Merge branch 'main' into fix_submitterId

.github/workflows/format-backend-on-request.yml

@@ -0,0 +1,40 @@
+name: Format Backend Code
+on:
+  workflow_dispatch:
+  pull_request:
+    types: [synchronize, labeled]
+    paths:
+      - "backend/**"
+jobs:
+  format:
+    if: github.event_name == 'workflow_dispatch' || (github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'format_me'))
+    permissions:
+      contents: write
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.head_ref }}
+
+      - name: Set up JDK
+        uses: actions/setup-java@v4
+        with:
+          java-version: "21"
+          distribution: "adopt"
+
+      - name: Setup Gradle
+        uses: gradle/actions/setup-gradle@v3
+
+      - name: Format Backend Code
+        run: ./gradlew ktlintFormat
+        working-directory: ./backend
+
+      - name: Commit and Push Changes
+        run: |
+          git config --global user.name 'Loculus bot'
+          git config --global user.email 'bot@loculus.org'
+          git add -A
+          git commit -m "Automated backend code formatting" || echo "No changes to commit"
+          git push origin HEAD:${{ github.head_ref }}

keycloak/keycloakify/src/email/messages/messages_en.properties

@@ -1,6 +1,6 @@
-emailVerificationSubject=Verify email
-emailVerificationBody=Someone has created a new account with this email address. If this was you, click the link below to verify your email address\n\n{0}\n\nThis link will expire within {3}.\n\nIf you didn''t create this account, just ignore this message.
-emailVerificationBodyHtml=<p>Someone has created a new account with this email address. If this was you, click the link below to verify your email address</p><p><a href="{0}">Link to e-mail address verification</a></p><p>This link will expire within {3}.</p><p>If you didn''t create this account, just ignore this message.</p>
+emailVerificationSubject=Verify email to complete account creation
+emailVerificationBody=Welcome!\n\nWe''ve received a request to create a new account using this email address. To complete your registration and verify your email, please click the link below:\n\n{0}\n\nFor your security, this verification link will expire in {3}.\n\nIf you didn''t initiate this account creation, no action is needed. You can safely disregard this message.\n\nIf you have any questions or concerns, please contact our support team.
+emailVerificationBodyHtml=<p>Welcome!</p><p>We''ve received a request to create a new account using this email address. To complete your registration and verify your email, please click the link below:</p><p><a href="{0}">Verify your email address</a></p><p>For your security, this verification link will expire in {3}.</p><p>If you didn''t initiate this account creation, no action is needed. You can safely disregard this message.</p><p>If you have any questions or concerns, please contact our support team.</p>
 emailUpdateConfirmationSubject=Verify new email
 emailUpdateConfirmationBody=To update your {2} account with email address {1}, click the link below\n\n{0}\n\nThis link will expire within {3}.\n\nIf you don''t want to proceed with this modification, just ignore this message.
 emailUpdateConfirmationBodyHtml=<p>To update your {2} account with email address {1}, click the link below</p><p><a href="{0}">{0}</a></p><p>This link will expire within {3}.</p><p>If you don''t want to proceed with this modification, just ignore this message.</p>

