Revert "Merge branch 'chore/nodeSelector' of P129679/molgenis-ops-docker-helm into master"

This reverts commit f94e6da6e3, reversing
changes made to b73fd578ea.

README.md

@@ -104,6 +104,7 @@ This repository is serves also as a catalogue for Rancher. We have serveral apps
 - [Jenkins](molgenis-jenkins/README.md)
 - [NEXUS](molgenis-nexus/README.md)
 - [HTTPD](molgenis-httpd/README.md)
+- [MOLGENIS](molgenis/README.md)
 - [MOLGENIS preview](molgenis-preview/README.md)
 - [MOLGENIS vault](molgenis-vault/README.md)
 
@@ -122,6 +123,26 @@ You can you need to know to easily develop and deploy helm-charts
   
   Do it in the root of the project where the Chart.yaml is located
   It installs a release of a kubernetes stack. You also store this as an artifact in a kubernetes repository
+- ```helm package .```
+  
+  You can create a package which can be uploaded in the molgenis helm repository
+  
+- ```helm publish```
+  You still have to create an ```index.yaml``` for the chart. You can do this by executing this command: ```helm repo index #directory name of helm chart#```
+  
+  Then you can upload it by executing:
+  
+  - ```curl -v --user #username#:#password# --upload-file index.yaml  https://registry.molgenis.org/repository/helm/#chart name#/index.yml```
+  - ```curl -v --user #username#:#password# --upload-file #chart name#-#version#.tgz https://registry.molgenis.org/repository/helm/#chart name#/#chart name#-#version#.tgz```
+  
+  Now you have to add the repository locally to use in your ```requirements.yaml```.
+  
+  - ```helm repo add #repository name# https://registry.molgenis.org/repository/helm/molgenis```
+
+- ```helm dep build```
+  
+  You can build your dependencies (create a ```charts``` directory and install the chart in it) of the helm-chart. 
+
 - ```helm list```
   
   Lists all installed releases

molgenis-jenkins/Chart.yaml

@@ -1,6 +1,6 @@
 name: molgenis-jenkins
 home: https://jenkins.io/
-version: 0.7.0
+version: 0.8.0
 appVersion: 2.121
 description: Molgenis installation for the jenkins chart.
 sources:

molgenis-jenkins/README.md

@@ -75,6 +75,10 @@ Token used by Jenkins to authenticate on the [RuG Webhosting Gogs](https://git.w
 | `secret.gogs.user`  | username for the account | `p281392` |
 | `secret.gogs.token` | token for the account    | `xxxx`    |
 
+
+#### Slack
+The Slack integration is done mostly in the Jenkinsfile of each project. It is sufficient to only add the plugin to the Jenkins configuration in Helm.
+
 #### Legacy:
 
 ##### Docker Hub

molgenis-jenkins/requirements.lock

@@ -1,6 +1,6 @@
 dependencies:
 - name: jenkins
   repository: https://kubernetes-charts.storage.googleapis.com/
-  version: 0.16.4
+  version: 0.18.0
 digest: sha256:39f694515489598fa545c9a5a4f1347749e8f2a8d7fae6ccae3e2acae1564685
-generated: 2018-06-27T14:36:23.172954738+02:00
+generated: 2018-09-27T11:00:15.795416984+02:00

molgenis-jenkins/resources/README.md

@@ -0,0 +1,8 @@
+# Helm in Jenkins
+
+To be able to run helm inside a jenkins pod, you'll need to 
+* create a role in the namespace where tiller is installed
+* bind that role to the user that jenkins pods run as
+
+This directory contains yaml for these resources.
+See also https://github.com/helm/helm/blob/master/docs/rbac.md

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/values.yaml

@@ -3,17 +3,18 @@ jenkins:
     HostName: jenkins.molgenis.org
     ServiceType: ClusterIP
     InstallPlugins:
-      - kubernetes:1.12.0
+      - kubernetes:1.12.6
       - workflow-aggregator:2.5
-      - workflow-job:2.21
+      - workflow-job:2.25
       - credentials-binding:1.16
       - git:3.9.1
       - github-branch-source:2.3.6
-      - kubernetes-credentials-provider:0.9
+      - kubernetes-credentials-provider:0.10
-      - blueocean:1.6.2
+      - blueocean:1.8.3
       - github-oauth:0.29
       - gogs-webhook:1.0.14
-      - sauce-ondemand:1.176
+      - github-scm-trait-commit-skip:0.1.1
+      - slack:2.3
     Security:
       UseGitHub: false
       GitHub:
@@ -82,6 +83,18 @@ jenkins:
                   <strategyId>1</strategyId>
                   <trust class="org.jenkinsci.plugins.github_branch_source.ForkPullRequestDiscoveryTrait$TrustPermission"/>
                 </org.jenkinsci.plugins.github__branch__source.ForkPullRequestDiscoveryTrait>
+                <org.jenkinsci.plugins.scm__filter.GitHubCommitSkipTrait plugin="github-scm-trait-commit-skip@0.1.1"/>
+                <jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
+                  <extension class="hudson.plugins.git.extensions.impl.LocalBranch">
+                    <localBranch>**</localBranch>
+                  </extension>
+                </jenkins.plugins.git.traits.LocalBranchTrait>
+                <jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
+                  <extension class="hudson.plugins.git.extensions.impl.UserIdentity">
+                    <name>MOLGENIS Jenkins</name>
+                    <email>molgenis+ci@gmail.com</email>
+                  </extension>
+                </jenkins.plugins.git.traits.UserIdentityTrait>
               </traits>
             </org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator>
           </navigators>
@@ -131,6 +144,17 @@ jenkins:
                   <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
                   <traits>
                     <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                    <jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.LocalBranch">
+                        <localBranch>**</localBranch>
+                      </extension>
+                    </jenkins.plugins.git.traits.LocalBranchTrait>
+                    <jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.UserIdentity">
+                        <name>MOLGENIS Jenkins</name>
+                        <email>molgenis+ci@gmail.com</email>
+                      </extension>
+                    </jenkins.plugins.git.traits.UserIdentityTrait>
                   </traits>
                 </source>
                 <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@@ -184,6 +208,17 @@ jenkins:
                   <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
                   <traits>
                     <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                    <jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.LocalBranch">
