chore (Jenkinsfile): Only deploy if branch is master

This reverts commit f94e6da6e3, reversing
changes made to b73fd578ea.

.gitignore

@@ -1,2 +1,3 @@
 .idea
-*.iml
+*.iml
+target

Jenkinsfile

@@ -0,0 +1,40 @@
+pipeline {
+    agent {
+        kubernetes {
+            label 'helm'
+        }
+    }
+    stages {
+        stage('Test') {
+            steps {
+                container('chart-testing') {
+                    sh "chart_test.sh --no-install --all"
+                }
+            }
+        }
+        stage('Package') {
+            steps {
+                container('chart-testing'){
+                    sh 'mkdir target'
+                    sh 'for dir in charts/*; do helm package --destination target "$dir"; done'
+                }
+            }
+        }
+        stage('Deploy') {
+            when {
+                branch 'master'
+            }
+            steps {
+                container('vault') {
+                    script {
+                        env.NEXUS_USER = sh(script: 'vault read -field=username secret/ops/account/nexus', returnStdout: true)
+                        env.NEXUS_PWD = sh(script: 'vault read -field=password secret/ops/account/nexus', returnStdout: true)
+                    }
+                }
+                container('alpine') {
+                    sh 'set +x; for chart in target/*; do curl -L -u $NEXUS_USER:$NEXUS_PWD http://registry.molgenis.org/repository/helm/ --upload-file "$chart"; done'
+                }
+            }
+        }
+    }
+}

README.md

@@ -104,6 +104,7 @@ This repository is serves also as a catalogue for Rancher. We have serveral apps
 - [Jenkins](molgenis-jenkins/README.md)
 - [NEXUS](molgenis-nexus/README.md)
 - [HTTPD](molgenis-httpd/README.md)
+- [MOLGENIS](molgenis/README.md)
 - [MOLGENIS preview](molgenis-preview/README.md)
 - [MOLGENIS vault](molgenis-vault/README.md)
 
@@ -122,6 +123,26 @@ You can you need to know to easily develop and deploy helm-charts
   
   Do it in the root of the project where the Chart.yaml is located
   It installs a release of a kubernetes stack. You also store this as an artifact in a kubernetes repository
+- ```helm package .```
+  
+  You can create a package which can be uploaded in the molgenis helm repository
+  
+- ```helm publish```
+  You still have to create an ```index.yaml``` for the chart. You can do this by executing this command: ```helm repo index #directory name of helm chart#```
+  
+  Then you can upload it by executing:
+  
+  - ```curl -v --user #username#:#password# --upload-file index.yaml  https://registry.molgenis.org/repository/helm/#chart name#/index.yml```
+  - ```curl -v --user #username#:#password# --upload-file #chart name#-#version#.tgz https://registry.molgenis.org/repository/helm/#chart name#/#chart name#-#version#.tgz```
+  
+  Now you have to add the repository locally to use in your ```requirements.yaml```.
+  
+  - ```helm repo add #repository name# https://registry.molgenis.org/repository/helm/molgenis```
+
+- ```helm dep build```
+  
+  You can build your dependencies (create a ```charts``` directory and install the chart in it) of the helm-chart. 
+
 - ```helm list```
   
   Lists all installed releases

charts/molgenis-httpd/Chart.yaml

@@ -5,4 +5,8 @@ name: molgenis-httpd
 version: 0.1.0
 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-httpd/catalogIcon-molgenis-httpd.svg
+icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-httpd/catalogIcon-molgenis-httpd.svg
+home: http://httpd.apache.org
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/molgenis-httpd/values.yaml

@@ -48,4 +48,4 @@ nodeSelector: {}
 
 tolerations: []
 
-affinity: {}
+affinity: {}

charts/molgenis-jenkins/Chart.yaml

@@ -1,8 +1,11 @@
 name: molgenis-jenkins
 home: https://jenkins.io/
-version: 0.7.0
-appVersion: 2.121
+version: 0.8.1
+appVersion: 2.138.1
 description: Molgenis installation for the jenkins chart.
 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-jenkins/catalogIcon-molgenis-jenkins.svg
+maintainers:
+- name: fdlk
+- name: sidohaakma

charts/molgenis-jenkins/README.md

@@ -75,6 +75,10 @@ Token used by Jenkins to authenticate on the [RuG Webhosting Gogs](https://git.w
 | `secret.gogs.user`  | username for the account | `p281392` |
 | `secret.gogs.token` | token for the account    | `xxxx`    |
 
+
+#### Slack
+The Slack integration is done mostly in the Jenkinsfile of each project. It is sufficient to only add the plugin to the Jenkins configuration in Helm.
+
 #### Legacy:
 
 ##### Docker Hub

charts/molgenis-jenkins/requirements.lock

@@ -1,6 +1,6 @@
 dependencies:
 - name: jenkins
   repository: https://kubernetes-charts.storage.googleapis.com/
-  version: 0.16.4
+  version: 0.18.0
 digest: sha256:39f694515489598fa545c9a5a4f1347749e8f2a8d7fae6ccae3e2acae1564685
-generated: 2018-06-27T14:36:23.172954738+02:00
+generated: 2018-09-27T11:00:15.795416984+02:00

charts/molgenis-jenkins/resources/README.md

@@ -0,0 +1,8 @@
+# Helm in Jenkins
+
+To be able to run helm inside a jenkins pod, you'll need to 
+* create a role in the namespace where tiller is installed
+* bind that role to the user that jenkins pods run as
+
+This directory contains yaml for these resources.
