README.md

@@ -104,7 +104,6 @@ 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)
 
@@ -123,26 +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

molgenis-jenkins/Chart.yaml

@@ -1,6 +1,6 @@
 name: molgenis-jenkins
 home: https://jenkins.io/
-version: 0.7.1
+version: 0.7.0
 appVersion: 2.121
 description: Molgenis installation for the jenkins chart.
 sources:

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

@@ -3,17 +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
+      - kubernetes-credentials-provider:0.9
-      - blueocean:1.8.3
+      - blueocean:1.6.2
       - github-oauth:0.29
       - gogs-webhook:1.0.14
-      - github-scm-trait-commit-skip:0.1.1
+      - sauce-ondemand:1.176
     Security:
       UseGitHub: false
       GitHub:
@@ -82,7 +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>

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

@@ -19,7 +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: volume-mount-nexus
+        image: busybox
+        command: ["sh", "-c", "chown -R 200:200 {{ .Values.persistence.mountPath }}"]
+        volumeMounts:
+        - name: {{ .Values.persistence.name }}
+          mountPath: "{{ .Values.persistence.mountPath }}"
       containers:
       - name: {{ .Values.nexus.name }}
         image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
@@ -28,31 +39,6 @@ spec:
         - containerPort: {{ .Values.nexus.port.ui }}
         - containerPort: {{ .Values.nexus.port.docker }}
         volumeMounts:
-          - name: molgenis-nexus-nfs
+        - name: {{ .Values.persistence.name }}
           mountPath: "/nexus-data"
-          livenessProbe:
-            httpGet:
-              path: /
-              port: {{ .Values.nexus.port.ui }}
-            initialDelaySeconds: 90
-            periodSeconds: 20
-            failureThreshold: 5
-            successThreshold: 1
-          readinessProbe:
-            httpGet:
-              path: /
-              port: {{ .Values.nexus.port.ui }}
-            initialDelaySeconds: 90
-            periodSeconds: 5
-            failureThreshold: 5
-            successThreshold: 1
 
-      volumes:
-        - name: molgenis-nexus-nfs
-          persistentVolumeClaim:
-            claimName: {{ .Values.persistence.claim }}
-
-    {{- with .Values.nodeSelector }}
-      nodeSelector:
-{{ toYaml . | indent 8 }}
-    {{- end }}

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: 90
-          periodSeconds: 5
-          failureThreshold: 5
-          successThreshold: 1
-        readinessProbe:
-          httpGet:
-            path: /
-            port: {{ .Values.nexusProxy.port }}
-          initialDelaySeconds: 90
-          periodSeconds: 5
-          failureThreshold: 5
-          successThreshold: 1
-
-    {{- with .Values.nodeSelector }}
-      nodeSelector:
-{{ toYaml . | indent 8 }}
-    {{- end }}

molgenis-nexus/templates/ingress.yaml

@@ -25,8 +25,8 @@ spec:
       paths:
         - path: {{ default "/" .path }}
           backend:
-            serviceName: {{ $.Values.nexusProxy.name }}
+            serviceName: httpd
-            servicePort: {{ $.Values.nexusProxy.port }}
+            servicePort: 80
 {{- if .tls }}
   tls:
   - hosts:

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 }}

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/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 }}

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

@@ -24,12 +24,12 @@ nexus:
   service:
     type: ClusterIP
 
-nexusProxy:
+httpd:
-  name: nexus-proxy
+  name: httpd
   hostname: registry.molgenis.org
   strategy:
     type: Recreate
-  selector: nexus-proxy
+  selector: httpd
   restartPolicy: Always
   image:
     repository: registry.webhosting.rug.nl/molgenis/httpd
@@ -43,22 +43,39 @@ nexusProxy:
 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:
-  enabled: true
+  name: molgenis-nexus-data
-  claim: molgenis-nexus
+  storageClass: nfs-class
-  size: 500Gi
+  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: {
+nodeSelector: {}
-  deployPod: "true"
-}
 
 tolerations: []
 

molgenis-preview/.helmignore

@@ -0,0 +1,21 @@
+# Patterns to ignore when building packages.
+# This supports shell glob matching, relative path matching, and
+# negation (prefixed with !). Only one pattern per line.
+.DS_Store
+# Common VCS dirs
+.git/
+.gitignore
+.bzr/
+.bzrignore
+.hg/
+.hgignore
+.svn/
+# Common backup files
+*.swp
+*.bak
+*.tmp
+*~
+# Various IDEs
+.project
+.idea/
+*.tmproj

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/NOTES.txt

@@ -0,0 +1,19 @@
+1. Get the application URL by running these commands:
+{{- if .Values.ingress.enabled }}
+{{- range .Values.ingress.hosts }}
+  http{{ if $.Values.ingress.tls }}s{{ end }}://{{ . }}{{ $.Values.ingress.path }}
+{{- end }}
+{{- else if contains "NodePort" .Values.service.type }}
+  export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ template "molgenis.fullname" . }})
+  export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
+  echo http://$NODE_IP:$NODE_PORT
+{{- else if contains "LoadBalancer" .Values.service.type }}
+     NOTE: It may take a few minutes for the LoadBalancer IP to be available.
+           You can watch the status of by running 'kubectl get svc -w {{ template "molgenis.fullname" . }}'
+  export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ template "molgenis.fullname" . }} -o jsonpath='{.status.loadBalancer.ingress[0].ip}')
+  echo http://$SERVICE_IP:{{ .Values.service.port }}
+{{- else if contains "ClusterIP" .Values.service.type }}
+  export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app={{ template "molgenis.name" . }},release={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
+  echo "Visit http://127.0.0.1:8080 to use your application"
+  kubectl port-forward $POD_NAME 8080:80
+{{- end }}

molgenis-preview/templates/_helpers.tpl

@@ -0,0 +1,32 @@
+{{/* vim: set filetype=mustache: */}}
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "molgenis.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 "molgenis.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 "molgenis.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
+{{- end -}}