+                        <localBranch>**</localBranch>
+                      </extension>
+                    </jenkins.plugins.git.traits.LocalBranchTrait>
+                    <jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.UserIdentity">
+                        <name>MOLGENIS Jenkins</name>
+                        <email>molgenis+ci@gmail.com</email>
+                      </extension>
+                    </jenkins.plugins.git.traits.UserIdentityTrait>
                   </traits>
                 </source>
                 <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@@ -237,6 +272,17 @@ jenkins:
                   <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
                   <traits>
                     <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                    <jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.LocalBranch">
+                        <localBranch>**</localBranch>
+                      </extension>
+                    </jenkins.plugins.git.traits.LocalBranchTrait>
+                    <jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.UserIdentity">
+                        <name>MOLGENIS Jenkins</name>
+                        <email>molgenis+ci@gmail.com</email>
+                      </extension>
+                    </jenkins.plugins.git.traits.UserIdentityTrait>
                   </traits>
                 </source>
                 <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@@ -290,6 +336,17 @@ jenkins:
                   <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
                   <traits>
                     <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                    <jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.LocalBranch">
+                        <localBranch>**</localBranch>
+                      </extension>
+                    </jenkins.plugins.git.traits.LocalBranchTrait>
+                    <jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.UserIdentity">
+                        <name>MOLGENIS Jenkins</name>
+                        <email>molgenis+ci@gmail.com</email>
+                      </extension>
+                    </jenkins.plugins.git.traits.UserIdentityTrait>
                   </traits>
                 </source>
                 <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@@ -343,6 +400,17 @@ jenkins:
                   <credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
                   <traits>
                     <jenkins.plugins.git.traits.BranchDiscoveryTrait/>
+                    <jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.LocalBranch">
+                        <localBranch>**</localBranch>
+                      </extension>
+                    </jenkins.plugins.git.traits.LocalBranchTrait>
+                    <jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
+                      <extension class="hudson.plugins.git.extensions.impl.UserIdentity">
+                        <name>MOLGENIS Jenkins</name>
+                        <email>molgenis+ci@gmail.com</email>
+                      </extension>
+                    </jenkins.plugins.git.traits.UserIdentityTrait>
                   </traits>
                 </source>
                 <strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@@ -416,6 +484,12 @@ jenkins:
               key: VAULT_ADDR
               secretName: molgenis-pipeline-vault-secret
               secretKey: addr
+        helm:
+          Image: "lachlanevenson/k8s-helm"
+          ImageTag: "v2.10.0"
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
       NodeSelector: {}
     node:
       Label: node-carbon
@@ -447,6 +521,69 @@ jenkins:
               secretName: molgenis-pipeline-vault-secret
               secretKey: addr
       NodeSelector: {}
+    molgenis-it:
+      InheritFrom: molgenis
+      Label: molgenis-it
+      NodeUsageMode: EXCLUSIVE
+      Containers:
+        elasticsearch:
+          Image: docker.elastic.co/elasticsearch/elasticsearch
+          ImageTag: 5.5.3
+          resources:
+            requests:
+              cpu: "100m"
+              memory: "1Gi"
+            limits:
+              cpu: "1"
+              memory: "1500Mi"
+          EnvVars:
+          - type: KeyValue
+            key: ES_JAVA_OPTS
+            value: "-Xms512m -Xmx512m"
+          - type: KeyValue
+            key: cluster.name
+            value: molgenis
+          - type: KeyValue
+            key: bootstrap.memory_lock
+            value: "true"
+          - type: KeyValue
+            key: xpack.security.enabled
+            value: "false"
+          - type: KeyValue
+            key: discovery.type
+            value: single-node
+        postgres:
+          Image: postgres
+          ImageTag: 9.6-alpine
+          resources:
+            requests:
+              cpu: "100m"
+              memory: "250Mi"
+            limits:
+              cpu: "1"
+              memory: "250Mi"
+          EnvVars:
+          - type: KeyValue
+            key: POSTGRES_USER
+            value: molgenis
+          - type: KeyValue
+            key: POSTGRES_PASSWORD
+            value: molgenis
+          - type: KeyValue
+            key: POSTGRES_DB
+            value: molgenis
+        opencpu:
+          Image: molgenis/opencpu
+          AlwaysPullImage: true
+          resources:
+            requests:
+              cpu: "100m"
+              memory: "256Mi"
+            limits:
+              cpu: "1"
+              memory: "512Mi"
+      NodeSelector: {}
+
 #secret contains configuration for the kubernetes secrets that jenkins can access
 secret:
   # vault configures the vault secret

molgenis-nexus/Chart.yaml

@@ -2,7 +2,7 @@ apiVersion: v1
 appVersion: "1.0"
 description: Nexus stack for MOLGENIS
 name: molgenis-nexus
-version: 0.3.0
+version: 0.4.2
 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

@@ -6,8 +6,44 @@ NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
 
 This chart will deploy:
 
+- 1 NEXUS-nfs initialization container
+
+  We need this container to avoid permission issues on the NEXUS docker
 - 1 NEXUS container
-- 1 MOLGENIS-httpd container ()to proxy the registry and docker to one domain)
+- 1 MOLGENIS-httpd container (to proxy the registry and docker to one domain)
+
+## Backup restore
+There are two steps in restoring the NEXUS.
