initial commit

.gitignore

@@ -0,0 +1,2 @@
+*.iml
+.idea

Jenkinsfile

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+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

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+# Third party - Helm templates
+
+These are the Helm templates that we will use for MOLGENIS operations. 
+ 
+## Kubernetes
+When you want to use kubernetes there are some commands you need to know. Also running on a remote cluster will be a must have to control your whole DTAP.
+
+### Basic concepts
+Basic concepts in respect to docker you need to know.
+
+**Deployments**
+
+Are a set of pods that will be deployed according to configuration that is usually managed bij Helm. These pods interact with eachother by being in the same namespace created by kubernetes according to the deployment configuration. 
+
+**Pods**
+
+A pod is wrapper around a container. It will recreate the container when it is shutdown for some reason and interact with other pods when needed.
+
+**Containers**
+
+A container is a docker-container that is created from a docker image. It could be seen as an VM for example
+
+**Images**
+
+An image is a template for a container some sort of boot script but also contains the os for example. A build dockerfile, if you will.
+
+**Prerequisites**
+
+There are some prerequisites you need.
+
+- docker
+- minikube
+
+### Useful commands
+Commands that can be used to get information from a kubernetes cluster
+
+**Pods**
+
+- ```kubectl get pods (optional: [--all-namspaces])```
+  
+  Gets alls running instances of containers from a certain deployment
+
+- ```kubectl describe pod #pod name# --namespace=#namesspace#```
+
+  Describes the pod initialization, also displays error messages more accurately if they occur
+
+- ```kubectl remove pod #pod name# --namespace=#namespace# (optional: [--force] [--grace-period=0])```
+
+  Removes a pod from the system (but will restart if the option is set in the deployment,yaml *[see note]*). 
+  
+  **note:** You can not do this while the deployment of the service is still there
+
+**Services**
+
+- ```kubectl get services```
+
+  Gets all services from a deployment
+
+**Volumes**
+  
+- ```kubectl get pv```
+  
+  Gets all persistant volumes
+- ```kubectl get pvc```
+  
+  Gets all persistent volume claims
+
+**Deployments**
+
+- ```kubectl get deployments```
+  
+  Gets all deployments (comparable with docker-compose)
+    
+## Helm
+
+This repository is serves also as a catalogue for Rancher. We have several apps that are served through this repository. e.g.
+
+- [Opal](charts/opal/README.md)
+
+### Useful commands
+You can you need to know to easily develop and deploy helm-charts
+
+- ```helm lint .```
+
+  To test your helm chart for code errors.
+
+- ```helm install . --dry-run --debug```
+
+  Check if your configuration deploys on a kubernetes cluster and check the configuration
+
+- ```helm install . #release name# --namespace #remote namespace#```
+  
+  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
+- ```helm delete #release#```
+  
+  Performs a sort of mvn clean on your workspace. Very handy for zombie persistent volumes or claims.
+
+- ```install tiller on remote cluster```
+
+  To install tiller on a remote cluster you need an rbac-config.yml.
+  ```kubectl create -f rbac-config.yaml```
+
+  When you have defined the yaml you can add the tiller to the cluster by following the steps below.
+  ```helm init --service-account tiller```  
+  
+  

charts/opal/Chart.yaml

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+apiVersion: v1
+appVersion: "1.0"
+description: Opal - helm stack (in BETA)
+name: opal
+version: 0.5.4
+sources:
+- https://git.webhosting.rug.nl/opal/opal-ops-docker-helm.git
+icon: https://git.webhosting.rug.nl/opal/opal-ops-docker-helm/
+home: https://obiba.org
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/opal/README.md

