diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/rqtl2/entry.py | 13 | ||||
| -rw-r--r-- | scripts/rqtl2/phenotypes_qc.py | 9 |
2 files changed, 10 insertions, 12 deletions
diff --git a/scripts/rqtl2/entry.py b/scripts/rqtl2/entry.py index e837aa8..e0e00e7 100644 --- a/scripts/rqtl2/entry.py +++ b/scripts/rqtl2/entry.py @@ -20,18 +20,13 @@ def build_main( [Redis, Connection, str, Namespace, logging.Logger], int ], - loggername: str + logger: logging.Logger ) -> Callable[[],int]: """Build a function to be used as an entry-point for scripts.""" def main(): - logging.basicConfig( - format=( - "%(asctime)s - %(levelname)s %(name)s: " - "(%(pathname)s: %(lineno)d) %(message)s"), - level=args.loglevel) - logger = logging.getLogger(loggername) with (Redis.from_url(args.redisuri, decode_responses=True) as rconn, database_connection(args.databaseuri) as dbconn): + logger.setLevel(args.loglevel.upper()) fqjobid = jobs.job_key(args.redisprefix, args.jobid) try: @@ -41,7 +36,7 @@ def build_main( fqjobid, f"{fqjobid}:log-messages", args.redisexpiry)) - logger.addHandler(StreamHandler(stream=sys.stdout)) + logger.addHandler(StreamHandler(stream=sys.stderr)) check_db(args.databaseuri) check_redis(args.redisuri) @@ -49,7 +44,7 @@ def build_main( logger.error("File not found: '%s'.", args.rqtl2bundle) return 2 - returncode = run_fn(rconn, dbconn, fqjobid, args, logger) + returncode = run_fn(rconn, dbconn, fqjobid, args) if returncode == 0: rconn.hset(fqjobid, "status", "completed:success") return returncode diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py index 76ecb8d..a9097d5 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -36,6 +36,10 @@ from scripts.cli_parser import init_cli_parser, add_global_data_arguments from scripts.rqtl2.bundleutils import build_line_joiner, build_line_splitter __MODULE__ = "scripts.rqtl2.phenotypes_qc" +logging.basicConfig( + format=("%(asctime)s - %(levelname)s %(name)s: " + "(%(pathname)s: %(lineno)d) %(message)s")) +logger = logging.getLogger(__MODULE__) def validate(phenobundle: Path, logger: Logger) -> dict: """Check that the bundle is generally valid""" @@ -369,8 +373,7 @@ def run_qc(# pylint: disable=[too-many-locals] rconn: Redis, dbconn: mdb.Connection, fullyqualifiedjobid: str, - args: Namespace, - logger: Logger + args: Namespace ) -> int: """Run quality control checks on the bundle.""" logger.debug("Beginning the quality assurance checks.") @@ -509,5 +512,5 @@ if __name__ == "__main__": type=Path) return parser.parse_args() - main = build_main(cli_args(), run_qc, __MODULE__) + main = build_main(cli_args(), run_qc, logger) sys.exit(main()) |