Parse entire namespace object rather than individual values.

3 files changed, 19 insertions, 18 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.")
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)