7998461 --challengeLogFolder syn9974718 --configFile config.json --mountedVolumes /home/ubuntu/sc2/Celgene-Multiple-Myeloma-Challenge/docker_agent/test-data:/test-data:ro /.synapseCache:/.synapseCache:ro -u $SYNAPSE_USER -p $SYNAPSE_PASS --outputDir /home/ubuntu/sc2/Celgene-Multiple-Myeloma-Challenge/docker_agent/9636069 --send-messages --notifications
args = parser.parse_args()
print "\n" * 2, "=" * 75
print datetime.utcnow().isoformat()
# Acquire lock, don't run two scoring scripts at once
try:
submission_lock = lock.acquire_lock_or_fail(
args.submissionId, max_age=timedelta(hours=9000))
except lock.LockedException:
print u"Is the scoring script already running? Can't acquire lock."
# can't acquire lock, so return error code 75 which is a
# temporary error according to /usr/include/sysexits.h
return 75
try:
syn = synapseclient.Synapse(debug=args.debug)
if not args.user:
args.user = os.environ.get('SYNAPSE_USER', None)
if not args.password:
args.password = os.environ.get('SYNAPSE_PASSWORD', None)
syn.login(email=args.user, password=args.password)
#Add client into arguments
client = docker.from_env()
client.login(args.user,
args.password,
registry="http://docker.synapse.org")
#Add syn and client into arguments
args.syn = syn
args.client = client
## initialize messages
messages.syn = syn
messages.dry_run = args.dry_run
messages.send_messages = args.send_messages
messages.send_notifications = args.notifications
messages.acknowledge_receipt = args.acknowledge_receipt
command_run(args)
except Exception as ex1:
sys.stderr.write('Error in scoring script:\n')
st = StringIO()
traceback.print_exc(file=st)
sys.stderr.write(st.getvalue())
sys.stderr.write('\n')
if ADMIN_USER_IDS:
messages.error_notification(userIds=ADMIN_USER_IDS,
message=st.getvalue(),
queue_name=CHALLENGE_NAME)
finally:
submission_lock.release()
print "\ndone: ", datetime.utcnow().isoformat()
print "=" * 75, "\n" * 2
def main():
parser = argparse.ArgumentParser()
parser.add_argument("-u", "--user", help="UserName", default=None)
parser.add_argument("-p", "--password", help="Password", default=None)
parser.add_argument("-c",
"--config",
help="Challenge Config File",
required=True)
parser.add_argument(
"--storeEvalConfig",
help="Store Evaluation quota configuration through the config file",
action="store_true")
parser.add_argument(
"--dry-run",
help=
"Perform the requested command without updating anything in Synapse",
action="store_true")
parser.add_argument(
"--debug",
help="Show verbose error output from Synapse API calls",
action="store_true")
subparsers = parser.add_subparsers(title="subcommand")
parser_validate = subparsers.add_parser(
'validate', help="Validate all RECEIVED submissions to an evaluation")
parser_validate.add_argument("evaluation",
metavar="EVALUATION-ID",
nargs='?',
default=None)
parser_validate.add_argument("--all", action="store_true", default=False)
parser_validate.add_argument("--canCancel",
action="store_true",
default=False)
parser_validate.set_defaults(func=command_validate)
args = parser.parse_args()
logger.info("\n" * 2 + "=" * 75)
syn = synapseclient.Synapse(debug=args.debug)
try:
syn.login(email=args.user, password=args.password, rememberMe=True)
except Exception as error:
logger.error("Please provide correct Synapse credentials")
raise error
with open(args.config) as config:
args.challenge_config = readYaml(config)
checkAndConfigEval(syn, args.challenge_config, args.setEvalConfig)
## Acquire lock, don't run two scoring scripts at once
try:
update_lock = lock.acquire_lock_or_fail('challenge',
max_age=timedelta(hours=4))
except lock.LockedException:
logger.error(
"Is the scoring script already running? Can't acquire lock.")
# can't acquire lock, so return error code 75 which is a
# temporary error according to /usr/include/sysexits.h
return 75
try:
args.func(syn, args)
except Exception as ex1:
logger.error('Error in scoring harness:\n')
st = StringIO()
traceback.print_exc(file=st)
logger.error(st.getvalue())
logger.error('\n')
finally:
update_lock.release()
logger.info("DONE EVAL\n\n" + "=" * 75)
