Merge branch 'add-pvs-to-molgenis' of p281392/molgenis-ops-docker-helm into master

molgenis/Chart.yaml

@@ -2,7 +2,7 @@ apiVersion: v1
 appVersion: "1.0"
 description: MOLGENIS - helm stack (in BETA)
 name: molgenis-beta
-version: 0.1.0
+version: 0.3.0
 sources:
 - https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
 icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis/catalogIcon-molgenis.svg

molgenis/README.md

@@ -79,5 +79,44 @@ Specify memory usage for Java JVM:
 
 Select the resources you need dependant on the customer you need to serve.
 
+## Persistence
+You can enable persistence on your MOLGENIS stack by specifying the following property.
+
+- ```persistence.enabled```
+
+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:
+
+```
+kubectl get pv
+```
+
+You can now view the persistent volume claims and the attached volumes.
+
+| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
+| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
+| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-solverd/molgenis-nfs-claim | nfs-provisioner-retain | | | 33d |
+| pvc-3984723d-220f-14e8-a98a-skjhf88823kk | 30G | RWO | | Delete | Bound | molgenis-test/molgenis-nfs-claim | nfs-provisioner | | | 33d |
+
+You see the ```molgenis-test/molgenis-nfs-claim``` is bound to the volume: ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
+When you want to view the data in the this volume you can go to the nfs-provisioning pod and execute the shell. Go to the directory ```export``` and lookup the directory ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```. 
+
 ## Firewall
 Is defined at cluster level. This chart does not facilitate firewall configuration.

molgenis/questions.yml

@@ -81,7 +81,7 @@ questions:
 - variable: molgenis.resources.requests.memory
   label: Container memory reservation
   default: 1250Mi
-  description: "Memory reservation for this MOLGENIS container"
+  description: "Memory reservation for this MOLGENIS container (must fit in the selected memory limit for the container)"
   type: enum
   options:
   - "1250Mi"
@@ -96,4 +96,36 @@ questions:
   options:
   - "1g"
   - "2g"
-  group: "Resources"
+  group: "Resources"
+- variable: persistence.enabled
+  default: false
+  description: "Do you want to use persistence"
+  type: boolean
+  required: true
+  group: "Persistence"
+  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 (PostgreSQL and ElasticSearch excluded)"
+    type: enum
+    options:
+    - "30Gi"
+    - "50Gi"
+    - "100Gi"
+    label: Size MOLGENIS filestore
+  - variable: elasticsearch.persistence.size
+    default: "50Gi"
+    description: "Size of ElasticSearch data (directory that is persist: /usr/share/elasticsearch/data)"
+    type: enum
+    options:
+    - "50Gi"
+    - "100Gi"
+    - "200Gi"
+    label: Size for ElasticSearch data

molgenis/templates/deployment.yaml

@@ -49,6 +49,11 @@ spec:
               value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
           ports:
             - containerPort: 8080
+          {{- if $.Values.persistence.enabled }}
+          volumeMounts:
+          - name: molgenis-nfs
+            mountPath: /home/molgenis
+          {{- end }}
           livenessProbe:
             httpGet:
               path: /
@@ -87,10 +92,25 @@ spec:
           ports:
             - containerPort: 9200
             - containerPort: 9300
+          {{- if $.Values.persistence.enabled }}
+          volumeMounts:
+          - name: elasticsearch-nfs
+            mountPath: /usr/share/elasticsearch/data
+          {{- end }}
+
           resources:
 {{ toYaml .resources | indent 12 }}
         {{- end }}
 
+{{- if .Values.persistence.enabled }}
+      volumes:
+        - name: molgenis-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.molgenis.persistence.claim }}
+        - name: elasticsearch-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.elasticsearch.persistence.claim }}
+{{- end }}
 
     {{- with .Values.nodeSelector }}
       nodeSelector:

molgenis/templates/persistence/elasticsearchPVC.yaml

@@ -0,0 +1,19 @@
+{{- 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 }}

molgenis/templates/persistence/molgenisPVC.yaml

@@ -0,0 +1,19 @@
+{{- if .Values.persistence.enabled -}}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Values.molgenis.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.molgenis.persistence.size }}
+{{- end }}

molgenis/values.yaml

@@ -25,12 +25,15 @@ molgenis:
   javaOpts:
     maxHeapSpace: "1g"
   resources:
-   limits:
+    limits:
-    cpu: 1
+      cpu: 1
-    memory: 1250Mi
+      memory: 1250Mi
-   requests:
+    requests:
-    cpu: 200m
+      cpu: 200m
-    memory: 1250Mi
+      memory: 1250Mi
+  persistence:
+    claim: molgenis-nfs-claim
+    size: 30Gi
   services:
     opencpu:
       host: localhost
@@ -57,8 +60,17 @@ elasticsearch:
    requests:
     cpu: 100m
     memory: 1Gi
+  persistence:
+    claim: elasticsearch-nfs-claim
+    size: 50Gi
 
-nodeSelector: {}
+persistence:
+  enabled: false
+  retain: false
+
+nodeSelector: {
+  deployPod: "true"
+}
 
 tolerations: []