feat: Add resources for helm role

Needs to run under service account created by the etcd-operator subchart so there's some template magic needed to figure out what it's called.

README.md

@@ -1,39 +1,140 @@
 # MOLGENIS Helm templates
 
-These are the Helm templates that we will use for MOLGENIS operations. There are some prerequisites you need.
+These are the Helm templates that we will use for MOLGENIS operations. 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 for Kubernetes
+## 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.
+
+### Useful commands
 
 Commands that can be used to get information from a kubernetes cluster
 
-- kubectl get pods
+**Pods**
+
+- ```kubectl get pods (optional: [--all-namspaces])```
+  
   Gets alls running instances of containers from a certain deployment
-- kubectl get services
+
+- ```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
-- kubectl get pv
+
+**Volumes**
+  
+- ```kubectl get pv```
+  
   Gets all persistant volumes
-- kubectl get pvc
+- ```kubectl get pvc```
+  
   Gets all persistent volume claims
-- kubectl get deployments
+
+**Deployments**
+
+- ```kubectl get deployments```
+  
   Gets all deployments (comparable with docker-compose)
+    
+
+## Remote clusters
 
 When you want to see what is running on the clusters at the CIT you have to make a context switch.
 You can access the cluster with kubeconfig-files. You can obtain these by downloading them from the 
 MOLGENIS kubernetes cluster.
 
-- Goto https://rancher.molgenis.org:7443
-- Goto 
+- Go to https://rancher.molgenis.org:7777 and login
+- Go to Rancher --> Cluster: *#name#* --> *Kubeconfig File*
+- Go to a **Terminal** where ```kubectl``` is available
+- Add this configuration to ~/.kube/config (or place a new file besides this one)
+  
+  *Example*: 
+```bash
+# When you added the MOLGENIS configuration to the original configuration
+kubectl config use-context molgenis
 
+# or when you placed the MOLGENIS configuration besides the original one
+kubectl config use-context molgenis --kubeconfig=*full path to molgenis config*
+```
+- You can now access all facilities of the MOLGENIS cluster like it is running locally
+  
+  *Example:*
+```bash
+kubectl get pods --namespace=*#namespace of application#*
+```
 
-## Useful commands for Helm
+## Helm
 
-- helm install .
+This repository is serves also as a catalogue for Rancher. We have serveral apps that are served through this repoistory. e.g.
+
+- [Jenkins](molgenis-jenkins/README.md)
+- [NEXUS](molgenis-nexus/README.md)
+- [HTTPD](molgenis-httpd/README.md)
+- [MOLGENIS preview](molgenis-preview/README.md)
+- [MOLGENIS vault](molgenis-vault/README.md)
+
+### Useful commands
+You can you need to know to easily develop and deploy helm-charts
+
+- ```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 list
+- ```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.
+- ```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/index.yaml

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

httpd/v0.1.x/Chart.yaml

@@ -1,5 +0,0 @@
-apiVersion: v1
-appVersion: "1.0"
-description: A Helm chart for Kubernetes
-name: httpd
-version: 0.1.2

httpd/v0.1.x/questions.yml

@@ -1,64 +0,0 @@
-categories:
-- MOLGENIS
-questions:
-- variable: molgenisUsername
-  default: "molgenis"
-  description: "User of the application"
-  type: string
-  required: true
-  label: MOLGENIS username
-  group: "MOLGENIS Settings"
-- variable: molgenisEmail
-  default: "admin@molgenis.org"
-  description: "Admin email"
-  type: string
-  required: true
-  label: MOLGENIS admin email
-  group: "MOLGENIS Settings"
-- variable: persistence.enabled
-  default: "false"
-  description: "Enable persistent volume for MOLGENIS"
-  type: boolean
-  required: true
-  label: MOLGENIS Persistent Volume Enabled
-  show_subquestion_if: true
-  group: "MOLGENIS Settings"
-  subquestions:
-  - variable: persistence.size
-    default: "10Gi"
-    description: "Persistent Volume Size"
-    type: string
-    label: MOLGENIS Volume Size
-  - variable: persistence.storageClass
-    default: ""
-    description: "If undefined or null, uses the default StorageClass. Default to null"
-    type: storageclass
-    label: Default StorageClass for MOLGENIS
-- 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: httpd.hostname
-  default: "test.molgenis.org"
-  description: "Hostname for your services (comma separated, example: [hostname]:[port])"
-  type: string
-  required: false
-  group: "Apache configuration"
-  label: Hostname
-- variable: httpd.proxy
-  default: ""
-  description: "Proxy for your services (comma separated, example: [service]:[port]:[path])"
-  type: string
-  required: false
-  group: "Apache configuration"
-  label: Proxy
-- variable: httpd.redirect
-  default: ""
-  description: "Redirection urls for your services (comma separated, example: [redirection_url])"
-  type: string
-  required: false
-  group: "Apache configuration"
-  label: Redirection

molgenis-httpd/Chart.yaml

@@ -0,0 +1,8 @@
+apiVersion: v1
+appVersion: "1.0"
+description: HTTPD for MOLGENIS
+name: molgenis-httpd
+version: 0.1.0
+sources:
+- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
+icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-httpd/catalogIcon-molgenis-httpd.svg

molgenis-httpd/README.md

@@ -0,0 +1,15 @@
+# MOLGENIS - HTTPD Helm Chart
+
+HTTPD (web)server for kubernetes to deploy on a kubernetes cluster with NFS-share
+
+## Chart Details
+
+This chart will deploy:
+
+- 1 HTTPD container
+
+## Installing the Chart
+
+etc.
+
+

molgenis-httpd/questions.yml

@@ -0,0 +1,31 @@
+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: httpd.hostname
+  default: "test.molgenis.org"
+  description: "Hostname for your services (comma separated, example: [hostname]:[port])"
+  type: string
+  required: false
+  group: "Apache configuration"
+  label: Hostname
+- variable: httpd.proxy
+  default: ""
+  description: "Proxy for your services (comma separated, example: [service]:[port]:[path])"
+  type: string
+  required: false
+  group: "Apache configuration"
+  label: Proxy
+- variable: httpd.redirect
+  default: ""
+  description: "Redirection urls for your services (comma separated, example: [redirection_url])"
+  type: string
+  required: false
+  group: "Apache configuration"
+  label: Redirection

molgenis-httpd/templates/deployment.yaml

@@ -24,9 +24,8 @@ spec:
           image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}"
           imagePullPolicy: {{ .Values.image.pullPolicy }}
           ports:
-            - name: http
-              containerPort: 80
-              protocol: TCP
+            - name: {{ .Values.service.name }}
+              containerPort: {{ .Values.service.port }}
           env:
             - name: SERVER_NAME
               value: "{{ .Values.httpd.hostname }}"

molgenis-httpd/templates/service.yaml

@@ -10,10 +10,9 @@ metadata:
 spec:
   type: {{ .Values.service.type }}
   ports:
-    - port: {{ .Values.service.port }}
-      targetPort: http
-      protocol: TCP
-      name: http
+  - name: {{ .Values.service.name }}
+    port: {{ .Values.service.port }}
+
   selector:
     app: {{ template "httpd.name" . }}
     release: {{ .Release.Name }}

molgenis-httpd/values.yaml

@@ -10,6 +10,7 @@ image:
   pullPolicy: Always
 
 service:
+  name: httpd
   type: ClusterIP
   port: 80
 
@@ -17,12 +18,9 @@ httpd:
   proxy: httpd:80:/
   redirect: redirect.molgenis.local
   hostname: test.molgenis.local
-  volume:
-    username: molgenis
-    email: admin@molgenis.org
 
 ingress:
-  enabled: false
+  enabled: true
   annotations: {}
     # kubernetes.io/ingress.class: nginx
     # kubernetes.io/tls-acme: "true"

molgenis-jenkins/Chart.yaml

@@ -1,7 +1,7 @@
 name: molgenis-jenkins
 home: https://jenkins.io/
-version: 0.2.1
-appVersion: 2.107
+version: 0.7.0
+appVersion: 2.121
 description: Molgenis installation for the jenkins chart.
 sources:
 - https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git

molgenis-jenkins/README.md

@@ -1,10 +1,7 @@
 # Molgenis Jenkins Helm Chart
 
-Jenkins master and slave cluster utilizing the Jenkins Kubernetes plugin
-
-* https://wiki.jenkins-ci.org/display/JENKINS/Kubernetes+Plugin
-
-Inspired by the awesome work of Carlos Sanchez <mailto:carlos@apache.org>
+Jenkins master and slave cluster utilizing the Jenkins Kubernetes plugin.
+Wraps [the kuberenetes jenkins chart](https://github.com/kubernetes/charts/tree/master/stable/jenkins), see documentation there!
 
 ## Chart Details
 
@@ -15,223 +12,100 @@ This chart will do the following:
 
 ## Installing the Chart
 
-In the rancher UI, choose the molgenis-jenkins app from the catalog and deploy it.
+Usually, you'll be deploying this to the molgenis cluster.
+In the [Rancher Catalog](https://rancher.molgenis.org:7443/g/catalog), add the latest version of this repository.
+In the [molgenis cluster management page](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/apps), choose the 
+catalog, pick the molgenis-jenkins app from the catalog and deploy it.
 
 ## Configuration
 
-The following tables list the configurable parameters of the Jenkins chart and their default values.
-You can paste these values into the Rancher Answers if you like.
-Array values can be added as {value, value, value}, e.g.
+When deploying, you can paste values into the Rancher Answers to override the defaults in this chart.
+Array values can be added as {value, value, value}.
 ```
-jenkins.Master.InstallPlugins={kubernetes:1.8.4, workflow-aggregator:2.5, workflow-job:2.21, credentials-binding:1.16, git:3.9.1}
+jenkins.Master.HostName=jenkins.molgenis.org
+jenkins.Master.AdminPassword=pa$$word
+jenkins.Persistence.Enabled=false
+jenkins.Master.InstallPlugins={kubernetes:1.8.4, workflow-aggregator:2.5, workflow-job:2.21, credentials-binding:1.16, git:3.9.1, blueocean:1.6.2, github-oauth:0.29}
+jenkins.Master.Security.UseGitHub=false
+## if UseGitHub=true
+jenkins.Master.Security.GitHub.ClientID=id
+jenkins.Master.Security.GitHub.ClientSecret=S3cr3t
+## end UseGitHub=true
+PipelineSecrets.Env.PGPPassphrase=literal:S3cr3t
 ```
-> Because we use jenkins as a sub-chart, you should prefix all values with `jenkins`!
 
