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/process_rqtl2_bundle.py | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

(limited to 'scripts/process_rqtl2_bundle.py')

diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py
index 20cfd3b..ade9862 100644
--- a/scripts/process_rqtl2_bundle.py
+++ b/scripts/process_rqtl2_bundle.py
@@ -2,6 +2,7 @@
 import sys
 import uuid
 import json
+import argparse
 import traceback
 from typing import Any
 from pathlib import Path
@@ -94,10 +95,11 @@ def process_bundle(dbconn: mdb.Connection,
             logger.info("Processing geno files.")
             genoexit = install_genotypes(
                 dbconn,
-                meta["speciesid"],
-                meta["populationid"],
-                meta["geno-dataset-id"],
-                Path(meta["rqtl2-bundle-file"]),
+                argparse.Namespace(
+                    speciesid=meta["speciesid"],
+                    populationid=meta["populationid"],
+                    datasetid=meta["geno-dataset-id"],
+                    rqtl2bundle=Path(meta["rqtl2-bundle-file"])),
                 logger)
             if genoexit != 0:
                 raise Exception("Processing 'geno' file failed.")
@@ -109,10 +111,11 @@ def process_bundle(dbconn: mdb.Connection,
         if has_pheno_file(thejob):
             phenoexit = install_pheno_files(
                 dbconn,
-                meta["speciesid"],
-                meta["platformid"],
-                meta["probe-dataset-id"],
-                Path(meta["rqtl2-bundle-file"]),
+                argparse.Namespace(
+                    speciesid=meta["speciesid"],
+                    platformid=meta["platformid"],
+                    dataset_id=meta["probe-dataset-id"],
+                    rqtl2bundle=Path(meta["rqtl2-bundle-file"])),
                 logger)
             if phenoexit != 0:
                 raise Exception("Processing 'pheno' file failed.")
-- 
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