From 2e7e765f50f3f3e4215b0e5319941fbafc99eff0 Mon Sep 17 00:00:00 2001
From: "Anna (Anya) Parker" <50943381+anna-parker@users.noreply.github.com>
Date: Wed, 11 Sep 2024 07:22:56 +0200
Subject: [PATCH] Check for empty lines in silo_import_job

---
 kubernetes/loculus/silo_import_job.sh | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/kubernetes/loculus/silo_import_job.sh b/kubernetes/loculus/silo_import_job.sh
index 48a737b04..f261de1b4 100755
--- 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"