+See also https://github.com/helm/helm/blob/master/docs/rbac.md

charts/molgenis-jenkins/resources/jenkins-default-tiller-user-rolebinding.yaml

@@ -0,0 +1,13 @@
+apiVersion: rbac.authorization.k8s.io/v1beta1
+kind: RoleBinding
+metadata:
+  name: tiller-jenkins-binding
+  namespace: kube-system
+roleRef:
+  apiGroup: rbac.authorization.k8s.io
+  kind: Role
+  name: tiller-user
+subjects:
+- kind: ServiceAccount
+  name: default
+  namespace: molgenis-jenkins

charts/molgenis-jenkins/resources/tiller-user-role.yaml

@@ -0,0 +1,18 @@
+apiVersion: rbac.authorization.k8s.io/v1beta1
+kind: Role
+metadata:
+  name: tiller-user
+  namespace: kube-system
+rules:
+- apiGroups:
+  - ""
+  resources:
+  - pods/portforward
+  verbs:
+  - create
+- apiGroups:
+  - ""
+  resources:
+  - pods
+  verbs:
+  - list

charts/molgenis-jenkins/values.yaml

@@ -3,17 +3,18 @@ jenkins:
     HostName: jenkins.molgenis.org
     ServiceType: ClusterIP
     InstallPlugins:
-      - kubernetes:1.12.0
+      - kubernetes:1.12.6
       - workflow-aggregator:2.5
-      - workflow-job:2.21
+      - workflow-job:2.25
       - credentials-binding:1.16
       - git:3.9.1
       - github-branch-source:2.3.6
-      - kubernetes-credentials-provider:0.9
-      - blueocean:1.6.2
+      - kubernetes-credentials-provider:0.10
+      - blueocean:1.8.3
       - github-oauth:0.29
       - gogs-webhook:1.0.14
-      - sauce-ondemand:1.176
+      - github-scm-trait-commit-skip:0.1.1
+      - slack:2.3
     Security:
       UseGitHub: false
       GitHub:
@@ -82,6 +83,18 @@ jenkins:
                   <strategyId>1</strategyId>
                   <trust class="org.jenkinsci.plugins.github_branch_source.ForkPullRequestDiscoveryTrait$TrustPermission"/>
                 </org.jenkinsci.plugins.github__branch__source.ForkPullRequestDiscoveryTrait>
+                <org.jenkinsci.plugins.scm__filter.GitHubCommitSkipTrait plugin="github-scm-trait-commit-skip@0.1.1"/>
+                <jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
+                  <extension class="hudson.plugins.git.extensions.impl.LocalBranch">
+                    <localBranch>**</localBranch>
+                  </extension>
+                </jenkins.plugins.git.traits.LocalBranchTrait>
+                <jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
+                  <extension class="hudson.plugins.git.extensions.impl.UserIdentity">
+                    <name>MOLGENIS Jenkins</name>
+                    <email>molgenis+ci@gmail.com</email>
+                  </extension>
+                </jenkins.plugins.git.traits.UserIdentityTrait>
               </traits>
             </org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator>
           </navigators>
@@ -131,6 +144,17 @@ jenkins:
                   <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
                   <traits>
                     <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                    <jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.LocalBranch">
+                        <localBranch>**</localBranch>
+                      </extension>
+                    </jenkins.plugins.git.traits.LocalBranchTrait>
+                    <jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.UserIdentity">
+                        <name>MOLGENIS Jenkins</name>
+                        <email>molgenis+ci@gmail.com</email>
+                      </extension>
+                    </jenkins.plugins.git.traits.UserIdentityTrait>
                   </traits>
                 </source>
                 <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@@ -184,6 +208,17 @@ jenkins:
                   <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
                   <traits>
                     <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                    <jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.LocalBranch">
+                        <localBranch>**</localBranch>
+                      </extension>
+                    </jenkins.plugins.git.traits.LocalBranchTrait>
+                    <jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.UserIdentity">
+                        <name>MOLGENIS Jenkins</name>
+                        <email>molgenis+ci@gmail.com</email>
+                      </extension>
+                    </jenkins.plugins.git.traits.UserIdentityTrait>
                   </traits>
                 </source>
                 <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@@ -237,6 +272,17 @@ jenkins:
                   <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
                   <traits>
                     <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                    <jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.LocalBranch">
+                        <localBranch>**</localBranch>
+                      </extension>
+                    </jenkins.plugins.git.traits.LocalBranchTrait>
+                    <jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.UserIdentity">
+                        <name>MOLGENIS Jenkins</name>
+                        <email>molgenis+ci@gmail.com</email>
+                      </extension>
+                    </jenkins.plugins.git.traits.UserIdentityTrait>
                   </traits>
                 </source>
                 <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@@ -290,6 +336,17 @@ jenkins:
                   <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
                   <traits>
                     <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                    <jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.LocalBranch">
+                        <localBranch>**</localBranch>
+                      </extension>
+                    </jenkins.plugins.git.traits.LocalBranchTrait>
+                    <jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.UserIdentity">
+                        <name>MOLGENIS Jenkins</name>
+                        <email>molgenis+ci@gmail.com</email>
+                      </extension>
+                    </jenkins.plugins.git.traits.UserIdentityTrait>
                   </traits>
                 </source>
                 <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@@ -343,6 +400,17 @@ jenkins:
                   <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
                   <traits>
                     <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                    <jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.LocalBranch">
+                        <localBranch>**</localBranch>
+                      </extension>
+                    </jenkins.plugins.git.traits.LocalBranchTrait>
+                    <jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.UserIdentity">
+                        <name>MOLGENIS Jenkins</name>
+                        <email>molgenis+ci@gmail.com</email>
+                      </extension>
+                    </jenkins.plugins.git.traits.UserIdentityTrait>
                   </traits>
                 </source>
                 <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@@ -416,6 +484,12 @@ jenkins:
               key: VAULT_ADDR
               secretName: molgenis-pipeline-vault-secret
               secretKey: addr
+        helm:
+          Image: "lachlanevenson/k8s-helm"
+          ImageTag: "v2.10.0"
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
       NodeSelector: {}
     node:
       Label: node-carbon
@@ -447,7 +521,104 @@ jenkins:
               secretName: molgenis-pipeline-vault-secret
               secretKey: addr
       NodeSelector: {}
-#secret contains configuration for the kubernetes secrets that jenkins can access
+    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
+            key: ES_JAVA_OPTS
+            value: "-Xms512m -Xmx512m"
+          - type: KeyValue
+            key: cluster.name
+            value: molgenis
+          - type: KeyValue
+            key: bootstrap.memory_lock
+            value: "true"
+          - type: KeyValue
+            key: xpack.security.enabled
+            value: "false"
+          - 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: {}
+    helm:
+      Label: helm
+      NodeUsageMode: EXCLUSIVE
+      Containers:
+        chart-testing:
+          Image: "quay.io/helmpack/chart-testing"
+          ImageTag: v1.1.0
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
+        alpine:
+          Image: "spotify/alpine"
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
+        vault:
+          Image: "vault"
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
+          EnvVars:
+            - type: Secret
+              key: VAULT_TOKEN
+              secretName: molgenis-pipeline-vault-secret
+              secretKey: token
+            - type: Secret
+              key: VAULT_SKIP_VERIFY
+              secretName: molgenis-pipeline-vault-secret
+              secretKey: skipVerify
+            - type: Secret
+              key: VAULT_ADDR
+              secretName: molgenis-pipeline-vault-secret
+              secretKey: addr
+      NodeSelector: {}
+
+# secret contains configuration for the kubernetes secrets that jenkins can access
 secret:
   # vault configures the vault secret
   vault:
@@ -469,4 +640,4 @@ secret:
   # dockerHubPassword contains password for hub.docker.com
   dockerHub:
     user: molgenisci
-    password: xxxx
+    password: xxxx

charts/molgenis-nexus/Chart.yaml

@@ -2,7 +2,11 @@ apiVersion: v1
 appVersion: "1.0"
 description: Nexus stack for MOLGENIS
 name: molgenis-nexus
-version: 0.3.0
+version: 0.4.2
 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-nexus/catalogIcon-molgenis-nexus.svg
+icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-nexus/catalogIcon-molgenis-nexus.svg
+home: https://www.sonatype.com/nexus-repository-oss
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/molgenis-nexus/README.md

@@ -0,0 +1,69 @@
+# MOLGENIS - NEXUS Helm Chart
+
+NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
+
+## Chart Details
+
+This chart will deploy:
+
+- 1 NEXUS-nfs initialization container
+
+  We need this container to avoid permission issues on the NEXUS docker
+- 1 NEXUS container
+- 1 MOLGENIS-httpd container (to proxy the registry and docker to one domain)
+
+## Backup restore
+There are two steps in restoring the NEXUS.
+
+- Database
+- Blobstore
+
+### Restore the database
+Go to the commandline:
+
+```bash
+kubectl get pv
+```
+
+```bash
+| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
+| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
+| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-nexus/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 |
+```
+
+The persistent volume is the one in the molgenis-nexus namespace. 
+
+Go to the NFS-provisioner to the path of the persistent volume:
+
+```bash
+ls -t --full-time | head -7 | xargs cp ../restore-from-backup/
+```
+
+### Restore the blobstore
+You can copy the directory ```blobs``` to the target persistent volume ```/ blobs```.
+
+You can now bring the NEXUS back up.
