README.md

@@ -1,6 +1,6 @@
 # Third party - Helm templates
 
-These are the Helm templates that we will use for third-party operations. 
+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.
@@ -76,8 +76,6 @@ Commands that can be used to get information from a kubernetes cluster
 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)
-- [RStudio](charts/rstudio/README.md)
-- [MOLGENIS website](charts/website/README.md)
 
 ### Useful commands
 You can you need to know to easily develop and deploy helm-charts

charts/opal/Chart.yaml

@@ -0,0 +1,12 @@
+apiVersion: v1
+appVersion: "1.0"
+description: Opal - helm stack (in BETA)
+name: opal
+version: 0.0.1
+sources:
+- https://git.webhosting.rug.nl/molgenis/thirdparty-ops-docker-helm.git
+icon: https://git.webhosting.rug.nl/molgenis/thirdparty-ops-docker-helm/
+home: https://obiba.org
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/opal/README.md

@@ -0,0 +1,13 @@
+# Opal
+This chart is used for acceptance and production use cases.
+
+## Containers
+The created containers are:
+
+- Opal
+- MongoDB
+- RServer
+
+## Provisioning
+You can choose from which registry you want to pull. There is 1 one registry:
+- https://hub.docker.com

charts/opal/questions.yml

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

charts/opal/requirements.lock

@@ -0,0 +1,6 @@
+dependencies:
+- name: mysql
+  repository: https://kubernetes-charts.storage.googleapis.com/
+  version: 0.10.2
+digest: sha256:77710fe100fb005d51e006d2e19643f9af2b1aadd1c2249c67ffc5be6a095f30
+generated: 2018-11-06T15:57:20.530933765Z

charts/opal/requirements.yaml

@@ -0,0 +1,4 @@
+dependencies:
+  - name: mysql
+    version: ^0.10.2
+    repository: https://kubernetes-charts.storage.googleapis.com/

charts/opal/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 }}

charts/opal/templates/_helpers.tpl

@@ -0,0 +1,32 @@
+{{/* 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 +1,83 @@
+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_ADMINISTRATOR_PASSWORD
+              value: "{{ .adminPassword }}"
+          ports:
+            - containerPort: {{ $.Values.service.port }}
+          {{- if $.Values.persistence.enabled }}
+          volumeMounts:
+          - name: opal-nfs
+            mountPath: /home/opal
+          {{- end }}
+          livenessProbe:
+            httpGet:
+              path: /
+              port: {{ $.Values.service.port }}
+            initialDelaySeconds: 60
+            periodSeconds: 5
+            failureThreshold: 25
+            successThreshold: 1
+          resources:
+{{ toYaml .resources | indent 12 }}
+        {{- end }}
+        - name: rserver
+        {{- with .Values.rserver }}
+          image: {{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}
+          imagePullPolicy: {{ .image.pullPolicy }}
+          ports:
+            - containerPort: 6612
+            - containerPort: 6311
+          resources:
+{{ toYaml .resources | indent 12 }}
+        {{- end }}
+
+{{- if .Values.persistence.enabled }}
+      volumes:
+        - name: opal-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Release.Name }}-{{ .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 +1,40 @@
+{{- if .Values.ingress.enabled -}}
+{{- $fullName := include "opal.fullname" . -}}
+{{- $ingressPath := .Values.ingress.path -}}
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: "{{ $.Release.Name }}-ingress"
+  labels:
+    app: {{ $.Values.service.name }}
+    chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
+    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 .Values.ingress.hosts }}
+  {{- range $host := .Values.ingress.hosts }}
+    - host: {{ $host }}
+      http:
+        paths:
+          - path: {{ $ingressPath }}
+            backend:
+              serviceName: {{ $.Values.service.name }}
+              servicePort: {{ $.Values.service.port }}
+  {{- end }}
+  {{- end }}
+{{- end }}

charts/opal/templates/opal-pvc.yaml

@@ -0,0 +1,19 @@
+{{- if .Values.persistence.enabled -}}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Release.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:
+      storage: {{ .Values.opal.persistence.size }}
+{{- end }}

