Add monitor scripts, dev edit for d3i

.github/workflows/build_gb_monitor.yml

@@ -0,0 +1,44 @@
+name: geoBoundaries Base Image Build
+run-name: gB Base Build
+on:
+  push:
+    branches: ['main']
+    paths: ['geoBoundaryBuilder/images/**']
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+    - name: Check out the repository
+      uses: actions/checkout@v3
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v2
+
+    - name: Log in to GitHub Container Registry
+      uses: docker/login-action@v2
+      with:
+        registry: ghcr.io
+        username: ${{ github.actor }}
+        password: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Define lowercase repository owner
+      id: repo
+      run: echo "REPO_OWNER=$(echo ${{ github.repository_owner }} | tr '[:upper:]' '[:lower:]')" >> $GITHUB_ENV
+
+    - name: Build and push Docker image
+      uses: docker/build-push-action@v3
+      with:
+        context: .
+        file: ./geoBoundaryBuilder/images/gBMonitor.Dockerfile
+        push: true
+        tags: ghcr.io/${{ env.REPO_OWNER }}/gb-monitor:latest
+        build-args: BUILDKIT_STEP_LOG_MAX_SIZE=10485760 BUILDKIT_STEP_LOG_MAX_SPEED=100000000
+      env:
+        # Enable Docker CLI debug output
+        DOCKER_BUILDKIT: 1
+        DOCKER_CLI_EXPERIMENTAL: enabled
+        DEBUG: 1

geoBoundaryBuilder/debug/debug.yml

@@ -0,0 +1,48 @@
+apiVersion: v1
+kind: Pod
+metadata:
+  name: worker-operator
+  namespace: geoboundaries
+  labels:
+    app: worker-operator
+spec:
+  restartPolicy: Never  # Restart policy at the Pod level
+  securityContext:
+    runAsUser: 71032    # User ID for accessing NFS
+    runAsGroup: 9915    # Group ID for accessing NFS
+  affinity:
+    nodeAffinity:
+      requiredDuringSchedulingIgnoredDuringExecution:
+        nodeSelectorTerms:
+        - matchExpressions:
+          - key: kubernetes.io/hostname
+            operator: In
+            values:
+            - dss
+            - d3i00.sciclone.wm.edu
+  containers:
+    - name: worker-operator
+      image: ghcr.io/wmgeolab/gb-base:latest
+      command: ["/bin/bash", "-c"]
+      args:
+        - |
+          export KUBECONFIG=/sciclone/geograd/geoBoundaries/.kube && \
+          cd /sciclone/geograd/geoBoundaries/geoBoundaryBot/geoBoundaryBuilder/modules/
+          python worker_operator.py
+      env:
+        - name: DB_SERVICE
+          value: "geoboundaries-postgres-service"
+        - name: DB_NAME
+          value: "geoboundaries"
+        - name: DB_USER
+          value: "geoboundaries"
+        - name: DB_PASSWORD
+          value: ""
+      volumeMounts:
+        - name: sciclone-volume
+          mountPath: /sciclone  # Mount kubeconfig directory
+  volumes:
+    - name: sciclone-volume
+      nfs:
+        server: 128.239.59.144
+        path: /sciclone

geoBoundaryBuilder/debug/debug_server.yml

@@ -0,0 +1,55 @@
+apiVersion: v1
+kind: Pod
+metadata:
+  name: geoboundaries-postgres
+  namespace: geoboundaries
+  labels:
+    app: geoboundaries-postgres
+spec:
+  securityContext:
+    runAsUser: 71032  # Required for NFS compatibility
+    runAsGroup: 9915  # Required for NFS group access
+    fsGroup: 9915     # Ensures group ownership for the data directory
+  containers:
+  - name: postgres
+    image: postgis/postgis:14-3.3  # PostGIS-enabled PostgreSQL image
+    ports:
+    - containerPort: 5432
+    env:
+    - name: POSTGRES_USER
+      value: "geoboundaries"  # User to be created on first run
+    - name: POSTGRES_PASSWORD
+      value: ""  # Empty password (trust authentication enabled)
+    - name: POSTGRES_DB
+      value: "geoboundaries"  # Database to be created on first run
+    - name: POSTGRES_HOST_AUTH_METHOD
+      value: "trust"  # Allow connections without a password
+    volumeMounts:
+    - name: postgres-data
+      mountPath: /var/lib/postgresql/data  # Persistent data directory
+    resources:
+      requests:
+        memory: "8Gi"
+        cpu: "2"
+      limits:
+        memory: "16Gi"
+        cpu: "4"
+  volumes:
+  - name: postgres-data
+    nfs:
+      server: 128.239.59.144  # Replace with your NFS server IP
+      path: /sciclone/geograd/geoBoundaries/postgres  # NFS path for PostgreSQL data storage
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: geoboundaries-postgres-service
+  namespace: geoboundaries
+spec:
+  selector:
+    app: geoboundaries-postgres
+  ports:
+  - protocol: TCP
+    port: 5432
+    targetPort: 5432
+  type: ClusterIP

geoBoundaryBuilder/images/gBMonitor.Dockerfile

@@ -0,0 +1,14 @@
+FROM python:3.9-slim
+
+WORKDIR /app
+
+RUN pip install --no-cache-dir \
+    Flask==2.3.3 \
+    psycopg2-binary==2.9.7 \
+    Werkzeug==2.3.7
+
+COPY ./geoBoundaryBuilder/monitor /app/
+
+EXPOSE 5000
+
+CMD ["python", "app.py"]

geoBoundaryBuilder/k8s_manifests/monitor.yml

@@ -0,0 +1,46 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: geoboundaries-monitor
+  namespace: geoboundaries
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: geoboundaries-monitor
+  template:
+    metadata:
+      labels:
+        app: geoboundaries-monitor
+    spec:
+      containers:
+      - name: monitor
+        image: ghcr.io/wmgeolab/gb-monitor:latest
+        ports:
+        - containerPort: 5000
+        env:
+        - name: DB_SERVICE
+          value: "geoboundaries-postgres-service"
+        - name: DB_NAME
+          value: "geoboundaries"
+        - name: DB_USER
+          value: "geoboundaries"
+        - name: DB_PASSWORD
+          valueFrom:
+            secretKeyRef:
+              name: postgres-secret
+              key: password
+---
+apiVersion: v1
+kind: Service
+metadata:
+  name: geoboundaries-monitor-service
+  namespace: geoboundaries
+spec:
+  type: NodePort
+  ports:
+  - port: 80
+    targetPort: 5000
+    nodePort: 30081  # Similar to adminer's setup
+  selector:
+    app: geoboundaries-monitor

geoBoundaryBuilder/k8s_manifests/worker_operator.yml

@@ -10,6 +10,16 @@ spec:
   securityContext:
     runAsUser: 71032    # User ID for accessing NFS
     runAsGroup: 9915    # Group ID for accessing NFS
+  affinity:
+    nodeAffinity:
+      requiredDuringSchedulingIgnoredDuringExecution:
+        nodeSelectorTerms:
+        - matchExpressions:
+          - key: kubernetes.io/hostname
+            operator: In
+            values:
+            - dss
+            - d3i00.sciclone.wm.edu
   containers:
     - name: worker-operator
       image: ghcr.io/wmgeolab/gb-base:latest