scripts: Pass in logger to get detailed updates.

1 files changed, 13 insertions, 11 deletions

diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py
index 21b5f00..a6cdacc 100644
--- a/scripts/rqtl2/install_phenos.py
+++ b/scripts/rqtl2/install_phenos.py
@@ -1,10 +1,10 @@
 """Load pheno from R/qtl2 bundle into the database."""
 import sys
-import logging
 import traceback
 from pathlib import Path
 from zipfile import ZipFile
 from functools import reduce
+from logging import Logger, getLogger, StreamHandler
 
 import MySQLdb as mdb
 from MySQLdb.cursors import DictCursor
@@ -16,9 +16,6 @@ from scripts.cli_parser import init_cli_parser, add_global_data_arguments
 from r_qtl import r_qtl2 as rqtl2
 
 from functional_tools import take
-stderr_handler = logging.StreamHandler(stream=sys.stderr)
-logger = logging.getLogger("install_phenos")
-logger.addHandler(stderr_handler)
 
 def insert_probesets(dbconn: mdb.Connection,
                      platformid: int,
@@ -95,11 +92,13 @@ def cross_reference_probeset_data(dbconn: mdb.Connection,
             } for row in dataids))
         return cursor.rowcount
 
-def install_pheno_files(dbconn: mdb.Connection,
-                        speciesid: int,
-                        platformid: int,
-                        datasetid: int,
-                        rqtl2bundle: Path) -> int:
+def install_pheno_files(#pylint: disable=[too-many-arguments, too-many-locals]
+        dbconn: mdb.Connection,
+        speciesid: int,
+        platformid: int,
+        datasetid: int,
+        rqtl2bundle: Path,
+        logger: Logger = getLogger()) -> int:
     """Load data in `pheno` files and other related files into the database."""
     with ZipFile(str(rqtl2bundle), "r") as zfile:
         try:
@@ -155,13 +154,16 @@ if __name__ == "__main__":
 
         return parser.parse_args()
 
+    thelogger = getLogger("install_phenos")
+    thelogger.addHandler(StreamHandler(stream=sys.stderr))
     main = build_main(
         cli_args(),
         lambda dbconn, args: install_pheno_files(dbconn,
                                                  args.speciesid,
                                                  args.platformid,
                                                  args.datasetid,
-                                                 args.rqtl2bundle),
-        logger,
+                                                 args.rqtl2bundle,
+                                                 thelogger),
+        thelogger,
         "DEBUG")
     sys.exit(main())