charts/opal/templates/service.yaml

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

charts/opal/values.yaml

@@ -0,0 +1,84 @@
+# Default values for molgenis.
+
+replicaCount: 1
+
+service:
+  name: opal
+  type: ClusterIP
+  port: 8080
+
+ingress:
+  enabled: true
+  annotations:
+    nginx.ingress.kubernetes.io/proxy-body-size: "0"
+  hosts:
+    - opal.dev.molgenis.org
+  path: /
+  tls: []
+
+opal:
+  advanced: false
+  javaOpts:
+    maxHeapSpace: "4g"
+  resources:
+    limits:
+    cpu: 1
+    memory: 2Gi
+  requests:
+    cpu: 200m
+    memory: 4Gi
+  persistence:
+    size: 10Gi
+  image:
+    repository: registry.hub.docker.com
+    name: obiba/opal
+    tag: latest
+    pullPolicy: Always
+  adminPassword: ?01LifeCycle!
+  persistence:
+    claim: pvc-opal
+    size: 10Gi
+  containerPorts:
+    - 8080
+
+rserver:
+  image:
+    repository: registry.hub.docker.com
+    name: obiba/opal-rserver
+    tag: latest
+    pullPolicy: IfNotPresent
+  resources:
+    limits:
+      cpu: 1
+      memory: 2Gi
+  containerPorts:
+   - 6612
+   - 6311
+
+mysql:
+  persistence:
+    enabled: false
+  mysqlRootPassword: ParaD0xa
+  mysqlUser: opal
+  mysqlPassword: ?opal01!
+  initializationFiles:
+    opal-ids.sql: |-
+      CREATE DATABASE IF NOT EXISTS opal_ids DEFAULT CHARACTER SET utf8 DEFAULT COLLATE utf8_general_ci;
+      GRANT ALL PRIVILEGES ON opal_ids.* TO "opal"@"%" IDENTIFIED BY "?opal01!";
+      FLUSH PRIVILEGES;
+    opal-data.sql: |-
+      CREATE DATABASE IF NOT EXISTS opal_data DEFAULT CHARACTER SET utf8 DEFAULT COLLATE utf8_general_ci;
+      GRANT ALL PRIVILEGES ON opal_data.* TO "opal"@"%" IDENTIFIED BY "?opal01!";
+      FLUSH PRIVILEGES;
+
+persistence:
+  enabled: false
+  retain: false
+
+nodeSelector: {
+  deployPod: "true"
+}
+
+tolerations: []
+
+affinity: {}

charts/rstudio/Chart.yaml

@@ -1,12 +1,12 @@
 apiVersion: v1
 appVersion: "1.0"
-description: MOLGENIS Helm chart for OpenCPU
+description: RStudio stack
-name: molgenis-website
+name: rstudio
 version: 0.0.1
 sources:
 - https://git.webhosting.rug.nl/molgenis/thirdparty-ops-docker-helm.git
-icon: https://raw.git.webhosting.rug.nl/molgenis/thirdparty-ops-docker-helm/raw/master/charts/molgenis-website/catalogIcon-molgenis-website.png
+icon: https://raw.git.webhosting.rug.nl/molgenis/thirdparty-ops-docker-helm/master/charts/rstudio/catalog-molgenis-rstudio.svg
-home: https://www.molgenis.org
+home: https://www.rocker.org
 maintainers:
 - name: sidohaakma
 - name: fdlk

charts/rstudio/README.md

@@ -0,0 +1,37 @@
+# MOLGENIS - RStudio Helm Chart
+
+An RStudio instance to support DataSHIELD users in setting up a central analysis server instance.
+
+## Containers
+
+This chart will deploy the following container:
+
+- molgenis-rstudio (with DataSHIELD packages)
+
+## Provisioning
+You can choose for the RStudio 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.
+
+- ```rstudio.image.repository```
+- ```rstudio.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.
+
+```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/rstudio/questions.yml

