added persistence properties to values and deployment

molgenis/questions.yml

@@ -101,3 +101,10 @@ questions:
   required: true
   group: "Persistence"
   label: Persistence
+  show_subquestion_if: true
+  - variable: molgenis.persistence.size
+    default: "10Gi"
+    description: "Size of MOLGENIS filestore (not the database size)"
+    type: string
+    label: Size filestore
+

molgenis/templates/deployment.yaml

@@ -49,10 +49,11 @@ spec:
               value: {{ .javaOpts }}
           ports:
             - containerPort: 8080
+          {{- if .persistence.enabled }}
           volumeMounts:
           - name: molgenis-nfs
-            mountPath: "/home/molgenis"
+            mountPath: /home/molgenis
-          restartPolicy: "Never"
+          {{- end }}
           livenessProbe:
             httpGet:
               path: /
@@ -67,10 +68,12 @@ spec:
             periodSeconds: 5
           resources:
 {{ toYaml .resources | indent 12 }}
+        {{- if .persistence.enabled }}
         volumes:
         - name: molgenis-nfs
           persistentVolumeClaim:
-            claimName: molgenis-nfs-claim
+            claimName: {{ .Values.persistence.name }}
+        {{- end }}
         {{- end }}
 
         - name: elasticsearch

molgenis/templates/persistence/molgenisPVC.yaml

@@ -0,0 +1,15 @@
+{{- if .Values.molgenis.persistence.enabled }}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Values.molgenis.persistence.name }}
+  annotations:
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
+  spec:
+    accessModes:
+      - ReadWriteMany
+    resources:
+      requests:
+        storage: {{ .Values.molgenis.persistence.size }}
+{{- end }}

molgenis/templates/persistence/molgenisPersistenceClaim.yaml

@@ -1,15 +0,0 @@
-{{- if .Values.molgenis.persistence.enabled -}}
-apiVersion: extensions/v1beta1
-kind: PersistentVolumeClaim
-apiVersion: v1
-metadata:
-  name: molgenis-nfs-claim
-  annotations:
-    volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
-spec:
-  accessModes:
-    - ReadWriteMany
-  resources:
-    requests:
-storage: 1Gi
-{{- end }}

molgenis/values.yaml

@@ -32,13 +32,8 @@ molgenis:
       memory: 1Gi
   persistence:
     enabled: false
-    name: molgenis-nexus-data
+    name: molgenis-nfs-claim
-    storageClass: nfs-class
     size: 30G
-    reclaimPolicy: Retain
-    server: 192.168.64.12
-    accessMode: ReadWriteMany
-    mountPath: /gcc/molgenis/nexus
   services:
     opencpu:
       host: localhost