+
+## Installing the Chart
+
+You can test in install the chart by executing:
+
+```helm lint .```
+
+To test if your helm chart-syntax is right and:
+
+```helm install . --dry-run --debug```
+
+To test if your hem chart works and:
+
+```helm install .```
+
+To deploy it on the cluster.
+
+```curl -L -u xxxx:xxxx http://registry.molgenis.org/repository/helm/ --upload-file molgenis-x.x.x.tgz```
+
+To push it to the registry
+
+
+

charts/molgenis-nexus/templates/deployments/nexus-deployment.yaml

@@ -19,18 +19,14 @@ spec:
         app: {{ .Values.nexus.name }}
       creationTimestamp: null
     spec:
-      volumes:
-      - name: {{ .Values.persistence.name }}
-        persistentVolumeClaim:
-          claimName: {{ .Values.persistence.name }}
       restartPolicy: {{ .Values.nexus.restartPolicy }}
       initContainers:
-      - name: volume-mount-nexus
+      - name: nexus-nfs
         image: busybox
-        command: ["sh", "-c", "chown -R 200:200 {{ .Values.persistence.mountPath }}"]
+        command: ["sh", "-c", "chown -R 200:200 /nexus-data"]
         volumeMounts:
-        - name: {{ .Values.persistence.name }}
-          mountPath: "{{ .Values.persistence.mountPath }}"
+        - name: molgenis-nexus-nfs
+          mountPath: "/nexus-data"
       containers:
       - name: {{ .Values.nexus.name }}
         image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
@@ -39,6 +35,31 @@ spec:
         - containerPort: {{ .Values.nexus.port.ui }}
         - containerPort: {{ .Values.nexus.port.docker }}
         volumeMounts:
-        - name: {{ .Values.persistence.name }}
-          mountPath: "/nexus-data"
+        - name: molgenis-nexus-nfs
+          mountPath: /nexus-data
+        livenessProbe:
+          httpGet:
+            path: /
+            port: {{ .Values.nexus.port.ui }}
+          initialDelaySeconds: 120
+          periodSeconds: 20
+          failureThreshold: 15
+          successThreshold: 1
+        readinessProbe:
+          httpGet:
+            path: /
+            port: {{ .Values.nexus.port.ui }}
+          initialDelaySeconds: 120
+          periodSeconds: 20
+          failureThreshold: 15
+          successThreshold: 1
 
+      volumes:
+        - name: molgenis-nexus-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.persistence.claim }}
+
+    {{- with .Values.nodeSelector }}
+      nodeSelector:
+{{ toYaml . | indent 8 }}
+    {{- end }}

charts/molgenis-nexus/templates/deployments/nexusProxy-deployment.yaml

@@ -0,0 +1,55 @@
+apiVersion: extensions/v1beta1
+kind: Deployment
+metadata:
+  creationTimestamp: null
+  name: {{ .Values.nexusProxy.name }}
+  labels:
+    app: {{ .Values.nexusProxy.name }}
+    environment: {{ .Values.environment }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  strategy:
+    type: {{ .Values.nexusProxy.strategy.type }}
+  selector:
+    matchLabels:
+      app: {{ .Values.nexusProxy.selector }}
+  template:
+    metadata:
+      labels:
+        app: {{ .Values.nexusProxy.name }}
+      creationTimestamp: null
+    spec:
+      restartPolicy: {{ .Values.nexusProxy.restartPolicy }}
+      containers:
+      - name: {{ .Values.nexusProxy.name }}
+        image: "{{ .Values.nexusProxy.image.repository }}:{{ .Values.nexusProxy.image.tag }}"
+        imagePullPolicy: {{ .Values.nexusProxy.image.pullPolicy }}
+        env:
+        - name: PROXY_SERVICE
+          value: "{{ .Values.nexus.name }}:{{ .Values.nexus.port.ui }},{{ .Values.nexus.name }}:{{ .Values.nexus.port.docker }}:{{ .Values.nexus.path.dockerV2 }}"
+        - name: SERVER_NAME
+          value: {{ .Values.nexusProxy.hostname }}
+        ports:
+        - containerPort: {{ .Values.nexusProxy.port }}
+        resources: {}
+        livenessProbe:
+          httpGet:
+            path: /
+            port: {{ .Values.nexusProxy.port }}
+          initialDelaySeconds: 1500
+          periodSeconds: 20
+          failureThreshold: 5
+          successThreshold: 1
+        readinessProbe:
+          httpGet:
+            path: /
+            port: {{ .Values.nexusProxy.port }}
+          initialDelaySeconds: 150
+          periodSeconds: 20
+          failureThreshold: 15
+          successThreshold: 1
+
+    {{- with .Values.nodeSelector }}
+      nodeSelector:
+{{ toYaml . | indent 8 }}
+    {{- end }}

charts/molgenis-nexus/templates/ingress.yaml

@@ -5,7 +5,7 @@ kind: Ingress
 metadata:
   name: "{{ $.Release.Name }}-ingress"
   labels:
-    app: httpd
+    app: {{ $.Values.nexusProxy.name }}
     chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
     release: "{{ $.Release.Name }}"
     heritage: "{{ $.Release.Service }}"
@@ -25,8 +25,8 @@ spec:
       paths:
         - path: {{ default "/" .path }}
           backend:
-            serviceName: httpd
-            servicePort: 80
+            serviceName: {{ $.Values.nexusProxy.name }}
+            servicePort: {{ $.Values.nexusProxy.port }}
 {{- if .tls }}
   tls:
   - hosts:

charts/molgenis-nexus/templates/persistence/nexusPVC.yaml

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

charts/molgenis-nexus/templates/services/nexusProxy-service.yaml

@@ -0,0 +1,13 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Values.nexusProxy.name }}
+  labels:
+    app: {{ .Values.nexusProxy.name }}
+spec:
+  type: {{ .Values.nexusProxy.service.type }}
+  ports:
+  - name: {{ .Values.nexusProxy.name }}
+    port: {{ .Values.nexusProxy.port }}
+  selector:
+    app: {{ .Values.nexusProxy.selector }}

charts/molgenis-nexus/values.yaml

@@ -0,0 +1,65 @@
+# Default values for nexus.
+# This is a YAML-formatted file.
+# Declare variables to be passed into your templates.
+
+replicaCount: 1
+
+environment: production
+
+nexus:
+  name: nexus
+  strategy:
+    type: Recreate
+  selector: nexus
+  restartPolicy: Always
+  image:
+    repository: molgenis/nexus3
+    tag: latest
+    pullPolicy: Always
+  port:
+    docker: 5000
+    ui: 8081
+  path:
+    dockerV2: v2
+  service:
+    type: ClusterIP
+
+nexusProxy:
+  name: nexus-proxy
+  hostname: registry.molgenis.org
+  strategy:
+    type: Recreate
+  selector: nexus-proxy
+  restartPolicy: Always
+  image:
+    repository: molgenis/httpd
+    tag: latest
+    pullPolicy: Always
+  port: 80
+  service:
+    type: LoadBalancer
+
+
+ingress:
+  enabled: true
+  annotations: {}
+  path: /
+  hosts:
+  - name: registry.molgenis.org
+  tls: []
+
+persistence:
+  enabled: true
+  claim: molgenis-nexus
+  size: 500Gi
+
+
+resources: {}
+
+nodeSelector: {
+  deployPod: "true"
+}
+
+tolerations: []
+
+affinity: {}

charts/molgenis-opencpu/Chart.yaml

@@ -0,0 +1,12 @@
+apiVersion: v1
+appVersion: "1.0"
+description: Opencpu stack for MOLGENIS
+name: molgenis-opencpu
+version: 0.1.1
+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-opencpu/catalogIcon-molgenis-opencpu.svg
+home: https://www.opencpu.org
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/molgenis-opencpu/README.md

@@ -0,0 +1,38 @@
+# MOLGENIS - OpenCPU Helm Chart
+
+NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
+
+## Containers
+
+This chart will deploy the following containers:
+
+- OpenCPU
+- MOLGENIS-httpd (to proxy the registry and docker to one domain)
+
+## Provisioning
+You can choose for the OpenCPU image from which repository you want to pull. Experimental builds are pushed to registry.molgenis.org and the stable builds to hub.docker.com. 