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+# Opal
+This chart is used for acceptance and production use cases.
+
+## Containers
+The created containers are:
+
+- MOLGENIS
+- ElasticSearch
+- PostgreSQL **(optional)**
+
+## Provisioning
+You can choose from which registry you want to pull. There are 2 registries:
+- https://registry.molgenis.org
+- https://hub.docker.com
+
+The registry.molgenis.org contains the bleeding edge versions (PR's and master merges). The hub.docker.com contains the released artifacts (MOLGENIS releases and release candidates).
+
+The three properties you need to specify are:
+- ```molgenis.image.repository```
+- ```molgenis.image.name```
+- ```molgenis.image.tag```
+
+Besides determining which image you want to pull, you also have to set an administrator password. You can do this by specifying the following property. 
+- ```molgenis.adminPassword```
+
+### Firewall
+Is defined at service level you can specify this attribute in the values:
+
+- ```molgenis.firewall.enabled``` default 'false' 
+
+If set to 'true' the following options are available. One of the options below has to be set.
+
+- ```molgenis.firewall.umcg.enabled``` default 'false'  
+- ```molgenis.firewall.cluster.enabled``` default 'false'
+
+UMCG = only available within the UMCG.
+Cluster = only available within the GCC cluster environment.
+
+## Services
+When you start MOLGENIS you need:
+- an elasticsearch instance (5.5.6) 
+- an postgres instance (9.6)
+
+You can attach additional services like:
+- an opencpu instance
+
+### Elasticsearch
+You can configure elasticsearch by giving in the cluster location.
+
+To configure the transport address you can address the node communication channel but also the native JAVA API. Which MOLGENIS uses to communicate with Elasticsearch.
+From Elasticsearch version 6 and further the JAVA API is not supported anymore. At this moment you can only use Elastic instance till major version 5.
+- ```molgenis.services.elasticsearch.transportAddresses: localhost:9300```
+
+To configure the index on a Elasticsearch cluster you can specify the clusterName property.
+- ```molgenis.services.elasticsearch.clusterName: molgenis```
+
+### Postgres
+You can specify the location of the postgres instance by specify the following property:
+- ```molgenis.services.postgres.host: localhost```
+
+You can specify the schema by filling out this property:
+- ```molgenis.services.postgres.scheme: molgenis```
+
+You can specify credentials for the database scheme by specifying the following properties:
+- ```molgenis.services.postgres.user: molgenis```
+- ```molgenis.services.postgres.password: molgenis```
+
+To test you can use the **PostgreSQL**-helm chart of Kubernetes and specify these answers:
+
+```bash
+# answers for postgresql chart
+postgresUser=molgenis
+postgresPassword=molgenis
+postgresDatabase=molgenis
+persistence.enabled=false
+```
+
+### OpenCPU
+You can specify the location of the OpenCPU cluster by specifying this property:
+- ```molgenis.services.opencpu.host: localhost```
+
+You can test OpenCPU settings using the **OpenCPU**-helm chart of MOLGENIS.
+
+## Resources
+You can specify resources by resource type. There are 2 resource types.
+- memory of container
+- maximum heap space JVM
+
+Specify memory usage of container:
+- ```molgenis.resources.limits.memory```
+
+Specify memory usage for Java JVM:
+- ```molgenis.javaOpts.maxHeapSpace```
+
+Select the resources you need dependant on the customer you need to serve.
+
+## Persistence
+You can enable persistence on your MOLGENIS stack by specifying the following property.
+
+- ```persistence.enabled``` default 'true'
+
+You can also choose to retain the volume of the NFS.
+- ```persistence.retain``` default 'false'
+
+The size and claim name can be specified per service. There are now two services that can be persist.
+
+- MOLGENIS
+- ElasticSearch
+- PostgreSQL **(optional)**
+
+MOLGENIS persistent properties.
+- ```molgenis.persistence.claim```
+- ```molgenis.persistence.size```
+
+ElasticSearch persistent properties.
+- ```elasticsearch.persistence.claim```
+- ```elasticsearch.persistence.size```
+
+PostgreSQL persistent properties.
+- ```postgres.persistence.claim```
+- ```postgres.persistence.size```
+
+### Resolve you persistent volume
+You do not know which volume is attached to your MOLGENIS instance. You can resolve this by executing:
+
+```
+kubectl get pv
+```
+
+You can now view the persistent volume claims and the attached volumes.
+
+| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
+| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
+| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-solverd/molgenis-nfs-claim | nfs-provisioner-retain | | | 33d |
+| pvc-3984723d-220f-14e8-a98a-skjhf88823kk | 30G | RWO | | Delete | Bound | molgenis-test/molgenis-nfs-claim | nfs-provisioner | | | 33d |
+
+You see the ```molgenis-test/molgenis-nfs-claim``` is bound to the volume: ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
+When you want to view the data in the this volume you can go to the nfs-provisioning pod and execute the shell. Go to the directory ```export``` and lookup the directory ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```. 