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

@@ -0,0 +1,38 @@
+{{- if .Values.ingress.enabled -}}
+{{- $fullName := include "molgenis.fullname" . -}}
+{{- $ingressPath := .Values.ingress.path -}}
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: {{ $fullName }}
+  labels:
+    app: {{ template "molgenis.name" . }}
+    chart: {{ template "molgenis.chart" . }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+{{- with .Values.ingress.annotations }}
+  annotations:
+{{ toYaml . | indent 4 }}
+{{- end }}
+spec:
+{{- if .Values.ingress.tls }}
+  tls:
+  {{- range .Values.ingress.tls }}
+    - hosts:
+      {{- range .hosts }}
+        - {{ . }}
+      {{- end }}
+      secretName: {{ .secretName }}
+  {{- end }}
+{{- end }}
+  rules:
+  {{- range .Values.ingress.hosts }}
+    - host: {{ .name }}
+      http:
+        paths:
+          - path: {{ $ingressPath }}
+            backend:
+              serviceName: {{ $fullName }}
+              servicePort: 8080
+  {{- end }}
+{{- end }}

molgenis-preview/templates/service.yaml

@@ -0,0 +1,17 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ template "molgenis.fullname" . }}
+  labels:
+    app: {{ template "molgenis.name" . }}
+    chart: {{ template "molgenis.chart" . }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  type: {{ .Values.service.type }}
+  ports:
+    - name: molgenis
+      port: {{ .Values.service.port }}
+  selector:
+    app: {{ template "molgenis.name" . }}
+    release: {{ .Release.Name }}

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/Chart.yaml

@@ -1,8 +1,8 @@
 apiVersion: v1
 appVersion: "1.0"
 description: MOLGENIS - helm stack (in BETA)
-name: molgenis
+name: molgenis-beta
-version: 0.4.3
+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:
@@ -136,3 +117,6 @@ You can now view the persistent volume claims and the attached volumes.
 
 You see the ```molgenis-test/molgenis-nfs-claim``` is bound to the volume: ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
 When you want to view the data in the this volume you can go to the nfs-provisioning pod and execute the shell. Go to the directory ```export``` and lookup the directory ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```. 
+
+## Firewall
+Is defined at cluster level. This chart does not facilitate firewall configuration.

molgenis/questions.yml

@@ -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"
@@ -58,19 +40,10 @@ 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
-  required: true
-  group: "Services"
-  show_subquestion_if: false
-  subquestions:
 - variable: molgenis.services.postgres.host
   label: Postgres cluster location
-    default: ""
+  default: "postgresql.molgenis-postgresql.svc"
-    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)"
+  description: "Set the location of the postgres cluster"
   type: string
   required: true
   group: "Services"
@@ -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"
+    - "30Gi"
-    - "10Gi"
+    - "50Gi"
-    - "20Gi"
+    - "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"
+    - "100Gi"
+    - "200Gi"
     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

molgenis/templates/deployment.yaml

@@ -17,8 +17,6 @@ spec:
     matchLabels:
       app: {{ template "molgenis.name" . }}
       release: {{ .Release.Name }}
-  strategy:
-    type: Recreate
   template:
     metadata:
       labels:
@@ -99,33 +97,11 @@ spec:
           - name: elasticsearch-nfs
             mountPath: /usr/share/elasticsearch/data
           {{- end }}
+
           resources:
 {{ toYaml .resources | indent 12 }}
         {{- end }}
 
-        - name: postgres
-        {{- with .Values.postgres }}
-          image: "{{ .image.repository }}:{{ .image.tag }}"
-          imagePullPolicy: {{ .image.pullPolicy }}
-          env:
-            - name: POSTGRES_USER
-              value: {{ $.Values.molgenis.services.postgres.user }}
-            - name: POSTGRES_PASSWORD
-              value: {{ $.Values.molgenis.services.postgres.password }}
-            - name: POSTGRES_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 }}
-
-
 {{- if .Values.persistence.enabled }}
       volumes:
         - name: molgenis-nfs
@@ -134,9 +110,6 @@ spec:
         - name: elasticsearch-nfs
           persistentVolumeClaim:
             claimName: {{ .Values.elasticsearch.persistence.claim }}
-        - name: postgres-nfs
-          persistentVolumeClaim:
-            claimName: {{ .Values.postgres.persistence.claim }}
 {{- end }}
 
     {{- with .Values.nodeSelector }}

molgenis/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/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/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/values.yaml

@@ -4,15 +4,6 @@ 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:
@@ -42,7 +33,7 @@ molgenis:
       memory: 1250Mi
   persistence:
     claim: molgenis-nfs-claim
-    size: 5Gi
+    size: 30Gi
   services:
     opencpu:
       host: localhost
@@ -50,7 +41,6 @@ molgenis:
       transportAddresses: localhost:9300
       clusterName: molgenis
     postgres:
-      embedded: false
       host: localhost
       scheme: molgenis
       user: molgenis
@@ -72,26 +62,10 @@ elasticsearch:
     memory: 1Gi
   persistence:
     claim: elasticsearch-nfs-claim
-    size: 5Gi
+    size: 50Gi
-
-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
+  enabled: false
   retain: false
 
 nodeSelector: {