1 files changed, 21 insertions, 14 deletions
diff --git a/scripts/process_rqtl2_bundle.py b/scripts/process_rqtl2_bundle.py
index 4da3936..e2ce420 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
@@ -10,16 +11,16 @@ from logging import Logger, getLogger, StreamHandler
 
 import MySQLdb as mdb
 from redis import Redis
+from gn_libs.mysqldb import database_connection
 
 from functional_tools import take
 
-import r_qtl.errors as rqe
 import r_qtl.r_qtl2 as rqtl2
 import r_qtl.r_qtl2_qc as rqc
+import r_qtl.exceptions as rqe
 
-from qc_app import jobs
-from qc_app.db_utils import database_connection
-from qc_app.check_connections import check_db, check_redis
+from uploader import jobs
+from uploader.check_connections import check_db, check_redis
 
 from scripts.cli_parser import init_cli_parser
 from scripts.redis_logger import setup_redis_logger
@@ -93,14 +94,17 @@ def process_bundle(dbconn: mdb.Connection,
         if has_geno_file(thejob):
             logger.info("Processing geno files.")
             genoexit = install_genotypes(
+                rconn,
                 dbconn,
-                meta["speciesid"],
-                meta["populationid"],
-                meta["geno-dataset-id"],
-                Path(meta["rqtl2-bundle-file"]),
+                f"{rprefix}:{jobid}",
+                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.")
+                raise Exception("Processing 'geno' file failed.")# pylint: disable=[broad-exception-raised]
             logger.debug(
                 "geno file processing completed successfully. (ExitCode: %s)",
                 genoexit)
@@ -108,14 +112,17 @@ def process_bundle(dbconn: mdb.Connection,
 
         if has_pheno_file(thejob):
             phenoexit = install_pheno_files(
+                rconn,
                 dbconn,
-                meta["speciesid"],
-                meta["platformid"],
-                meta["probe-dataset-id"],
-                Path(meta["rqtl2-bundle-file"]),
+                f"{rprefix}:{jobid}",
+                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.")
+                raise Exception("Processing 'pheno' file failed.")# pylint: disable=[broad-exception-raised]
             logger.debug(
                 "pheno file processing completed successfully. (ExitCode: %s)",
                 phenoexit)