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validate_round2.py
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#!/usr/bin/env python3
"""Imputation challenge validation script for round2
Author:
Jin Lee ([email protected])
"""
import os
import re
import time
import shutil
import math
#import gc
import traceback
import synapseclient
import multiprocessing
from validate import validate
from io import StringIO
from rank import get_team_name, parse_team_name_tsv
from score import parse_submission_filename
from score_leaderboard import mkdir_p, send_message
from score_leaderboard import WIKI_TEMPLATE_SUBMISSION_STATUS, RE_PATTERN_SUBMISSION_FNAME
from logger import log
BIG_INT = 99999999 # for multiprocessing
ROUND2_VALID_CELL_ASSAY = [
'C05M17',
'C05M18',
'C05M20',
'C05M29',
'C06M16',
'C06M17',
'C06M18',
'C07M20',
'C07M29',
'C12M01',
'C12M02',
'C14M01',
'C14M02',
'C14M16',
'C14M17',
'C14M22',
'C19M16',
'C19M17',
'C19M18',
'C19M20',
'C19M22',
'C19M29',
'C22M16',
'C22M17',
'C28M17',
'C28M18',
'C28M22',
'C28M29',
'C31M01',
'C31M02',
'C31M16',
'C31M29',
'C38M01',
'C38M02',
'C38M17',
'C38M18',
'C38M20',
'C38M22',
'C38M29',
'C39M16',
'C39M17',
'C39M18',
'C39M20',
'C39M22',
'C39M29',
'C40M16',
'C40M17',
'C40M18',
'C40M20',
'C40M22',
'C40M29',
'C51M16',
'C51M17',
'C51M18',
'C51M20',
'C51M29'
]
def is_valid_round2_cell_assay(cell, assay):
return (cell + assay) in ROUND2_VALID_CELL_ASSAY
def update_wiki_for_round2(syn, team_name_dict, args):
# calculate ranks and update round2 wiki
log.info('Updating wiki...')
wiki_id_map = {
k.split(':')[0]: k.split(':')[1] for k in args.round2_wiki_id.split(',')
}
for k, wiki_id in wiki_id_map.items():
w = syn.getWiki(args.project_id, wiki_id)
if k == 'submission_status':
title = 'Submission status'
markdown = WIKI_TEMPLATE_SUBMISSION_STATUS.format(
eval_queue_id=args.eval_queue_id)
else:
raise Exception('invalid wiki type')
w.markdown = markdown
w.title = title
w = syn.store(w)
return None
def parse_arguments():
import argparse
import os
py_path = os.path.dirname(os.path.realpath(__file__))
parser = argparse.ArgumentParser(
description='ENCODE Imputation Challenge round2 script. ')
parser.add_argument('eval_queue_id',
help='Synapse evaluation queue ID to retreive submissions from.')
p_score = parser.add_argument_group(
title='Scoring parameters')
p_score.add_argument('--window-size', default=25, type=int,
help='Window size for bigwig in bp')
p_score.add_argument('--update-wiki-only', action='store_true',
help='Update wiki based on DB file (--db-file) without '
'scoring submissions')
p_sys = parser.add_argument_group(
title='System and resource settings')
p_sys.add_argument('--nth', type=int, default=1,
help='Number of threads to parallelize scoring (per) submission')
p_sys.add_argument('--team-name-tsv',
help='TSV file with team_id/team_name (1st col/2nd col).')
p_syn = parser.add_argument_group(
title='Communitation with synapse')
p_syn.add_argument('--dry-run', action='store_true',
help='Do not update submission\'s status on synapse.')
p_syn.add_argument('--project-id', default='syn17083203',
help='Synapse project ID.')
p_syn.add_argument('--round2-wiki-id',
default='submission_status:594312',
help='Comma-delimited Synapse wiki ID for round2.')
p_syn.add_argument('--submission-dir', default='./submissions',
help='Download submissions here.')
