Merge

.github/scripts/collect_kubernetes_logs.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+set -e
+
+pods=$(kubectl get pods -l app=loculus -n loculus -o jsonpath='{.items[*].metadata.name}' || true)
+for pod in $pods; do
+  containers=$(kubectl get pod "$pod" -n loculus -o jsonpath='{.spec.containers[*].name}' || true)
+  for container in $containers; do
+    mkdir "kubernetes_logs" -p
+    file="kubernetes_logs/$pod-$container.txt"
+    echo "Logs from $pod - $container:" >> "$file"
+    kubectl logs "$pod" -n loculus -c "$container" >> "$file" 2>/dev/null || true
+  done
+done

.github/scripts/wait_for_pods_to_be_ready.py

@@ -0,0 +1,54 @@
+#!/usr/bin/env python3
+
+import json
+import subprocess
+import time
+
+
+def main():
+    end_time = time.time() + 480
+
+    while True:
+        pods = get_pods()
+
+        if time.time() > end_time:
+            print("Aborting, timeout reached")
+            exit(1)
+
+        try:
+            if all_pods_are_ready(pods):
+                print("All pods are up and running!")
+                break
+        except KeyError as e:
+            print("KeyError:", e, "continuing...")
+
+        print("Sleeping for 10 seconds...")
+        time.sleep(10)
+
+
+def get_pods():
+    cmd = ['kubectl', 'get', 'pods', '-l', 'app=loculus', '-n', 'loculus', '-o', 'json']
+    result = subprocess.run(cmd, capture_output=True, text=True)
+    return json.loads(result.stdout)['items']
+
+
+def all_pods_are_ready(pods):
+    for pod in pods:
+        print("Status of:", pod['metadata']['name'], "-", pod['status']['phase'])
+        if pod['status']['phase'] == 'Succeeded':
+            continue
+        if has_container_that_is_not_ready(pod):
+            return False
+    return True
+
+
+def has_container_that_is_not_ready(pod):
+    for container_status in pod['status']['containerStatuses']:
+        if container_status['ready'] is False:
+            print(container_status['name'], "is not ready")
+            return True
+    return False
+
+
+if __name__ == "__main__":
+    main()

.github/workflows/backend.yml

@@ -19,10 +19,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up JDK 20
-        uses: actions/setup-java@v3
+      - name: Set up JDK
+        uses: actions/setup-java@v4
         with:
-          java-version: '20'
+          java-version: '21'
           distribution: 'adopt'
       - name: Execute Tests
         uses: gradle/gradle-build-action@v2
@@ -44,10 +44,10 @@ jobs:
       checks: read
     steps:
       - uses: actions/checkout@v4
-      - name: Set up JDK 20
-        uses: actions/setup-java@v3
+      - name: Set up JDK
+        uses: actions/setup-java@v4
         with:
-          java-version: '20'
+          java-version: '21'
           distribution: 'adopt'
 
       - name: Login to GitHub Container Registry
@@ -65,17 +65,27 @@ jobs:
           tags: |
             type=ref,event=branch,enable=${{ github.ref != 'refs/heads/main' }}
             type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' }}
+            type=sha,prefix=commit-
+      - name: Extract Docker Tags
+        id: extractTag
+        run: |
+          FIRST_TAG=$(echo "${{ steps.dockerMetadata.outputs.tags }}" | head -n 1)
+          echo "::set-output name=firstTag::$FIRST_TAG"
 
+          SECOND_TAG=$(echo "${{ steps.dockerMetadata.outputs.tags }}" | head -n 2 | tail -n 1)
+          echo "::set-output name=secondTag::$SECOND_TAG"
       - name: Build Docker Image For Branch
         uses: gradle/gradle-build-action@v2
         env:
           USER: ${{ github.actor }}
           TOKEN: "${{ secrets.GITHUB_TOKEN }}"
         with:
-          arguments: bootBuildImage --imageName=${{ steps.dockerMetadata.outputs.tags }}
+          arguments: bootBuildImage --imageName=${{steps.extractTag.outputs.firstTag }}
           build-root-directory: ./backend
 
-      - name: Push Docker Image For Branch
-        run: docker push ${{ steps.dockerMetadata.outputs.tags }}
-
-
+      - name: Tag With SHA tag
+        run: docker tag ${{ steps.extractTag.outputs.firstTag  }} ${{ steps.extractTag.outputs.secondTag  }}
+      - name: Push 1st Docker Image
+        run: docker push ${{ steps.extractTag.outputs.firstTag  }}
+      - name: Push 2nd Docker Image
+        run: docker push ${{ steps.extractTag.outputs.secondTag  }}