charts/opal/questions.yml

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+
+categories:
+- OPAL
+questions:
+- variable: opal.environment
+  label: Environment
+  default: "test"
+  description: "Environment of Opal instance"
+  type: enum
+  options:
+   - development
+   - test
+   - acceptance
+   - production
+  required: true
+  group: "Provisioning"
+- variable: molgenis.type.kind
+  label: Type
+  default: "medium"
+  description: "Type of MOLGENIS resources"
+  type: enum
+  options:
+   - small
+   - medium
+   - large
+  required: true
+  group: "Provisioning"
+- variable: molgenis.image.tag
+  label: Version
+  default: "stable"
+  description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for released tags)"
+  type: string
+  required: true
+  group: "Provisioning"
+- variable: molgenis.adminPassword
+  label: Administrator password
+  default: ""
+  description: "Enter an administrator password"
+  type: password
+  required: true
+  group: "Provisioning"
+- variable: service.firewall.enabled
+  label: Firewall enabled
+  default: false
+  description: "Firewall enabled (can be cluster or UMCG scoped)"
+  type: boolean
+  required: true
+  group: "Services"
+  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.advanced
+  label: Advanced mode
+  default: false
+  description: "Do you want to override the default values in advanced mode"
+  type: boolean
+  required: true
+  group: "Advanced"
+  show_subquestion_if: true
+  subquestions:
+  - variable: molgenis.image.repository
+    label: Registry
+    default: "registry.hub.docker.com"
+    description: "Select a registry to pull from"
+    type: enum
+    options:
+    - "registry.hub.docker.com"
+    - "registry.molgenis.org"
+    required: true
+    group: "Provisioning"
+  - variable: molgenis.services.opencpu.host
+    label: OpenCPU cluster
+    default: "molgenis-opencpu.opencpu"
+    description: "Specify the OpenCPU cluster"
+    type: string
+    required: true
+    group: "Services"
+  - variable: molgenis.services.postgres.embedded
+    label: Postgres embedded
+    default: true
+    description: "Do you want an embedded postgres"
+    type: boolean
+    required: true
+    group: "Services"
+  - variable: molgenis.services.postgres.host
+    label: Postgres cluster location
+    default: "localhost"
+    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: persistence.retain
+    default: false
+    description: "Do you want to retain the persistent volume"
+    type: boolean
+    label: Retain volume
+    group: "Persistence"
+  - variable: persistence.molgenis.size
+    default: "default"
+    description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
+    type: enum
+    options:
+    - "default"
+    - "5Gi"
+    - "10Gi"
+    - "30Gi"
+    label: Size MOLGENIS filestore
+    group: "Persistence"

charts/opal/requirements.yaml

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+dependencies:
+  - name: mysql
+    version: ^0.16
+    repository: https://kubernetes-charts.storage.googleapis.com/

charts/opal/templates/NOTES.txt

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+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 }}