+You need to fill out 2 properties to determine which repository you are going to use.
+
+- ```opencpu.image.repository```
+- ```opencpu.image.tag```
+
+You can do this in the questions in Rancher or in the ```values.yaml```.
+
+
+
+## Development
+You can test in install the chart by executing:
+
+```helm lint .```
+
+To test if your helm chart-syntax is right and:
+
+```helm install . --dry-run --debug```
+
+To test if your hem chart works and:
+
+```helm install .```
+
+To deploy it on the cluster.
+
+

charts/molgenis-opencpu/questions.yml

@@ -0,0 +1,28 @@
+
+categories:
+- MOLGENIS
+questions:
+- variable: ingress.enabled
+  label: Enable ingress
+  default: false
+  description: "Enable ingress"
+  type: boolean
+  required: true
+  group: "Load balancing"
+- variable: opencpu.image.repository
+  label: Registry
+  default: "registry.hub.docker.com"
+  description: "Select a registry to pull from"
+  type: enum
+  options:
+  - "registry.hub.docker.com"
+  - "registry.molgenis.org"
+  required: true
+  group: "Provisioning"
+- variable: opencpu.image.tag
+  label: Version
+  default: ""
+  description: "Select a OpenCPU version (check the registry.molgenis.org or hub.docker.com for released tags)"
+  type: string
+  required: true
+  group: "Provisioning"

charts/molgenis-opencpu/templates/_helpers.tpl

@@ -0,0 +1,32 @@
+{{/* vim: set filetype=mustache: */}}
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "opencpu.name" -}}
+{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
+{{- end -}}
+
+{{/*
+Create a default fully qualified app name.
+We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
+If release name contains chart name it will be used as a full name.
+*/}}
+{{- define "opencpu.fullname" -}}
+{{- if .Values.fullnameOverride -}}
+{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
+{{- else -}}
+{{- $name := default .Chart.Name .Values.nameOverride -}}
+{{- if contains $name .Release.Name -}}
+{{- .Release.Name | trunc 63 | trimSuffix "-" -}}
+{{- else -}}
+{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}}
+{{- end -}}
+{{- end -}}
+{{- end -}}
+
+{{/*
+Create chart name and version as used by the chart label.
+*/}}
+{{- define "opencpu.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
+{{- end -}}

charts/molgenis-opencpu/templates/deployment.yaml

@@ -0,0 +1,35 @@
+apiVersion: extensions/v1beta1
+kind: Deployment
+metadata:
+  {{- with .Values.ingress.annotations }}
+  annotations:
+{{ toYaml . | indent 4 }}
+  {{- end }}
+  name: {{ template "opencpu.fullname" . }}
+  labels:
+    app: {{ template "opencpu.name" . }}
+    chart: {{ template "opencpu.chart" . }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app: {{ template "opencpu.name" . }}
+      release: {{ .Release.Name }}
+  template:
+    metadata:
+      labels:
+        app: {{ template "opencpu.name" . }}
+        release: {{ .Release.Name }}
+    spec:
+      containers:
+      {{- with .Values.opencpu }}
+      - name: {{ .name }}
+        image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
+        imagePullPolicy: {{ .image.pullPolicy }}
+        ports:
+        - containerPort: {{ .service.port }}
+      {{- end }}
+
+

charts/molgenis-opencpu/templates/ingress.yaml

@@ -0,0 +1,36 @@
+{{- if .Values.ingress.enabled }}
+{{- range .Values.ingress.hosts }}
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: "{{ $.Release.Name }}-ingress"
+  labels:
+    app:  {{ $.Values.opencpu.name }}
+    chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
+    release: "{{ $.Release.Name }}"
+    heritage: "{{ $.Release.Service }}"
+  annotations:
+    {{- if .tls }}
+    ingress.kubernetes.io/secure-backends: "true"
+    {{- end }}
+    {{- range $key, $value := .annotations }}
+    {{ $key }}: {{ $value | quote }}
+    {{- end }}
+spec:
+  rules:
+  - host: {{ .name }}
+    http:
+      paths:
+        - path: {{ default "/" .path }}
+          backend:
+            serviceName: {{ $.Values.opencpu.service.name }}
+            servicePort: {{ $.Values.opencpu.service.port }}
+{{- if .tls }}
+  tls:
+  - hosts:
+    - {{ .name }}
+    secretName: {{ .tlsSecret }}
+{{- end }}
+---
+{{- end }}
+{{- end }}

charts/molgenis-opencpu/templates/service.yaml

@@ -0,0 +1,20 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Values.opencpu.service.name }}
+  labels:
+    app: {{ .Values.opencpu.service.name }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  type: {{ .Values.opencpu.service.type }}
+  loadBalancerSourceRanges:
+  {{- range $index, $rule := .Values.opencpu.service.firewall }}
+    - {{ $rule }}
+  {{- end }}
+  ports:
+    - name: {{ .Values.opencpu.service.name }}
+      port: {{ .Values.opencpu.service.port }}
+  selector:
+    app: {{ template "opencpu.name" . }}
+    release: {{ .Release.Name }}

charts/molgenis-opencpu/values.yaml

@@ -0,0 +1,41 @@
+# Default values for nexus.
+# This is a YAML-formatted file.
+# Declare variables to be passed into your templates.
+
+replicaCount: 1
+
+environment: production
+
+opencpu:
+  name: opencpu
+  strategy:
+    type: Recreate
+  restartPolicy: Always
+  image:
+    repository: registry.hub.docker.com
+    name: molgenis/opencpu
+    tag: stable
+    pullPolicy: Always
+  service:
+    name: opencpu
+    type: LoadBalancer
+    port: 8004
+    firewall:
+    - 145.100.224.1/24
+
+ingress:
+  enabled: false
+  annotations: {
+    kubernetes.io/ingress.class: "nginx",
+    nginx.ingress.kubernetes.io/proxy-body-size: "0"
+  }
+  path: /
+  hosts:
+  - name: opencpu.molgenis.org
+  tls: []
+
+nodeSelector: {}
+
+tolerations: []
+
+affinity: {}

charts/molgenis-vault/Chart.yaml

@@ -4,3 +4,7 @@ description: MOLGENIS vault
 name: molgenis-vault
 version: 0.1.1
 icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-vault/catalogIcon-molgenis-vault.svg
+home: https://github.com/coreos/vault-operator
+maintainers:
+- name: fdlk
+- name: sidohaakma

charts/molgenis-vault/values.yaml

@@ -70,10 +70,10 @@ ui:
     # limits:
     #  cpu: 100m
     #  memory: 128Mi
-    #requests:
+    # requests:
     #  cpu: 100m
     #  memory: 128Mi
   nodeSelector: {}
   vault:
     auth: GITHUB
-    url: https://vault.vault-operator:8200
+    url: https://vault.vault-operator:8200

charts/molgenis/Chart.yaml

@@ -1,8 +1,12 @@
 apiVersion: v1
 appVersion: "1.0"
-description: A Helm chart for Kubernetes
+description: MOLGENIS - helm stack (in BETA)
 name: molgenis
-version: 0.2.0
+version: 0.4.3
 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-preview/catalogIcon-molgenis.svg
+icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis/catalogIcon-molgenis.svg
+home: http://molgenis.org
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/molgenis/README.md

@@ -0,0 +1,138 @@
+# MOLGENIS
+This chart is used for acceptance and production use cases.
