Pass in the logger, rather than the name of the logger.

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())