+
+- Database
+- Blobstore
+
+### Restore the database
+Go to the commandline:
+
+```bash
+kubectl get pv
+```
+
+```bash
+| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
+| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
+| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-nexus/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 |
+```
+
+The persistent volume is the one in the molgenis-nexus namespace. 
+
+Go to the NFS-provisioner to the path of the persistent volume:
+
+```bash
+ls -t --full-time | head -7 | xargs cp ../restore-from-backup/
+```
+
+### Restore the blobstore
+You can copy the directory ```blobs``` to the target persistent volume ```/ blobs```.
+
+You can now bring the NEXUS back up.
 
 ## Installing the Chart
 
@@ -25,4 +61,9 @@ To test if your hem chart works and:
 
 To deploy it on the cluster.
 
+```curl -L -u xxxx:xxxx http://registry.molgenis.org/repository/helm/ --upload-file molgenis-x.x.x.tgz```
+
+To push it to the registry
+
+
 

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

@@ -1,34 +0,0 @@
-apiVersion: extensions/v1beta1
-kind: Deployment
-metadata:
-  creationTimestamp: null
-  name: {{ .Values.httpd.name }}
-  labels:
-    app: {{ .Values.httpd.name }}
-    environment: {{ .Values.environment }}
-spec:
-  replicas: {{ .Values.replicaCount }}
-  strategy:
-    type: {{ .Values.httpd.strategy.type }}
-  selector:
-    matchLabels:
-      app: {{ .Values.httpd.selector }}
-  template:
-    metadata:
-      labels:
-        app: {{ .Values.httpd.name }}
-      creationTimestamp: null
-    spec:
-      restartPolicy: {{ .Values.httpd.restartPolicy }}
-      containers:
-      - name: {{ .Values.httpd.name }}
-        image: "{{ .Values.httpd.image.repository }}:{{ .Values.httpd.image.tag }}"
-        imagePullPolicy: {{ .Values.httpd.image.pullPolicy }}
-        env:
-        - name: PROXY_SERVICE
-          value: "{{ .Values.nexus.name }}:{{ .Values.nexus.port.ui }},{{ .Values.nexus.name }}:{{ .Values.nexus.port.docker }}:{{ .Values.nexus.path.dockerV2 }}"
-        - name: SERVER_NAME
-          value: {{ .Values.httpd.hostname }}
-        ports:
-        - containerPort: {{ .Values.httpd.port }}
-        resources: {}

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

@@ -19,18 +19,14 @@ spec:
         app: {{ .Values.nexus.name }}
       creationTimestamp: null
     spec:
-      volumes:
-      - name: {{ .Values.persistence.name }}
-        persistentVolumeClaim:
-          claimName: {{ .Values.persistence.name }}
       restartPolicy: {{ .Values.nexus.restartPolicy }}
       initContainers:
-      - name: volume-mount-nexus
+      - name: nexus-nfs
         image: busybox
-        command: ["sh", "-c", "chown -R 200:200 {{ .Values.persistence.mountPath }}"]
+        command: ["sh", "-c", "chown -R 200:200 /nexus-data"]
         volumeMounts:
-        - name: {{ .Values.persistence.name }}
+        - name: molgenis-nexus-nfs
-          mountPath: "{{ .Values.persistence.mountPath }}"
+          mountPath: "/nexus-data"
       containers:
       - name: {{ .Values.nexus.name }}
         image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
@@ -39,6 +35,31 @@ spec:
         - containerPort: {{ .Values.nexus.port.ui }}
         - containerPort: {{ .Values.nexus.port.docker }}
         volumeMounts:
-        - name: {{ .Values.persistence.name }}
+        - name: molgenis-nexus-nfs
-          mountPath: "/nexus-data"
+          mountPath: /nexus-data
+        livenessProbe:
+          httpGet:
+            path: /
+            port: {{ .Values.nexus.port.ui }}
+          initialDelaySeconds: 120
+          periodSeconds: 20
+          failureThreshold: 15
+          successThreshold: 1
+        readinessProbe:
+          httpGet:
+            path: /
+            port: {{ .Values.nexus.port.ui }}
+          initialDelaySeconds: 120
+          periodSeconds: 20
+          failureThreshold: 15
+          successThreshold: 1
 
+      volumes:
+        - name: molgenis-nexus-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.persistence.claim }}
+
+    {{- with .Values.nodeSelector }}
+      nodeSelector:
+{{ toYaml . | indent 8 }}
+    {{- end }}

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

@@ -0,0 +1,55 @@
+apiVersion: extensions/v1beta1
+kind: Deployment
+metadata:
+  creationTimestamp: null
+  name: {{ .Values.nexusProxy.name }}
+  labels:
+    app: {{ .Values.nexusProxy.name }}
+    environment: {{ .Values.environment }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  strategy:
+    type: {{ .Values.nexusProxy.strategy.type }}
+  selector:
+    matchLabels:
+      app: {{ .Values.nexusProxy.selector }}
+  template:
+    metadata:
+      labels:
+        app: {{ .Values.nexusProxy.name }}
+      creationTimestamp: null
+    spec:
