Merge branch 'master' of https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm

molgenis-jenkins/README.md

@@ -40,57 +40,62 @@ You can use [all configuration values of the jenkins subchart](https://github.co
 ### GitHub Authentication delegation
 You need to setup a MOLGENIS - Jenkins GitHub OAuth App. You can do this by accessing this url: [add new OAuth app](https://github.com/settings/applications/new).
 
-### Additional configuration
+### Secrets
-There is one additional group of configuration items specific for this chart, so not prefixed with `jenkins`:
 
-* PipelineSecrets
+   When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins.
-
-   When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins and mounted in the jenkins 
-   build pods. The secrets, like the rest of the deployment, is namespaced so multiple instances can run beside
-   each other with their own secrets.
 
    You can override the values at deploy time but otherwise also configure them 
    [in Rancher](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/secrets) or through kubectl.
 
-*  Vault
+#### Vault
 
-   New vault token to be used by the pods to retrieve their tokens from the vault.
+The vault secret gets mounted in the vault pod so pipeline scripts can retrieve secrets from the vault.
 
-   | Parameter                          | Description                                | Default                                        |
+| Parameter                 | Description                                | Default                                        |
-   | ---------------------------------- | ------------------------------------------ | ---------------------------------------------- |
+| ------------------------- | ------------------------------------------ | ---------------------------------------------- |
-   | `PipelineSecrets.Vault.Replace`    | Replace the molgenis-pipeline-vault secret | `true`                                         |
+| `secret.vault.token`      | Token to log into the hashicorp vault      | `xxxx`                                         |
-   | `PipelineSecrets.Vault.Token`      | Token to log into the hashicorp vault      | `xxxx`                                         |
+| `secret.vault.addr`       | Address of the vault                       | `https:vault-operator.vault-operator.svc:8200` |
-   | `PipelineSecrets.Vault.Addr`       | Address of the vault                       | `https:vault-operator.vault-operator.svc:8200` |
+| `secret.vault.skipVerify` | Skip verification of the https connection  | `1`                                            |
-   | `PipelineSecrets.Vault.SkipVerify` | Skip verification of the https connection  | `1`                                            |
 
-*  Env
+#### GitHub
 
-   Environment variables stored in molgenis-pipeline-env secret, to be added as environment variables
+Token used by Jenkins to authenticate on GitHub.
-   in the slave pods.
 
-   | Parameter                               | Description                               | Default         |
+| Parameter             | Description              | Default            |
-   | --------------------------------------- | ----------------------------------------- | --------------- |
+| --------------------- | ------------------------ | ------------------ |
-   | `PipelineSecrets.Env.Replace`           | Replace molgenis-pipeline-env secret      | `true`          |
+| `secret.gitHub.user`  | username for the account | `molgenis-jenkins` |
-   | `PipelineSecrets.Env.PGPPassphrase`     | passphrase for the pgp signing key        | `literal:xxxx`  |
+| `secret.gitHub.token` | token for the account    | `xxxx`             |
-   | `PipelineSecrets.Env.CodecovToken`      | token for codecov.io                      | `xxxx`          |
-   | `PipelineSecrets.Env.GitHubToken`       | token for GH molgenis-jenkins user        | `xxxx`          |
-   | `PipelineSecrets.Env.NexusPassword`     | token for molgenis-jenkins user in NEXUS  | `xxxx`          |
-   | `PipelineSecrets.Env.DockerHubPassword` | token for molgenis user in hub.docker.com | `xxxx`          |
-   | `PipelineSecrets.Env.SonarToken`        | token for sonarcloud.io                   | `xxxx`          |
-   | `PipelineSecrets.Env.NpmToken`          | token for npmjs.org                       | `xxxx`          | 
-   | `PipelineSecrets.Env.SauceAccessKey`    | token for saucelabs.com                   | `xxxx`          |
 
-* File
+#### Gogs
 
-  Environment variables stored in molgenis-pipeline-file secret, to be mounted as files
+Token used by Jenkins to authenticate on the [RuG Webhosting Gogs](https://git.webhosting.rug.nl).
-  in the `/root/.m2` directory of the slave pods.
-  > The settings.xml file references the 
 