-### Jenkins Master
-| Parameter                         | Description                          | Default                                                                      |
-| --------------------------------- | ------------------------------------ | ---------------------------------------------------------------------------- |
-| `nameOverride`                    | Override the resource name prefix    | `jenkins`                                                                    |
-| `fullnameOverride`                | Override the full resource names     | `jenkins-{release-name}` (or `jenkins` if release-name is `jenkins`)         |
-| `Master.Name`                     | Jenkins master name                  | `jenkins-master`                                                             |
-| `Master.Image`                    | Master image name                    | `jenkinsci/jenkins`                                                          |
-| `Master.ImageTag`                 | Master image tag                     | `lts`                                                                     |
-| `Master.ImagePullPolicy`          | Master image pull policy             | `Always`                                                                     |
-| `Master.ImagePullSecret`          | Master image pull secret             | Not set                                                                      |
-| `Master.Component`                | k8s selector key                     | `jenkins-master`                                                             |
-| `Master.UseSecurity`              | Use basic security                   | `true`                                                                       |
-| `Master.AdminUser`                | Admin username (and password) created as a secret if useSecurity is true | `admin`                                  |
-| `Master.Cpu`                      | Master requested cpu                 | `200m`                                                                       |
-| `Master.Memory`                   | Master requested memory              | `256Mi`                                                                      |
-| `Master.InitContainerEnv`         | Environment variables for Init Container                                 | Not set                                  |
-| `Master.ContainerEnv`             | Environment variables for Jenkins Container                              | Not set                                  |
-| `Master.RunAsUser`                | uid that jenkins runs with           | `0`                                                                          |
-| `Master.FsGroup`                  | uid that will be used for persistent volume | `0`                                                                   |
-| `Master.ServiceAnnotations`       | Service annotations                  | `{}`                                                                         |
-| `Master.ServiceType`              | k8s service type                     | `LoadBalancer`                                                               |
-| `Master.ServicePort`              | k8s service port                     | `8080`                                                                       |
-| `Master.NodePort`                 | k8s node port                        | Not set                                                                      |
-| `Master.HealthProbes`             | Enable k8s liveness and readiness probes | `true`                                                                   |
-| `Master.HealthProbesLivenessTimeout`      | Set the timeout for the liveness probe | `120`                                                       |
-| `Master.HealthProbesReadinessTimeout` | Set the timeout for the readiness probe | `60`                                                       |
-| `Master.HealthProbeLivenessFailureThreshold` | Set the failure threshold for the liveness probe | `12`                                                       |
-| `Master.ContainerPort`            | Master listening port                | `8080`                                                                       |
-| `Master.SlaveListenerPort`        | Listening port for agents            | `50000`                                                                      |
-| `Master.DisabledAgentProtocols`   | Disabled agent protocols             | `JNLP-connect JNLP2-connect`                                                                      |
-| `Master.CSRF.DefaultCrumbIssuer.Enabled` | Enable the default CSRF Crumb issuer | `true`                                                                      |
-| `Master.CSRF.DefaultCrumbIssuer.ProxyCompatability` | Enable proxy compatibility | `true`                                                                      |
-| `Master.CLI`                      | Enable CLI over remoting             | `false`                                                                      |
-| `Master.LoadBalancerSourceRanges` | Allowed inbound IP addresses         | `0.0.0.0/0`                                                                  |
-| `Master.LoadBalancerIP`           | Optional fixed external IP           | Not set                                                                      |
-| `Master.JMXPort`                  | Open a port, for JMX stats           | Not set                                                                      |
-| `Master.CustomConfigMap`          | Use a custom ConfigMap               | `false`                                                                      |
-| `Master.Ingress.Annotations`      | Ingress annotations                  | `{}`                                                                         |
-| `Master.Ingress.TLS`              | Ingress TLS configuration            | `[]`                                                                         |
-| `Master.InitScripts`              | List of Jenkins init scripts         | Not set                                                                      |
-| `Master.CredentialsXmlSecret`     | Kubernetes secret that contains a 'credentials.xml' file | Not set                                                  |
-| `Master.SecretsFilesSecret`       | Kubernetes secret that contains 'secrets' files | Not set                                                           |
-| `Master.Jobs`                     | Jenkins XML job configs              | Not set                                                                      |
-| `Master.InstallPlugins`           | List of Jenkins plugins to install   | `kubernetes:0.11 workflow-aggregator:2.5 credentials-binding:1.11 git:3.2.0` |
-| `Master.ScriptApproval`           | List of groovy functions to approve  | Not set                                                                      |
-| `Master.NodeSelector`             | Node labels for pod assignment       | `{}`                                                                         |
-| `Master.Affinity`                 | Affinity settings                    | `{}`                                                                         |
-| `Master.Tolerations`              | Toleration labels for pod assignment | `{}`                                                                         |
-| `NetworkPolicy.Enabled`           | Enable creation of NetworkPolicy resources. | `false`                                                               |
-| `NetworkPolicy.ApiVersion`        | NetworkPolicy ApiVersion             | `extensions/v1beta1`                                                         |
-| `rbac.install`                    | Create service account and ClusterRoleBinding for Kubernetes plugin | `false`                                       |
-| `rbac.apiVersion`                 | RBAC API version                     | `v1beta1`                                                                    |
-| `rbac.roleRef`                    | Cluster role name to bind to         | `cluster-admin`                                                              |
+You can use [all configuration values of the jenkins subchart](https://github.com/kubernetes/charts/tree/master/stable/jenkins).
+> Because we use jenkins as a sub-chart, you should prefix all value keys with `jenkins`!
 
-### Jenkins Agent
+### GitHub Authentication delegation
+You need to setup a MOLGENIS - Jenkins GitHub OAuth App. You can do this by accessing this url: [add new OAuth app](https://github.com/settings/applications/new).
 
-| Parameter               | Description                                     | Default                |
-| ----------------------- | ----------------------------------------------- | ---------------------- |
-| `Agent.AlwaysPullImage` | Always pull agent container image before build  | `false`                |
-| `Agent.Enabled`         | Enable Kubernetes plugin jnlp-agent podTemplate | `true`                 |
-| `Agent.Image`           | Agent image name                                | `jenkinsci/jnlp-slave` |
-| `Agent.ImagePullSecret` | Agent image pull secret                         | Not set                |
-| `Agent.ImageTag`        | Agent image tag                                 | `2.62`                 |
-| `Agent.Privileged`      | Agent privileged container                      | `false`                |
-| `Agent.Cpu`             | Agent requested cpu                             | `200m`                 |
-| `Agent.Memory`          | Agent requested memory                          | `256Mi`                |
-| `Agent.volumes`         | Additional volumes                              | `nil`                  |
+### Secrets
 
+   When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins.
+
+   You can override the values at deploy time but otherwise also configure them 
+   [in Rancher](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/secrets) or through kubectl.
+
+#### Vault
+
+The vault secret gets mounted in the vault pod so pipeline scripts can retrieve secrets from the vault.
+
+| Parameter                 | Description                                | Default                                        |
+| ------------------------- | ------------------------------------------ | ---------------------------------------------- |
+| `secret.vault.token`      | Token to log into the hashicorp vault      | `xxxx`                                         |
+| `secret.vault.addr`       | Address of the vault                       | `https:vault-operator.vault-operator.svc:8200` |
+| `secret.vault.skipVerify` | Skip verification of the https connection  | `1`                                            |
+
+#### GitHub
+
+Token used by Jenkins to authenticate on GitHub.
+
+| Parameter             | Description              | Default            |
+| --------------------- | ------------------------ | ------------------ |
+| `secret.gitHub.user`  | username for the account | `molgenis-jenkins` |
+| `secret.gitHub.token` | token for the account    | `xxxx`             |
+
+#### Gogs
+
+Token used by Jenkins to authenticate on the [RuG Webhosting Gogs](https://git.webhosting.rug.nl).
+
+| Parameter           | Description              | Default   |
+| ------------------- | ------------------------ | --------- |
+| `secret.gogs.user`  | username for the account | `p281392` |
+| `secret.gogs.token` | token for the account    | `xxxx`    |
+
+#### Legacy:
+
+##### Docker Hub
+   
+Account used in pipeline builds to push docker images to `hub.docker.com`.
+> They should read `secret/gcc/account/dockerhub` from vault instead!
+
+| Parameter                   | Description              | Default         |
+| --------------------------- | ------------------------ | --------------- |
+| `secret.dockerHub.user`     | username for the account | `molgenisci`    |
+| `secret.dockerHub.password` | password for the account | `xxxx`          |
+
+##### Registry
+   
+Account used in pipeline builds to push docker images to `registry.molgenis.org`.
+> They should read `secret/ops/account/nexus` from vault instead!
+
+| Parameter                   | Description              | Default   |
+| --------------------------- | ------------------------ | --------- |
+| `secret.dockerHub.user`     | username for the account | `admin`   |
+| `secret.dockerHub.password` | password for the account | `xxxx`    |
+
+## Command line use
 Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`.
 
-Alternatively, a YAML file that specifies the values for the parameters can be provided while installing the chart. For example,
+Alternatively, a YAML file that specifies the values for the parameters can be provided while installing the chart.
+For example,
 
 ```bash
-$ helm install --name my-release -f values.yaml stable/jenkins
+$ helm install --name jenkins -f values.yaml molgenis-jenkins
 ```
 
 > **Tip**: You can use the default [values.yaml](values.yaml)
 
-## Mounting volumes into your Agent pods
-
-Your Jenkins Agents will run as pods, and it's possible to inject volumes where needed:
-
-```yaml
-Agent:
-  volumes:
-  - type: Secret
-    secretName: jenkins-mysecrets
-    mountPath: /var/run/secrets/jenkins-mysecrets
-```
-
-The supported volume types are: `ConfigMap`, `EmptyDir`, `HostPath`, `Nfs`, `Pod`, `Secret`. Each type supports a different set of configurable attributes, defined by [the corresponding Java class](https://github.com/jenkinsci/kubernetes-plugin/tree/master/src/main/java/org/csanchez/jenkins/plugins/kubernetes/volumes).
-
-## NetworkPolicy
-
-To make use of the NetworkPolicy resources created by default,
-install [a networking plugin that implements the Kubernetes
-NetworkPolicy spec](https://kubernetes.io/docs/tasks/administer-cluster/declare-network-policy#before-you-begin).
-
-For Kubernetes v1.5 & v1.6, you must also turn on NetworkPolicy by setting
-the DefaultDeny namespace annotation. Note: this will enforce policy for _all_ pods in the namespace:
-
-    kubectl annotate namespace default "net.beta.kubernetes.io/network-policy={\"ingress\":{\"isolation\":\"DefaultDeny\"}}"
-
-Install helm chart with network policy enabled:
-
-    $ helm install stable/jenkins --set NetworkPolicy.Enabled=true
-
-## Persistence
-
-The Jenkins image stores persistence under `/var/jenkins_home` path of the container. A dynamically managed Persistent Volume
-Claim is used to keep the data across deployments, by default. This is known to work in GCE, AWS, and minikube. Alternatively,
-a previously configured Persistent Volume Claim can be used.
-
-It is possible to mount several volumes using `Persistence.volumes` and `Persistence.mounts` parameters.
-
-### Persistence Values
-
-| Parameter                   | Description                     | Default         |
-| --------------------------- | ------------------------------- | --------------- |
-| `Persistence.Enabled`       | Enable the use of a Jenkins PVC | `true`          |
-| `Persistence.ExistingClaim` | Provide the name of a PVC       | `nil`           |
-| `Persistence.AccessMode`    | The PVC access mode             | `ReadWriteOnce` |
-| `Persistence.Size`          | The size of the PVC             | `8Gi`           |
-| `Persistence.volumes`       | Additional volumes              | `nil`           |
-| `Persistence.mounts`        | Additional mounts               | `nil`           |
-
-#### Existing PersistentVolumeClaim
-
-1. Create the PersistentVolume
-1. Create the PersistentVolumeClaim
-1. Install the chart
-
-```bash
-$ helm install --name my-release --set Persistence.ExistingClaim=PVC_NAME stable/jenkins
-```
-
-## Custom ConfigMap
-
-When creating a new parent chart with this chart as a dependency, the `CustomConfigMap` parameter can be used to override the default config.xml provided.
-It also allows for providing additional xml configuration files that will be copied into `/var/jenkins_home`. In the parent chart's values.yaml,
-set the `jenkins.Master.CustomConfigMap` value to true like so
-
-```yaml
-jenkins:
-  Master:
-    CustomConfigMap: true
-```
-
-and provide the file `templates/config.tpl` in your parent chart for your use case. You can start by copying the contents of `config.yaml` from this chart into your parent charts `templates/config.tpl` as a basis for customization. Finally, you'll need to wrap the contents of `templates/config.tpl` like so:
-
-```yaml
-{{- define "override_config_map" }}
-    <CONTENTS_HERE>
-{{ end }}
-```
-
-## RBAC
-
-If running upon a cluster with RBAC enabled you will need to do the following:
-
-* `helm install stable/jenkins --set rbac.install=true`
-* Create a Jenkins credential of type Kubernetes service account with service account name provided in the `helm status` output.
-* Under configure Jenkins -- Update the credentials config in the cloud section to use the service account credential you created in the step above.
-
-## Run Jenkins as non root user
-
-The default settings of this helm chart let Jenkins run as root user with uid `0`.
-Due to security reasons you may want to run Jenkins as a non root user.
-Fortunately the default jenkins docker image `jenkins/jenkins` contains a user `jenkins` with uid `1000` that can be used for this purpose.
-
-Simply use the following settings to run Jenkins as `jenkins` user with uid `1000`.
-
-```yaml
-jenkins:
-  Master:
-    RunAsUser: 1000
-    FsGroup: 1000
-```
-
-Docs taken from https://github.com/jenkinsci/docker/blob/master/Dockerfile:
-_Jenkins is run with user `jenkins`, uid = 1000. If you bind mount a volume from the host or a data container,ensure you use the same uid_
-
-## Running behind a forward proxy
-
-The master pod uses an Init Container to install plugins etc. If you are behind a corporate proxy it may be useful to set `Master.InitContainerEnv` to add environment variables such as `http_proxy`, so that these can be downloaded.
-
-Additionally, you may want to add env vars for the Jenkins container, and the JVM (`Master.JavaOpts`).
-
-```yaml
-Master:
-  InitContainerEnv:
-    - name: http_proxy
-      value: "http://192.168.64.1:3128"
-    - name: https_proxy
-      value: "http://192.168.64.1:3128"
-    - name: no_proxy
-      value: ""
-  ContainerEnv:
-    - name: http_proxy
-      value: "http://192.168.64.1:3128"
-    - name: https_proxy
-      value: "http://192.168.64.1:3128"
-  JavaOpts: >-
-    -Dhttp.proxyHost=192.168.64.1
-    -Dhttp.proxyPort=3128
-    -Dhttps.proxyHost=192.168.64.1
-    -Dhttps.proxyPort=3128
-```