+      restartPolicy: {{ .Values.nexusProxy.restartPolicy }}
+      containers:
+      - name: {{ .Values.nexusProxy.name }}
+        image: "{{ .Values.nexusProxy.image.repository }}:{{ .Values.nexusProxy.image.tag }}"
+        imagePullPolicy: {{ .Values.nexusProxy.image.pullPolicy }}
+        env:
+        - name: PROXY_SERVICE
+          value: "{{ .Values.nexus.name }}:{{ .Values.nexus.port.ui }},{{ .Values.nexus.name }}:{{ .Values.nexus.port.docker }}:{{ .Values.nexus.path.dockerV2 }}"
+        - name: SERVER_NAME
+          value: {{ .Values.nexusProxy.hostname }}
+        ports:
+        - containerPort: {{ .Values.nexusProxy.port }}
+        resources: {}
+        livenessProbe:
+          httpGet:
+            path: /
+            port: {{ .Values.nexusProxy.port }}
+          initialDelaySeconds: 1500
+          periodSeconds: 20
+          failureThreshold: 5
+          successThreshold: 1
+        readinessProbe:
+          httpGet:
+            path: /
+            port: {{ .Values.nexusProxy.port }}
+          initialDelaySeconds: 150
+          periodSeconds: 20
+          failureThreshold: 15
+          successThreshold: 1
+
+    {{- with .Values.nodeSelector }}
+      nodeSelector:
+{{ toYaml . | indent 8 }}
+    {{- end }}

molgenis-nexus/templates/ingress.yaml

@@ -5,7 +5,7 @@ kind: Ingress
 metadata:
   name: "{{ $.Release.Name }}-ingress"
   labels:
-    app: httpd
+    app: {{ $.Values.nexusProxy.name }}
     chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
     release: "{{ $.Release.Name }}"
     heritage: "{{ $.Release.Service }}"
@@ -25,8 +25,8 @@ spec:
       paths:
         - path: {{ default "/" .path }}
           backend:
-            serviceName: httpd
+            serviceName: {{ $.Values.nexusProxy.name }}
-            servicePort: 80
+            servicePort: {{ $.Values.nexusProxy.port }}
 {{- if .tls }}
   tls:
   - hosts:

molgenis-nexus/templates/persistence/nexusPVC.yaml

@@ -0,0 +1,15 @@
+{{- if .Values.persistence.enabled -}}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Values.persistence.claim }}
+  annotations:
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
+spec:
+  accessModes:
+    - ReadWriteMany
+  resources:
+    requests:
+      storage: {{ .Values.persistence.size }}
+{{- end }}

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

@@ -1,13 +0,0 @@
-apiVersion: v1
-kind: Service
-metadata:
-  name: {{ .Values.httpd.name }}
-  labels:
-    app: {{ .Values.httpd.name }}
-spec:
-  type: {{ .Values.httpd.service.type }}
-  ports:
-  - name: {{ .Values.httpd.name }}
-    port: {{ .Values.httpd.port }}
-  selector:
-    app: {{ .Values.httpd.selector }}

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

@@ -0,0 +1,13 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Values.nexusProxy.name }}
+  labels:
+    app: {{ .Values.nexusProxy.name }}
+spec:
+  type: {{ .Values.nexusProxy.service.type }}
+  ports:
+  - name: {{ .Values.nexusProxy.name }}
+    port: {{ .Values.nexusProxy.port }}
+  selector:
+    app: {{ .Values.nexusProxy.selector }}

molgenis-nexus/templates/volumes/nexus-pv.yaml

@@ -1,16 +0,0 @@
-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

@@ -1,11 +0,0 @@
-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

@@ -13,7 +13,7 @@ nexus:
   selector: nexus
   restartPolicy: Always
   image:
-    repository: sonatype/nexus3
+    repository: molgenis/nexus3
     tag: latest
     pullPolicy: Always
   port:
@@ -24,16 +24,16 @@ nexus:
   service:
     type: ClusterIP
 
-httpd:
+nexusProxy:
-  name: httpd
+  name: nexus-proxy
   hostname: registry.molgenis.org
   strategy:
     type: Recreate
-  selector: httpd
+  selector: nexus-proxy
   restartPolicy: Always
   image:
-    repository: registry.webhosting.rug.nl/molgenis/httpd
+    repository: molgenis/httpd
-    tag: lts
+    tag: latest
     pullPolicy: Always
   port: 80
   service:
@@ -43,39 +43,22 @@ httpd:
 ingress:
   enabled: true
   annotations: {}
-    # kubernetes.io/ingress.class: nginx
-    # kubernetes.io/tls-acme: "true"
   path: /
   hosts:
   - name: registry.molgenis.org
   tls: []
-  #  - secretName: chart-example-tls
-  #    hosts:
-  #      - chart-example.local
 
 persistence:
-  name: molgenis-nexus-data
+  enabled: true
-  storageClass: nfs-class
+  claim: molgenis-nexus
-  size: 30G
+  size: 500Gi
-  reclaimPolicy: Retain
-  server: 192.168.64.12
-  accessMode: ReadWriteMany
-  mountPath: /gcc/molgenis/nexus
 
 
 resources: {}
-  # We usually recommend not to specify default resources and to leave this as a conscious
-  # choice for the user. This also increases chances charts run on environments with little
-  # resources, such as Minikube. If you do want to specify resources, uncomment the following
-  # lines, adjust them as necessary, and remove the curly braces after 'resources:'.