-  | Parameter                              | Description                           | Default                                                                         |
+| Parameter           | Description              | Default   |
-  | -------------------------------------- | ------------------------------------- | ------------------------------------------------------------------------------- |
+| ------------------- | ------------------------ | --------- |
-  | `PipelineSecrets.File.Replace`         | Replace molgenis-pipeline-file secret | `true`                                                                          |
+| `secret.gogs.user`  | username for the account | `p281392` |
-  | `PipelineSecrets.File.PGPPrivateKeyAsc`| pgp signing key in ascii form         | `-----BEGIN PGP PRIVATE KEY BLOCK-----xxxxx-----END PGP PRIVATE KEY BLOCK-----` |
+| `secret.gogs.token` | token for the account    | `xxxx`    |
-  | `PipelineSecrets.File.MavenSettingsXML`| Maven settings.xml file               | `<settings>[...]</settings>` (see actual [values.yaml](values.yaml))            |
+
+#### Legacy:
+
+##### Docker Hub
+   
+Account used in pipeline builds to push docker images to `hub.docker.com`.
+> They should read `secret/gcc/account/dockerhub` from vault instead!
+
+| Parameter                   | Description              | Default         |
+| --------------------------- | ------------------------ | --------------- |
+| `secret.dockerHub.user`     | username for the account | `molgenisci`    |
+| `secret.dockerHub.password` | password for the account | `xxxx`          |
+
+##### Registry
+   
+Account used in pipeline builds to push docker images to `registry.molgenis.org`.
+> They should read `secret/ops/account/nexus` from vault instead!
+
+| Parameter                   | Description              | Default   |
+| --------------------------- | ------------------------ | --------- |
+| `secret.dockerHub.user`     | username for the account | `admin`   |
+| `secret.dockerHub.password` | password for the account | `xxxx`    |
 
 ## Command line use
 Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`.

molgenis-jenkins/templates/molgenis-jenkins-dockerhub-secret.yaml

@@ -8,9 +8,9 @@ metadata:
     "jenkins.io/credentials-type": "usernamePassword"
   annotations: {
 # description - can not be a label as spaces are not allowed
-    "jenkins.io/credentials-description" : "user to authenticate against Docker Hub (hub.docker.com)"
+    "jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to Docker Hub (hub.docker.com)"
   }
 type: Opaque
 data:
-  username: {{ "molgenisci" | b64enc | quote }}
+  username: {{ .Values.secret.registry.user | b64enc | quote }}
-  password: {{ .Values.PipelineSecrets.Env.DockerHubPassword | b64enc | quote }}
+  password: {{ .Values.secret.registry.password | b64enc | quote }}

molgenis-jenkins/templates/molgenis-jenkins-github-secret.yaml

@@ -8,9 +8,9 @@ metadata:
     "jenkins.io/credentials-type": "usernamePassword"
   annotations: {
 # description - can not be a label as spaces are not allowed
-    "jenkins.io/credentials-description" : "oauth token for the molgenis-jenkins github user"
+    "jenkins.io/credentials-description" : "Oauth token for the {{.Values.secret.gitHub.user}} GitHub user"
   }
 type: Opaque
 data:
-  username: {{ "molgenis-jenkins" | b64enc | quote }}
+  username: {{ .Values.secret.gitHub.user | b64enc | quote }}
-  password: {{ .Values.PipelineSecrets.Env.GitHubToken | b64enc | quote }}
+  password: {{ .Values.secret.gitHub.token | b64enc | quote }}

molgenis-jenkins/templates/molgenis-jenkins-gogs-secret.yaml

@@ -8,9 +8,9 @@ metadata:
     "jenkins.io/credentials-type": "usernamePassword"
   annotations: {
 # description - can not be a label as spaces are not allowed
-    "jenkins.io/credentials-description" : "user to authenticate against GOGS (git.webhosting.rug.nl)"
+    "jenkins.io/credentials-description" : "Account used to authenticate against RuG Webhosting Gogs."
   }
 type: Opaque
 data:
-  username: {{ "p281392" | b64enc | quote }}
+  username: {{ .Values.secret.gogs.user | b64enc | quote }}
-  password: {{ .Values.PipelineSecrets.Env.GogsToken | b64enc | quote }}
+  password: {{ .Values.secret.gogs.token | b64enc | quote }}

