From 6fb2834489888937842d761cbbc7c2992a4f5a0d Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Thu, 24 Oct 2024 15:57:27 -0500
Subject: Parse entire namespace object rather than individual values.

---
 scripts/rqtl2/install_genotypes.py | 9 ++++-----
 scripts/rqtl2/install_phenos.py    | 9 ++++-----
 2 files changed, 8 insertions(+), 10 deletions(-)

(limited to 'scripts/rqtl2')

diff --git a/scripts/rqtl2/install_genotypes.py b/scripts/rqtl2/install_genotypes.py
index abc3f07..20a19da 100644
--- a/scripts/rqtl2/install_genotypes.py
+++ b/scripts/rqtl2/install_genotypes.py
@@ -1,7 +1,7 @@
 """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
@@ -187,13 +187,12 @@ def cross_reference_genotypes(
 
 def install_genotypes(#pylint: disable=[too-many-arguments, too-many-locals]
         dbconn: mdb.Connection,
-        speciesid: int,
-        populationid: int,
-        datasetid: int,
-        rqtl2bundle: Path,
+        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:
diff --git a/scripts/rqtl2/install_phenos.py b/scripts/rqtl2/install_phenos.py
index e96742f..a6e9fb2 100644
--- a/scripts/rqtl2/install_phenos.py
+++ b/scripts/rqtl2/install_phenos.py
@@ -1,7 +1,7 @@
 """Load pheno 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 logging import Logger, getLogger
@@ -97,12 +97,11 @@ def cross_reference_probeset_data(dbconn: mdb.Connection,
 
 def install_pheno_files(#pylint: disable=[too-many-arguments, too-many-locals]
         dbconn: mdb.Connection,
-        speciesid: int,
-        platformid: int,
-        datasetid: int,
-        rqtl2bundle: Path,
+        args: argparse.Namespace,
         logger: Logger = getLogger()) -> int:
     """Load data in `pheno` files and other related files into the database."""
+    (speciesid, platformid, datasetid, rqtl2bundle) = (
+        args.speciesid, args.platformid, args.datasetid, args.rqtl2bundle)
     with ZipFile(str(rqtl2bundle), "r") as zfile:
         try:
             rqc.validate_bundle(zfile)
-- 
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