From 53b1e7cb181380a24aab4cbc7a9634b2d8dd2d29 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 19 Jan 2024 08:29:04 +0300
Subject: scripts: Process R/qtl2 bundle

Build script to start the processing of the R/qtl2 bundle.
---
 scripts/rqtl2/entry.py             | 3 +--
 scripts/rqtl2/install_genotypes.py | 8 ++++----
 scripts/rqtl2/install_phenos.py    | 8 ++++----
 3 files changed, 9 insertions(+), 10 deletions(-)

(limited to 'scripts/rqtl2')

diff --git a/scripts/rqtl2/entry.py b/scripts/rqtl2/entry.py
index e2d70a6..eccc19d 100644
--- a/scripts/rqtl2/entry.py
+++ b/scripts/rqtl2/entry.py
@@ -11,13 +11,12 @@ from qc_app.check_connections import check_db, check_redis
 
 from scripts.redis_logger import setup_redis_logger
 
-def build_main(cli_args: Callable[[], Namespace],
+def build_main(args: Namespace,
                run_fn: Callable[[Connection, Namespace], int],
                logger: Logger,
                loglevel: str = "INFO") -> Callable[[],int]:
     """Build a function to be used as an entry-point for scripts."""
     def main():
-        args = cli_args()
         check_db(args.databaseuri)
         check_redis(args.redisuri)
         if not args.rqtl2bundle.exists():
diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index 77e7163..733ccf9 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -15,8 +15,8 @@ from r_qtl import r_qtl2 as rqtl2
 from functional_tools import take
 
 from scripts.rqtl2.entry import build_main
-from scripts.cli_parser import init_cli_parser
 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")
@@ -217,14 +217,14 @@ if __name__ == "__main__":
 
     def cli_args():
         """Process command-line arguments for install_genotypes"""
-        parser = add_common_arguments(init_cli_parser(
+        parser = add_common_arguments(add_global_data_arguments(init_cli_parser(
             "install_genotypes",
-            "Parse genotypes from R/qtl2 bundle into the database."))
+            "Parse genotypes from R/qtl2 bundle into the database.")))
 
         return parser.parse_args()
 
     main = build_main(
-        cli_args,
+        cli_args(),
         lambda dbconn, args: install_genotypes(dbconn,
                                                args.speciesid,
                                                args.populationid,
diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py
index 5c25866..21b5f00 100644
--- a/scripts/rqtl2/install_phenos.py
+++ b/scripts/rqtl2/install_phenos.py
@@ -10,8 +10,8 @@ import MySQLdb as mdb
 from MySQLdb.cursors import DictCursor
 
 from scripts.rqtl2.entry import build_main
-from scripts.cli_parser import init_cli_parser
 from scripts.rqtl2.cli_parser import add_common_arguments
+from scripts.cli_parser import init_cli_parser, add_global_data_arguments
 
 from r_qtl import r_qtl2 as rqtl2
 
@@ -143,9 +143,9 @@ if __name__ == "__main__":
 
     def cli_args():
         """Process command-line arguments for `install_phenos`"""
-        parser = init_cli_parser(
+        parser = add_global_data_arguments(init_cli_parser(
             "install_genotypes",
-            "Parse genotypes from R/qtl2 bundle into the database.")
+            "Parse genotypes from R/qtl2 bundle into the database."))
 
         parser.add_argument(
             "platformid",
@@ -156,7 +156,7 @@ if __name__ == "__main__":
         return parser.parse_args()
 
     main = build_main(
-        cli_args,
+        cli_args(),
         lambda dbconn, args: install_pheno_files(dbconn,
                                                  args.speciesid,
                                                  args.platformid,
-- 
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