+
+## Containers
+This chart spins up a MOLGENIS instance with HTTPD. The created containers are:
+
+- MOLGENIS
+- ElasticSearch
+- PostgreSQL **(optional)**
+
+## Provisioning
+You can choose from which registry you want to pull. There are 2 registries:
+- https://registry.molgenis.org
+- https://hub.docker.com
+
+The registry.molgenis.org contains the bleeding edge versions (PR's and master merges). The hub.docker.com contains the released artifacts (MOLGENIS releases and release candidates).
+
+The three properties you need to specify are:
+- ```molgenis.image.repository```
+- ```molgenis.image.name```
+- ```molgenis.image.tag```
+
+Besides determining which image you want to pull, you also have to set an administrator password. You can do this by specifying the following property. 
+- ```molgenis.adminPassword```
+
+### Firewall
+Is defined at service level you can specify this attribute in the values:
+
+- ```molgenis.firewall.enabled``` default 'false' 
+
+If set to 'true' the following options are available. One of the options below has to be set.
+
+- ```molgenis.firewall.umcg.enabled``` default 'false'  
+- ```molgenis.firewall.cluster.enabled``` default 'false'
+
+UMCG = only available within the UMCG.
+Cluster = only available within the GCC cluster environment.
+
+## Services
+When you start MOLGENIS you need:
+- an elasticsearch instance (5.5.6) 
+- an postgres instance (9.6)
+
+You can attach additional services like:
+- an opencpu instance
+
+### Elasticsearch
+You can configure elasticsearch by giving in the cluster location.
+
+To configure the transport address you can address the node communication channel but also the native JAVA API. Which MOLGENIS uses to communicate with Elasticsearch.
+From Elasticsearch version 6 and further the JAVA API is not supported anymore. At this moment you can only use Elastic instance till major version 5.
+- ```molgenis.services.elasticsearch.transportAddresses: localhost:9300```
+
+To configure the index on a Elasticsearch cluster you can specify the clusterName property.
+- ```molgenis.services.elasticsearch.clusterName: molgenis```
+
+### Postgres
+You can specify the location of the postgres instance by specify the following property:
+- ```molgenis.services.postgres.host: localhost```
+
+You can specify the schema by filling out this property:
+- ```molgenis.services.postgres.scheme: molgenis```
+
+You can specify credentials for the database scheme by specifying the following properties:
+- ```molgenis.services.postgres.user: molgenis```
+- ```molgenis.services.postgres.password: molgenis```
+
+To test you can use the **PostgreSQL**-helm chart of Kubernetes and specify these answers:
+
+```bash
+# answers for postgresql chart
+postgresUser=molgenis
+postgresPassword=molgenis
+postgresDatabase=molgenis
+persistence.enabled=false
+```
+
+### OpenCPU
+You can specify the location of the OpenCPU cluster by specifying this property:
+- ```molgenis.services.opencpu.host: localhost```
+
+You can test OpenCPU settings using the **OpenCPU**-helm chart of MOLGENIS.
+
+## Resources
+You can specify resources by resource type. There are 2 resource types.
+- memory of container
+- maximum heap space JVM
+
+Specify memory usage of container:
+- ```molgenis.resources.limits.memory```
+
+Specify memory usage for Java JVM:
+- ```molgenis.javaOpts.maxHeapSpace```
+
+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``` default 'true'
+
+You can also choose to retain the volume of the NFS.
+- ```persistence.retain``` default 'false'
+
+The size and claim name can be specified per service. There are now two services that can be persist.
+
+- MOLGENIS
+- ElasticSearch
+- PostgreSQL **(optional)**
+
+MOLGENIS persistent properties.
+- ```molgenis.persistence.claim```
+- ```molgenis.persistence.size```
+
+ElasticSearch persistent properties.
+- ```elasticsearch.persistence.claim```
+- ```elasticsearch.persistence.size```
+
+PostgreSQL persistent properties.
+- ```postgres.persistence.claim```
+- ```postgres.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```. 

charts/molgenis/questions.yml

@@ -0,0 +1,167 @@
+
+categories:
+- MOLGENIS
+questions:
+- variable: ingress.hosts[0].name
+  label: Hostname
+  default: "test.molgenis.org"
+  description: "Hostname for your stack"
+  type: hostname
+  required: true
+  group: "Load balancing"
+- variable: molgenis.image.repository
+  label: Registry
+  default: "registry.hub.docker.com"
+  description: "Select a registry to pull from"
+  type: enum
+  options:
+  - "registry.hub.docker.com"
+  - "registry.molgenis.org"
+  required: true
+  group: "Provisioning"
+- variable: molgenis.image.tag
+  label: Version
+  default: ""
+  description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for released tags)"
+  type: string
+  required: true
+  group: "Provisioning"
+- variable: molgenis.adminPassword
+  label: Administrator password
+  default: ""
+  description: "Enter an administrator password"
+  type: password
+  required: true
+  group: "Provisioning"
+- variable: service.firewall.enabled
+  label: Firewall enabled
+  default: false
+  description: "Firewall enabled (can be cluster or UMCG scoped)"
+  type: boolean
+  required: true
+  group: "Provisioning"
+  show_subquestion_if: true
+  subquestions:
+  - variable: service.firewall.kind
+    default: "umcg"
+    description: "Firewall kind. This can be 'umcg' or 'cluster' environment"
+    type: enum
+    required: true
+    options:
+    - umcg
+    - cluster
+    label: Firewall kind
+- variable: molgenis.services.opencpu.host
+  label: OpenCPU cluster
+  default: "localhost"
+  description: "Specify the OpenCPU cluster"
+  type: string
+  required: true
+  group: "Services"
+- variable: molgenis.services.postgres.embedded
+  label: Postgres embedded
+  default: false
+  description: "Do you want an embedded postgres"
+  type: boolean
+  required: true
+  group: "Services"
+  show_subquestion_if: false
+  subquestions:
+  - variable: molgenis.services.postgres.host
+    label: Postgres cluster location
+    default: ""
+    description: "Set the location of the postgres cluster. This can be localhost when the postgres is enabled else you need to specify a cluster location if you do not want a embedded postgres instance)"
+    type: string
+    required: true
+    group: "Services"
+  - variable: molgenis.services.postgres.scheme
+    label: Database scheme
+    default: "molgenis"
+    description: "Set the database scheme"
+    type: string
+    required: true
+    group: "Services"
+  - variable: molgenis.services.postgres.user
+    label: Database username
+    default: "molgenis"
+    description: "Set user of the database scheme"
+    type: string
+    required: true
+    group: "Services"
+  - variable: molgenis.services.postgres.password
+    label: Database password
+    default: "molgenis"
+    description: "Set the password of the database scheme"
+    type: string
+    required: true
+    group: "Services"
+- variable: molgenis.resources.limits.memory
+  label: Container memory limit
+  default: 1250Mi
+  description: "Memory limit for this MOLGENIS container"
+  type: enum
+  options:
+  - "1250Mi"
+  - "2500Mi"
+  required: true
+  group: "Resources"
+- variable: molgenis.resources.requests.memory
