diff --git a/.github/workflows/e2e-k3d.yml b/.github/workflows/e2e-k3d.yml index 43a12ccad..90483f16c 100644 --- a/.github/workflows/e2e-k3d.yml +++ b/.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 diff --git a/kubernetes/loculus/templates/_common-metadata.tpl b/kubernetes/loculus/templates/_common-metadata.tpl index e8960f9ac..8ef878c10 100644 --- a/kubernetes/loculus/templates/_common-metadata.tpl +++ b/kubernetes/loculus/templates/_common-metadata.tpl @@ -1,3 +1,16 @@ +{{- define "loculus.websiteUrl" -}} +{{- $websiteHost := "" }} +{{- if $.Values.codespaceName }} + {{- $websiteHost = printf "https://%s-3000.app.github.dev" $.Values.codespaceName }} +{{- else if eq $.Values.environment "server" }} + {{- $websiteHost = printf "https://%s" $.Values.host }} +{{- else }} + {{- $websiteHost = "http://localhost:3000" }} +{{- end }} +{{- printf $websiteHost }} +{{- end }} + + {{/* Get common metadata fields */}} {{- define "loculus.commonMetadata" }} fields: @@ -29,6 +42,9 @@ fields: type: int autocomplete: true header: Submission details + customDisplay: + type: link + url: {{ include "loculus.websiteUrl" $ -}} /group/__value__ - name: groupName type: string generateIndex: true diff --git a/kubernetes/loculus/templates/loculus-backend.yaml b/kubernetes/loculus/templates/loculus-backend.yaml index 9fb78bb77..4a54bf3d2 100644 --- a/kubernetes/loculus/templates/loculus-backend.yaml +++ b/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