molgenis-jenkins/resources/jenkins-default-tiller-user-rolebinding.yaml

@@ -0,0 +1,13 @@
+apiVersion: rbac.authorization.k8s.io/v1beta1
+kind: RoleBinding
+metadata:
+  name: tiller-jenkins-binding
+  namespace: kube-system
+roleRef:
+  apiGroup: rbac.authorization.k8s.io
+  kind: Role
+  name: tiller-user
+subjects:
+- kind: ServiceAccount
+  name: default
+  namespace: molgenis-jenkins

molgenis-jenkins/resources/tiller-user-role.yaml

@@ -0,0 +1,18 @@
+apiVersion: rbac.authorization.k8s.io/v1beta1
+kind: Role
+metadata:
+  name: tiller-user
+  namespace: kube-system
+rules:
+- apiGroups:
+  - ""
+  resources:
+  - pods/portforward
+  verbs:
+  - create
+- apiGroups:
+  - ""
+  resources:
+  - pods
+  verbs:
+  - list

molgenis-jenkins/templates/config.tpl

@@ -15,162 +15,126 @@ data:
       <authorizationStrategy class="hudson.security.FullControlOnceLoggedInAuthorizationStrategy">
         <denyAnonymousReadAccess>true</denyAnonymousReadAccess>
       </authorizationStrategy>
+{{- if .Values.Master.Security.UseGitHub }}
+      <securityRealm class="org.jenkinsci.plugins.GithubSecurityRealm">
+        <githubWebUri>https://github.com</githubWebUri>
+        <githubApiUri>https://api.github.com</githubApiUri>
+        <clientID>{{ .Values.Master.Security.GitHub.ClientID }}</clientID>
+        <clientSecret>{{ .Values.Master.Security.GitHub.ClientSecret }}</clientSecret>
+        <oauthScopes>read:org,user:email</oauthScopes>
+      </securityRealm>
+{{- else }}
       <securityRealm class="hudson.security.LegacySecurityRealm"/>
+{{- end }}
       <disableRememberMe>false</disableRememberMe>
       <projectNamingStrategy class="jenkins.model.ProjectNamingStrategy$DefaultProjectNamingStrategy"/>
       <workspaceDir>${JENKINS_HOME}/workspace/${ITEM_FULLNAME}</workspaceDir>
       <buildsDir>${ITEM_ROOTDIR}/builds</buildsDir>
       <markupFormatter class="hudson.markup.EscapedMarkupFormatter"/>
       <jdks/>
+      <primaryView>dev</primaryView>
       <viewsTabBar class="hudson.views.DefaultViewsTabBar"/>
       <myViewsTabBar class="hudson.views.DefaultMyViewsTabBar"/>
       <clouds>
         <org.csanchez.jenkins.plugins.kubernetes.KubernetesCloud plugin="kubernetes@{{ template "jenkins.kubernetes-version" . }}">
           <name>kubernetes</name>
           <templates>
-{{- if .Values.Agent.Enabled }}
+{{- range $podName, $pod := .Values.Pods }}
             <org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
-              <inheritFrom></inheritFrom>
-              <name>default</name>
+              <inheritFrom>{{ $pod.InheritFrom | default "" }}</inheritFrom>
+              <name>{{ $podName }}</name>
               <instanceCap>2147483647</instanceCap>
               <idleMinutes>0</idleMinutes>
-              <label>{{ .Release.Name }}-{{ .Values.Agent.Component }}</label>
+              <label>{{ .Label }}</label>
               <nodeSelector>
                 {{- $local := dict "first" true }}
-                {{- range $key, $value := .Values.Agent.NodeSelector }}
+                {{- range $key, $value := .NodeSelector }}
                   {{- if not $local.first }},{{- end }}
                   {{- $key }}={{ $value }}
                   {{- $_ := set $local "first" false }}
                 {{- end }}</nodeSelector>
-                <nodeUsageMode>EXCLUSIVE</nodeUsageMode>
+                <nodeUsageMode>{{ .NodeUsageMode }}</nodeUsageMode>
               <volumes>
-{{- range $index, $volume := .Values.Agent.volumes }}
-                <org.csanchez.jenkins.plugins.kubernetes.volumes.{{ $volume.type }}Volume>
+{{- range $index, $volume := .volumes }}
+                <org.csanchez.jenkins.plugins.kubernetes.volumes.{{ .type }}Volume>
 {{- range $key, $value := $volume }}{{- if not (eq $key "type") }}
                   <{{ $key }}>{{ $value }}</{{ $key }}>
 {{- end }}{{- end }}
-                </org.csanchez.jenkins.plugins.kubernetes.volumes.{{ $volume.type }}Volume>
+                </org.csanchez.jenkins.plugins.kubernetes.volumes.{{ .type }}Volume>
 {{- end }}
               </volumes>
               <containers>
+{{- range $containerName, $container := .Containers }}
                 <org.csanchez.jenkins.plugins.kubernetes.ContainerTemplate>
-                  <name>jnlp</name>
-                  <image>{{ .Values.Agent.Image }}:{{ .Values.Agent.ImageTag }}</image>
-{{- if .Values.Agent.Privileged }}
+                  <name>{{ $containerName }}</name>
+                  <image>{{ .Image }}:{{ .ImageTag | default "latest" }}</image>
+                  <ports>
+{{- range $index, $envVar := .Ports }}
+                    <org.csanchez.jenkins.plugins.kubernetes.PortMapping>
+                      <name>{{ .name }}</name>
+                      <containerPort>{{ .containerPort }}</containerPort>
+                      <hostPort>{{ .hostPort }}</hostPort>
+                    </org.csanchez.jenkins.plugins.kubernetes.PortMapping>
+{{- end }}
+                  </ports>
+{{- if .Privileged }}
                   <privileged>true</privileged>
 {{- else }}
                   <privileged>false</privileged>
 {{- end }}
-                  <alwaysPullImage>{{ .Values.Agent.AlwaysPullImage }}</alwaysPullImage>
-                  <workingDir>/home/jenkins</workingDir>
-                  <command></command>
-                  <args>${computer.jnlpmac} ${computer.name}</args>
-                  <ttyEnabled>false</ttyEnabled>
-                  <resourceRequestCpu>{{.Values.Agent.Cpu}}</resourceRequestCpu>
-                  <resourceRequestMemory>{{.Values.Agent.Memory}}</resourceRequestMemory>
-                  <resourceLimitCpu>{{.Values.Agent.Cpu}}</resourceLimitCpu>
-                  <resourceLimitMemory>{{.Values.Agent.Memory}}</resourceLimitMemory>
-                  <envVars>
-                    <org.csanchez.jenkins.plugins.kubernetes.ContainerEnvVar>
-                      <key>JENKINS_URL</key>
-                      <value>http://{{ template "jenkins.fullname" . }}:{{.Values.Master.ServicePort}}{{ default "" .Values.Master.JenkinsUriPrefix }}</value>
-                    </org.csanchez.jenkins.plugins.kubernetes.ContainerEnvVar>
-                  </envVars>
-                </org.csanchez.jenkins.plugins.kubernetes.ContainerTemplate>
-              </containers>
-              <envVars/>
-              <annotations/>
-{{- if .Values.Agent.ImagePullSecret }}
-              <imagePullSecrets>
-                <org.csanchez.jenkins.plugins.kubernetes.PodImagePullSecret>
-                  <name>{{ .Values.Agent.ImagePullSecret }}</name>
-                </org.csanchez.jenkins.plugins.kubernetes.PodImagePullSecret>
-              </imagePullSecrets>
+{{- if .AlwaysPullImage }}
+                  <alwaysPullImage>true</alwaysPullImage>
 {{- else }}
-              <imagePullSecrets/>
+                  <alwaysPullImage>false</alwaysPullImage>
 {{- end }}
-              <nodeProperties/>
-            </org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
-{{- end -}}
-{{- if .Values.Pod.Enabled }}
-            <org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
-              <inheritFrom></inheritFrom>
-              <name>{{ .Values.Pod.Label }}</name>
-              <instanceCap>2147483647</instanceCap>
-              <idleMinutes>0</idleMinutes>
-              <label>{{ .Values.Pod.Label }}</label>
-              <nodeSelector>
-                {{- $local := dict "first" true }}
-                {{- range $key, $value := .Values.Pod.NodeSelector }}
-                  {{- if not $local.first }},{{- end }}
-                  {{- $key }}={{ $value }}
-                  {{- $_ := set $local "first" false }}
-                {{- end }}</nodeSelector>
-                <nodeUsageMode>NORMAL</nodeUsageMode>
-              <volumes>
-{{- range $index, $volume := .Values.Pod.volumes }}
-                <org.csanchez.jenkins.plugins.kubernetes.volumes.{{ $volume.type }}Volume>
-{{- range $key, $value := $volume }}{{- if not (eq $key "type") }}
-                  <{{ $key }}>{{ $value }}</{{ $key }}>
-{{- end }}{{- end }}
-                </org.csanchez.jenkins.plugins.kubernetes.volumes.{{ $volume.type }}Volume>
-{{- end }}
-              </volumes>
-              <containers>
-                <org.csanchez.jenkins.plugins.kubernetes.ContainerTemplate>
-                  <name>{{ .Values.Pod.Label }}</name>
-                  <image>{{ .Values.Pod.Image }}:{{ .Values.Pod.ImageTag }}</image>
-{{- if .Values.Pod.Privileged }}
-                  <privileged>true</privileged>
-{{- else }}
-                  <privileged>false</privileged>
-{{- end }}
-                  <alwaysPullImage>{{ .Values.Pod.AlwaysPullImage }}</alwaysPullImage>
-                  <workingDir>/home/jenkins</workingDir>
-                  <command>{{ .Values.Pod.Command }}</command>
-                  <args>{{ .Values.Pod.Args }}</args>
-{{- if .Values.Pod.TTY }}
+                  <workingDir>{{ .WorkingDir | default "" }}</workingDir>
+                  <command>{{ .Command | default "" }}</command>
+                  <args>{{ .Args | default "" }}</args>
+{{- if .TTY }}
                   <ttyEnabled>true</ttyEnabled>
 {{- else }}
                   <ttyEnabled>false</ttyEnabled>
 {{- end }}
-                  <resourceRequestCpu>{{.Values.Pod.Cpu}}</resourceRequestCpu>
-                  <resourceRequestMemory>{{.Values.Pod.Memory}}</resourceRequestMemory>
-                  <resourceLimitCpu>{{.Values.Pod.Cpu}}</resourceLimitCpu>
-                  <resourceLimitMemory>{{.Values.Pod.Memory}}</resourceLimitMemory>
+                  <envVars>
+{{- range $index, $envVar := .EnvVars }}
+                    <org.csanchez.jenkins.plugins.kubernetes.model.{{ .type }}EnvVar>
+{{- range $key, $value := $envVar }}{{- if not (eq $key "type") }}
+                      <{{ $key }}>{{ $value }}</{{ $key }}>
+{{- end }}{{- end }}
+                    </org.csanchez.jenkins.plugins.kubernetes.model.{{ .type }}EnvVar>
+{{- end }}
+                  </envVars>
+{{- if .resources }}
+{{- if .resources.requests }}
+                  <resourceRequestCpu>{{ .resources.requests.cpu | default "" }}</resourceRequestCpu>
+                  <resourceRequestMemory>{{ .resources.requests.memory | default "" }}</resourceRequestMemory>
+{{- end }}
+{{- if .resources.limits }}
+                  <resourceLimitCpu>{{ .resources.limits.cpu | default "" }}</resourceLimitCpu>
+                  <resourceLimitMemory>{{ .resources.limits.memory | default "" }}</resourceLimitMemory>
+{{- end }}
+{{- end }}
                 </org.csanchez.jenkins.plugins.kubernetes.ContainerTemplate>
+{{- end }}
               </containers>
               <envVars>
-                <org.csanchez.jenkins.plugins.kubernetes.model.SecretEnvVar>
-                  <key>PGP_PASSPHRASE</key>
-                  <secretName>molgenis-pipeline-env-secret</secretName>
-                  <secretKey>pgpPassphrase</secretKey>
-                </org.csanchez.jenkins.plugins.kubernetes.model.SecretEnvVar>
-                <org.csanchez.jenkins.plugins.kubernetes.model.KeyValueEnvVar>
-                  <key>PGP_SECRETKEY</key>
-                  <value>keyfile:/root/.m2/key.asc</value>
-                </org.csanchez.jenkins.plugins.kubernetes.model.KeyValueEnvVar>
-                <org.csanchez.jenkins.plugins.kubernetes.model.SecretEnvVar>
-                  <key>SONAR_TOKEN</key>
-                  <secretName>molgenis-pipeline-env-secret</secretName>
-                  <secretKey>sonarToken</secretKey>
-                </org.csanchez.jenkins.plugins.kubernetes.model.SecretEnvVar>
-                <org.csanchez.jenkins.plugins.kubernetes.model.SecretEnvVar>
-                  <key>CODECOV_TOKEN</key>
-                  <secretName>molgenis-pipeline-env-secret</secretName>
-                  <secretKey>codecovToken</secretKey>
-                </org.csanchez.jenkins.plugins.kubernetes.model.SecretEnvVar>
-                <org.csanchez.jenkins.plugins.kubernetes.model.SecretEnvVar>
-                  <key>GITHUB_TOKEN</key>
-                  <secretName>molgenis-pipeline-env-secret</secretName>
-                  <secretKey>githubToken</secretKey>
-                </org.csanchez.jenkins.plugins.kubernetes.model.SecretEnvVar>
+                  <org.csanchez.jenkins.plugins.kubernetes.model.KeyValueEnvVar>
+                    <key>JENKINS_URL</key>
+                    <value>http://{{ template "jenkins.fullname" $ }}:{{$.Values.Master.ServicePort}}{{ default "" $.Values.Master.JenkinsUriPrefix }}</value>
+                  </org.csanchez.jenkins.plugins.kubernetes.model.KeyValueEnvVar>
+{{- range $index, $envVar := .EnvVars }}
+                <org.csanchez.jenkins.plugins.kubernetes.model.{{ .type }}EnvVar>
+{{- range $key, $value := $envVar }}{{- if not (eq $key "type") }}
+                  <{{ $key }}>{{ $value }}</{{ $key }}>
+{{- end }}{{- end }}
+                </org.csanchez.jenkins.plugins.kubernetes.model.{{ .type }}EnvVar>
+{{- end }}
               </envVars>
               <annotations/>
-{{- if .Values.Pod.ImagePullSecret }}
+{{- if .ImagePullSecret }}
               <imagePullSecrets>
                 <org.csanchez.jenkins.plugins.kubernetes.PodImagePullSecret>
-                  <name>{{ .Values.Pod.ImagePullSecret }}</name>
+                  <name>{{ .ImagePullSecret }}</name>
                 </org.csanchez.jenkins.plugins.kubernetes.PodImagePullSecret>
               </imagePullSecrets>
 {{- else }}
@@ -178,14 +142,14 @@ data:
 {{- end }}
               <nodeProperties/>
             </org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
-{{- end -}}
+{{- end }}
           </templates>
           <serverUrl>https://kubernetes.default</serverUrl>
           <skipTlsVerify>false</skipTlsVerify>
           <namespace>{{ .Release.Namespace }}</namespace>
           <jenkinsUrl>http://{{ template "jenkins.fullname" . }}:{{.Values.Master.ServicePort}}{{ default "" .Values.Master.JenkinsUriPrefix }}</jenkinsUrl>
           <jenkinsTunnel>{{ template "jenkins.fullname" . }}-agent:50000</jenkinsTunnel>
-          <containerCap>10</containerCap>
+          <containerCap>50</containerCap>
           <retentionTimeout>5</retentionTimeout>
           <connectTimeout>0</connectTimeout>
           <readTimeout>0</readTimeout>
@@ -196,13 +160,40 @@ data:
       <views>
         <hudson.model.AllView>
           <owner class="hudson" reference="../../.."/>
-          <name>All</name>
+          <name>all</name>
           <filterExecutors>false</filterExecutors>
           <filterQueue>false</filterQueue>
           <properties class="hudson.model.View$PropertyList"/>
         </hudson.model.AllView>
+{{- range $viewName, $view := .Values.Master.Views }}
+        <listView>
+          <owner class="hudson" reference="../../.."/>
+          <name>{{ $viewName }}</name>
+          <filterExecutors>false</filterExecutors>
+          <filterQueue>false</filterQueue>
+          <properties class="hudson.model.View$PropertyList"/>
+          <jobNames>
+             <comparator class="hudson.util.CaseInsensitiveComparator" reference="../../../listView/jobNames/comparator"/>
+{{- range $index, $job := $view }}
+             <string>{{ $job }}</string>
+{{- end }}
+          </jobNames>
+          <jobFilters/>
+          <columns>
+            <hudson.views.StatusColumn/>
+            <hudson.views.WeatherColumn/>
+            <hudson.views.JobColumn/>
+            <hudson.views.LastSuccessColumn/>
+            <hudson.views.LastFailureColumn/>
+            <hudson.views.LastDurationColumn/>
+            <hudson.views.BuildButtonColumn/>
+            <hudson.plugins.favorite.column.FavoriteColumn plugin="favorite@2.3.2"/>
+          </columns>
+          <recurse>false</recurse>
+        </listView>
+{{- end }}
       </views>
-      <primaryView>All</primaryView>
+      <primaryView>{{ .Values.Master.DefaultView }}</primaryView>
       <slaveAgentPort>50000</slaveAgentPort>
       <disabledAgentProtocols>
 {{- range .Values.Master.DisabledAgentProtocols }}

