add MOLGENIS preview

README.md

@@ -104,6 +104,7 @@ This repository is serves also as a catalogue for Rancher. We have serveral apps
 - [Jenkins](molgenis-jenkins/README.md)
 - [NEXUS](molgenis-nexus/README.md)
 - [HTTPD](molgenis-httpd/README.md)
+- [MOLNIGES preview](molgenis-preview/README.md)
 
 ### Useful commands
 You can you need to know to easily develop and deploy helm-charts
@@ -116,7 +117,7 @@ You can you need to know to easily develop and deploy helm-charts
 
   Check if your configuration deploys on a kubernetes cluster and check the configuration
 
-- ```helm install .```
+- ```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
@@ -126,4 +127,13 @@ You can you need to know to easily develop and deploy helm-charts
 - ```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```  
+  
+  

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

@@ -5,7 +5,7 @@ metadata:
   labels:
     app: {{ .Values.httpd.name }}
 spec:
-  type: NodePort
+  type: {{ .Values.httpd.service.type }}
   ports:
   - name: {{ .Values.httpd.name }}
     port: {{ .Values.httpd.port }}

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

@@ -5,7 +5,7 @@ metadata:
   labels:
     app: {{ .Values.nexus.name }}
 spec:
-  type: ClusterIP
+  type: {{ .Values.nexus.service.type }}
   ports:
   - name: ui
     port: {{ .Values.nexus.port.ui }}

molgenis-nexus/values.yaml

@@ -6,10 +6,6 @@ replicaCount: 1
 
 environment: production
 
-service:
-  type: NodePort
-  port: 80
-
 nexus:
   name: nexus
   strategy:
@@ -25,6 +21,8 @@ nexus:
     ui: 8081
   path:
     dockerV2: v2
+  service:
+    type: ClusterIP
 
 httpd:
   name: httpd
@@ -38,6 +36,8 @@ httpd:
     tag: lts
     pullPolicy: Always
   port: 80
+  service:
+    type: LoadBalancer
 
 
 ingress:

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 +1,5 @@
+apiVersion: v1
+appVersion: "1.0"
+description: A Helm chart for Kubernetes
+name: molgenis
+version: 0.1.0

molgenis-preview/README.md

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

molgenis-preview/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 +1,120 @@
+apiVersion: apps/v1beta2
+kind: Deployment
+metadata:
+  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.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: {{ . }}
+      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/test.yaml

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

molgenis-preview/values.yaml

@@ -0,0 +1,82 @@
+# Default values for molgenis.
+
+replicaCount: 1
+
+service:
+  type: LoadBalancer
+  port: 8080
+
+ingress:
+  enabled: true
+  annotations: {}
+    # kubernetes.io/ingress.class: nginx
+    # kubernetes.io/tls-acme: "true"
+  path: /
+  hosts:
+    - test.molgenis.org
+  tls: []
+
+molgenis:
+  image:
+    repository: registry.molgenis.org/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: {}

rbac-config.yml

@@ -0,0 +1,18 @@
+apiVersion: v1
+kind: ServiceAccount
+metadata:
+  name: tiller
+  namespace: kube-system
+---
+apiVersion: rbac.authorization.k8s.io/v1beta1
+kind: ClusterRoleBinding
+metadata:
+  name: tiller
+roleRef:
+  apiGroup: rbac.authorization.k8s.io
+  kind: ClusterRole
+  name: cluster-admin
+subjects:
+  - kind: ServiceAccount
+    name: tiller
+    namespace: kube-system