feat: Add resources for helm role

.gitignore

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

Jenkinsfile

@@ -1,40 +0,0 @@
-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

@@ -101,11 +101,11 @@ kubectl get pods --namespace=*#namespace of application#*
 
 This repository is serves also as a catalogue for Rancher. We have serveral apps that are served through this repoistory. e.g.
 
-- [Jenkins](charts/molgenis-jenkins/README.md)
-- [NEXUS](charts/molgenis-nexus/README.md)
-- [HTTPD](charts/molgenis-httpd/README.md)
-- [MOLGENIS](charts/molgenis/README.md)
-- [MOLGENIS vault](charts/molgenis-vault/README.md)
+- [Jenkins](molgenis-jenkins/README.md)
+- [NEXUS](molgenis-nexus/README.md)
+- [HTTPD](molgenis-httpd/README.md)
+- [MOLGENIS preview](molgenis-preview/README.md)
+- [MOLGENIS vault](molgenis-vault/README.md)
 
 ### Useful commands
 You can you need to know to easily develop and deploy helm-charts
@@ -122,26 +122,6 @@ 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/index.yaml

@@ -0,0 +1,16 @@
+apiVersion: v1
+entries:
+  molgenis-preview:
+  - apiVersion: v1
+    appVersion: "1.0"
+    created: 2018-09-11T16:11:49.165533266+02:00
+    description: MOLGENIS - helm stack for testing purposes
+    digest: e1174bd0d8a71bf4d23f5463521cf4dbcac39dc93f16cd842c92cda1a963f6b2
+    icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-preview/catalogIcon-molgenis.svg
+    name: molgenis-preview
+    sources:
+    - https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
+    urls:
+    - molgenis-preview-0.2.0.tgz
+    version: 0.2.0
+generated: 2018-09-11T16:11:49.158086031+02:00

charts/molgenis-httpd/Chart.yaml

@@ -1,12 +0,0 @@
-apiVersion: v1
-appVersion: "1.0"
-description: HTTPD for MOLGENIS
-name: molgenis-httpd
-version: 0.1.0
-sources:
-- https://github.com/molgenis/molgenis-ops-docker-helm.git
-Icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis-httpd/catalogIcon-molgenis-httpd.svg
-home: http://httpd.apache.org
-maintainers:
-- name: sidohaakma
-- name: fdlk

charts/molgenis-jenkins/Chart.yaml

@@ -1,11 +0,0 @@
-name: molgenis-jenkins
-home: https://jenkins.io/
-version: 0.8.1
-appVersion: 2.138.1
-description: Molgenis installation for the jenkins chart.
-sources:
-- https://github.com/molgenis/molgenis-ops-docker-helm.git
-icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis-jenkins/catalogIcon-molgenis-jenkins.svg
-maintainers:
-- name: fdlk
-- name: sidohaakma

charts/molgenis-jenkins/resources/README.md

@@ -1,8 +0,0 @@
-# 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-nexus/Chart.yaml

@@ -1,12 +0,0 @@
-apiVersion: v1
-appVersion: "1.0"
-description: Nexus stack for MOLGENIS
-name: molgenis-nexus
-version: 0.4.2
-sources:
-- https://github.com/molgenis/molgenis-ops-docker-helm.git
-icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis-nexus/catalogIcon-molgenis-nexus.svg
-home: https://www.sonatype.com/nexus-repository-oss
-maintainers:
-- name: sidohaakma
-- name: fdlk

charts/molgenis-nexus/README.md

@@ -1,69 +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-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/nexusProxy-deployment.yaml

@@ -1,55 +0,0 @@
-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/persistence/nexusPVC.yaml

@@ -1,15 +0,0 @@
-{{- 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

@@ -1,13 +0,0 @@
-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

@@ -1,65 +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: 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