molgenis-jenkins/templates/molgenis-jenkins-dockerhub-secret.yaml

@@ -0,0 +1,16 @@
+apiVersion: v1
+kind: Secret
+metadata:
+# this is the jenkins id.
+  name: "molgenis-jenkins-dockerhub-secret"
+  labels:
+# so we know what type it is.
+    "jenkins.io/credentials-type": "usernamePassword"
+  annotations: {
+# description - can not be a label as spaces are not allowed
+    "jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to Docker Hub (hub.docker.com)"
+  }
+type: Opaque
+data:
+  username: {{ .Values.secret.registry.user | b64enc | quote }}
+  password: {{ .Values.secret.registry.password | b64enc | quote }}

molgenis-jenkins/templates/molgenis-jenkins-github-secret.yaml

@@ -0,0 +1,16 @@
+apiVersion: v1
+kind: Secret
+metadata:
+# this is the jenkins id.
+  name: "molgenis-jenkins-github-secret"
+  labels:
+# so we know what type it is.
+    "jenkins.io/credentials-type": "usernamePassword"
+  annotations: {
+# description - can not be a label as spaces are not allowed
+    "jenkins.io/credentials-description" : "Oauth token for the {{.Values.secret.gitHub.user}} GitHub user"
+  }
+type: Opaque
+data:
+  username: {{ .Values.secret.gitHub.user | b64enc | quote }}
+  password: {{ .Values.secret.gitHub.token | b64enc | quote }}

molgenis-jenkins/templates/molgenis-jenkins-gogs-secret.yaml

@@ -0,0 +1,16 @@
+apiVersion: v1
+kind: Secret
+metadata:
+# this is the jenkins id.
+  name: "molgenis-jenkins-gogs-secret"
+  labels:
+# so we know what type it is.
+    "jenkins.io/credentials-type": "usernamePassword"
+  annotations: {
+# description - can not be a label as spaces are not allowed
+    "jenkins.io/credentials-description" : "Account used to authenticate against RuG Webhosting Gogs."
+  }
+type: Opaque
+data:
+  username: {{ .Values.secret.gogs.user | b64enc | quote }}
+  password: {{ .Values.secret.gogs.token | b64enc | quote }}

molgenis-jenkins/templates/molgenis-jenkins-registry-secret.yaml

@@ -0,0 +1,17 @@
+apiVersion: v1
+kind: Secret
+metadata:
+  name: molgenis-jenkins-registry-secret
+  labels:
+    app: {{ template "jenkins.fullname" . }}
+    chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
+    release: "{{ .Release.Name }}"
+    heritage: "{{ .Release.Service }}"
+  annotations: {
+# description - can not be a label as spaces are not allowed
+    "jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to registry.molgenis.org."
+  }
+type: Opaque
+data:
+  username: {{ .Values.secret.registry.user | b64enc | quote }}
+  password: {{ .Values.secret.registry.password | b64enc | quote }}

molgenis-jenkins/templates/molgenis-pipeline-env-secret.yaml

@@ -1,17 +0,0 @@
-{{- if .Values.PipelineSecrets.Env.Replace }}
-apiVersion: v1
-kind: Secret
-metadata:
-  name: molgenis-pipeline-env-secret
-  labels:
-    app: {{ template "jenkins.fullname" . }}
-    chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
-    release: "{{ .Release.Name }}"
-    heritage: "{{ .Release.Service }}"
-type: Opaque
-data:
-  pgpPassphrase: {{ .Values.PipelineSecrets.Env.PGPPassphrase | b64enc | quote }}
-  codecovToken: {{ .Values.PipelineSecrets.Env.CodecovToken | b64enc | quote }}
-  githubToken: {{ .Values.PipelineSecrets.Env.GithubToken | b64enc | quote }}
-  sonarToken: {{ .Values.PipelineSecrets.Env.SonarToken | b64enc | quote }}
-{{- end }}

