Merge pull request #460 from EBISPOT/issue-449

issue-449: create separate k8s config for dev cluster
EBISPOT · Aug 8, 2023 · fdadedb · fdadedb
2 parents f4c4c42 + 98b2b66
commit fdadedb
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Showing 31 changed files with 478 additions and 30 deletions.
diff --git a/k8chart-dev/dataserver/Chart.yaml b/k8chart-dev/dataserver/Chart.yaml
@@ -0,0 +1,5 @@
+apiVersion: v1
+appVersion: "1.0"
+description: ols4 dataserver deployment
+name: ols4
+version: 0.1.0
diff --git a/k8chart-dev/dataserver/templates/ols4-dataserver-deployment.yaml b/k8chart-dev/dataserver/templates/ols4-dataserver-deployment.yaml
@@ -0,0 +1,40 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ .Release.Name }}
+  labels:
+    app: {{ .Release.Name }}
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: {{ .Release.Name }}
+  template:
+    metadata:
+      labels:
+        app: {{ .Release.Name }}
+    spec:
+      affinity:
+        nodeAffinity:
+          requiredDuringSchedulingIgnoredDuringExecution:
+            nodeSelectorTerms:
+              - matchExpressions:
+                - key: kubernetes.io/hostname
+                  operator: In
+                  values:
+                    - hh-rke-wp-webadmin-56-worker-1.caas.ebi.ac.uk
+      containers:
+        - name: dataserver
+          image: nginx:1.23.3
+          ports:
+            - containerPort: 80
+          volumeMounts:
+            - name: {{.Release.Name}}-data
+              mountPath: "/usr/share/nginx/html"
+          resources:
+            requests:
+              memory: 2Gi
+      volumes:
+      - name: {{.Release.Name}}-data
+        persistentVolumeClaim:
+          claimName: {{.Release.Name}}-pvc
diff --git a/k8chart-dev/dataserver/templates/ols4-dataserver-pvc.yaml b/k8chart-dev/dataserver/templates/ols4-dataserver-pvc.yaml
@@ -0,0 +1,13 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  creationTimestamp: null
+  name: {{ .Release.Name }}-pvc
+spec:
+  storageClassName: standard-nfs-production
+  accessModes:
+    - ReadWriteOnce
+  resources:
+    requests:
+      storage: 80Gi
+
diff --git a/k8chart-dev/dataserver/templates/ols4-dataserver-service.yaml b/k8chart-dev/dataserver/templates/ols4-dataserver-service.yaml
@@ -0,0 +1,14 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Release.Name }}
+  labels:
+    app: {{ .Release.Name }}
+spec:
+  ports:
+      - port: 80
+        targetPort: 80
+        name: http
+        protocol: TCP
+  selector:
+    app: {{ .Release.Name }}
diff --git a/k8chart-dev/dataserver/values.yaml b/k8chart-dev/dataserver/values.yaml
diff --git a/k8chart-dev/ols4/.helmignore b/k8chart-dev/ols4/.helmignore
@@ -0,0 +1,22 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj
+.vscode/
diff --git a/k8chart-dev/ols4/Chart.yaml b/k8chart-dev/ols4/Chart.yaml
@@ -0,0 +1,5 @@
+apiVersion: v1
+appVersion: "1.0"
+description: ols4 deployment
+name: ols4
+version: 0.1.0
diff --git a/k8chart-dev/ols4/templates/_helpers.tpl b/k8chart-dev/ols4/templates/_helpers.tpl
diff --git a/k8chart-dev/ols4/templates/ols4-backend-deployment.yaml b/k8chart-dev/ols4/templates/ols4-backend-deployment.yaml
@@ -0,0 +1,44 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ .Release.Name }}-backend
+  labels:
+    app: {{ .Release.Name }}-backend
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: {{ .Release.Name }}-backend
+  template:
+    metadata:
+      labels:
+        app: {{ .Release.Name }}-backend
+    spec:
+      affinity:
+        nodeAffinity:
+          requiredDuringSchedulingIgnoredDuringExecution:
+            nodeSelectorTerms:
+              - matchExpressions:
+                - key: kubernetes.io/hostname
+                  operator: In
+                  values:
+                    - hh-rke-wp-webadmin-56-worker-3.caas.ebi.ac.uk
+      containers:
+        - name: web
+          image: ghcr.io/ebispot/ols4-backend:{{.Values.imageTag}}
+          imagePullPolicy: Always
+          ports:
+            - containerPort: 8080
+          resources:
+            requests:
+              memory: 14Gi
+          env:
+            - name: OLS_SOLR_HOST
+              value: http://{{ .Release.Name }}-solr:8983
+            - name: OLS_NEO4J_HOST
+              value: bolt://{{ .Release.Name }}-neo4j:7687
+            - name: SERVER_SERVLET_CONTEXT_PATH
+              value: /ols4
+            - name: JAVA_OPTIONS
+              value: -Xmx6G
+
diff --git a/k8chart-dev/ols4/templates/ols4-backend-service.yaml b/k8chart-dev/ols4/templates/ols4-backend-service.yaml
@@ -0,0 +1,13 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Release.Name }}-backend
+  labels:
+    app: {{ .Release.Name }}-backend
+spec:
+  type: NodePort
+  ports:
+  - name: "application"
+    port: 8080
+  selector:
+    app: {{ .Release.Name }}-backend
diff --git a/k8chart-dev/ols4/templates/ols4-configmap.yaml b/k8chart-dev/ols4/templates/ols4-configmap.yaml
@@ -0,0 +1,6 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ .Release.Name }}-configmap
+data:
+  myvalue: "Hello World"
diff --git a/k8chart-dev/ols4/templates/ols4-frontend-deployment.yaml b/k8chart-dev/ols4/templates/ols4-frontend-deployment.yaml
@@ -0,0 +1,46 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name: {{ .Release.Name }}-frontend
+  labels:
+    app: {{ .Release.Name }}-frontend
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: {{ .Release.Name }}-frontend
+  template:
+    metadata:
+      labels:
+        app: {{ .Release.Name }}-frontend
+    spec:
+      affinity:
+        nodeAffinity:
+          requiredDuringSchedulingIgnoredDuringExecution:
+            nodeSelectorTerms:
+              - matchExpressions:
+                - key: kubernetes.io/hostname
+                  operator: In
+                  values:
+                    - hh-rke-wp-webadmin-56-worker-2.caas.ebi.ac.uk
+      containers:
+        - name: web
+          image: ghcr.io/ebispot/ols4-frontend:{{.Values.imageTag}}
+          imagePullPolicy: Always
+          resources:
+              requests:
+                cpu: 2
+                memory: 4G          
+          ports:
+            - containerPort: 8080
+          env:
+            - name: REACT_APP_APIURL
+              value: https://www.ebi.ac.uk/ols4/
+            - name: PUBLIC_URL
+              value: /ols4
+            - name: OLS_MINIFY
+              value: 'true'
+          command: ["/bin/bash", "-c"]
+          args: ["/opt/ols4-frontend/entrypoint.dockersh"]
+
+
diff --git a/k8chart-dev/ols4/templates/ols4-frontend-service.yaml b/k8chart-dev/ols4/templates/ols4-frontend-service.yaml
@@ -0,0 +1,13 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Release.Name }}-frontend
+  labels:
+    app: {{ .Release.Name }}-frontend
+spec:
+  type: NodePort
+  ports:
+  - name: "application"
+    port: 8080
+  selector:
+    app: {{ .Release.Name }}-frontend
diff --git a/k8chart-dev/ols4/templates/ols4-ingress.yaml b/k8chart-dev/ols4/templates/ols4-ingress.yaml
@@ -0,0 +1,18 @@
+apiVersion: networking.k8s.io/v1
+kind: Ingress
+metadata:
+  name: {{ .Release.Name }}-ingress
+  annotations:
+    nginx.ingress.kubernetes.io/rewrite-target: /
+spec:
+  rules:
+  - http:
+      paths:
+      - path: /
+        pathType: Prefix