molgenis-jenkins/templates/molgenis-jenkins-nexus-secret.yaml

@@ -1,16 +0,0 @@
-apiVersion: v1
-kind: Secret
-metadata:
-# this is the jenkins id.
-  name: "molgenis-jenkins-nexus-secret"
-  labels:
-# so we know what type it is.
-    "jenkins.io/credentials-type": "usernamePassword"
-  annotations: {
-# description - can not be a label as spaces are not allowed
-    "jenkins.io/credentials-description" : "user to authenticate against NEXUS"
-  }
-type: Opaque
-data:
-  username: {{ "admin" | b64enc | quote }}
-  password: {{ .Values.PipelineSecrets.Env.NexusPassword | b64enc | quote }}

molgenis-jenkins/templates/molgenis-jenkins-registry-secret.yaml

@@ -0,0 +1,17 @@
+apiVersion: v1
+kind: Secret
+metadata:
+  name: molgenis-jenkins-registry-secret
+  labels:
+    app: {{ template "jenkins.fullname" . }}
+    chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
+    release: "{{ .Release.Name }}"
+    heritage: "{{ .Release.Service }}"
+  annotations: {
+# description - can not be a label as spaces are not allowed
+    "jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to registry.molgenis.org."
+  }
+type: Opaque
+data:
+  username: {{ .Values.secret.registry.user | b64enc | quote }}
+  password: {{ .Values.secret.registry.password | b64enc | quote }}

molgenis-jenkins/templates/molgenis-jenkins-saucelabs-secret.yaml

@@ -1,16 +0,0 @@
-apiVersion: v1
-kind: Secret
-metadata:
-# this is the jenkins id.
-  name: "molgenis-jenkins-saucelabs-secret"
-  labels:
-# so we know what type it is.
-    "jenkins.io/credentials-type": "usernamePassword"
-  annotations: {
-# description - can not be a label as spaces are not allowed
-    "jenkins.io/credentials-description" : "user to authenticate against Saucelabs (saucelabs.com)"
-  }
-type: Opaque
-data:
-  username: {{ "molgenis-jenkins" | b64enc | quote }}
-  password: {{ .Values.PipelineSecrets.Env.SauceAccessKey | b64enc | quote }}

molgenis-jenkins/templates/molgenis-pipeline-env-secret.yaml

@@ -1,18 +0,0 @@
-{{- if .Values.PipelineSecrets.Env.Replace }}
-apiVersion: v1
-kind: Secret
-metadata:
-  name: molgenis-pipeline-env-secret
-  labels:
-    app: {{ template "jenkins.fullname" . }}
-    chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
-    release: "{{ .Release.Name }}"
-    heritage: "{{ .Release.Service }}"
-type: Opaque
-data:
-  pgpPassphrase: {{ .Values.PipelineSecrets.Env.PGPPassphrase | b64enc | quote }}
-  codecovToken: {{ .Values.PipelineSecrets.Env.CodecovToken | b64enc | quote }}
-  githubToken: {{ .Values.PipelineSecrets.Env.GitHubToken | b64enc | quote }}
-  sonarToken: {{ .Values.PipelineSecrets.Env.SonarToken | b64enc | quote }}
-  npmToken: {{ .Values.PipelineSecrets.Env.NpmToken | b64enc | quote }}
-{{- end }}

molgenis-jenkins/templates/molgenis-pipeline-file-secret.yaml

@@ -1,15 +0,0 @@
-{{- if .Values.PipelineSecrets.File.Replace }}
-apiVersion: v1
-kind: Secret
-metadata:
-  name: molgenis-pipeline-file-secret
-  labels:
-    app: {{ template "jenkins.fullname" . }}
-    chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
-    release: "{{ .Release.Name }}"
-    heritage: "{{ .Release.Service }}"
-type: Opaque
-data:
-  key.asc: {{ .Values.PipelineSecrets.File.PGPPrivateKeyAsc | b64enc | quote }}
-  settings.xml: {{ .Values.PipelineSecrets.File.MavenSettingsXML | b64enc | quote }}
-{{- end }}