-  # limits:
-  #  cpu: 100m
-  #  memory: 128Mi
-  # requests:
-  #  cpu: 100m
-  #  memory: 128Mi
 
-nodeSelector: {}
+nodeSelector: {
+  deployPod: "true"
+}
 
 tolerations: []
 

molgenis-opencpu/Chart.yaml

@@ -1,8 +1,8 @@
 apiVersion: v1
 appVersion: "1.0"
-description: MOLGENIS - helm stack for testing purposes
+description: Opencpu stack for MOLGENIS
-name: molgenis-preview
+name: molgenis-opencpu
-version: 0.2.0
+version: 0.1.1
 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
+icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-opencpu/catalogIcon-molgenis-opencpu.svg

molgenis-opencpu/README.md

@@ -0,0 +1,38 @@
+# MOLGENIS - OpenCPU Helm Chart
+
+NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
+
+## Containers
+
+This chart will deploy the following containers:
+
+- OpenCPU
+- MOLGENIS-httpd (to proxy the registry and docker to one domain)
+
+## Provisioning
+You can choose for the OpenCPU image from which repository you want to pull. Experimental builds are pushed to registry.molgenis.org and the stable builds to hub.docker.com. 
+You need to fill out 2 properties to determine which repository you are going to use.
+
+- ```opencpu.image.repository```
+- ```opencpu.image.tag```
+
+You can do this in the questions in Rancher or in the ```values.yaml```.
+
+
+
+## Development
+You can test in install the chart by executing:
+
+```helm lint .```
+
+To test if your helm chart-syntax is right and:
+
+```helm install . --dry-run --debug```
+
+To test if your hem chart works and:
+
+```helm install .```
+
+To deploy it on the cluster.
+
+

molgenis-opencpu/catalog-molgenis-opencpu.svg

@@ -0,0 +1 @@
+<svg id="svg" version="1.1" width="400" height="211.2" viewBox="0 0 400 211.2" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" ><g id="svgg"><path id="path0" d="M146.487 22.310 C 145.632 22.523,145.088 22.783,144.947 23.047 C 144.827 23.271,144.534 23.455,144.295 23.455 C 143.805 23.455,141.997 25.207,141.997 25.682 C 141.997 25.852,141.807 26.181,141.574 26.413 C 141.342 26.646,141.152 27.073,141.152 27.362 C 141.152 27.660,140.968 28.003,140.729 28.153 C 140.181 28.495,140.059 35.922,140.601 35.922 C 140.951 35.922,141.152 36.375,141.152 37.164 C 141.152 37.538,141.407 37.993,141.884 38.468 C 142.288 38.869,142.620 39.283,142.624 39.387 C 142.633 39.636,144.518 41.416,144.773 41.416 C 144.880 41.416,145.022 41.556,145.088 41.727 C 145.153 41.898,145.555 42.099,145.979 42.173 C 146.404 42.248,146.962 42.440,147.219 42.602 C 147.924 43.043,154.517 43.023,154.886 42.578 C 155.031 42.404,155.408 42.261,155.725 42.261 C 156.041 42.261,156.472 42.071,156.683 41.838 C 156.893 41.606,157.162 41.416,157.280 41.416 C 157.398 41.416,157.905 40.988,158.406 40.465 C 158.907 39.942,159.413 39.514,159.532 39.514 C 159.650 39.514,159.746 39.370,159.746 39.195 C 159.746 39.020,159.937 38.713,160.169 38.514 C 160.401 38.315,160.592 37.996,160.592 37.805 C 160.592 37.614,160.782 37.216,161.014 36.921 C 161.247 36.625,161.437 36.168,161.437 35.905 C 161.437 35.642,161.592 35.256,161.781 35.047 C 162.303 34.470,162.323 30.318,161.807 29.588 C 161.603 29.301,161.437 28.769,161.437 28.406 C 161.437 28.015,161.265 27.591,161.014 27.364 C 160.782 27.154,160.592 26.808,160.592 26.597 C 160.592 26.192,157.426 22.847,156.658 22.440 C 155.872 22.022,148.043 21.923,146.487 22.310 M308.399 43.013 C 307.702 43.170,306.704 43.305,306.181 43.313 C 305.658 43.321,304.848 43.500,304.382 43.712 C 303.916 43.923,303.156 44.167,302.692 44.253 C 301.885 44.403,299.535 45.069,297.517 45.720 C 296.518 46.042,295.426 46.540,293.514 47.545 C 292.882 47.877,292.216 48.203,292.035 48.269 C 290.977 48.653,285.499 52.278,284.000 53.587 C 282.400 54.984,278.352 59.082,277.941 59.722 C 277.726 60.055,277.265 60.644,276.916 61.030 C 276.567 61.416,275.831 62.414,275.280 63.249 C 274.730 64.083,274.183 64.880,274.065 65.020 C 273.947 65.161,273.851 65.341,273.851 65.421 C 273.851 65.501,273.533 66.052,273.144 66.645 C 272.397 67.784,271.699 69.225,270.880 71.315 C 270.607 72.013,270.288 72.712,270.172 72.869 C 270.056 73.026,269.814 73.594,269.634 74.132 C 269.230 75.343,268.375 75.960,266.837 76.152 C 264.656 76.424,259.843 77.698,258.659 78.316 C 258.356 78.474,257.949 78.603,257.754 78.604 C 257.559 78.605,257.270 78.735,257.111 78.894 C 256.797 79.208,254.829 80.296,254.575 80.296 C 254.438 80.296,253.118 81.167,250.363 83.075 C 246.291 85.895,241.602 91.295,239.291 95.827 C 238.699 96.989,237.986 98.368,237.707 98.891 C 237.429 99.414,237.086 100.269,236.946 100.792 C 236.805 101.315,236.448 102.606,236.152 103.660 C 235.856 104.714,235.474 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96.401,361.699 96.371,361Line truncated

molgenis-opencpu/questions.yml

@@ -0,0 +1,28 @@
+
+categories:
+- MOLGENIS
+questions:
+- variable: ingress.enabled
+  label: Enable ingress
+  default: false
+  description: "Enable ingress"
+  type: boolean
+  required: true
+  group: "Load balancing"
+- variable: opencpu.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: opencpu.image.tag
+  label: Version
+  default: ""
+  description: "Select a OpenCPU version (check the registry.molgenis.org or hub.docker.com for released tags)"
+  type: string
+  required: true
+  group: "Provisioning"

molgenis-opencpu/templates/_helpers.tpl

@@ -2,7 +2,7 @@
 {{/*
 Expand the name of the chart.
