1 files changed, 23 insertions, 14 deletions
diff --git a/scripts/insert_samples.py b/scripts/insert_samples.py
index 8431462..fc029f9 100644
--- a/scripts/insert_samples.py
+++ b/scripts/insert_samples.py
@@ -3,14 +3,16 @@ import sys
 import logging
 import pathlib
 import argparse
+import traceback
 
 import MySQLdb as mdb
 from redis import Redis
+from gn_libs.mysqldb import database_connection
 
-from qc_app.db_utils import database_connection
-from qc_app.check_connections import check_db, check_redis
-from qc_app.db import species_by_id, population_by_id
-from qc_app.samples import (
+from uploader.check_connections import check_db, check_redis
+from uploader.species.models import species_by_id
+from uploader.population.models import population_by_id
+from uploader.samples.models import (
     save_samples_data,
     read_samples_file,
     cross_reference_samples)
@@ -32,7 +34,7 @@ class SeparatorAction(argparse.Action):
         """Process the value passed in."""
         setattr(namespace, self.dest, (chr(9) if values == "\\t" else values))
 
-def insert_samples(conn: mdb.Connection,# pylint: disable=[too-many-arguments]
+def insert_samples(conn: mdb.Connection,# pylint: disable=[too-many-arguments, too-many-positional-arguments]
                    rconn: Redis,# pylint: disable=[unused-argument]
                    speciesid: int,
                    populationid: int,
@@ -72,6 +74,7 @@ def insert_samples(conn: mdb.Connection,# pylint: disable=[too-many-arguments]
     print("Samples upload successfully completed.")
     return 0
 
+
 if __name__ == "__main__":
 
     def cli_args():
@@ -126,7 +129,7 @@ if __name__ == "__main__":
 
     def main():
         """Run script to insert samples into the database."""
-
+        status_code = 1 # Exit with an Exception
         args = cli_args()
         check_db(args.databaseuri)
         check_redis(args.redisuri)
@@ -136,13 +139,19 @@ if __name__ == "__main__":
 
         with (Redis.from_url(args.redisuri, decode_responses=True) as rconn,
               database_connection(args.databaseuri) as dbconn):
-            return insert_samples(dbconn,
-                                  rconn,
-                                  args.speciesid,
-                                  args.populationid,
-                                  args.samplesfile,
-                                  args.separator,
-                                  args.firstlineheading,
-                                  args.quotechar)
+
+            try:
+                status_code = insert_samples(dbconn,
+                                             rconn,
+                                             args.speciesid,
+                                             args.populationid,
+                                             args.samplesfile,
+                                             args.separator,
+                                             args.firstlineheading,
+                                             args.quotechar)
+            except Exception as _exc:# pylint: disable=[broad-exception-caught]
+                print(traceback.format_exc(), file=sys.stderr)
+
+        return status_code
 
     sys.exit(main())