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"""Run Quality Control checks on R/qtl2 bundle."""
import sys
import json
from zipfile import ZipFile
from argparse import Namespace
from typing import Union, Sequence
from logging import Logger, getLogger, StreamHandler
from redis import Redis
from quality_control.errors import InvalidValue
from qc_app import jobs
from qc_app.db_utils import database_connection
from qc_app.check_connections import check_db, check_redis
from r_qtl import r_qtl2 as rqtl2
from r_qtl import r_qtl2_qc as rqc
from r_qtl import fileerrors as rqfe
from scripts.cli_parser import init_cli_parser
from scripts.process_rqtl2_bundle import parse_job
from scripts.redis_logger import setup_redis_logger
def dict2tuple(dct: dict) -> tuple:
"""Utility to convert items in dicts to pairs of tuples."""
return tuple((key, val) for key,val in dct.items())
def add_to_errors(rconn: Redis,
fqjobid: str,
key: str,
errors: Sequence[Union[InvalidValue, rqfe.MissingFile]]):
"""Add `errors` to a given list of errors"""
errs = tuple(dict(item) for item in set(
[dict2tuple(old) for old in
json.loads(rconn.hget(fqjobid, key) or "[]")] +
[dict2tuple({"type": type(error).__name__, **error._asdict()})
for error in errors]))
rconn.hset(fqjobid, key, json.dumps(errs))
def qc_missing_files(rconn: Redis,
fqjobid: str,
zfile: ZipFile,
logger: Logger) -> bool:
"""Run QC for files listed in control file that don't exist in bundle."""
logger.info("Checking for missing files…")
missing = rqc.missing_files(zfile)
add_to_errors(rconn, fqjobid, "errors-generic", tuple(
rqfe.MissingFile(
mfile[0], mfile[1], (
f"File '{mfile[1]}' is listed in the control file under "
f"the '{mfile[0]}' key, but it does not actually exist in "
"the bundle."))
for mfile in missing))
if len(missing) > 0:
logger.error("Missing files in the bundle!")
return True
return False
def qc_geno_errors(rconn, fqjobid, zfile, logger) -> bool:
"""Check for errors in `geno` file(s)."""
logger.info("Checking for errors in the 'geno' file…")
cdata = rqtl2.control_data(zfile)
if "geno" in cdata:
gerrs = tuple(rqc.geno_errors(zfile))
add_to_errors(rconn, fqjobid, "errors-generic", tuple(
err for err in gerrs if isinstance(err, rqfe.MissingFile)))
add_to_errors(rconn, fqjobid, "errors-geno", tuple(
err for err in gerrs if not isinstance(err, rqfe.MissingFile)))
if len(gerrs) > 0:
logger.error("The 'geno' file has errors.")
return True
logger.info("No errors found in the 'geno' file.")
return False
def qc_pheno_errors(rconn, fqjobid, zfile, logger) -> bool:
"""Check for errors in `pheno` file(s)."""
logger.info("Checking for errors in the 'pheno' file…")
cdata = rqtl2.control_data(zfile)
if "pheno" in cdata:
perrs = tuple(rqc.pheno_errors(zfile))
add_to_errors(rconn, fqjobid, "errors-generic", tuple(
err for err in perrs if isinstance(err, rqfe.MissingFile)))
add_to_errors(rconn, fqjobid, "errors-pheno", tuple(
err for err in perrs if not isinstance(err, rqfe.MissingFile)))
if len(perrs) > 0:
logger.error("The 'pheno' file has errors.")
return True
logger.info("No errors found in the 'pheno' file.")
return False
def qc_phenose_errors(rconn, fqjobid, zfile, logger) -> bool:
"""Check for errors in `phenose` file(s)."""
logger.info("Checking for errors in the 'phenose' file…")
cdata = rqtl2.control_data(zfile)
if "phenose" in cdata:
perrs = tuple(rqc.phenose_errors(zfile))
add_to_errors(rconn, fqjobid, "errors-generic", tuple(
err for err in perrs if isinstance(err, rqfe.MissingFile)))
add_to_errors(rconn, fqjobid, "errors-phenose", tuple(
err for err in perrs if not isinstance(err, rqfe.MissingFile)))
if len(perrs) > 0:
logger.error("The 'phenose' file has errors.")
return True
logger.info("No errors found in the 'phenose' file.")
return False
def qc_phenocovar_errors(_rconn, _fqjobid, _zfile, _logger) -> bool:
"""Check for errors in `phenocovar` file(s)."""
return False
def run_qc(rconn: Redis,
args: Namespace,
logger: Logger) -> int:
"""Run the QC programs."""
fqjobid = jobs.job_key(args.redisprefix, args.jobid)
thejob = parse_job(rconn, args.redisprefix, args.jobid)
jobmeta = thejob["job-metadata"]
with ZipFile(jobmeta["rqtl2-bundle-file"], "r") as zfile:
if qc_missing_files(rconn, fqjobid, zfile, logger):
return 1
return (
1 if any((
qc_geno_errors(rconn, fqjobid, zfile, logger),
qc_pheno_errors(rconn, fqjobid, zfile, logger),
qc_phenose_errors(rconn, fqjobid, zfile, logger),
qc_phenocovar_errors(rconn, fqjobid, zfile, logger)))
else 0)
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(rconn, args, logger)
rconn.hset(
jobs.job_key(args.redisprefix, args.jobid), "exitcode", exitcode)
return exitcode
sys.exit(main())
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