 */}}
-{{- define "molgenis.name" -}}
+{{- define "opencpu.name" -}}
 {{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
 {{- end -}}
 
@@ -11,7 +11,7 @@ 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" -}}
+{{- define "opencpu.fullname" -}}
 {{- if .Values.fullnameOverride -}}
 {{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
 {{- else -}}
@@ -27,6 +27,6 @@ If release name contains chart name it will be used as a full name.
 {{/*
 Create chart name and version as used by the chart label.
 */}}
-{{- define "molgenis.chart" -}}
+{{- define "opencpu.chart" -}}
 {{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
 {{- end -}}

molgenis-opencpu/templates/deployment.yaml

@@ -0,0 +1,35 @@
+apiVersion: extensions/v1beta1
+kind: Deployment
+metadata:
+  {{- with .Values.ingress.annotations }}
+  annotations:
+{{ toYaml . | indent 4 }}
+  {{- end }}
+  name: {{ template "opencpu.fullname" . }}
+  labels:
+    app: {{ template "opencpu.name" . }}
+    chart: {{ template "opencpu.chart" . }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  selector:
+    matchLabels:
+      app: {{ template "opencpu.name" . }}
+      release: {{ .Release.Name }}
+  template:
+    metadata:
+      labels:
+        app: {{ template "opencpu.name" . }}
+        release: {{ .Release.Name }}
+    spec:
+      containers:
+      {{- with .Values.opencpu }}
+      - name: {{ .name }}
+        image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
+        imagePullPolicy: {{ .image.pullPolicy }}
+        ports:
+        - containerPort: {{ .service.port }}
+      {{- end }}
+
+

molgenis-opencpu/templates/ingress.yaml

@@ -0,0 +1,36 @@
+{{- if .Values.ingress.enabled }}
+{{- range .Values.ingress.hosts }}
+apiVersion: extensions/v1beta1
+kind: Ingress
+metadata:
+  name: "{{ $.Release.Name }}-ingress"
+  labels:
+    app:  {{ $.Values.opencpu.name }}
+    chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
+    release: "{{ $.Release.Name }}"
+    heritage: "{{ $.Release.Service }}"
+  annotations:
+    {{- if .tls }}
+    ingress.kubernetes.io/secure-backends: "true"
+    {{- end }}
+    {{- range $key, $value := .annotations }}
+    {{ $key }}: {{ $value | quote }}
+    {{- end }}
+spec:
+  rules:
+  - host: {{ .name }}
+    http:
+      paths:
+        - path: {{ default "/" .path }}
+          backend:
+            serviceName: {{ $.Values.opencpu.service.name }}
+            servicePort: {{ $.Values.opencpu.service.port }}
+{{- if .tls }}
+  tls:
+  - hosts:
+    - {{ .name }}
+    secretName: {{ .tlsSecret }}
+{{- end }}
+---
+{{- end }}
+{{- end }}

molgenis-opencpu/templates/service.yaml

@@ -0,0 +1,20 @@
+apiVersion: v1
+kind: Service
+metadata:
+  name: {{ .Values.opencpu.service.name }}
+  labels:
+    app: {{ .Values.opencpu.service.name }}
+    release: {{ .Release.Name }}
+    heritage: {{ .Release.Service }}
+spec:
+  type: {{ .Values.opencpu.service.type }}
+  loadBalancerSourceRanges:
+  {{- range $index, $rule := .Values.opencpu.service.firewall }}
+    - {{ $rule }}
+  {{- end }}
+  ports:
+    - name: {{ .Values.opencpu.service.name }}
+      port: {{ .Values.opencpu.service.port }}
+  selector:
+    app: {{ template "opencpu.name" . }}
+    release: {{ .Release.Name }}

molgenis-opencpu/values.yaml

@@ -0,0 +1,41 @@
+# Default values for nexus.
+# This is a YAML-formatted file.
+# Declare variables to be passed into your templates.