molgenis-jenkins/templates/molgenis-pipeline-file-secret.yaml

@@ -1,15 +0,0 @@
-{{- if .Values.PipelineSecrets.File.Replace }}
-apiVersion: v1
-kind: Secret
-metadata:
-  name: molgenis-pipeline-env-secret
-  labels:
-    app: {{ template "jenkins.fullname" . }}
-    chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
-    release: "{{ .Release.Name }}"
-    heritage: "{{ .Release.Service }}"
-type: Opaque
-data:
-  maven.xml: {{ .Values.PipelineSecrets.File.MavenSettingsXML | b64enc | quote }}
-  key.asc: {{ .Values.PipelineSecrets.File.PGPPrivateKeyAsc | b64enc | quote }}
-{{- end }}

molgenis-jenkins/templates/molgenis-pipeline-vault-secret.yaml

@@ -0,0 +1,14 @@
+apiVersion: v1
+kind: Secret
+metadata:
+  name: molgenis-pipeline-vault-secret
+  labels:
+    app: {{ template "jenkins.fullname" . }}
+    chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
+    release: "{{ .Release.Name }}"
+    heritage: "{{ .Release.Service }}"
+type: Opaque
+data:
+  token: {{ .Values.secret.vault.token | b64enc | quote }}
+  addr: {{ .Values.secret.vault.addr | b64enc | quote }}
+  skipVerify: {{ .Values.secret.vault.skipVerify | b64enc | quote }}

molgenis-jenkins/values.yaml

@@ -3,63 +3,359 @@ jenkins:
     HostName: jenkins.molgenis.org
     ServiceType: ClusterIP
     InstallPlugins:
-      - kubernetes:1.8.4
+      - kubernetes:1.12.0
       - workflow-aggregator:2.5
       - workflow-job:2.21
       - credentials-binding:1.16
       - git:3.9.1
+      - github-branch-source:2.3.6
+      - kubernetes-credentials-provider:0.9
+      - blueocean:1.6.2
+      - github-oauth:0.29
+      - gogs-webhook:1.0.14
+      - sauce-ondemand:1.176
+    Security:
+      UseGitHub: false
+      GitHub:
+        ClientID: ""
+        ClienSecret: ""
+    DefaultView: dev
+    Views:
+      dev:
+        - molgenis
+      ops:
+        - molgenis-ops-docker-httpd
+        - molgenis-ops-docker-maven
+        - molgenis-ops-docker-node
+        - molgenis-ops-tools
+        - molgenis-ops-tomcat
     Jobs: |-
       molgenis: |-
+        <?xml version='1.1' encoding='UTF-8'?>
+        <jenkins.branch.OrganizationFolder plugin="branch-api@2.0.20">
+          <actions/>
+          <description></description>
+          <properties>
+            <org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
+              <dockerLabel></dockerLabel>
+              <registry plugin="docker-commons@1.13"/>
+            </org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
+            <jenkins.branch.NoTriggerOrganizationFolderProperty>
+              <branches>.*</branches>
+            </jenkins.branch.NoTriggerOrganizationFolderProperty>
+          </properties>
+          <folderViews class="jenkins.branch.OrganizationFolderViewHolder">
+            <owner reference="../.."/>
+          </folderViews>
+          <healthMetrics>
+            <com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
+              <nonRecursive>false</nonRecursive>
+            </com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
+          </healthMetrics>
+          <icon class="jenkins.branch.MetadataActionFolderIcon">
+            <owner class="jenkins.branch.OrganizationFolder" reference="../.."/>
+          </icon>
+          <orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
+            <pruneDeadBranches>true</pruneDeadBranches>
+            <daysToKeep>-1</daysToKeep>
+            <numToKeep>-1</numToKeep>
+          </orphanedItemStrategy>
+          <triggers>
+            <com.cloudbees.hudson.plugins.folder.computed.PeriodicFolderTrigger plugin="cloudbees-folder@6.5.1">
+              <spec>H H * * *</spec>
+              <interval>86400000</interval>
+            </com.cloudbees.hudson.plugins.folder.computed.PeriodicFolderTrigger>
+          </triggers>
+          <disabled>false</disabled>
+          <navigators>
+            <org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator plugin="github-branch-source@2.3.6">
+              <repoOwner>molgenis</repoOwner>
+              <credentialsId>molgenis-jenkins-github-secret</credentialsId>
+              <traits>
+                <org.jenkinsci.plugins.github__branch__source.BranchDiscoveryTrait>
+                  <strategyId>1</strategyId>
+                </org.jenkinsci.plugins.github__branch__source.BranchDiscoveryTrait>
+                <org.jenkinsci.plugins.github__branch__source.OriginPullRequestDiscoveryTrait>
+                  <strategyId>1</strategyId>
+                </org.jenkinsci.plugins.github__branch__source.OriginPullRequestDiscoveryTrait>
+                <org.jenkinsci.plugins.github__branch__source.ForkPullRequestDiscoveryTrait>
+                  <strategyId>1</strategyId>
+                  <trust class="org.jenkinsci.plugins.github_branch_source.ForkPullRequestDiscoveryTrait$TrustPermission"/>
+                </org.jenkinsci.plugins.github__branch__source.ForkPullRequestDiscoveryTrait>
+              </traits>
+            </org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator>
+          </navigators>
+          <projectFactories>
+            <org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProjectFactory plugin="workflow-multibranch@2.19">
+              <scriptPath>Jenkinsfile</scriptPath>
+            </org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProjectFactory>
+          </projectFactories>
+          <buildStrategies/>
+        </jenkins.branch.OrganizationFolder>
+      molgenis-ops-docker-httpd: |-
         <?xml version='1.1' encoding='UTF-8'?>
         <org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
-            <actions/>
-            <description></description>
-            <properties>
-                <org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3">
-                    <dockerLabel></dockerLabel>
-                    <registry plugin="docker-commons@1.13"/>
-                </org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
-            </properties>
-            <folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
-                <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
-            </folderViews>
-            <healthMetrics>
-                <com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
-                    <nonRecursive>false</nonRecursive>
-                </com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
-            </healthMetrics>
-            <icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
-                <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
-            </icon>
-            <orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
-                <pruneDeadBranches>true</pruneDeadBranches>
-                <daysToKeep>-1</daysToKeep>
-                <numToKeep>-1</numToKeep>
-            </orphanedItemStrategy>
-            <triggers/>
-            <disabled>false</disabled>
-            <sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
-                <data>
-                    <jenkins.branch.BranchSource>
-                        <source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
-                            <id>a1f535cd-ab83-4d42-8993-0c3e59cf139f</id>
-                            <remote>http://github.com/molgenis/molgenis.git</remote>
-                            <credentialsId></credentialsId>
-                            <traits>
-                                <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
-                            </traits>
-                        </source>
-                        <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
-                            <properties class="empty-list"/>
-                        </strategy>
-                    </jenkins.branch.BranchSource>
-                </data>
-                <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
-            </sources>
-            <factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
-                <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
-                <scriptPath>Jenkinsfile</scriptPath>
-            </factory>
+          <actions/>
+          <description>HTTPD server that can be used for redirection and proxieing</description>
+          <displayName>molgenis-ops-docker-httpd</displayName>
+          <properties>
+            <org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
+              <dockerLabel></dockerLabel>
+              <registry plugin="docker-commons@1.13"/>
+            </org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
+          </properties>
+          <folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </folderViews>
+          <healthMetrics>
+            <com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
+              <nonRecursive>false</nonRecursive>
+            </com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
+          </healthMetrics>
+          <icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </icon>
+          <orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
+            <pruneDeadBranches>true</pruneDeadBranches>
+            <daysToKeep>-1</daysToKeep>
+            <numToKeep>-1</numToKeep>
+          </orphanedItemStrategy>
+          <triggers/>
+          <disabled>false</disabled>
+          <sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
+            <data>
+              <jenkins.branch.BranchSource>
+                <source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
+                  <id>a756941d-6c9d-4492-bcf9-327041764be6</id>
+                  <remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-httpd.git</remote>
+                  <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
+                  <traits>
+                    <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                  </traits>
+                </source>
+                <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
+                  <properties class="empty-list"/>
+                </strategy>
+              </jenkins.branch.BranchSource>
+            </data>
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </sources>
+          <factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+            <scriptPath>Jenkinsfile</scriptPath>
+          </factory>
+        </org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
+      molgenis-ops-docker-node: |-
+        <?xml version='1.1' encoding='UTF-8'?>
+        <org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
+          <actions/>
+          <description>NodeJS build container with Curl</description>
+          <displayName>molgenis-ops-docker-node</displayName>
+          <properties>
+            <org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
+              <dockerLabel></dockerLabel>
+              <registry plugin="docker-commons@1.13"/>
+            </org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
+          </properties>
+          <folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </folderViews>
+          <healthMetrics>
+            <com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
+              <nonRecursive>false</nonRecursive>
+            </com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
+          </healthMetrics>
+          <icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </icon>
+          <orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
+            <pruneDeadBranches>true</pruneDeadBranches>
+            <daysToKeep>-1</daysToKeep>
+            <numToKeep>-1</numToKeep>
+          </orphanedItemStrategy>
+          <triggers/>
+          <disabled>false</disabled>
+          <sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
+            <data>
+              <jenkins.branch.BranchSource>
+                <source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
+                  <id>a756941d-6c9d-4492-bcf9-327041764be6</id>
+                  <remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-node.git</remote>
+                  <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
+                  <traits>
+                    <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                  </traits>
+                </source>
+                <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
+                  <properties class="empty-list"/>
+                </strategy>
+              </jenkins.branch.BranchSource>
+            </data>
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </sources>
+          <factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+            <scriptPath>Jenkinsfile</scriptPath>
+          </factory>
+        </org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
+      molgenis-ops-docker-maven: |-
+        <?xml version='1.1' encoding='UTF-8'?>
+        <org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
+          <actions/>
+          <description>MAVEN build container with RPMbuild and Curl</description>
+          <displayName>molgenis-ops-docker-maven</displayName>
+          <properties>
+            <org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
+              <dockerLabel></dockerLabel>
+              <registry plugin="docker-commons@1.13"/>
+            </org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
+          </properties>
+          <folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </folderViews>
+          <healthMetrics>
+            <com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
+              <nonRecursive>false</nonRecursive>
+            </com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
+          </healthMetrics>
+          <icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </icon>
+          <orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
+            <pruneDeadBranches>true</pruneDeadBranches>
+            <daysToKeep>-1</daysToKeep>
+            <numToKeep>-1</numToKeep>
+          </orphanedItemStrategy>
+          <triggers/>
+          <disabled>false</disabled>
+          <sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
+            <data>
+              <jenkins.branch.BranchSource>
+                <source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
+                  <id>4702479a-6988-4a85-b4b7-e77fa2d05ffa</id>
+                  <remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-maven.git</remote>
+                  <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
+                  <traits>
+                    <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                  </traits>
+                </source>
+                <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
+                  <properties class="empty-list"/>
+                </strategy>
+              </jenkins.branch.BranchSource>
+            </data>
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </sources>
+          <factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+            <scriptPath>Jenkinsfile</scriptPath>
+          </factory>
+        </org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
+      molgenis-ops-tomcat: |-
+        <?xml version='1.1' encoding='UTF-8'?>
+        <org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
+          <actions/>
+          <description>MOLGENIS tomcat package to manage tomcat version on CentOS</description>
+          <displayName>molgenis-ops-tomcat</displayName>
+          <properties>
+            <org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
+              <dockerLabel></dockerLabel>
+              <registry plugin="docker-commons@1.13"/>
+            </org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
+          </properties>
+          <folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </folderViews>
+          <healthMetrics>
+            <com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
+              <nonRecursive>false</nonRecursive>
+            </com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
+          </healthMetrics>
+          <icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </icon>
+          <orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
+            <pruneDeadBranches>true</pruneDeadBranches>
+            <daysToKeep>-1</daysToKeep>
+            <numToKeep>-1</numToKeep>
+          </orphanedItemStrategy>
+          <triggers/>
+          <disabled>false</disabled>
+          <sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
+            <data>
+              <jenkins.branch.BranchSource>
+                <source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
+                  <id>4702479a-6988-4a85-b4b7-e77fa2d05ffa</id>
+                  <remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-tomcat.git</remote>
+                  <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
+                  <traits>
+                    <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                  </traits>
+                </source>
+                <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
+                  <properties class="empty-list"/>
+                </strategy>
+              </jenkins.branch.BranchSource>
+            </data>
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </sources>
+          <factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+            <scriptPath>Jenkinsfile</scriptPath>
+          </factory>
+        </org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
+      molgenis-ops-tools: |-
+        <?xml version='1.1' encoding='UTF-8'?>
+        <org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
+          <actions/>
+          <description>MOLGENIS operations tools-package to configure firewall, apache, sudoers, etc.</description>
+          <displayName>molgenis-ops-tools</displayName>
+          <properties>
+            <org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
+              <dockerLabel></dockerLabel>
+              <registry plugin="docker-commons@1.13"/>
+            </org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig>
+          </properties>
+          <folderViews class="jenkins.branch.MultiBranchProjectViewHolder" plugin="branch-api@2.0.20">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </folderViews>
+          <healthMetrics>
+            <com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric plugin="cloudbees-folder@6.5.1">
+              <nonRecursive>false</nonRecursive>
+            </com.cloudbees.hudson.plugins.folder.health.WorstChildHealthMetric>
+          </healthMetrics>
+          <icon class="jenkins.branch.MetadataActionFolderIcon" plugin="branch-api@2.0.20">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </icon>
+          <orphanedItemStrategy class="com.cloudbees.hudson.plugins.folder.computed.DefaultOrphanedItemStrategy" plugin="cloudbees-folder@6.5.1">
+            <pruneDeadBranches>true</pruneDeadBranches>
+            <daysToKeep>-1</daysToKeep>
+            <numToKeep>-1</numToKeep>
+          </orphanedItemStrategy>
+          <triggers/>
+          <disabled>false</disabled>
+          <sources class="jenkins.branch.MultiBranchProject$BranchSourceList" plugin="branch-api@2.0.20">
+            <data>
+              <jenkins.branch.BranchSource>
+                <source class="jenkins.plugins.git.GitSCMSource" plugin="git@3.9.1">
+                  <id>4702479a-6988-4a85-b4b7-e77fa2d05ffa</id>
+                  <remote>https://git.webhosting.rug.nl/molgenis/molgenis-ops-tools.git</remote>
+                  <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
+                  <traits>
+                    <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                  </traits>
+                </source>
+                <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
+                  <properties class="empty-list"/>
+                </strategy>
+              </jenkins.branch.BranchSource>
+            </data>
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+          </sources>
+          <factory class="org.jenkinsci.plugins.workflow.multibranch.WorkflowBranchProjectFactory">
+            <owner class="org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject" reference="../.."/>
+            <scriptPath>Jenkinsfile</scriptPath>
+          </factory>
         </org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject>
     # Kubernetes secret that contains a 'credentials.xml' for Jenkins
     # CredentialsXmlSecret: jenkins-credentials
@@ -70,80 +366,107 @@ jenkins:
     CustomConfigMap: true
   rbac:
     install: true
-  # A second pod template for maven builds
-  Pod:
-    Enabled: true
-    Image: "webhost12.service.rug.nl/molgenis/molgenis-maven"
-    ImageTag: latest
-  # ImagePullSecret: jenkins
-    Label: "molgenis-maven"
-    Privileged: false
-    Cpu: ""
-    Memory: ""
-    # You may want to change this to true while testing a new image
-    AlwaysPullImage: false
-    Command: "/bin/sh -c"
-    Args: "cat"
-    TTY: true
-    # You can define the volumes that you want to mount for this container
-    # Allowed types are: ConfigMap, EmptyDir, HostPath, Nfs, Pod, Secret
-    # Configure the attributes as they appear in the corresponding Java class for that type
-    # https://github.com/jenkinsci/kubernetes-plugin/tree/master/src/main/java/org/csanchez/jenkins/plugins/kubernetes/volumes
-    volumes:
-      - type: HostPath
-        hostPath: "/var/run/docker.sock"
-        mountPath: "/var/run/docker.sock"
-      - type: Secret
-        secretName: molgenis-pipeline-file-secret
-        mountPath: "keyfile:/root/.m2"
-    NodeSelector: {}
-    # Key Value selectors. Ex:
-    # jenkins-agent: v1
-PipelineSecrets:
-  Env:
-    # Set to false to keep existing secret
-    Replace: true
-    # Passphrase for the pgp private key file
-    pgpPassphrase: xxxx
-    # Token for codecov.io service
-    codecovToken: xxxx
-    # Token for github bot account
-    githubToken: xxxx
-    # Token for sonarcloud.io
-    sonarToken: xxxx
-  File:
-    # Set to false to keep existing secret
-    Replace: true
-    # PGP Private key in ascii format used to sign artifacts
-    PGPPrivateKeyAsc: |-
-      -----BEGIN PGP PRIVATE KEY BLOCK-----
-      xxxxx
-      -----END PGP PRIVATE KEY BLOCK-----
-    # maven.settings file
-    MavenSettingsXML: |-
-      <settings>
-        <!-- sets the local maven repository outside of the ~/.m2 folder for easier mounting of secrets and repo -->
-        <localRepository>${user.home}/.mvnrepository</localRepository>
-        <!-- lets disable the download progress indicator that fills up logs -->
-        <interactiveMode>false</interactiveMode>
-        <mirrors>
-          <mirror>
-            <id>nexus</id>
-            <mirrorOf>external:*</mirrorOf>
-            <url>https://registry.molgenis.org/repository/maven-central/</url>
-          </mirror>
-        </mirrors>
-        <servers>
-          <server>
-            <id>local-nexus</id>
-            <url>https://registry.molgenis.org/repository/maven-central/</url>
-            <username>admin</username>
-            <password>xxxxx</password>
-          </server>
-          <server>
-            <id>oss-sonatype-staging</id>
-            <username>molgenis</username>
-            <password>xxxxx</password>
-          </server>
-        </servers>
-      </settings>
+  Pods:
+    molgenis:
+      Label: molgenis
+      NodeUsageMode: NORMAL
+      volumes:
+        - type: HostPath
+          hostPath: "/var/run/docker.sock"
+          mountPath: "/var/run/docker.sock"
+      Containers:
+        maven:
+          Image: "registry.webhosting.rug.nl/molgenis/maven"
+          ImageTag: lts
+          AlwaysPullImage: true
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
+          resources:
+            requests:
+              cpu: "1"
+              memory: "4Gi"
+          EnvVars:
+            - type: KeyValue
+              key: MAVEN_OPTS
+              value: "-Duser.home=/home/jenkins"
+            - type: KeyValue
+              key: MAVEN_CONFIG
+              value: "/home/jenkins/.m2"
+        alpine:
+          Image: "spotify/alpine"
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
+        vault:
+          Image: "vault"
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
+          EnvVars:
+            - type: Secret
+              key: VAULT_TOKEN
+              secretName: molgenis-pipeline-vault-secret
+              secretKey: token
+            - type: Secret
+              key: VAULT_SKIP_VERIFY
+              secretName: molgenis-pipeline-vault-secret
+              secretKey: skipVerify
+            - type: Secret
+              key: VAULT_ADDR
+              secretName: molgenis-pipeline-vault-secret
+              secretKey: addr
+      NodeSelector: {}
+    node:
+      Label: node-carbon
+      NodeUsageMode: EXCLUSIVE
+      Containers:
+        node:
+          Image: "registry.webhosting.rug.nl/molgenis/node"
+          ImageTag: lts
+          AlwaysPullImage: true
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
+        vault:
+          Image: "vault"
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
+          EnvVars:
+            - type: Secret
+              key: VAULT_TOKEN
+              secretName: molgenis-pipeline-vault-secret
+              secretKey: token
+            - type: Secret
+              key: VAULT_SKIP_VERIFY
+              secretName: molgenis-pipeline-vault-secret
+              secretKey: skipVerify
+            - type: Secret
+              key: VAULT_ADDR
+              secretName: molgenis-pipeline-vault-secret
+              secretKey: addr
+      NodeSelector: {}
+#secret contains configuration for the kubernetes secrets that jenkins can access
+secret:
+  # vault configures the vault secret
+  vault:
+    token: xxxx
+    addr: "https://vault-operator.vault-operator.svc:8200"
+    skipVerify: "1"
+  # githubToken contains access token for jenkins bot account on github.com
+  gitHub:
+    user: "molgenis-jenkins"
+    token: xxxx
+  # gogs contains access token for jenkins bot account on RuG GoGs
+  gogs:
+    user: p281392
+    token: xxxx
+  # registry contains credentials for registry.molgenis.org
+  registry:
+    user: admin
+    password: xxxx
+  # dockerHubPassword contains password for hub.docker.com
+  dockerHub:
+    user: molgenisci
+    password: xxxx