@@ -1,12 +0,0 @@
-apiVersion: v1
-appVersion: "1.0"
-description: Opencpu stack for MOLGENIS
-name: molgenis-opencpu
-version: 0.1.1
-sources:
-- https://github.com/molgenis/molgenis-ops-docker-helm.git
-icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis-opencpu/catalog-molgenis-opencpu.svg
-home: https://www.opencpu.org
-maintainers:
-- name: sidohaakma
-- name: fdlk

charts/molgenis-opencpu/README.md

@@ -1,38 +0,0 @@
-# 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

@@ -1,28 +0,0 @@
-
-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/deployment.yaml

@@ -1,35 +0,0 @@
-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

@@ -1,36 +0,0 @@
-{{- 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

@@ -1,20 +0,0 @@
-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

@@ -1,41 +0,0 @@
-# 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

@@ -1,12 +0,0 @@
-apiVersion: v1
-appVersion: "1.0"
-description: MOLGENIS vault
-name: molgenis-vault
-version: 0.1.1
-sources:
-- https://github.com/molgenis/molgenis-ops-docker-helm.git
-icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis-vault/catalogIcon-molgenis-vault.svg
-home: https://github.com/coreos/vault-operator
-maintainers:
-- name: fdlk
-- name: sidohaakma

charts/molgenis/Chart.yaml

@@ -1,12 +0,0 @@
-apiVersion: v1
-appVersion: "1.0"
-description: MOLGENIS - helm stack (in BETA)
-name: molgenis
-version: 0.4.3
-sources:
-- https://github.com/molgenis/molgenis-ops-docker-helm.git
-icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis/catalogIcon-molgenis.svg
-home: http://molgenis.org
-maintainers:
-- name: sidohaakma
-- name: fdlk

charts/molgenis/templates/persistence/postgresPVC.yaml

@@ -1,21 +0,0 @@
-{{- 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 }}

molgenis-httpd/Chart.yaml

@@ -0,0 +1,8 @@
+apiVersion: v1
+appVersion: "1.0"
+description: HTTPD for MOLGENIS
+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

molgenis-httpd/values.yaml

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

molgenis-jenkins/Chart.yaml

@@ -0,0 +1,8 @@
+name: molgenis-jenkins
+home: https://jenkins.io/
+version: 0.7.0
+appVersion: 2.121
+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

molgenis-jenkins/README.md

@@ -75,10 +75,6 @@ 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

molgenis-jenkins/requirements.lock

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

molgenis-jenkins/values.yaml

@@ -3,18 +3,17 @@ jenkins:
     HostName: jenkins.molgenis.org
     ServiceType: ClusterIP
     InstallPlugins:
-      - kubernetes:1.12.6
+      - kubernetes:1.12.0
       - workflow-aggregator:2.5
-      - workflow-job:2.25
+      - workflow-job:2.21
       - credentials-binding:1.16
       - git:3.9.1
       - github-branch-source:2.3.6
-      - kubernetes-credentials-provider:0.10
-      - blueocean:1.8.3
+      - kubernetes-credentials-provider:0.9
+      - blueocean:1.6.2
       - github-oauth:0.29
       - gogs-webhook:1.0.14
-      - github-scm-trait-commit-skip:0.1.1
-      - slack:2.3
+      - sauce-ondemand:1.176
     Security:
       UseGitHub: false
       GitHub:
@@ -83,18 +82,6 @@ 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>
@@ -144,17 +131,6 @@ 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">
@@ -208,17 +184,6 @@ 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">
@@ -272,17 +237,6 @@ 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">
@@ -336,17 +290,6 @@ 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">
@@ -400,17 +343,6 @@ 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">
@@ -484,12 +416,6 @@ 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
@@ -521,104 +447,7 @@ jenkins:
               secretName: molgenis-pipeline-vault-secret
               secretKey: addr
       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
-            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 contains configuration for the kubernetes secrets that jenkins can access
 secret:
   # vault configures the vault secret
   vault:
@@ -640,4 +469,4 @@ secret:
   # dockerHubPassword contains password for hub.docker.com
   dockerHub:
     user: molgenisci
-    password: xxxx
+    password: xxxx

molgenis-nexus/Chart.yaml

@@ -0,0 +1,8 @@
+apiVersion: v1
+appVersion: "1.0"
+description: Nexus stack for MOLGENIS
+name: molgenis-nexus
+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-nexus/catalogIcon-molgenis-nexus.svg

molgenis-nexus/README.md

@@ -0,0 +1,28 @@
+# 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

@@ -0,0 +1,34 @@
+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/deployments/nexus-deployment.yaml