+
+replicaCount: 1
+
+environment: production
+
+opencpu:
+  name: opencpu
+  strategy:
+    type: Recreate
+  restartPolicy: Always
+  image:
+    repository: registry.hub.docker.com
+    name: molgenis/opencpu
+    tag: stable
+    pullPolicy: Always
+  service:
+    name: opencpu
+    type: LoadBalancer
+    port: 8004
+    firewall:
+    - 145.100.224.1/24
+
+ingress:
+  enabled: false
+  annotations: {
+    kubernetes.io/ingress.class: "nginx",
+    nginx.ingress.kubernetes.io/proxy-body-size: "0"
+  }
+  path: /
+  hosts:
+  - name: opencpu.molgenis.org
+  tls: []
+
+nodeSelector: {}
+
+tolerations: []
+
+affinity: {}

molgenis-preview/README.md

@@ -1,16 +0,0 @@
-# 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

@@ -1,61 +0,0 @@
-
-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

@@ -1,19 +0,0 @@
-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/deployment.yaml

@@ -1,124 +0,0 @@
-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

@@ -1,38 +0,0 @@
-{{- 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

@@ -1,17 +0,0 @@
-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

@@ -1,82 +0,0 @@
-# Default values for molgenis.
-
-replicaCount: 1
-
-service:
-  type: LoadBalancer
-  port: 8080
-
-ingress:
-  enabled: true
-  annotations:
-    nginx.ingress.kubernetes.io/proxy-body-size: "0"
-  path: /
-  hosts:
-  - name: test.molgenis.org
-  tls: []
-
-molgenis:
-  image:
-    repository: registry.molgenis.org
-    name: molgenis/molgenis-app
-    tag: 7.0.0-SNAPSHOT
-    pullPolicy: Always
-  adminPassword: admin
-  javaOpts: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
-  resources:
-   limits:
-    cpu: 1
-    memory: 1250Mi
-   requests:
-    cpu: 200m
-    memory: 1Gi
-
-postgres:
-  image:
-    repository: postgres
-    tag: 9.6-alpine
-    pullPolicy: IfNotPresent
-  user: molgenis
-  password: molgenis
-  db: molgenis
-  resources:
-   limits:
-    cpu: 1
-    memory: 250Mi
-   requests:
-    cpu: 100m
-    memory: 250Mi
-
-elasticsearch:
-  image:
-    repository: docker.elastic.co/elasticsearch/elasticsearch
-    tag: 5.5.3
-    pullPolicy: IfNotPresent
-  javaOpts: "-Xms512m -Xmx512m"
-  clusterName: molgenis
-  resources:
-   limits:
-    cpu: 1
-    memory: 1500Mi
-   requests:
-    cpu: 100m
-    memory: 1Gi
-
-opencpu:
-  image:
-    repository: molgenis/opencpu
-    tag: latest
-    pullPolicy: Always
-  resources:
-    limits:
-      cpu: 1
-      memory: 512Mi
-    requests:
-      cpu: 100m
-      memory: 256Mi
-
-nodeSelector: {}
-
-tolerations: []
-
-affinity: {}

molgenis/Chart.yaml

@@ -1,8 +1,8 @@
 apiVersion: v1
 appVersion: "1.0"
 description: MOLGENIS - helm stack (in BETA)
-name: molgenis-beta
+name: molgenis
-version: 0.3.0
+version: 0.4.3
 sources:
 - https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
 icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis/catalogIcon-molgenis.svg

molgenis/README.md

@@ -5,6 +5,8 @@ This chart is used for acceptance and production use cases.
 This chart spins up a MOLGENIS instance with HTTPD. The created containers are:
 
 - MOLGENIS
+- ElasticSearch
+- PostgreSQL **(optional)**
 
 ## Provisioning
 You can choose from which registry you want to pull. There are 2 registries:
@@ -21,6 +23,19 @@ The three properties you need to specify are:
 Besides determining which image you want to pull, you also have to set an administrator password. You can do this by specifying the following property. 
 - ```molgenis.adminPassword```
 
+### Firewall
+Is defined at service level you can specify this attribute in the values:
+
+- ```molgenis.firewall.enabled``` default 'false' 
+
+If set to 'true' the following options are available. One of the options below has to be set.
+
+- ```molgenis.firewall.umcg.enabled``` default 'false'  
+- ```molgenis.firewall.cluster.enabled``` default 'false'
+
+UMCG = only available within the UMCG.
+Cluster = only available within the GCC cluster environment.
+
 ## Services
 When you start MOLGENIS you need:
 - an elasticsearch instance (5.5.6) 
@@ -82,15 +97,16 @@ 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```
+- ```persistence.enabled``` default 'true'
 
 You can also choose to retain the volume of the NFS.
-- ```persistence.retain```
+- ```persistence.retain``` default 'false'
 
 The size and claim name can be specified per service. There are now two services that can be persist.
 
 - MOLGENIS
 - ElasticSearch
+- PostgreSQL **(optional)**
 
 MOLGENIS persistent properties.
 - ```molgenis.persistence.claim```
@@ -100,6 +116,9 @@ ElasticSearch persistent properties.
 - ```elasticsearch.persistence.claim```
 - ```elasticsearch.persistence.size```
 
+PostgreSQL persistent properties.
+- ```postgres.persistence.claim```
+- ```postgres.persistence.size```
 
 ### Resolve you persistent volume
 You do not know which volume is attached to your MOLGENIS instance. You can resolve this by executing:
@@ -117,6 +136,3 @@ You can now view the persistent volume claims and the attached volumes.