charts/opal/templates/_helpers.tpl

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

charts/opal/templates/deployment.yaml

@@ -0,0 +1,103 @@
+apiVersion: apps/v1beta2
+kind: Deployment
+metadata:
+  {{- with .Values.ingress.annotations }}
+  annotations:
+{{ toYaml . | indent 4 }}
+  {{- end }}
+  name: {{ template "opal.fullname" . }}
+  labels:
+    app: {{ template "opal.name" . }}
+    chart: {{ template "opal.chart" . }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app: {{ template "opal.name" . }}
+      release: {{ .Release.Name }}
+  strategy:
+    type: Recreate
+  template:
+    metadata:
+      labels:
+        app: {{ template "opal.name" . }}
+        release: {{ .Release.Name }}
+    spec:
+      containers:
+        - name: opal
+        {{- with .Values.opal }}
+          image: {{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}
+          imagePullPolicy: {{ .image.pullPolicy }}
+          env:
+            - name: opal.home
+              value: /home/opal
+            - name: db_uri
+              value: jdbc:postgresql://localhost/opal
+            - name: db_user
+              value: opal
+            - name: db_password
+              value: opal
+            - name: admin.password
+              value: "{{ .adminPassword }}"
+            - name: CATALINA_OPTS
+            {{- if eq .type.kind "small" }}
+              value: "-Xmx{{ .type.small.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
+            {{- else if eq .type.kind "medium"}}
+              value: "-Xmx{{ .type.medium.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
+            {{- else }}
+              value: "-Xmx{{ .type.large.javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
+            {{- end }}
+          ports:
+            - containerPort: 8080
+          {{- if $.Values.persistence.enabled }}
+          volumeMounts:
+          - name: opal-nfs
+            mountPath: /home/opal
+          {{- end }}
+          livenessProbe:
+            httpGet:
+              path: /
+              port: 8080
+            initialDelaySeconds: 60
+            periodSeconds: 5
+            failureThreshold: 25
+            successThreshold: 1
+          readinessProbe:
+            httpGet:
+              path: /api/v2/version
+              port: 8080
+            initialDelaySeconds: 120
+            periodSeconds: 30
+            failureThreshold: 3
+            successThreshold: 1
+          resources:
+          {{- if eq .type.kind "small" }}
+{{ toYaml .type.small.resources | indent 12 }}
+          {{- else if eq .type.kind "medium" }}
+{{ toYaml .type.medium.resources | indent 12 }}
+          {{- else }}
+{{ toYaml .type.large.resources | indent 12 }}
+          {{- end }}
+        {{- end }}
+
+{{- if .Values.persistence.enabled }}
+      volumes:
+        - name: opal-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.opal.persistence.claim }}
+{{- 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 }}

charts/opal/templates/ingress.yaml

@@ -0,0 +1,44 @@
+{{- if .Values.ingress.enabled -}}
+{{- $fullName := include "opal.fullname" . -}}
+{{- $ingressPath := .Values.ingress.path -}}
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: "{{ $.Release.Name }}-ingress"
+  labels:
+    app: {{ template "opal.name" . }}
+    chart: {{ template "opal.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:
+    {{- if eq $.Values.opal.environment "development" }}
+    - host: {{ .Release.Name }}.dev.opal.org
+    {{- else if eq $.Values.opal.environment "test" }}
+    - host: {{ .Release.Name }}.test.opal.org
+    {{- else if eq $.Values.opal.environment "acceptance" }}
+    - host: {{ .Release.Name }}.accept.opal.org
+    {{- else }}
+    - host: {{ .Release.Name }}.opal.org
+    {{- end }}
+      http:
+        paths:
+          - path: {{ $ingressPath }}
+            backend:
+              serviceName: {{ $fullName }}
+              servicePort: {{ $.Values.service.port }}
+{{- end }}

charts/opal/templates/persistence/mysqlPVC.yaml

@@ -0,0 +1,29 @@
+{{- if .Values.persistence.enabled }}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Values.mysql.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:
+    {{- if eq .Values.persistence.mysql.size "default" }}
+      {{- if eq .Values.opal.type.kind "small" }}
+      storage: {{ .Values.mysql.type.small.persistence.size }}
+      {{- else if eq .Values.opal.type.kind "medium" }}
+      storage: {{ .Values.mysql.type.medium.persistence.size }}
+      {{- else }}
+      storage: {{ .Values.mysql.type.large.persistence.size }}
+      {{- end }}
+    {{ else }}
+        storage: {{ .Values.persistence.mysql.size }}
+    {{- end }}
+{{- end }}