p_syn.add_argument('--send-msg-to-admin', action='store_true',
help='Send message to admin.')
p_syn.add_argument('--send-msg-to-user', action='store_true',
help='Send message to user.')
p_syn.add_argument('--period', default=1800,
help='Time period in second to download submissions from synapse '
'and score them')
p_syn.add_argument('--admin-id', nargs='+', default=['3345120'],
help='Admin\'s Synapse ID (as string) ')
args = parser.parse_args()
return args
def validate_submission(submission, status, args, syn):
status['status'] = 'INVALID'
submission_dir = os.path.join(
os.path.abspath(args.submission_dir), submission.id)
mkdir_p(submission_dir)
metadata = {
'id': submission.id,
'team': 'undefined'
}
try:
metadata['team'] = get_team_name(syn, None, submission.teamId)
log.info('Downloading submission... {}'.format(submission.id))
submission = syn.getSubmission(
submission,
downloadLocation=submission_dir,
ifcollision='overwrite.local'
)
print()
submission_fname = submission.filePath
cell, assay = parse_submission_filename(submission_fname)
if not is_valid_round2_cell_assay(cell, assay):
raise Exception('Invalid cell/assay combination for '
'round2 round')
log.info('Downloading done {}, {}, {}, {}, {}'.format(
submission_fname, submission.id,
submission.teamId, cell, assay))
# read pred npy (submission)
log.info('Validating bigwig...{}'.format(submission.id))
valid, message = validate(submission_fname, args.window_size)
if valid:
status['status'] = 'VALIDATED'
subject = 'Successfully validated submission %s %s %s:\n' % (
submission.name, submission.id, submission.teamId)
message += '\nSuccess!\n'
else:
subject = 'Invalid submission %s %s %s:\n' % (
submission.name, submission.id, submission.teamId)
# delete file
shutil.rmtree(submission_dir)
log.info(subject + message)
except Exception as ex1:
if 'teamId' in submission:
teamId = submission.teamId
else:
teamId = 'undefined'
subject = 'Error validating submission %s %s %s:\n' % (
submission.name, submission.id, teamId)
st = StringIO()
traceback.print_exc(file=st)
message = st.getvalue()
log.error(subject + message)
# delete file
shutil.rmtree(submission_dir)
# send message
users_to_send_msg = []
if args.send_msg_to_user:
users_to_send_msg.append(submission.userId)
if args.send_msg_to_admin:
users_to_send_msg.extend(args.admin_id)
send_message(syn, users_to_send_msg, subject, message)
if not args.dry_run:
status['annotations'] = synapseclient.annotations.to_submission_status_annotations(
metadata, is_private=False)
status = syn.store(status)
return status
def main():
log.info('Parsing arguments...')
args = parse_arguments()
if args.team_name_tsv is not None:
team_name_dict = parse_team_name_tsv(args.team_name_tsv)
else:
team_name_dict = None
print(team_name_dict)
syn = synapseclient.login()
t0 = time.perf_counter()
while True:
try:
if not args.update_wiki_only:
evaluation = syn.getEvaluation(args.eval_queue_id)
# init multiprocessing
pool = multiprocessing.Pool(args.nth)
# distribute jobs
ret_vals = []
for submission, status in syn.getSubmissionBundles(evaluation, status='RECEIVED'):
ret_vals.append(
pool.apply_async(validate_submission,
(submission, status, args, syn)))
# gather
for r in ret_vals:
r.get(BIG_INT)
pool.close()
pool.join()
update_wiki_for_round2(syn, team_name_dict, args)
except Exception as ex1:
st = StringIO()
traceback.print_exc(file=st)
message = st.getvalue()
subject = 'Server error:'
if args.send_msg_to_admin:
send_message(syn, args.admin_id, subject, message)
log.error(message)
log.info('Waiting for new submissions...')
while time.perf_counter() - t0 < args.period:
time.sleep(60)
t0 = time.perf_counter()
log.info('All done')
if __name__ == '__main__':
main()