added elasticsearch persistence

molgenis/README.md

@@ -80,13 +80,27 @@ Specify memory usage for Java JVM:
 Select the resources you need dependant on the customer you need to serve.
 
 ## Persistence
-You can define your own volume by enabling persistence on your MOLGENIS instance. You can also choose to retain the volume of the NFS and specify the size of the volume.
+You can enable persistence on your MOLGENIS stack by specifying the following property.
-The following properties will setup the persistence for you.
 
-- ```molgenis.persistence.enabled```
+- ```persistence.enabled```
-- ```molgenis.persistence.retain```
+
+You can also choose to retain the volume of the NFS.
+- ```persistence.retain```
+
+The size and claim name can be specified per service. There are now two services that can be persist.
+
+- MOLGENIS
+- ElasticSearch
+
+MOLGENIS persistent properties.
+- ```molgenis.persistence.claim```
 - ```molgenis.persistence.size```
 
+ElasticSearch persistent properties.
+- ```elasticsearch.persistence.claim```
+- ```elasticsearch.persistence.size```
+
+
 ### Resolve you persistent volume
 You do not know which volume is attached to your MOLGENIS instance. You can resolve this by executing:
 

molgenis/questions.yml

@@ -97,7 +97,7 @@ questions:
   - "1g"
   - "2g"
   group: "Resources"
-- variable: molgenis.persistence.enabled
+- variable: persistence.enabled
   default: false
   description: "Do you want to use persistence"
   type: boolean
@@ -106,18 +106,26 @@ questions:
   label: Persistence
   show_subquestion_if: true
   subquestions:
+  - variable: persistence.retain
+    default: false
+    description: "Do you want to retain the persistent volume"
+    type: boolean
+    label: Retain volume
   - variable: molgenis.persistence.size
+    default: "30Gi"
+    description: "Size of MOLGENIS filestore"
+    type: enum
+    options:
+    - "30Gi"
+    - "50Gi"
+    - "100Gi"
+    label: Size filestore
+  - variable: elasticsearch.persistence.size
     default: "50Gi"
-    description: "Size of MOLGENIS filestore (not the database size)"
+    description: "Size of ElasticSearch data"
     type: enum
     options:
     - "50Gi"
     - "100Gi"
     - "200Gi"
-    - "300Gi"
+    label: Size for ElasticSearch data
-    label: Size filestore
-  - variable: molgenis.persistence.retain
-    default: false
-    description: "Do you want to retain the persistence volume"
-    type: boolean
-    label: Retain volume

molgenis/templates/deployment.yaml

@@ -49,7 +49,7 @@ spec:
               value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
           ports:
             - containerPort: 8080
-          {{- if .persistence.enabled }}
+          {{- if $.Values.persistence.enabled }}
           volumeMounts:
           - name: molgenis-nfs
             mountPath: /home/molgenis
@@ -92,15 +92,25 @@ spec:
           ports:
             - containerPort: 9200
             - containerPort: 9300
+          {{- if $.Values.persistence.enabled }}
+          volumeMounts:
+          - name: elastic-nfs
+            mountPath: /usr/share/elasticsearch/data
+          {{- end }}
+
           resources:
 {{ toYaml .resources | indent 12 }}
         {{- end }}
 
-{{- if .Values.molgenis.persistence.enabled }}
+{{- if .Values.persistence.enabled }}
       volumes:
         - name: molgenis-nfs
           persistentVolumeClaim:
-            claimName: {{ .Values.molgenis.persistence.name }}
+            claimName: {{ .Values.molgenis.persistence.claim }}
+      volumes:
+        - name: elasticsearch-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.elasticsearch.persistence.claim }}
 {{- end }}
 
     {{- with .Values.nodeSelector }}

molgenis/templates/persistence/elasticsearchPVC.yaml

@@ -0,0 +1,20 @@
+{{- if .Values.persistence.enabled -}}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Values.elasticsearch.persistence.claim }}
+  annotations:
+    {{- if .Values.persistence.retain }}
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
+    {{- else }}
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
+    {{- end }}
+spec:
+  accessModes:
+    - ReadWriteMany
+  resources:
+    requests:
+      storage: {{ .Values.elasticsearch.persistence.size }}
+{{- end }}
+{{- end }}

molgenis/templates/persistence/molgenisPVC.yaml

@@ -1,12 +1,11 @@
-{{- with .Values.molgenis.persistence }}
+{{- if .Values.persistence.enabled -}}
-{{- if .enabled -}}
 apiVersion: extensions/v1beta1
 kind: PersistentVolumeClaim
 apiVersion: v1
 metadata:
-  name: {{ .name }}
+  name: {{ .Values.molgenis.persistence.claim }}
   annotations:
-    {{- if .retain }}
+    {{- if .Values.persistence.retain }}
     volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
     {{- else }}
     volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
@@ -16,6 +15,6 @@ spec:
     - ReadWriteMany
   resources:
     requests:
-      storage: {{ .size }}
+      storage: {{ .Values.molgenis.persistence.size }}
 {{- end }}
 {{- end }}

molgenis/values.yaml

@@ -32,10 +32,8 @@ molgenis:
       cpu: 200m
       memory: 1250Mi
   persistence:
-    enabled: false
+    claim: molgenis-nfs-claim
-    retain: false
+    size: 30Gi
-    name: molgenis-nfs-claim
-    size: 50Gi
   services:
     opencpu:
       host: localhost
@@ -62,6 +60,13 @@ elasticsearch:
    requests:
     cpu: 100m
     memory: 1Gi
+  persistence:
+    claim: elasticsearch-nfs-claim
+    size: 50Gi
+
+persistence:
+  enabled: false
+  retain: false
 
 nodeSelector: {
   deployPod: "true"