kubernetes/appset.yaml

@@ -4,52 +4,57 @@ kind: ApplicationSet
 metadata:
   name: pp-preview
   namespace: argocd
-  resourceVersion: "33491144"
 spec:
-  goTemplate: true
   generators:
-    - pullRequest:
-        github:
-          owner: loculus-project
-          labels:
-            - preview
-          repo: loculus
-          tokenRef:
-            key: token
-            secretName: github-access-token
-        requeueAfterSeconds: 60
-    - git:
-        repoURL: https://github.com/loculus-project/argocd_metadata.git
-        revision: HEAD
-        files:
-          - path: "config.json"
+  - pullRequest:
+      github:
+        labels:
+        - preview
+        owner: loculus-project
+        repo: loculus
+        tokenRef:
+          key: token
+          secretName: github-access-token
+      requeueAfterSeconds: 60
+  - git:
+      files:
+      - path: config.json
+      repoURL: https://github.com/loculus-project/argocd_metadata.git
+      revision: HEAD
+  goTemplate: true
   template:
     metadata:
-      name: 'pp-{{ (printf "%.25s" .branch) | replace "_" "-" | replace "/" "-" | trimSuffix "-" | lower }}-{{.number}}'
+      name: pp-{{ (printf "%.25s" .branch) | replace "_" "-" | replace "/" "-" | trimSuffix      "-" | lower }}-{{.number}}
     spec:
       destination:
-        server: 'https://kubernetes.default.svc'
-        namespace: 'prev-{{ (printf "%.25s" .branch) | replace "_" "-" | replace "/" "-" | trimSuffix "-" | lower  }}'
+        namespace: prev-{{ (printf "%.25s" .branch) | replace "_" "-" | replace "/"   "-" | trimSuffix "-" | lower  }}
+        server: https://kubernetes.default.svc
       project: default
       source:
-        path: 'kubernetes/loculus/'
-        repoURL: 'https://github.com/loculus-project/loculus.git'
-        targetRevision: '{{.branch}}'
         helm:
           parameters:
-            - name: shortbranch
-              value: '{{ (printf "%.25s" .branch) | replace "_" "-" | replace "/" "-" | trimSuffix "-" | lower  }}'
-            - name: namespace # TODO(https://github.com/loculus-project/loculus/issues/979) delete this once no unsynced up branches need it
-              value: 'preview-{{ (printf "%.25s" .branch) | replace "_" "-" | replace "/" "-" | trimSuffix "-" | lower }}'
-            - name: sha
-              value: '{{.head_short_sha_7}}'
-            - name: branch
-              value: '{{.branch}}'
-            - name: host
-              value: '{{ (printf "%.25s" .branch) | replace "_" "-" | replace "/" "-" | trimSuffix "-" | lower  }}.loculus.org'
+          - name: shortbranch
+            value: '{{ (printf "%.25s" .branch) | replace "_" "-" | replace "/" "-"
+              | trimSuffix "-" | lower  }}'
+          - name: sha
+            value: '{{.head_short_sha_7}}'
+          - name: branch
+            value: '{{.branch}}'
+          - name: bannerMessage
+            value: Dev build, data will not be persisted. SHA {{.head_short_sha_7}}
+          - name: host
+            value: '{{ (printf "%.25s" .branch) | replace "_" "-" | replace "/" "-"
+              | trimSuffix "-" | lower  }}.loculus.org'
+          valueFiles:
+          - values.yaml
+          - values_preview_server.yaml
+        path: kubernetes/loculus/
+        repoURL: https://github.com/loculus-project/loculus.git
+        targetRevision: '{{.branch}}'
       syncPolicy:
-        syncOptions:
-          - CreateNamespace=true
         automated:
-          selfHeal: true
           prune: true
+          selfHeal: true
+        syncOptions:
+        - CreateNamespace=true
+        - ServerSideApply=true

kubernetes/loculus/templates/_config-processor.tpl

@@ -9,6 +9,13 @@
       mountPath: /output
   command: ["python3"]
   args: ["/app/config-processor.py", "/input", "/output"]
+  resources:
+    requests:
+      cpu: 100m
+      memory: 128Mi
+    limits:
+      cpu: 500m
+      memory: 256Mi
   env:
     - name: LOCULUSSUB_smtpPassword
       valueFrom:

kubernetes/loculus/templates/ena-submission-deployment.yaml

@@ -23,6 +23,13 @@ spec:
       initContainers:
         - name: ena-submission-flyway
           image: "ghcr.io/loculus-project/ena-submission-flyway:{{ $dockerTag }}"
+          resources:
+            requests:
+              cpu: 100m
+              memory: 128Mi
+            limits:
+              cpu: 500m
+              memory: 256Mi
           command: ['flyway', 'migrate']
           env:
             - name: FLYWAY_URL

kubernetes/loculus/templates/keycloak-deployment.yaml

@@ -32,6 +32,13 @@ spec:
       initContainers:
 {{- include "loculus.configProcessor" (dict "name" "keycloak-config" "dockerTag" $dockerTag) | nindent 8 }}
         - name: keycloak-theme-prep
+          resources:
+            requests:
+              cpu: 100m
+              memory: 128Mi
+            limits:
+              cpu: 500m
+              memory: 256Mi
           image: "ghcr.io/loculus-project/keycloakify:{{ $dockerTag }}"
           volumeMounts:
             - name: theme-volume

kubernetes/loculus/values.yaml

@@ -1162,8 +1162,8 @@ insecureCookies: false
 bannerMessage: "This is a development environment. Data will not be persisted."
 additionalHeadHTML: '<script defer data-domain="main.loculus.org" src="https://plausible.io/js/script.js"></script>'
 images:
-  lapisSilo: "ghcr.io/genspectrum/lapis-silo:0.2.7"
-  lapis: "ghcr.io/genspectrum/lapis:0.2.3"
+  lapisSilo: "ghcr.io/genspectrum/lapis-silo:0.2.11"
+  lapis: "ghcr.io/genspectrum/lapis:0.2.7"
 secrets:
   smtp-password:
     type: raw