@@ -0,0 +1,31 @@
+
+categories:
+- MOLGENIS
+questions:
+- variable: rstudio.environment
+  label: Environment
+  default: development
+  type: enum
+  options:
+  - development
+  - test
+  - acceptence
+  - production
+  group: "Provisioning"
+- variable: rstudio.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: rstudio.image.tag
+  label: Version
+  default: ""
+  description: "Select a RStudio version (check the registry.molgenis.org or hub.docker.com for released tags)"
+  type: string
+  required: true
+  group: "Provisioning"

charts/rstudio/templates/_helpers.tpl

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

charts/rstudio/templates/deployment.yaml

@@ -0,0 +1,46 @@
+apiVersion: extensions/v1beta1
+kind: Deployment
+metadata:
+  {{- with .Values.ingress.annotations }}
+  annotations:
+{{ toYaml . | indent 4 }}
+  {{- end }}
+  name: {{ template "rstudio.fullname" . }}
+  labels:
+    app: {{ template "rstudio.name" . }}
+    chart: {{ template "rstudio.chart" . }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app: {{ template "rstudio.name" . }}
+      release: {{ .Release.Name }}
+  template:
+    metadata:
+      labels:
+        app: {{ template "rstudio.name" . }}
+        release: {{ .Release.Name }}
+    spec:
+      containers:
+      {{- with .Values.rstudio }}
+      - name: {{ .name }}
+        image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
+        imagePullPolicy: {{ .image.pullPolicy }}
+        env:
+        - name: PASSWORD
+          value: "{{ .adminPassword }}"
+        ports:
+        - containerPort: {{ .service.port }}
+        livenessProbe:
+          httpGet:
+            path: /
+            port: {{ .service.port }}
+          initialDelaySeconds: 60
+          periodSeconds: 5
+          failureThreshold: 25
+          successThreshold: 1
+      {{- end }}
+
+

charts/rstudio/templates/ingress.yaml

@@ -0,0 +1,36 @@
+{{- if .Values.ingress.enabled }}
+{{- range .Values.ingress.hosts }}
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: "{{ $.Release.Name }}-ingress"
+  labels:
+    app:  "{{ .Release.Name}}-{{ .Values.rstudio.service.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: "{{ .Release.Name}}-{{ .Values.rstudio.service.name }}"
+            servicePort: {{ $.Values.rstudio.service.port }}
+{{- if .tls }}
+  tls:
+  - hosts:
+    - {{ .name }}
+    secretName: {{ .tlsSecret }}
+{{- end }}
+---
+{{- end }}
+{{- end }}

charts/rstudio/templates/service.yaml

@@ -0,0 +1,16 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: "{{ .Release.Name}}-{{ .Values.rstudio.service.name }}"
+  labels:
+    app: "{{ .Release.Name}}-{{ .Values.rstudio.service.name }}"
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  type: {{ .Values.rstudio.service.type }}
+  ports:
+    - name: "{{ .Release.Name}}-{{ .Values.rstudio.service.name }}"
+      port: {{ .Values.rstudio.service.port }}
+  selector:
+    app: {{ template "rstudio.name" . }}
+    release: {{ .Release.Name }}

charts/rstudio/values.yaml

@@ -0,0 +1,40 @@
+# Default values for nexus.
+# This is a YAML-formatted file.
+# Declare variables to be passed into your templates.
+
+replicaCount: 1
+
+environment: production
+
+rstudio:
+  name: rstudio
+  strategy:
+    type: Recreate
+  restartPolicy: Always
+  adminPassword: ?01LifeCycle!
+  image:
+    repository: registry.hub.docker.com
+    name: molgenis/rstudio
+    tag: beta
+    pullPolicy: Always
+  service:
+    name: rstudio
+    type: ClusterIP
+    port: 8787
+
+ingress:
+  enabled: true
+  annotations: {
+    kubernetes.io/ingress.class: "nginx",
+    nginx.ingress.kubernetes.io/proxy-body-size: "0"
+  }
+  path: /
+  hosts:
+  - name: analysis.dev.molgenis.org
+  tls: []
+
+nodeSelector: {}
+
+tolerations: []
+
+affinity: {}

charts/website/.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

charts/website/Chart.yaml

@@ -0,0 +1,12 @@
+apiVersion: v1
+appVersion: "1.0"
+description: MOLGENIS Helm chart for OpenCPU
+name: molgenis-website
+version: 0.0.1
+sources:
+- https://github.com/molgenis/molgenis-ops-docker-helm.git
+icon: https://raw.githubusercontent.com/molgenis/molgenis-ops-docker-helm/master/charts/molgenis-website/catalog-molgenis-website.svg
+home: https://www.molgenis.org
+maintainers:
+- name: sidohaakma
+- name: fdlk