molgenis-nexus/Chart.yaml

@@ -0,0 +1,8 @@
+apiVersion: v1
+appVersion: "1.0"
+description: Nexus stack for MOLGENIS
+name: molgenis-nexus
+version: 0.3.0
+sources:
+- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
+icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-nexus/catalogIcon-molgenis-nexus.svg

molgenis-nexus/README.md

@@ -0,0 +1,28 @@
+# MOLGENIS - NEXUS Helm Chart
+
+NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
+
+## Chart Details
+
+This chart will deploy:
+
+- 1 NEXUS container
+- 1 MOLGENIS-httpd container ()to proxy the registry and docker to one domain)
+
+## Installing the Chart
+
+You can test in install the chart by executing:
+
+```helm lint .```
+
+To test if your helm chart-syntax is right and:
+
+```helm install . --dry-run --debug```
+
+To test if your hem chart works and:
+
+```helm install .```
+
+To deploy it on the cluster.
+
+

molgenis-nexus/templates/deployments/nexus-deployment.yaml

@@ -20,17 +20,17 @@ spec:
       creationTimestamp: null
     spec:
       volumes:
-      - name: molgenis-nexus-data
+      - name: {{ .Values.persistence.name }}
         persistentVolumeClaim:
-          claimName: molgenis-nexus-data
+          claimName: {{ .Values.persistence.name }}
       restartPolicy: {{ .Values.nexus.restartPolicy }}
       initContainers:
       - name: volume-mount-nexus
         image: busybox
-        command: ["sh", "-c", "chown -R 200:200 /gcc/molgenis/nexus"]
+        command: ["sh", "-c", "chown -R 200:200 {{ .Values.persistence.mountPath }}"]
         volumeMounts:
-        - name: molgenis-nexus-data
-          mountPath: "/nexus-data"
+        - name: {{ .Values.persistence.name }}
+          mountPath: "{{ .Values.persistence.mountPath }}"
       containers:
       - name: {{ .Values.nexus.name }}
         image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
@@ -39,6 +39,6 @@ spec:
         - containerPort: {{ .Values.nexus.port.ui }}
         - containerPort: {{ .Values.nexus.port.docker }}
         volumeMounts:
-        - name: molgenis-nexus-data
+        - name: {{ .Values.persistence.name }}
           mountPath: "/nexus-data"
 

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/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

@@ -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:
@@ -53,6 +53,16 @@ ingress:
   #    hosts:
   #      - chart-example.local
 