+  label: Container memory reservation
+  default: 1250Mi
+  description: "Memory reservation for this MOLGENIS container (must fit in the selected memory limit for the container)"
+  type: enum
+  options:
+  - "1250Mi"
+  - "2500Mi"
+  required: true
+  group: "Resources"
+- variable: molgenis.javaOpts.maxHeapSpace
+  label: Maximum heap space (JVM)
+  default: "1g"
+  description: "Maximum heap space MOLGENIS container JVM. Please not this should fit in your container memory limit"
+  type: enum
+  options:
+  - "1g"
+  - "2g"
+  group: "Resources"
+- variable: persistence.enabled
+  default: true
+  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: "5Gi"
+    description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
+    type: enum
+    options:
+    - "5Gi"
+    - "10Gi"
+    - "20Gi"
+    label: Size MOLGENIS filestore
+  - variable: elasticsearch.persistence.size
+    default: "5Gi"
+    description: "Size of ElasticSearch data (directory that is persist: /usr/share/elasticsearch/data)"
+    type: enum
+    options:
+    - "5Gi"
+    - "10Gi"
+    - "50Gi"
+    label: Size for ElasticSearch data
+  - variable: postgres.persistence.size
+    default: "5Gi"
+    description: "Size of PostgreSQL data (directory that is persist: /var/lib/postgresql/data/pgdata)"
+    type: enum
+    options:
+    - "5Gi"
+    - "10Gi"
+    - "50Gi"
+    label: Size for PostgreSQL data

charts/molgenis/templates/deployment.yaml

@@ -17,6 +17,8 @@ spec:
     matchLabels:
       app: {{ template "molgenis.name" . }}
       release: {{ .Release.Name }}
+  strategy:
+    type: Recreate
   template:
     metadata:
       labels:
@@ -26,37 +28,50 @@ spec:
       containers:
         - name: molgenis
         {{- with .Values.molgenis }}
-          image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
+          image: {{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}
           imagePullPolicy: {{ .image.pullPolicy }}
           env:
             - name: molgenis.home
               value: /home/molgenis
             - name: opencpu.uri.host
-              value: localhost
+              value: {{ .services.opencpu.host }}
             - name: elasticsearch.transport.addresses
-              value: localhost:9300
+              value: {{ .services.elasticsearch.transportAddresses }}
             - name: elasticsearch.cluster.name
-              value: {{ $.Values.elasticsearch.clusterName }}
+              value: {{ .services.elasticsearch.clusterName }}
             - name: db_uri
-              value: "jdbc:postgresql://localhost/{{ $.Values.postgres.db }}"
+              value: jdbc:postgresql://{{ .services.postgres.host }}/{{ .services.postgres.scheme }}
             - name: db_user
-              value: {{ $.Values.postgres.user }}
+              value: {{ .services.postgres.user }}
             - name: db_password
-              value: {{ $.Values.postgres.password }}
+              value: {{ .services.postgres.password }}
             - name: admin.password
               value: {{ .adminPassword }}
             - name: CATALINA_OPTS
-              value: "{{ .javaOpts }}"
+              value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
           ports:
             - containerPort: 8080
-#          livenessProbe:
-#            httpGet:
-#              path: /
-#              port: 8080
-#          readinessProbe:
-#            httpGet:
-#              path: /api/v2/version
-#              port: 8080
+          {{- if $.Values.persistence.enabled }}
+          volumeMounts:
+          - name: molgenis-nfs
+            mountPath: /home/molgenis
+          {{- end }}
+          livenessProbe:
+            httpGet:
+              path: /
+              port: 8080
+            initialDelaySeconds: 60
+            periodSeconds: 5
+            failureThreshold: 25
+            successThreshold: 1
+          readinessProbe:
+            httpGet:
+              path: /api/v2/version
+              port: 8080
+            initialDelaySeconds: 120
+            periodSeconds: 30
+            failureThreshold: 3
+            successThreshold: 1
           resources:
 {{ toYaml .resources | indent 12 }}
         {{- end }}
@@ -79,6 +94,11 @@ 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 }}
@@ -89,26 +109,35 @@ spec:
           imagePullPolicy: {{ .image.pullPolicy }}
           env:
             - name: POSTGRES_USER
-              value: {{ .user }}
+              value: {{ $.Values.molgenis.services.postgres.user }}
             - name: POSTGRES_PASSWORD
-              value: {{ .password }}
+              value: {{ $.Values.molgenis.services.postgres.password }}
             - name: POSTGRES_DB
-              value: {{ .db }}
+              value: {{ $.Values.molgenis.services.postgres.scheme }}
           ports:
             - containerPort: 5432
           resources:
 {{ toYaml .resources | indent 12 }}
+          {{- if $.Values.persistence.enabled }}
+          volumeMounts:
+          - name: postgres-nfs
+            mountPath: /var/lib/postgresql/data
+          {{- end }}
         {{- end }}
 
-        - name: opencpu
-        {{- with .Values.opencpu }}
-          image: "{{ .image.repository }}:{{ .image.tag }}"
-          imagePullPolicy: {{ .image.pullPolicy }}
-          ports:
-            - containerPort: 8004
-          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 }}
+        - name: postgres-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.postgres.persistence.claim }}
+{{- end }}
 
     {{- with .Values.nodeSelector }}
       nodeSelector:

charts/molgenis/templates/ingress.yaml

@@ -4,7 +4,7 @@
 apiVersion: extensions/v1beta1
 kind: Ingress
 metadata:
-  name: {{ $fullName }}
+  name: "{{ $.Release.Name }}-ingress"
   labels:
     app: {{ template "molgenis.name" . }}
     chart: {{ template "molgenis.chart" . }}
@@ -33,6 +33,6 @@ spec:
           - path: {{ $ingressPath }}
             backend:
               serviceName: {{ $fullName }}
-              servicePort: 8080
+              servicePort: {{ $.Values.service.port }}
   {{- end }}
 {{- end }}

charts/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 }}

charts/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 }}

charts/molgenis/templates/persistence/postgresPVC.yaml

@@ -0,0 +1,21 @@
+{{- if .Values.molgenis.services.postgres.embedded }}
+{{- if .Values.persistence.enabled }}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Values.postgres.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.postgres.persistence.size }}
+{{- end }}
+{{- end }}

charts/molgenis/templates/service.yaml

@@ -9,6 +9,18 @@ metadata:
     heritage: {{ .Release.Service }}
 spec:
   type: {{ .Values.service.type }}
+{{- if .Values.service.firewall.enabled }}
+  loadBalancerSourceRanges:
+{{- if .Values.service.firewall.kind eq "umcg" }}
+    {{- range $index, $rule := .Values.service.firewall.umcg.rules }}
+    - {{ $rule }}
+    {{- end }}
+{{- else }}
+    {{- range $index, $rule := .Values.service.firewall.cluster.rules }}
+    - {{ $rule }}
+    {{- end }}
+{{- end }}
+{{- end }}
   ports:
     - name: molgenis
       port: {{ .Values.service.port }}

charts/molgenis/values.yaml

@@ -0,0 +1,103 @@
+# Default values for molgenis.