molgenis-jenkins/templates/molgenis-pipeline-vault-secret.yaml

@@ -1,4 +1,3 @@
-{{- if .Values.PipelineSecrets.Vault.Replace }}
 apiVersion: v1
 kind: Secret
 metadata:
@@ -10,7 +9,6 @@ metadata:
     heritage: "{{ .Release.Service }}"
 type: Opaque
 data:
-  token: {{ .Values.PipelineSecrets.Vault.Token | b64enc | quote }}
+  token: {{ .Values.secret.vault.token | b64enc | quote }}
-  addr: {{ .Values.PipelineSecrets.Vault.Addr | b64enc | quote }}
+  addr: {{ .Values.secret.vault.addr | b64enc | quote }}
-  skipVerify: {{ .Values.PipelineSecrets.Vault.SkipVerify | b64enc | quote }}
+  skipVerify: {{ .Values.secret.vault.skipVerify | b64enc | quote }}
-{{- end }}

molgenis-jenkins/values.yaml

@@ -368,8 +368,8 @@ jenkins:
     install: true
   Pods:
     molgenis:
-      Label: molgenisv2
+      Label: molgenis
-      NodeUsageMode: EXCLUSIVE
+      NodeUsageMode: NORMAL
       volumes:
         - type: HostPath
           hostPath: "/var/run/docker.sock"
@@ -417,39 +417,6 @@ jenkins:
               secretName: molgenis-pipeline-vault-secret
               secretKey: addr
       NodeSelector: {}
-    molgenis-legacy:
-      InheritFrom: molgenis
-      Label: molgenis
-      NodeUsageMode: NORMAL
-      volumes:
-        - type: Secret
-          secretName: molgenis-pipeline-file-secret
-          mountPath: "/home/jenkins/.m2"
-      Containers:
-      EnvVars:
-        - type: Secret
-          key: PGP_PASSPHRASE
-          secretName: molgenis-pipeline-env-secret
-          secretKey: pgpPassphrase
-        - type: KeyValue
-          key: PGP_SECRETKEY
-          value: "keyfile:/home.jenkins/.m2/key.asc"
-        - type: KeyValue
-          key: npm_config_registry
-          value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
-        - type: Secret
-          key: SONAR_TOKEN
-          secretName: molgenis-pipeline-env-secret
-          secretKey: sonarToken
-        - type: Secret
-          key: CODECOV_TOKEN
-          secretName: molgenis-pipeline-env-secret
-          secretKey: codecovToken
-        - type: Secret
-          key: GITHUB_TOKEN
-          secretName: molgenis-pipeline-env-secret
-          secretKey: githubToken
-      NodeSelector: {}
     node:
       Label: node-carbon
       NodeUsageMode: EXCLUSIVE
@@ -461,155 +428,45 @@ jenkins:
           Command: cat
           WorkingDir: /home/jenkins
           TTY: true
-      EnvVars:
+        vault:
-        - type: KeyValue
+          Image: "vault"
-          key: npm_config_registry
+          Command: cat
-          value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
+          WorkingDir: /home/jenkins
-        - type: Secret
+          TTY: true
-          key: CODECOV_TOKEN
-          secretName: molgenis-pipeline-env-secret
-          secretKey: codecovToken
-        - type: Secret
-          key: GITHUB_TOKEN
-          secretName: molgenis-pipeline-env-secret
-          secretKey: githubToken
-        - type: Secret
-          key: NPM_TOKEN
-          secretName: molgenis-pipeline-env-secret
-          secretKey: npmToken
-      NodeSelector: {}
-    molgenis-it:
-      InheritFrom: molgenis
-      Label: molgenis-it
-      NodeUsageMode: EXCLUSIVE
-      Containers:
-        elasticsearch:
-          Image: docker.elastic.co/elasticsearch/elasticsearch
-          ImageTag: 5.5.3
-          resources:
-            requests:
-              cpu: "100m"
-              memory: "1Gi"
-            limits:
-              cpu: "1"
-              memory: "1500Mi"
           EnvVars:
-          - type: KeyValue
+            - type: Secret
-            key: ES_JAVA_OPTS
+              key: VAULT_TOKEN
-            value: "-Xms512m -Xmx512m"
+              secretName: molgenis-pipeline-vault-secret
-          - type: KeyValue
+              secretKey: token
-            key: cluster.name
+            - type: Secret
-            value: molgenis
+              key: VAULT_SKIP_VERIFY
-          - type: KeyValue
+              secretName: molgenis-pipeline-vault-secret
-            key: bootstrap.memory_lock
+              secretKey: skipVerify
-            value: "true"
+            - type: Secret
-          - type: KeyValue
+              key: VAULT_ADDR
-            key: xpack.security.enabled