charts/opal/templates/persistence/opalPVC.yaml

@@ -0,0 +1,29 @@
+{{- if .Values.persistence.enabled -}}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Values.opal.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:
+    {{- if eq .Values.persistence.opal.size "default" }}
+      {{- if eq .Values.opal.type.kind "small" }}
+      storage: {{ .Values.opal.type.small.persistence.size }}
+      {{- else if eq .Values.opal.type.kind "medium" }}
+      storage: {{ .Values.opal.type.medium.persistence.size }}
+      {{- else }}
+      storage: {{ .Values.opal.type.large.persistence.size }}
+      {{- end }}
+    {{ else }}
+      storage: {{ .Values.persistence.opal.size }}
+    {{- end }}
+{{- end }}

charts/opal/templates/service.yaml

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

charts/opal/values.yaml

@@ -0,0 +1,143 @@
+# Default values for molgenis.
+
+replicaCount: 1
+
+service:
+  type: LoadBalancer
+  firewall:
+    enabled: false
+    kind: "umcg"
+    umcg:
+      rules:
+      - 127.0.0.1/32
+    cluster:
+      rules:
+      - 127.0.0.1/32
+  port: 8080
+
+ingress:
+  enabled: true
+  annotations:
+    nginx.ingress.kubernetes.io/proxy-body-size: "0"
+  # This will be used again when external domains need be attached to the instance
+  # hosts:
+  # - name: test
+  path: /
+  tls: []
+
+opal:
+  advanced: false
+  type:
+    kind: medium
+    small:
+      javaOpts:
+        maxHeapSpace: "2g"
+      resources:
+        limits:
+          cpu: 2
+          memory: 2Gi
+        requests:
+          cpu: 200m
+          memory: 2Gi
+      persistence:
+        size: 5Gi
+    medium:
+      javaOpts:
+        maxHeapSpace: "3g"
+      resources:
+        limits:
+          cpu: 3
+          memory: 3Gi
+        requests:
+          cpu: 200m
+          memory: 3Gi
+      persistence:
+        size: 10Gi
+    large:
+      javaOpts:
+        maxHeapSpace: "4g"
+      resources:
+        limits:
+          cpu: 4
+          memory: 4Gi
+        requests:
+          cpu: 200m
+          memory: 4Gi
+      persistence:
+        size: 30Gi
+  environment: test
+  image:
+    repository: registry.hub.docker.com
+    name: obiba/opal
+    tag: stable
+    pullPolicy: Always
+  adminPassword:
+  persistence:
+    claim: opal-nfs-claim
+  services:
+    rserver:
+      host: localhost
+    mysql:
+      host: localhost
+
+
+rserver:
+  image:
+    repository: obiba/opal-rserver
+    tag: stable
+    pullPolicy: IfNotPresent
+
+mysql:
+  type:
+    small:
+      resources:
+        limits:
+          cpu: 1
+          memory: 512Mi
+        requests:
+          cpu: 100m
+          memory: 512Mi
+      persistence:
+        size: 5Gi
+    medium:
+      resources:
+        limits:
+          cpu: 2
+          memory: 2Gi
+        requests:
+          cpu: 100m
+          memory: 2Gi
+      persistence:
+        size: 10Gi
+    large:
+      resources:
+        limits:
+          cpu: 4
+          memory: 4Gi
+        requests:
+          cpu: 100m
+          memory: 4Gi
+      persistence:
+        size: 15Gi
+  image:
+    repository: postgres
+    tag: 9.6-alpine
+    pullPolicy: IfNotPresent
+  persistence:
+    claim: mysql-nfs-claim
+
+persistence:
+  enabled: true
+  retain: false
+  opal:
+    size: "default"
+  mysql:
+    size: "default"
+
+nodeSelector: {
+  deployPod: "true"
+}
+
+tolerations: []
+
+affinity: {}