+
+replicaCount: 1
+
+service:
+  type: LoadBalancer
+  firewall:
+    enabled: false
+    kind: "umcg"
+    umcg:
+      rules:
+      - 127.0.0.1/32
+    cluster:
+      rules:
+      - 127.0.0.1/32
+  port: 8080
+
+ingress:
+  enabled: true
+  annotations:
+    nginx.ingress.kubernetes.io/proxy-body-size: "0"
+  path: /
+  hosts:
+  - name: test.molgenis.org
+  tls: []
+
+molgenis:
+  image:
+    repository: registry.hub.docker.com
+    name: molgenis/molgenis-app
+    tag: stable
+    pullPolicy: Always
+  adminPassword:
+  javaOpts:
+    maxHeapSpace: "1g"
+  resources:
+    limits:
+      cpu: 1
+      memory: 1250Mi
+    requests:
+      cpu: 200m
+      memory: 1250Mi
+  persistence:
+    claim: molgenis-nfs-claim
+    size: 5Gi
+  services:
+    opencpu:
+      host: localhost
+    elasticsearch:
+      transportAddresses: localhost:9300
+      clusterName: molgenis
+    postgres:
+      embedded: false
+      host: localhost
+      scheme: molgenis
+      user: molgenis
+      password: molgenis
+
+elasticsearch:
+  image:
+    repository: docker.elastic.co/elasticsearch/elasticsearch
+    tag: 5.5.3
+    pullPolicy: IfNotPresent
+  javaOpts: "-Xms1g -Xmx1g"
+  clusterName: molgenis
+  resources:
+    limits:
+      cpu: 2
+      memory: 3Gi
+    requests:
+      cpu: 100m
+      memory: 1Gi
+  persistence:
+    claim: elasticsearch-nfs-claim
+    size: 5Gi
+
+postgres:
+  image:
+    repository: postgres
+    tag: 9.6-alpine
+    pullPolicy: IfNotPresent
+  resources:
+    limits:
+      cpu: 1
+      memory: 250Mi
+    requests:
+      cpu: 100m
+      memory: 250Mi
+  persistence:
+    claim: postgres-nfs-claim
+    size: 5Gi
+
+persistence:
+  enabled: true
+  retain: false
+
+nodeSelector: {
+  deployPod: "true"
+}
+
+tolerations: []
+
+affinity: {}

molgenis-nexus/README.md

@@ -1,28 +0,0 @@
-# MOLGENIS - NEXUS Helm Chart
-
-NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
-
-## Chart Details
-
-This chart will deploy:
-
-- 1 NEXUS container
-- 1 MOLGENIS-httpd container ()to proxy the registry and docker to one domain)
-
-## Installing the Chart
-
-You can test in install the chart by executing:
-
-```helm lint .```
-
-To test if your helm chart-syntax is right and:
-
-```helm install . --dry-run --debug```
-
-To test if your hem chart works and:
-
-```helm install .```
-
-To deploy it on the cluster.
-
-

molgenis-nexus/templates/deployments/httpd-deployment.yaml

@@ -1,34 +0,0 @@
-apiVersion: extensions/v1beta1
-kind: Deployment
-metadata:
-  creationTimestamp: null
-  name: {{ .Values.httpd.name }}
-  labels:
-    app: {{ .Values.httpd.name }}
-    environment: {{ .Values.environment }}
-spec:
-  replicas: {{ .Values.replicaCount }}
-  strategy:
-    type: {{ .Values.httpd.strategy.type }}
-  selector:
-    matchLabels:
-      app: {{ .Values.httpd.selector }}
-  template:
-    metadata:
-      labels:
-        app: {{ .Values.httpd.name }}
-      creationTimestamp: null
-    spec:
-      restartPolicy: {{ .Values.httpd.restartPolicy }}
-      containers:
-      - name: {{ .Values.httpd.name }}
-        image: "{{ .Values.httpd.image.repository }}:{{ .Values.httpd.image.tag }}"
-        imagePullPolicy: {{ .Values.httpd.image.pullPolicy }}
-        env:
-        - name: PROXY_SERVICE
-          value: "{{ .Values.nexus.name }}:{{ .Values.nexus.port.ui }},{{ .Values.nexus.name }}:{{ .Values.nexus.port.docker }}:{{ .Values.nexus.path.dockerV2 }}"
-        - name: SERVER_NAME
-          value: {{ .Values.httpd.hostname }}
-        ports:
-        - containerPort: {{ .Values.httpd.port }}
-        resources: {}

molgenis-nexus/templates/services/httpd-service.yaml

@@ -1,13 +0,0 @@
-apiVersion: v1
-kind: Service
-metadata:
-  name: {{ .Values.httpd.name }}
-  labels:
-    app: {{ .Values.httpd.name }}
-spec:
-  type: {{ .Values.httpd.service.type }}
-  ports:
-  - name: {{ .Values.httpd.name }}
-    port: {{ .Values.httpd.port }}
-  selector:
-    app: {{ .Values.httpd.selector }}

molgenis-nexus/templates/volumes/nexus-pv.yaml

@@ -1,16 +0,0 @@
-apiVersion: v1
-kind: PersistentVolume
-metadata:
-  name: {{ .Values.persistence.name }}
-  labels:
-    name: nfs2
-spec:
-  storageClassName: {{ .Values.persistence.storageClass }}
-  capacity:
-    storage: {{ .Values.persistence.size }}
-  accessModes:
-    - {{ .Values.persistence.accessMode }}
-  persistentVolumeReclaimPolicy: {{ .Values.persistence.reclaimPolicy }}
-  nfs:
-    server: {{ .Values.persistence.server }}
-    path: {{ .Values.persistence.mountPath }}

molgenis-nexus/templates/volumes/nexus-pvc.yaml

@@ -1,11 +0,0 @@
-kind: PersistentVolumeClaim
-apiVersion: v1
-metadata:
-  name: {{ .Values.persistence.name }}
-spec:
-  storageClassName: {{ .Values.persistence.storageClass }}
-  accessModes:
-    - {{ .Values.persistence.accessMode }}
-  resources:
-    requests:
-      storage: {{ .Values.persistence.size }}

molgenis-nexus/values.yaml

@@ -1,82 +0,0 @@
-# Default values for nexus.
-# This is a YAML-formatted file.
-# Declare variables to be passed into your templates.
-
-replicaCount: 1
-
-environment: production
-
-nexus:
-  name: nexus
-  strategy:
-    type: Recreate
-  selector: nexus
-  restartPolicy: Always
-  image:
-    repository: sonatype/nexus3
-    tag: latest
-    pullPolicy: Always
-  port:
-    docker: 5000
-    ui: 8081
-  path:
-    dockerV2: v2
-  service:
-    type: ClusterIP
-
-httpd:
-  name: httpd
-  hostname: registry.molgenis.org
-  strategy:
-    type: Recreate
-  selector: httpd
-  restartPolicy: Always
-  image:
-    repository: registry.webhosting.rug.nl/molgenis/httpd
-    tag: lts
-    pullPolicy: Always
-  port: 80
-  service:
-    type: LoadBalancer
-
-
-ingress:
-  enabled: true
-  annotations: {}
-    # kubernetes.io/ingress.class: nginx
-    # kubernetes.io/tls-acme: "true"
-  path: /
-  hosts:
-  - name: registry.molgenis.org
-  tls: []
-  #  - secretName: chart-example-tls
-  #    hosts:
-  #      - chart-example.local
-
-persistence:
-  name: molgenis-nexus-data
-  storageClass: nfs-class
-  size: 30G
-  reclaimPolicy: Retain
-  server: 192.168.64.12
-  accessMode: ReadWriteMany
-  mountPath: /gcc/molgenis/nexus
-
-
-resources: {}
-  # We usually recommend not to specify default resources and to leave this as a conscious
-  # choice for the user. This also increases chances charts run on environments with little
-  # resources, such as Minikube. If you do want to specify resources, uncomment the following
-  # lines, adjust them as necessary, and remove the curly braces after 'resources:'.
