From c3de3a4e933a9768d2e1c784813accf4d466b111 Mon Sep 17 00:00:00 2001 From: Theo Sanderson Date: Mon, 26 Feb 2024 17:29:11 +0000 Subject: [PATCH 1/2] Clean up after failed curl in silo_import --- kubernetes/loculus/silo_import_job.sh | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/kubernetes/loculus/silo_import_job.sh b/kubernetes/loculus/silo_import_job.sh index 3602e1fca..006c3ca23 100755 --- a/kubernetes/loculus/silo_import_job.sh +++ b/kubernetes/loculus/silo_import_job.sh @@ -48,7 +48,19 @@ download_data() { released_data_endpoint="$BACKEND_BASE_URL/get-released-data" echo "calling $released_data_endpoint" + + set +e curl -o "$data_dir/data.ndjson" --fail-with-body "$released_data_endpoint" -H "Authorization: Bearer $jwt" + exit_code=$? + set -e + + if [ $exit_code -ne 0 ]; then + echo "Curl command failed with exit code $exit_code, cleaning up and exiting." + + rm -rf "$data_dir" + + exit $exit_code + fi echo "downloaded $(wc -l < "$data_dir/data.ndjson") sequences" echo From 8d61b93509e68c788f0a05d516a265aecf492c84 Mon Sep 17 00:00:00 2001 From: Theo Sanderson Date: Mon, 26 Feb 2024 17:30:42 +0000 Subject: [PATCH 2/2] Update silo_import_job.sh --- kubernetes/loculus/silo_import_job.sh | 2 -- 1 file changed, 2 deletions(-) diff --git a/kubernetes/loculus/silo_import_job.sh b/kubernetes/loculus/silo_import_job.sh index 006c3ca23..1601e3b4d 100755 --- a/kubernetes/loculus/silo_import_job.sh +++ b/kubernetes/loculus/silo_import_job.sh @@ -56,9 +56,7 @@ download_data() { if [ $exit_code -ne 0 ]; then echo "Curl command failed with exit code $exit_code, cleaning up and exiting." - rm -rf "$data_dir" - exit $exit_code fi