1 files changed, 12 insertions, 18 deletions
diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index 6b89142..8762655 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -1,12 +1,13 @@
 """Load genotypes from R/qtl2 bundle into the database."""
 import sys
+import argparse
 import traceback
-from pathlib import Path
 from zipfile import ZipFile
 from functools import reduce
 from typing import Iterator, Optional
-from logging import Logger, getLogger, StreamHandler
+from logging import Logger, getLogger
 
+from redis import Redis
 import MySQLdb as mdb
 from MySQLdb.cursors import DictCursor
 
@@ -19,6 +20,8 @@ from scripts.rqtl2.entry import build_main
 from scripts.rqtl2.cli_parser import add_common_arguments
 from scripts.cli_parser import init_cli_parser, add_global_data_arguments
 
+__MODULE__ = "scripts.rqtl2.install_genotypes"
+
 def insert_markers(
         dbconn: mdb.Connection,
         speciesid: int,
@@ -183,15 +186,16 @@ def cross_reference_genotypes(
         cursor.executemany(insertquery, insertparams)
         return cursor.rowcount
 
-def install_genotypes(#pylint: disable=[too-many-arguments, too-many-locals]
+def install_genotypes(#pylint: disable=[too-many-locals]
+        rconn: Redis,#pylint: disable=[unused-argument]
         dbconn: mdb.Connection,
-        speciesid: int,
-        populationid: int,
-        datasetid: int,
-        rqtl2bundle: Path,
+        fullyqualifiedjobid: str,#pylint: disable=[unused-argument]
+        args: argparse.Namespace,
         logger: Logger = getLogger(__name__)
 ) -> int:
     """Load any existing genotypes into the database."""
+    (speciesid, populationid, datasetid, rqtl2bundle) = (
+         args.speciesid, args.populationid, args.datasetid, args.rqtl2bundle)
     count = 0
     with ZipFile(str(rqtl2bundle.absolute()), "r") as zfile:
         try:
@@ -253,15 +257,5 @@ if __name__ == "__main__":
 
         return parser.parse_args()
 
-    thelogger = getLogger("install_genotypes")
-    thelogger.addHandler(StreamHandler(stream=sys.stderr))
-    main = build_main(
-        cli_args(),
-        lambda dbconn, args: install_genotypes(dbconn,
-                                               args.speciesid,
-                                               args.populationid,
-                                               args.datasetid,
-                                               args.rqtl2bundle),
-        thelogger,
-        "INFO")
+    main = build_main(cli_args(), install_genotypes, __MODULE__)
     sys.exit(main())