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

molgenis-nexus/templates/ingress.yaml

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

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

@@ -0,0 +1,13 @@
+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

@@ -0,0 +1,16 @@
+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

@@ -0,0 +1,11 @@
+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

@@ -0,0 +1,82 @@
+# 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/Chart.yaml

@@ -0,0 +1,8 @@
+apiVersion: v1
+appVersion: "1.0"
+description: MOLGENIS - helm stack for testing purposes
+name: molgenis-preview
+version: 0.2.0
+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-preview/catalogIcon-molgenis.svg

molgenis-preview/README.md

@@ -0,0 +1,16 @@
+# MOLGENIS preview
+This chart is used for testing purposes. It can be used by data managers or developers to test MOLGENIS (e.g. integration testing).
+
+## Containers
+This chart spins up a complete stack to run MOLGENIS. The created containers are:
+
+- MOLGENIS
+- PostgreSQL
+- Elasticsearch
+- OpenCPU
+
+## Rancher
+You can spin up a test instance by navigating to https://rancher.molgenis.org:7777 and login with your LDAP-account.
+
+Go to the test-environment and click on "Launch". Search for MOLGENIS.
+

molgenis-preview/questions.yml

@@ -0,0 +1,61 @@
+
+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/templates/deployment.yaml

@@ -0,0 +1,124 @@
+apiVersion: apps/v1beta2
+kind: Deployment
+metadata:
+  {{- with .Values.ingress.annotations }}
+  annotations:
+{{ toYaml . | indent 4 }}
+  {{- end }}
+  name: {{ template "molgenis.fullname" . }}
+  labels:
+    app: {{ template "molgenis.name" . }}
+    chart: {{ template "molgenis.chart" . }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app: {{ template "molgenis.name" . }}
+      release: {{ .Release.Name }}
+  template:
+    metadata:
+      labels:
+        app: {{ template "molgenis.name" . }}
+        release: {{ .Release.Name }}
+    spec:
+      containers:
+        - name: molgenis
+        {{- with .Values.molgenis }}
+          image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
+          imagePullPolicy: {{ .image.pullPolicy }}
+          env:
+            - name: molgenis.home
+              value: /home/molgenis
+            - name: opencpu.uri.host
+              value: localhost
+            - name: elasticsearch.transport.addresses
+              value: localhost:9300
+            - name: elasticsearch.cluster.name
+              value: {{ $.Values.elasticsearch.clusterName }}
+            - name: db_uri
+              value: "jdbc:postgresql://localhost/{{ $.Values.postgres.db }}"
+            - name: db_user
+              value: {{ $.Values.postgres.user }}
+            - name: db_password
+              value: {{ $.Values.postgres.password }}
+            - name: admin.password
+              value: {{ .adminPassword }}
+            - name: CATALINA_OPTS
+              value: "{{ .javaOpts }}"
+          ports:
+            - containerPort: 8080
+#          livenessProbe:
+#            httpGet:
+#              path: /
+#              port: 8080
+#          readinessProbe:
+#            httpGet:
+#              path: /api/v2/version
+#              port: 8080
+          resources:
+{{ toYaml .resources | indent 12 }}
+        {{- end }}
+
+        - name: elasticsearch
+        {{- with .Values.elasticsearch }}
+          image: "{{ .image.repository }}:{{ .image.tag }}"
+          imagePullPolicy: {{ .image.pullPolicy }}
+          env:
+            - name: cluster.name
+              value: {{ .clusterName }}
+            - name: bootstrap.memory_lock
+              value: "true"
+            - name: ES_JAVA_OPTS
+              value: "{{ .javaOpts }}"
+            - name: xpack.security.enabled
+              value: "false"
+            - name: discovery.type
+              value: single-node
+          ports:
+            - containerPort: 9200
+            - containerPort: 9300
+          resources:
+{{ toYaml .resources | indent 12 }}
+        {{- end }}
+
+        - name: postgres
+        {{- with .Values.postgres }}
+          image: "{{ .image.repository }}:{{ .image.tag }}"
+          imagePullPolicy: {{ .image.pullPolicy }}
+          env:
+            - name: POSTGRES_USER
+              value: {{ .user }}
+            - name: POSTGRES_PASSWORD
+              value: {{ .password }}
+            - name: POSTGRES_DB
+              value: {{ .db }}
+          ports:
+            - containerPort: 5432
+          resources:
+{{ toYaml .resources | indent 12 }}
+        {{- end }}
+
+        - name: opencpu
+        {{- with .Values.opencpu }}
+          image: "{{ .image.repository }}:{{ .image.tag }}"
+          imagePullPolicy: {{ .image.pullPolicy }}
+          ports:
+            - containerPort: 8004
+          resources:
+{{ toYaml .resources | indent 12 }}
+        {{- end }}
+
+    {{- with .Values.nodeSelector }}
+      nodeSelector:
+{{ toYaml . | indent 8 }}
+    {{- end }}
+    {{- with .Values.affinity }}
+      affinity:
+{{ toYaml . | indent 8 }}
+    {{- end }}
+    {{- with .Values.tolerations }}
+      tolerations:
+{{ toYaml . | indent 8 }}
+    {{- end }}

