fix(k8s): check if backendExtraArgs is set, add test for default temp…

…late (#2010)

Recently merged PR expects backendExtraArgs to be present in values.yaml

It isn't, so default way of generating helm templates crashes. Fixing and adding test to avoid this in future.

.github/workflows/e2e-k3d.yml

@@ -61,7 +61,12 @@ jobs:
         run: |
           ./deploy.py --verbose cluster
 
-      - name: Template with helm
+      - name: Default template with helm
+        uses: WyriHaximus/github-action-helm3@v4
+        with:
+          exec: helm template loculus kubernetes/loculus
+
+      - name: E2E Template with helm
         uses: WyriHaximus/github-action-helm3@v4
         with:
           exec: ./deploy.py --verbose helm --branch ${{ github.ref_name }} --sha ${{ env.sha }} --for-e2e --template > /tmp/helm_template.yaml
@@ -71,6 +76,7 @@ jobs:
         with:
           name: helm-template
           path: /tmp/helm_template.yaml
+
       - name: Deploy with helm
         run: |
           ./deploy.py --verbose helm --branch ${{ github.ref_name }} --sha ${{ env.sha }} --for-e2e

kubernetes/loculus/templates/loculus-backend.yaml

@@ -59,7 +59,9 @@ spec:
             - "--spring.datasource.username=$(DB_USERNAME)"
             - "--spring.security.oauth2.resourceserver.jwt.jwk-set-uri=http://loculus-keycloak-service:8083/realms/loculus/protocol/openid-connect/certs"
             - "--loculus.cleanup.task.reset-stale-in-processing-after-seconds={{- .Values.preprocessingTimeout | default 120 }}"
-            {{ .Values.backendExtraArgs | toYaml | nindent 12 }}
+            {{- if .Values.backendExtraArgs }}
+              {{- .Values.backendExtraArgs | toYaml | nindent 12 }}
+            {{- end }}
           env:
             - name: JVM_OPTS
               value: -XX:+UseContainerSupport -XX:+UseG1GC -XX:MaxHeapFreeRatio=5 -XX:MinHeapFreeRatio=2