+        backend:
+          service:
+            name:  {{ .Release.Name }}-frontend
+            port:
+              number: 8081
+
diff --git a/k8chart-dev/ols4/templates/ols4-neo4j-deployment.yaml b/k8chart-dev/ols4/templates/ols4-neo4j-deployment.yaml
@@ -0,0 +1,43 @@
+apiVersion: apps/v1
+kind: Deployment
+metadata:
+  name:  {{ .Release.Name }}-neo4j
+  labels:
+    app: {{ .Release.Name }}-neo4j
+spec:
+  replicas: 1
+  selector:
+    matchLabels:
+      app: {{ .Release.Name }}-neo4j
+  template:
+    metadata:
+      labels:
+        app: {{ .Release.Name }}-neo4j
+    spec:
+      volumes:
+        - name: {{ .Release.Name }}-neo4j-storage
+          persistentVolumeClaim:
+            claimName: {{ .Release.Name }}-neo4j-pvc
+      containers:
+        - name: neo4j
+          image: ghcr.io/ebispot/ols4-neo4j:4.4.9-community
+          volumeMounts:
+            - mountPath: "/data"
+              name: {{ .Release.Name }}-neo4j-storage
+          command: ["/bin/bash", "-c"]
+          args: ["rm -rf /data/* && wget -qO- $NEO4J_TARBALL_URL | tar -xz -C /data/ && tini -g -- /startup/docker-entrypoint.sh neo4j"]
+          resources:
+            requests:
+              memory: 20Gi
+          env:
+            - name: NEO4J_HEAP_MEMORY
+              value: 10g
+            - name: NEO4J_dbms_memory_heap_maxSize
+              value: 8g
+            - name: NEO4J_TARBALL_URL
+              value: {{.Values.neo4jTarballUrl}}
+            - name: NEO4J_AUTH
+              value: none
+          ports:
+            - containerPort: 7474
+            - containerPort: 7687
diff --git a/k8chart-dev/ols4/templates/ols4-neo4j-pv.yaml b/k8chart-dev/ols4/templates/ols4-neo4j-pv.yaml
@@ -0,0 +1,26 @@
+apiVersion: v1
+kind: PersistentVolume
+metadata:
+  annotations:
+  finalizers:
+  - kubernetes.io/pv-protection
+  name: ols4-neo4j-pv
+spec:
+  accessModes:
+  - ReadWriteOnce
+  capacity:
+    storage: 250Gi
+  local:
+    path: /var/local-disk
+  nodeAffinity:
+    required:
+      nodeSelectorTerms:
+      - matchExpressions:
+        - key: kubernetes.io/hostname
+          operator: In
+          values:
+          - hh-rke-wp-webadmin-56-worker-2.caas.ebi.ac.uk
+  persistentVolumeReclaimPolicy: Retain
+  storageClassName: local-storage
+  volumeMode: Filesystem
+
diff --git a/k8chart-dev/ols4/templates/ols4-neo4j-pvc.yaml b/k8chart-dev/ols4/templates/ols4-neo4j-pvc.yaml
@@ -0,0 +1,13 @@
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: ols4-neo4j-pvc
+spec:
+  storageClassName: local-storage
+  volumeName: ols4-neo4j-pv
+  accessModes:
+    - ReadWriteOnce
+  resources:
+    requests:
+      storage: 250Gi
+
diff --git a/k8chart-dev/ols4/templates/ols4-neo4j-service.yaml b/k8chart-dev/ols4/templates/ols4-neo4j-service.yaml
@@ -0,0 +1,18 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Release.Name }}-neo4j
+  labels:
+    app: {{ .Release.Name }}-neo4j
+spec:
+  ports:
+      - port: 7474
+        targetPort: 7474
+        name: http
+        protocol: TCP
+      - port: 7687
+        targetPort: 7687
+        name: bolt
+        protocol: TCP
+  selector:
+    app: {{ .Release.Name }}-neo4j
diff --git a/k8chart-dev/ols4/templates/ols4-proxy-configmap.yaml b/k8chart-dev/ols4/templates/ols4-proxy-configmap.yaml
@@ -0,0 +1,10 @@
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ .Release.Name }}-proxy-configmap
+data:
+  HTTP_PROXY: http://hx-wwwcache.ebi.ac.uk:3128
+  HTTPS_PROXY: http://hx-wwwcache.ebi.ac.uk:3128
+  http_proxy: http://hx-wwwcache.ebi.ac.uk:3128
+  https_proxy: http://hx-wwwcache.ebi.ac.uk:3128
+  no_proxy: localhost,.cluster.local