Check for empty lines in silo_import_job

loculus-project · Sep 11, 2024 · 2e7e765 · 2e7e765
1 parent f073e72
commit 2e7e765
Showing 1 changed file with 7 additions and 0 deletions.
diff --git a/kubernetes/loculus/silo_import_job.sh b/kubernetes/loculus/silo_import_job.sh
@@ -37,6 +37,13 @@ download_data() {
   exit_code=$?
   set -e
 
+  c=`tail -c 2 $new_input_data`
+  if [ "$c" != "" ]; then
+      echo "No 2 newlines at end of $new_input_data, instead $c, stream not completed, cleaning up and exiting"
+      rm -rf "$new_input_data_dir"
+      exit $exit_code
+  fi
+
   if [ $exit_code -ne 0 ]; then
     echo "Curl command failed with exit code $exit_code, cleaning up and exiting."
     rm -rf "$new_input_data_dir"