molgenis-preview/templates/ingress.yaml

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

molgenis-preview/templates/service.yaml

@@ -9,18 +9,6 @@ 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 }}

molgenis-preview/values.yaml

@@ -0,0 +1,82 @@
+# 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: {}

molgenis-vault/Chart.yaml

@@ -0,0 +1,6 @@
+apiVersion: v1
+appVersion: "1.0"
+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

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

molgenis/Chart.yaml

@@ -0,0 +1,8 @@
+apiVersion: v1
+appVersion: "1.0"
+description: MOLGENIS - helm stack (in BETA)
+name: molgenis-beta
+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

@@ -5,8 +5,6 @@ This chart is used for acceptance and production use cases.
 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:
@@ -23,19 +21,6 @@ The three properties you need to specify are:
 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) 
@@ -97,16 +82,15 @@ 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'
+- ```persistence.enabled```
 
 You can also choose to retain the volume of the NFS.
-- ```persistence.retain``` default 'false'
+- ```persistence.retain```
 
 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```
@@ -116,9 +100,6 @@ 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:
@@ -135,4 +116,7 @@ You can now view the persistent volume claims and the attached volumes.
 | 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```. 
+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

@@ -8,7 +8,7 @@ questions:
   description: "Hostname for your stack"
   type: hostname
   required: true
-  group: "Load balancing"
+  group: "Load Balancing"
 - variable: molgenis.image.repository
   label: Registry
   default: "registry.hub.docker.com"
@@ -33,24 +33,6 @@ questions:
   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"
@@ -58,43 +40,34 @@ questions:
   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
+- variable: molgenis.services.postgres.host
+  label: Postgres cluster location
+  default: "postgresql.molgenis-postgresql.svc"
+  description: "Set the location of the postgres cluster"
+  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"
-  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
@@ -125,7 +98,7 @@ questions:
   - "2g"
   group: "Resources"
 - variable: persistence.enabled
-  default: true
+  default: false
   description: "Do you want to use persistence"
   type: boolean
   required: true
@@ -139,29 +112,20 @@ questions:
     type: boolean
     label: Retain volume
   - variable: molgenis.persistence.size
-    default: "5Gi"
+    default: "30Gi"
     description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
     type: enum
     options:
-    - "5Gi"
-    - "10Gi"
-    - "20Gi"
+    - "30Gi"
+    - "50Gi"
+    - "100Gi"
     label: Size MOLGENIS filestore
   - variable: elasticsearch.persistence.size
-    default: "5Gi"
+    default: "50Gi"
     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
+    - "100Gi"
+    - "200Gi"
+    label: Size for ElasticSearch data