From 6ca397279e09d968679930f429d6341798be990e Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 22 Jan 2024 09:27:58 +0300
Subject: scripts: Pass in logger to get detailed updates.

---
 scripts/rqtl2/install_genotypes.py | 16 ++++++++--------
 scripts/rqtl2/install_phenos.py    | 24 +++++++++++++-----------
 2 files changed, 21 insertions(+), 19 deletions(-)

(limited to 'scripts/rqtl2')

diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index 733ccf9..bfe17b8 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -1,11 +1,11 @@
 """Load genotypes 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 typing import Iterator, Optional
+from logging import Logger, getLogger, StreamHandler
 
 import MySQLdb as mdb
 from MySQLdb.cursors import DictCursor
@@ -18,10 +18,6 @@ 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
 
-stderr_handler = logging.StreamHandler(stream=sys.stderr)
-logger = logging.getLogger("install_genotypes")
-logger.addHandler(stderr_handler)
-
 def insert_markers(dbconn: mdb.Connection,
                    speciesid: int,
                    markers: tuple[str, ...],
@@ -158,11 +154,13 @@ def cross_reference_genotypes(dbconn: mdb.Connection,
             } for row in dataids))
         return cursor.rowcount
 
-def install_genotypes(dbconn: mdb.Connection,
+def install_genotypes(#pylint: disable=[too-many-arguments, too-many-locals]
+        dbconn: mdb.Connection,
                       speciesid: int,
                       populationid: int,
                       datasetid: int,
-                      rqtl2bundle: Path) -> int:
+                      rqtl2bundle: Path,
+                      logger: Logger = getLogger()) -> int:
     """Load any existing genotypes into the database."""
     count = 0
     with ZipFile(str(rqtl2bundle.absolute()), "r") as zfile:
@@ -223,6 +221,8 @@ 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,
@@ -230,6 +230,6 @@ if __name__ == "__main__":
                                                args.populationid,
                                                args.datasetid,
                                                args.rqtl2bundle),
-        logger,
+        thelogger,
         "INFO")
     sys.exit(main())
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())
-- 
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