-  # limits:
-  #  cpu: 100m
-  #  memory: 128Mi
-  # requests:
-  #  cpu: 100m
-  #  memory: 128Mi
-
-nodeSelector: {}
-
-tolerations: []
-
-affinity: {}

molgenis-preview/README.md

@@ -1,11 +0,0 @@
-# MOLGENIS preview
-Is used for integration testing purposes.
-
-## Containers
-This chart spins up a complete stack to run MOLGENIS. The created containers are:
-
-- MOLGENIS
-- PostgreSQL
-- Elasticsearch
-- OpenCPU
-

molgenis-preview/questions.yml

@@ -1,61 +0,0 @@
-
-categories:
-- MOLGENIS
-questions:
-- variable: ingress.hosts[0].name
-  default: "test.molgenis.org"
-  description: "Hostname for your stack"
-  type: hostname
-  required: true
-  group: "Services and Load Balancing"
-  label: Hostname
-- variable: molgenis.image.repository
-  default: "registry.hub.docker.com"
-  description: "Select a registry to pull from"
-  type: enum
-  options:
-  - "registry.hub.docker.com"
-  - "registry.molgenis.org"
-  required: true
-  group: "MOLGENIS - Version"
-  label: Registry
-- variable: molgenis.image.tag
-  default: "stable"
-  description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for other tags)"
-  type: string
-  required: true
-  group: "MOLGENIS - Version"
-  label: Version
-- variable: molgenis.resources.limits.cpu
-  default: 1
-  description: "CPU limit for this MOLGENIS instance"
-  type: enum
-  options:
-  - "1"
-  - "2"
-  - "3"
-  - "4"
-  required: true
-  group: "MOLGENIS - Resource limits"
-  label: CPU limit
-- variable: molgenis.resources.limits.memory
-  default: 1250Mi
-  description: "Memory limit for this MOLGENIS instance"
-  type: enum
-  options:
-  - "1250Mi"
-  - "1500Mi"
-  - "2000Mi"
-  - "2500Mi"
-  required: true
-  group: "MOLGENIS - Resource limits"
-  label: Memory limit
-- variable: molgenis.javaOpts
-  default: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-  description: "Java runtime options for the MOLGENIS instance"
-  type: enum
-  options:
-  - "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-  - "-Xmx2g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-  group: "MOLGENIS - Resource limits"
-  label: Java memory options

molgenis-preview/test.yaml

@@ -1,120 +0,0 @@
-# Source: molgenis/templates/deployment.yaml
-apiVersion: apps/v1beta2
-kind: Deployment
-metadata:
-  name: lanky-ragdoll-molgenis
-  labels:
-    app: molgenis
-    chart: molgenis-0.1.0
-    release: lanky-ragdoll
-    heritage: Tiller
-spec:
-  replicas: 1
-  selector:
-    matchLabels:
-      app: molgenis
-      release: lanky-ragdoll
-  template:
-    metadata:
-      labels:
-        app: molgenis
-        release: lanky-ragdoll
-    spec:
-      containers:
-        - name: molgenis
-          image: "registry.molgenis.org/molgenis/molgenis-app:latest"
-          imagePullPolicy: Always
-          env:
-            - name: molgenis.home
-              value: /home/molgenis
-            - name: opencpu.uri.host
-              value: opencpu
-            - name: elasticsearch.transport.addresses
-              value: elasticsearch:9300
-            - name: elasticsearch.cluster.name
-              value: molgenis
-            - name: db_uri
-              value: "jdbc:postgresql://postgres/molgenis"
-            - name: db_user
-              value: molgenis
-            - name: db_password
-              value: molgenis
-            - name: admin.password
-              value: admin
-            - name: CATALINA_OPTS
-              value: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-          ports:
-            - containerPort: 8080
-          livenessProbe:
-            httpGet:
-              path: /
-              port: http
-          readinessProbe:
-            httpGet:
-              path: /api/v2/version
-              port: http
-          resources:
-            limits:
-              cpu: 1
-              memory: 1250Mi
-            requests:
-              cpu: 200m
-              memory: 1Gi
-
-
-        - name: elasticsearch
-          image: "docker.elastic.co/elasticsearch/elasticsearch:5.5.3"
-          imagePullPolicy: IfNotPresent
-          env:
-            - name: cluster.name
-              value: molgenis
-            - name: bootstrap.memory_lock
-              value: true
-            - name: ES_JAVA_OPTS
-              value: "-Xms512m -Xmx512m"
-            - name: xpack.security.enabled
-              value: false
-            - name: discovery.type
-              value: single-node
-          ports:
-            - containerPort: 9200
-            - containerPort: 9300
-            limits:
-              cpu: 1
-              memory: 1500Mi
-            requests:
-              cpu: 100m
-              memory: 1Gi
-
-
-        - name: postgres
-          image: "postgres:9.6-alpine"
-          imagePullPolicy: IfNotPresent
-          env:
-            - name: POSTGRES_USER
-              value: molgenis
-            - name: POSTGRES_PASSWORD
-              value: molgenis
-            - name: POSTGRES_DB
-              value: molgenis
-          ports:
-            - containerPort: 5432
-            limits:
-              cpu: 1
-              memory: 250Mi
-            requests:
-              cpu: 100m
-              memory: 250Mi
-
-
-        - name: opencpu
-          image: "molgenis/opencpu:latest"
-          imagePullPolicy: Always
-          ports:
-            - containerPort: 8004
-            limits:
-              cpu: 1
-              memory: 512Mi
-            requests:
-              cpu: 100m
-              memory: 256Mi

molgenis-preview/values.yaml

@@ -1,82 +0,0 @@
-# Default values for molgenis.
-
-replicaCount: 1
-
-service:
-  type: LoadBalancer
-  port: 8080
-
-ingress:
-  enabled: true
-  annotations:
-    nginx.ingress.kubernetes.io/proxy-body-size: "0"
-  path: /
-  hosts:
-  - name: test.molgenis.org
-  tls: []
-
-molgenis:
-  image:
-    repository: registry.molgenis.org
-    name: molgenis/molgenis-app
-    tag: 7.0.0-SNAPSHOT
-    pullPolicy: Always
-  adminPassword: admin
-  javaOpts: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-  resources:
-   limits:
-    cpu: 1
-    memory: 1250Mi
-   requests:
-    cpu: 200m
-    memory: 1Gi
-
-postgres:
-  image:
-    repository: postgres
-    tag: 9.6-alpine
-    pullPolicy: IfNotPresent
-  user: molgenis
-  password: molgenis
-  db: molgenis
-  resources:
-   limits:
-    cpu: 1
-    memory: 250Mi
-   requests:
-    cpu: 100m
-    memory: 250Mi
-
-elasticsearch:
-  image:
-    repository: docker.elastic.co/elasticsearch/elasticsearch
-    tag: 5.5.3
-    pullPolicy: IfNotPresent
-  javaOpts: "-Xms512m -Xmx512m"
-  clusterName: molgenis
-  resources:
-   limits:
-    cpu: 1
-    memory: 1500Mi
-   requests:
-    cpu: 100m
-    memory: 1Gi
-
-opencpu:
-  image:
-    repository: molgenis/opencpu
-    tag: latest
-    pullPolicy: Always
-  resources:
-    limits:
-      cpu: 1
-      memory: 512Mi
-    requests:
-      cpu: 100m
-      memory: 256Mi
-
-nodeSelector: {}
-
-tolerations: []
-
-affinity: {}