+persistence:
+  name: molgenis-nexus-data
+  storageClass: nfs-class
+  size: 30G
+  reclaimPolicy: Retain
+  server: 192.168.64.12
+  accessMode: ReadWriteMany
+  mountPath: /gcc/molgenis/nexus
+
+
 resources: {}
   # We usually recommend not to specify default resources and to leave this as a conscious
   # choice for the user. This also increases chances charts run on environments with little

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-vault/.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-vault/Chart.yaml

@@ -0,0 +1,6 @@
+apiVersion: v1
+appVersion: "1.0"
+description: MOLGENIS vault
+name: molgenis-vault
+version: 0.1.1
+icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-vault/catalogIcon-molgenis-vault.svg

molgenis-vault/README.md

@@ -0,0 +1,52 @@
+# MOLGENIS Vault helm chart
+
+This chart creates a vault operator, but NO vault.
+The vault operator defines a new custom resource named `vault` that you can use to create vaults.
+
+After launching the operator, create the molgenis vault manually:
+`kubectl create -f resources/vault.yaml`
+
+That creates a new vault with two vault pods.
+
+See https://github.com/coreos/vault-operator/blob/master/doc/user/vault.md
+
+## Parameters
+
+### Azure cloud credentials
+Define credentials for backup to the Azure Blob Store.
+See [etcd-operator documentation](https://github.com/coreos/etcd-operator/blob/master/doc/user/abs_backup.md).
+
+| Parameter       | Description                   | Default            |
+| --------------- | ----------------------------- | ------------------ |
+| `abs.account`   | name of storage account       | `fdlkops`          |
+| `abs.accessKey` | access key of storage account | `xxxx`             |
+| `abs.cloud`     | name of cloud environment     | `AzurePublicCloud` |
+
+### Backup job
+Define the schedule of the backup job
+
+| Parameter            | Description                  | Default       |
+| -------------------- | ---------------------------- | ------------- |
+| `backupJob.enable`   | Enable backup cronjob        | `true`        |
+| `backupJob.schedule` | cron schedule for the backup | `0 12 * * 1`  |
+
+### UI
+
+Parameter | Description | Default
+--------- | ----------- | ------- 
+`ui.replicaCount` | desired number of Vault UI pod | `1`
+`ui.image.repository` | Vault UI container image repository | `djenriquez/vault-ui`
+`ui.image.tag` | Vault UI container image tag | `latest`
+`ui.resources` | Vault UI pod resource requests & limits | `{}`
+`ui.nodeSelector` | node labels for Vault UI pod assignment | `{}`
+`ui.ingress.enabled` | If true, Vault UI Ingress will be created | `true`
+`ui.ingress.annotations` | Vault UI Ingress annotations | `{}`
+`ui.ingress.host` | Vault UI Ingress hostname | `vault.molgenis.org`
+`ui.ingress.tls` | Vault UI Ingress TLS configuration (YAML) | `[]`
+`ui.vault.url` | Vault UI default vault url | `https://vault.vault-operator:8200`
+`ui.vault.auth` | Vault UI login method | `GITHUB`
+`ui.service.name` | Vault UI service name | `vault-ui`
+`ui.service.type` | type of ui service to create | `ClusterIP`
+`ui.service.externalPort` | Vault UI service target port | `8000`
+`ui.service.internalPort` | Vault UI container port | `8000`
+`ui.service.nodePort` | Port to be used as the service NodePort (ignored if `server.service.type` is not `NodePort`) | `0`

molgenis-vault/catalogIcon-molgenis-vault.svg

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+"
+     style="image-rendering:optimizeQuality"
+     preserveAspectRatio="none"
+     height="94.666664"
+     width="84" /><g
+     inkscape:groupmode="layer"
+     id="layer1"
+     inkscape:label="base"
+     style="opacity:1" /></svg>

molgenis-vault/requirements.lock

@@ -0,0 +1,9 @@
+dependencies:
+- name: vault-operator
+  repository: https://kubernetes-charts.storage.googleapis.com/
+  version: 0.1.1
+- name: etcd-operator
+  repository: https://kubernetes-charts.storage.googleapis.com/
+  version: 0.8.0
+digest: sha256:47aa645df7dfce9760905800321599de05995ae50090735d45310936dbaa46de
+generated: 2018-09-06T18:59:39.861922543+02:00

molgenis-vault/requirements.yaml

@@ -0,0 +1,7 @@
+dependencies:
+  - name: vault-operator
+    version: ^0.1.1
+    repository: https://kubernetes-charts.storage.googleapis.com/
+  - name: etcd-operator
+    version: ^0.8.0
+    repository: https://kubernetes-charts.storage.googleapis.com/

molgenis-vault/resources/restore.yaml

@@ -0,0 +1,15 @@
+# Use kubectl create -f restore.yaml to manually execute a restore of the vault
+apiVersion: "etcd.database.coreos.com/v1beta2"
+kind: "EtcdRestore"
+metadata:
+  # The restore CR name must be the same as spec.etcdCluster.name
+  name: vault-etcd
+  namespace: vault-operator
+spec:
+  etcdCluster:
+    # The namespace is the same as this EtcdRestore CR
+    name: vault-etcd
+  backupStorageType: ABS
+  abs:
+    path: vault/backup-<specify the backup name>
+    absSecret: abs

molgenis-vault/resources/vault.yaml

@@ -0,0 +1,9 @@
+# Use kubectl create -f vault.yaml to manually create a vault
+apiVersion: "vault.security.coreos.com/v1alpha1"
+kind: "VaultService"
+metadata:
+  name: "vault"
+  namespace: "vault-operator"
+spec:
+  nodes: 2
+  version: "0.9.1-0"

molgenis-vault/templates/NOTES.txt

@@ -0,0 +1,13 @@
+Vault operator created
+
+Next steps:
+
+* Manually create a vault using resources/vault.yaml
+* Manually restore a backup using resources/backup.yaml
+* Unseal the vault pods
+
+{{ if .Values.backupJob.enable }}
+!! Make sure to check if the backups succeed !!
+{{ else }}
+!!!!!! NO BACKUPS CONFIGURED !!!!!!
+{{ end }}

molgenis-vault/templates/_helpers.tpl

@@ -0,0 +1,54 @@
+{{/*
+Define vault ui fullname
+*/}}
+{{- define "vault.ui.fullname" -}}
+{{- printf "%s-ui" .Release.Name | trunc 63 | trimSuffix "-" -}}
+{{- end -}}
+
+{{/*
+Define vault service url for the ui
+*/}}
+{{- define "vault.service.url" -}}
+{{- printf "https://%s:8200" .Release.Name | trunc 63 | trimSuffix "-" -}}
+{{- end -}}
+
+{{/* See https://github.com/helm/helm/issues/4535 */}}
+{{- define "call-nested" }}
+{{- $dot := index . 0 }}
+{{- $subchart := index . 1 }}
+{{- $template := index . 2 }}
+{{- include $template (dict "Chart" (dict "Name" $subchart) "Values" (index $dot.Values $subchart) "Release" $dot.Release "Capabilities" $dot.Capabilities) }}
+{{- end }}
+
+{{/* vim: set filetype=mustache: */}}
+{{/*
+Expand the name of the chart.
+*/}}
+{{- define "molgenis-vault.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-vault.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-vault.chart" -}}
+{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
+{{- end -}}

molgenis-vault/templates/abs-secret.yaml

@@ -0,0 +1,10 @@
+# Secret to access microsoft azure blob store
+apiVersion: v1
+kind: Secret
+metadata:
+  name: abs
+type: Opaque
+stringData:
+  storage-account: {{ .Values.abs.account }}
+  storage-key: {{ .Values.abs.accessKey }}
+  cloud: {{ .Values.abs.cloud }}

molgenis-vault/templates/backup-configmap.yaml

@@ -0,0 +1,18 @@
+# configmap to use as a template by the backup cronjob to create etcdbackup instances
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: backup-config
+data:
+  backup_cr.yaml: |
+    apiVersion: "etcd.database.coreos.com/v1beta2"
+    kind: "EtcdBackup"
+    metadata:
+      generateName: vault-backup-
+    spec:
+      etcdEndpoints: ["https://vault-etcd-client:2379"]
+      storageType: ABS
+      clientTLSSecret: vault-etcd-client-tls
+      abs:
+        path: vault/backup.<NOW>
+        absSecret: abs

molgenis-vault/templates/backup-cronjob.yaml

@@ -0,0 +1,30 @@
+{{- if .Values.backupJob.enable }}
+# cronjob that creates etcdbackups using the etcd backup serviceaccount
+apiVersion: batch/v1beta1
+kind: CronJob
+metadata:
+  name: etcd-backup
+spec:
+  schedule: {{ .Values.backupJob.schedule | quote }}
+  jobTemplate:
+    spec:
+      template:
+        spec:
+          serviceAccountName: {{ include "call-nested" (list . "etcd-operator" "etcd-operator.serviceAccountName") }}
+          containers:
+          - name: etcd-backup
+            image: lachlanevenson/k8s-kubectl
+            command:
+            - /bin/sh
+            - "-ec"
+            - |
+              sed -e "s|<NOW>|$(date '+%Y-%m-%d_%H:%M:%S')|g" /var/etcd_backup/backup_cr.yaml | kubectl create -f -
+            volumeMounts:
+            - name: backup-config
+              mountPath: /var/etcd_backup
+          restartPolicy: OnFailure
+          volumes:
+          - name: backup-config
+            configMap:
+              name: backup-config
+{{- end }}

molgenis-vault/templates/ui-ingress.yaml

@@ -0,0 +1,30 @@
+{{- if .Values.ui.ingress.enabled -}}
+{{- $serviceName := include "vault.ui.fullname" . -}}
+{{- $servicePort := .Values.ui.service.externalPort -}}
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: {{ template "vault.ui.fullname" . }}
+  labels:
+    app: {{ template "molgenis-vault.name" . }}
+    chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+  annotations:
+    {{- range $key, $value := .Values.ui.ingress.annotations }}
+      {{ $key }}: {{ $value | quote }}
+    {{- end }}
+spec:
+  rules:
+    - host: {{ .Values.ui.ingress.host }}
+      http:
+        paths:
+          - path:
+            backend:
+              serviceName: {{ $serviceName }}
+              servicePort: {{ $servicePort }}
+  {{- if .Values.ui.ingress.tls }}
+  tls:
+{{ toYaml .Values.ui.ingress.tls | indent 4 }}
+  {{- end -}}
+{{- end -}}

molgenis-vault/templates/ui-service.yaml

@@ -0,0 +1,23 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ template "vault.ui.fullname" . }}
+  labels:
+    app: {{ template "vault-operator.name" . }}
+    chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  type: {{ .Values.ui.service.type }}
+  ports:
+    - port: {{ .Values.ui.service.externalPort }}
+      targetPort: {{ .Values.ui.service.internalPort }}
+      protocol: TCP
+      name: {{ .Values.ui.service.name }}
+    {{- if .Values.ui.service.nodePort }}
+      nodePort: {{ .Values.ui.service.nodePort }}
+    {{- end }}
+  selector:
+    app: {{ template "vault-operator.name" . }}
+    release: {{ .Release.Name }}
+    component: {{ .Values.ui.name }}

