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"""Run Quality Control checks on R/qtl2 bundle."""
import sys
from logging import getLogger, StreamHandler
from redis import Redis
from qc_app import jobs
from qc_app.db_utils import database_connection
from qc_app.check_connections import check_db, check_redis
from scripts.cli_parser import init_cli_parser
from scripts.redis_logger import setup_redis_logger
def run_qc(_args):
"""Run the QC programs."""
return 1
if __name__ == "__main__":
def main():
"""Enter R/qtl2 bundle QC runner."""
args = init_cli_parser(
"qc-on-rqtl2-bundle", "Run QC on R/qtl2 bundle.").parse_args()
check_redis(args.redisuri)
check_db(args.databaseuri)
logger = getLogger("qc-on-rqtl2-bundle")
logger.addHandler(StreamHandler(stream=sys.stderr))
logger.setLevel("DEBUG")
fqjobid = jobs.job_key(args.redisprefix, args.jobid)
with (database_connection(args.databaseuri) as _dbconn,
Redis.from_url(args.redisuri, decode_responses=True) as rconn):
logger.addHandler(setup_redis_logger(
rconn, fqjobid, f"{fqjobid}:log-messages",
args.redisexpiry))
exitcode = run_qc(args)
rconn.hset(
jobs.job_key(args.redisprefix, args.jobid), "exitcode", exitcode)
return exitcode
sys.exit(main())
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