Parse entire namespace object rather than individual values.

1 files changed, 11 insertions, 8 deletions

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.")