molgenis-vault/templates/vault-ui-deployment.yaml

@@ -0,0 +1,50 @@
+apiVersion: apps/v1beta1
+kind: Deployment
+metadata:
+  name: {{ template "vault.ui.fullname" . }}
+  labels:
+    app: {{ template "vault-operator.name" . }}
+    chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+    component: {{ .Values.ui.name }}
+spec:
+  replicas: {{ .Values.ui.replicaCount }}
+  template:
+    metadata:
+      labels:
+        app: {{ template "vault-operator.name" . }}
+        release: {{ .Release.Name }}
+        component: {{ .Values.ui.name }}
+    spec:
+      containers:
+        - name: {{ .Values.ui.name }}
+          image: "{{ .Values.ui.image.repository }}:{{ .Values.ui.image.tag }}"
+          imagePullPolicy: {{ .Values.imagePullPolicy }}
+          env:
+          - name: VAULT_URL_DEFAULT
+          {{- if .Values.ui.vault.url }}
+            value: {{ .Values.ui.vault.url }}
+          {{ else }}
+            value: {{ template "vault.service.url" . }}
+          {{- end }}
+          - name: VAULT_AUTH_DEFAULT
+            value: {{ .Values.ui.vault.auth }}
+          - name: NODE_TLS_REJECT_UNAUTHORIZED
+            value: '0'
+          ports:
+            - containerPort: {{ .Values.ui.service.internalPort }}
+          livenessProbe:
+            httpGet:
+              path: /
+              port: {{ .Values.ui.service.internalPort }}
+          readinessProbe:
+            httpGet:
+              path: /
+              port: {{ .Values.ui.service.internalPort }}
+          resources:
+{{ toYaml .Values.ui.resources | indent 12 }}
+    {{- if .Values.ui.nodeSelector }}
+      nodeSelector:
+{{ toYaml .Values.ui.nodeSelector | indent 8 }}
+    {{- end }}

molgenis-vault/values.yaml

@@ -0,0 +1,79 @@
+# Default values for molgenis-vault.
+# This is a YAML-formatted file.
+# Declare variables to be passed into your templates.
+
+# abs gives details of the credentials to reach the azure backup storage
+abs:
+  # account is the name of the Storage account
+  account: fdlkops
+  # access key for the Storage account
+  accessKey: xxxx
+  # default cloud
+  cloud: AzurePublicCloud
+
+# backupjob describes the backup cronjob
+backupJob:
+  # enable enables the backup job
+  enable: true
+  # schedule gives the cron schedule for the backup job
+  schedule: "0 12 * * 1"
+
+###
+# All of the config variables related to setting up the etcd-operator
+# If you want more information about the variables exposed, please visit:
+#   https://github.com/kubernetes/charts/tree/master/stable/etcd-operator#configuration
+###
+etcd-operator:
+  deployments:
+    etcdOperator: true
+    backupOperator: true
+    restoreOperator: true
+  serviceAccount:
+    etcdOperatorServiceAccount:
+      create: true
+    backupOperatorServiceAccount:
+      create: true
+    restoreOperatorServiceAccount:
+      create: true
+  etcdOperator:
+    image:
+      tag: v0.9.2
+  backupOperator:
+    image:
+      tag: v0.9.2
+  restoreOperator:
+    image:
+      tag: v0.9.2
+
+ui:
+  name: "vault-ui"
+  replicaCount: 1
+  image:
+    repository: djenriquez/vault-ui
+    tag: latest
+  service:
+    name: vault-ui
+    type: ClusterIP
+    externalPort: 8000
+    internalPort: 8000
+    # nodePort: 32001
+  ingress:
+    enabled: true
+    # Used to create Ingress record (should used with service.type: ClusterIP).
+    host: vault.molgenis.org
+
+  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: {}
+  vault:
+    auth: GITHUB
+    url: https://vault.vault-operator:8200

molgenis/Chart.yaml

@@ -0,0 +1,8 @@
+apiVersion: v1
+appVersion: "1.0"
+description: MOLGENIS - helm stack (in BETA)
+name: molgenis-beta
+version: 0.3.0
+sources:
+- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
+icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis/catalogIcon-molgenis.svg

molgenis/README.md

@@ -0,0 +1,122 @@
+# MOLGENIS
+This chart is used for acceptance and production use cases.
+
+## Containers
+This chart spins up a MOLGENIS instance with HTTPD. The created containers are:
+
+- MOLGENIS
+
+## 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```
+
+## 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```
+
+You can also choose to retain the volume of the NFS.
+- ```persistence.retain```
+
+The size and claim name can be specified per service. There are now two services that can be persist.
+
+- MOLGENIS
+- ElasticSearch
+
+MOLGENIS persistent properties.
+- ```molgenis.persistence.claim```
+- ```molgenis.persistence.size```
+
+ElasticSearch persistent properties.
+- ```elasticsearch.persistence.claim```
+- ```elasticsearch.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```. 
+
+## Firewall
+Is defined at cluster level. This chart does not facilitate firewall configuration.

molgenis/questions.yml

@@ -0,0 +1,131 @@
+
+categories:
+- MOLGENIS
+questions:
+- variable: ingress.hosts[0].name
+  label: Hostname
+  default: "test.molgenis.org"
+  description: "Hostname for your stack"
+  type: hostname
+  required: true
+  group: "Load Balancing"
+- 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.image.tag
+  label: Version
+  default: ""
+  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: molgenis.services.opencpu.host
+  label: OpenCPU cluster
+  default: "localhost"
+  description: "Specify the OpenCPU cluster"
+  type: string
+  required: true
+  group: "Services"
+- variable: molgenis.services.postgres.host
+  label: Postgres cluster location
+  default: "postgresql.molgenis-postgresql.svc"
+  description: "Set the location of the postgres cluster"
+  type: string
+  required: true
+  group: "Services"
+- variable: molgenis.services.postgres.scheme
+  label: Database scheme
+  default: "molgenis"
+  description: "Set the database scheme"
+  type: string
+  required: true
+  group: "Services"
+- variable: molgenis.services.postgres.user
+  label: Database username
+  default: "molgenis"
+  description: "Set user of the database scheme"
+  type: string
+  required: true
+  group: "Services"
+- variable: molgenis.services.postgres.password
+  label: Database password
+  default: "molgenis"
+  description: "Set the password of the database scheme"
+  type: string
+  required: true
+  group: "Services"
+- variable: molgenis.resources.limits.memory
+  label: Container memory limit
+  default: 1250Mi
+  description: "Memory limit for this MOLGENIS container"
+  type: enum
+  options:
+  - "1250Mi"
+  - "2500Mi"
+  required: true
+  group: "Resources"
+- variable: molgenis.resources.requests.memory
+  label: Container memory reservation
+  default: 1250Mi
+  description: "Memory reservation for this MOLGENIS container (must fit in the selected memory limit for the container)"
+  type: enum
+  options:
+  - "1250Mi"
+  - "2500Mi"
+  required: true
+  group: "Resources"
+- variable: molgenis.javaOpts.maxHeapSpace
+  label: Maximum heap space (JVM)
+  default: "1g"
+  description: "Maximum heap space MOLGENIS container JVM. Please not this should fit in your container memory limit"
+  type: enum
+  options:
+  - "1g"
+  - "2g"
+  group: "Resources"
+- variable: persistence.enabled
+  default: false
+  description: "Do you want to use persistence"
+  type: boolean
+  required: true
+  group: "Persistence"
+  label: Persistence
+  show_subquestion_if: true
+  subquestions:
+  - variable: persistence.retain
+    default: false
+    description: "Do you want to retain the persistent volume"
+    type: boolean
+    label: Retain volume
+  - variable: molgenis.persistence.size
+    default: "30Gi"
+    description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
+    type: enum
+    options:
+    - "30Gi"
+    - "50Gi"
+    - "100Gi"
+    label: Size MOLGENIS filestore
+  - variable: elasticsearch.persistence.size
+    default: "50Gi"
+    description: "Size of ElasticSearch data (directory that is persist: /usr/share/elasticsearch/data)"
+    type: enum
+    options:
+    - "50Gi"
+    - "100Gi"
+    - "200Gi"
+    label: Size for ElasticSearch data

molgenis/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/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/templates/deployment.yaml

@@ -0,0 +1,126 @@
+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: {{ .services.opencpu.host }}
+            - name: elasticsearch.transport.addresses
+              value: {{ .services.elasticsearch.transportAddresses }}
+            - name: elasticsearch.cluster.name
+              value: {{ .services.elasticsearch.clusterName }}
+            - name: db_uri
+              value: jdbc:postgresql://{{ .services.postgres.host }}/{{ .services.postgres.scheme }}
+            - name: db_user
+              value: {{ .services.postgres.user }}
+            - name: db_password
+              value: {{ .services.postgres.password }}
+            - name: admin.password
+              value: {{ .adminPassword }}
+            - name: CATALINA_OPTS
+              value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
+          ports:
+            - containerPort: 8080
+          {{- if $.Values.persistence.enabled }}
+          volumeMounts:
+          - name: molgenis-nfs
+            mountPath: /home/molgenis
+          {{- 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:
+{{ 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
+          {{- if $.Values.persistence.enabled }}
+          volumeMounts:
+          - name: elasticsearch-nfs
+            mountPath: /usr/share/elasticsearch/data
+          {{- end }}
+
+          resources:
+{{ toYaml .resources | indent 12 }}
+        {{- end }}
+
+{{- if .Values.persistence.enabled }}
+      volumes:
+        - name: molgenis-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.molgenis.persistence.claim }}
+        - name: elasticsearch-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.elasticsearch.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 }}

molgenis/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/templates/persistence/elasticsearchPVC.yaml

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

molgenis/templates/persistence/molgenisPVC.yaml

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

molgenis/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/values.yaml

@@ -0,0 +1,77 @@
+# 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.hub.docker.com
+    name: molgenis/molgenis-app
+    tag: stable
+    pullPolicy: Always
+  adminPassword:
+  javaOpts:
+    maxHeapSpace: "1g"
+  resources:
+    limits:
+      cpu: 1
+      memory: 1250Mi
+    requests:
+      cpu: 200m
+      memory: 1250Mi
+  persistence:
+    claim: molgenis-nfs-claim
+    size: 30Gi
+  services:
+    opencpu:
+      host: localhost
+    elasticsearch:
+      transportAddresses: localhost:9300
+      clusterName: molgenis
+    postgres:
+      host: localhost
+      scheme: molgenis
+      user: molgenis
+      password: molgenis
+
+elasticsearch:
+  image:
+    repository: docker.elastic.co/elasticsearch/elasticsearch
+    tag: 5.5.3
+    pullPolicy: IfNotPresent
+  javaOpts: "-Xms1g -Xmx1g"
+  clusterName: molgenis
+  resources:
+   limits:
+    cpu: 2
+    memory: 3Gi
+   requests:
+    cpu: 100m
+    memory: 1Gi
+  persistence:
+    claim: elasticsearch-nfs-claim
+    size: 50Gi
+
+persistence:
+  enabled: false
+  retain: false
+
+nodeSelector: {
+  deployPod: "true"
+}
+
+tolerations: []
+
+affinity: {}

nexus/v0.1.x/Chart.yaml

@@ -1,6 +0,0 @@
-apiVersion: v1
-appVersion: "1.0"
-description: Nexus stack for MOLGENIS
-name: nexus
-version: 0.1.2
-icon: https://github.com/sidohaakma/molgenis-docker-helm/blob/master/nexus/catalogIcon-molgenis-nexus.svg

nexus/v0.1.x/templates/volumes/nexus-pv.yaml

@@ -1,16 +0,0 @@
-apiVersion: v1
-kind: PersistentVolume
-metadata:
-  name: molgenis-nexus-data
-  labels:
-    name: nfs2
-spec:
-  storageClassName: nfs-class
-  capacity:
-    storage: 50Gi
-  accessModes:
-    - ReadWriteMany
-  persistentVolumeReclaimPolicy: Retain
-  nfs:
-    server: 192.168.64.12
-    path: /gcc/molgenis/nexus

nexus/v0.1.x/templates/volumes/nexus-pvc.yaml

@@ -1,11 +0,0 @@
-kind: PersistentVolumeClaim
-apiVersion: v1
-metadata:
-  name: molgenis-nexus-data
-spec:
-  storageClassName: nfs-class
-  accessModes:
-    - ReadWriteMany
-  resources:
-    requests:
-      storage: 50Gi