+              secretName: molgenis-pipeline-vault-secret
-            value: "false"
+              secretKey: addr
-          - type: KeyValue
-            key: discovery.type
-            value: single-node
-        postgres:
-          Image: postgres
-          ImageTag: 9.6-alpine
-          resources:
-            requests:
-              cpu: "100m"
-              memory: "250Mi"
-            limits:
-              cpu: "1"
-              memory: "250Mi"
-          EnvVars:
-          - type: KeyValue
-            key: POSTGRES_USER
-            value: molgenis
-          - type: KeyValue
-            key: POSTGRES_PASSWORD
-            value: molgenis
-          - type: KeyValue
-            key: POSTGRES_DB
-            value: molgenis
-        opencpu:
-          Image: molgenis/opencpu
-          AlwaysPullImage: true
-          resources:
-            requests:
-              cpu: "100m"
-              memory: "256Mi"
-            limits:
-              cpu: "1"
-              memory: "512Mi"
       NodeSelector: {}
-PipelineSecrets:
+#secret contains configuration for the kubernetes secrets that jenkins can access
-  Vault:
+secret:
-    Replace: true
+  # vault configures the vault secret
-    Token: xxxx
+  vault:
-    Addr: "https://vault-operator.vault-operator.svc:8200"
+    token: xxxx
-    SkipVerify: 1
+    addr: "https://vault-operator.vault-operator.svc:8200"
-  Env:
+    skipVerify: "1"
-    # Set to false to keep existing secret
+  # githubToken contains access token for jenkins bot account on github.com
-    Replace: true
+  gitHub:
-    # Passphrase for the pgp private key file, prefixed with literal:
+    user: "molgenis-jenkins"
-    PGPPassphrase: literal:xxxx
+    token: xxxx
-    # Token for codecov.io service
+  # gogs contains access token for jenkins bot account on RuG GoGs
-    CodecovToken: xxxx
+  gogs:
-    # Token for github bot account
+    user: p281392
-    GitHubToken: xxxx
+    token: xxxx
-    # Token for github bot account
+  # registry contains credentials for registry.molgenis.org
-    GogsToken: xxxx
+  registry:
-    # Token for sonarcloud.io
+    user: admin
-    SonarToken: xxxx
+    password: xxxx
-    # Token for npmjs.org
+  # dockerHubPassword contains password for hub.docker.com
-    NpmToken: xxxx
+  dockerHub:
-    # Password Local NEXUS
+    user: molgenisci
-    NexusPassword: xxxx
+    password: xxxx
-    # Password hub.docker.com
-    DockerHubPassword: xxxx
-    # Access key for saucelabs.com
-    SauceAccessKey: xxxx
-  File:
-    # Set to false to keep existing secret
-    Replace: true
-    # PGP Private key in ascii format used to sign artifacts
-    PGPPrivateKeyAsc: |-
-      -----BEGIN PGP PRIVATE KEY BLOCK-----
-      xxxxx
-      -----END PGP PRIVATE KEY BLOCK-----
-    # maven.settings file
-    MavenSettingsXML: |-
-      <settings>
-        <localRepository>${user.home}/.mvnrepository</localRepository>
-        <interactiveMode>false</interactiveMode>
-        <mirrors>
-          <mirror>
-            <id>nexus</id>
-            <mirrorOf>external:*</mirrorOf>
-            <url>http://nexus.molgenis-nexus:8081/repository/maven-central/</url>
-          </mirror>
-        </mirrors>
-        <servers>
-          <!-- for snapshot builds of the master -->
-          <server>
-            <id>sonatype-nexus-staging</id>
-            <username>molgenis</username>
-            <password>xxxx</password>
-          </server>
-          <server>
-            <id>local-nexus</id>
-            <url>http://nexus.molgenis-nexus:8081/repository/maven-snapshots/</url>
-            <username>admin</username>
-            <password>xxxxx</password>
-          </server>
-          <!-- for docker images-->
-          <server>
-            <id>registry.molgenis.org</id>
-            <username>admin</username>
-            <password>xxxx</password>
-          </server>
-          <server>
-            <id>registry.hub.docker.com</id>
-            <username>molgenisci</username>
-            <password>xxxx</password>
-          </server>
-        </servers>
-      </settings>

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"
@@ -97,3 +97,35 @@ questions:
   - "1g"
   - "2g"
   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: []