 
 You see the ```molgenis-test/molgenis-nfs-claim``` is bound to the volume: ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
 When you want to view the data in the this volume you can go to the nfs-provisioning pod and execute the shell. Go to the directory ```export``` and lookup the directory ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```. 
-
-## Firewall
-Is defined at cluster level. This chart does not facilitate firewall configuration.

molgenis/questions.yml

@@ -8,7 +8,7 @@ questions:
   description: "Hostname for your stack"
   type: hostname
   required: true
-  group: "Load Balancing"
+  group: "Load balancing"
 - variable: molgenis.image.repository
   label: Registry
   default: "registry.hub.docker.com"
@@ -33,6 +33,24 @@ questions:
   type: password
   required: true
   group: "Provisioning"
+- variable: service.firewall.enabled
+  label: Firewall enabled
+  default: false
+  description: "Firewall enabled (can be cluster or UMCG scoped)"
+  type: boolean
+  required: true
+  group: "Provisioning"
+  show_subquestion_if: true
+  subquestions:
+  - variable: service.firewall.kind
+    default: "umcg"
+    description: "Firewall kind. This can be 'umcg' or 'cluster' environment"
+    type: enum
+    required: true
+    options:
+    - umcg
+    - cluster
+    label: Firewall kind
 - variable: molgenis.services.opencpu.host
   label: OpenCPU cluster
   default: "localhost"
@@ -40,28 +58,37 @@ questions:
   type: string
   required: true
   group: "Services"
-- variable: molgenis.services.postgres.host
+- variable: molgenis.services.postgres.embedded
+  label: Postgres embedded
+  default: false
+  description: "Do you want an embedded postgres"
+  type: boolean
+  required: true
+  group: "Services"
+  show_subquestion_if: false
+  subquestions:
+  - variable: molgenis.services.postgres.host
     label: Postgres cluster location
-  default: "postgresql.molgenis-postgresql.svc"
+    default: ""
-  description: "Set the location of the postgres cluster"
+    description: "Set the location of the postgres cluster. This can be localhost when the postgres is enabled else you need to specify a cluster location if you do not want a embedded postgres instance)"
     type: string
     required: true
     group: "Services"
-- variable: molgenis.services.postgres.scheme
+  - 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
+  - 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
+  - variable: molgenis.services.postgres.password
     label: Database password
     default: "molgenis"
     description: "Set the password of the database scheme"
@@ -98,7 +125,7 @@ questions:
   - "2g"
   group: "Resources"
 - variable: persistence.enabled
-  default: false
+  default: true
   description: "Do you want to use persistence"
   type: boolean
   required: true
@@ -112,20 +139,29 @@ questions:
     type: boolean
     label: Retain volume
   - variable: molgenis.persistence.size
-    default: "30Gi"
+    default: "5Gi"
     description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
     type: enum
     options:
-    - "30Gi"
+    - "5Gi"
-    - "50Gi"
+    - "10Gi"
-    - "100Gi"
+    - "20Gi"
     label: Size MOLGENIS filestore
   - variable: elasticsearch.persistence.size
-    default: "50Gi"
+    default: "5Gi"
     description: "Size of ElasticSearch data (directory that is persist: /usr/share/elasticsearch/data)"
     type: enum
     options:
+    - "5Gi"
+    - "10Gi"
     - "50Gi"
-    - "100Gi"
-    - "200Gi"
     label: Size for ElasticSearch data
+  - variable: postgres.persistence.size
+    default: "5Gi"
+    description: "Size of PostgreSQL data (directory that is persist: /var/lib/postgresql/data/pgdata)"
+    type: enum
+    options:
+    - "5Gi"
+    - "10Gi"
+    - "50Gi"
+    label: Size for PostgreSQL data

molgenis/templates/deployment.yaml

@@ -17,6 +17,8 @@ spec:
     matchLabels:
       app: {{ template "molgenis.name" . }}
       release: {{ .Release.Name }}
+  strategy:
+    type: Recreate
   template:
     metadata:
       labels:
@@ -97,11 +99,33 @@ spec:
           - name: elasticsearch-nfs
             mountPath: /usr/share/elasticsearch/data
           {{- end }}
-
           resources:
 {{ toYaml .resources | indent 12 }}
         {{- end }}
 
+        - name: postgres
+        {{- with .Values.postgres }}
+          image: "{{ .image.repository }}:{{ .image.tag }}"
+          imagePullPolicy: {{ .image.pullPolicy }}
+          env:
+            - name: POSTGRES_USER
+              value: {{ $.Values.molgenis.services.postgres.user }}
+            - name: POSTGRES_PASSWORD
+              value: {{ $.Values.molgenis.services.postgres.password }}
+            - name: POSTGRES_DB
+              value: {{ $.Values.molgenis.services.postgres.scheme }}
+          ports:
+            - containerPort: 5432
+          resources:
+{{ toYaml .resources | indent 12 }}
+          {{- if $.Values.persistence.enabled }}
+          volumeMounts:
+          - name: postgres-nfs
+            mountPath: /var/lib/postgresql/data
+          {{- end }}
+        {{- end }}
+
+
 {{- if .Values.persistence.enabled }}
       volumes:
         - name: molgenis-nfs
@@ -110,6 +134,9 @@ spec:
         - name: elasticsearch-nfs
           persistentVolumeClaim:
             claimName: {{ .Values.elasticsearch.persistence.claim }}
+        - name: postgres-nfs
+          persistentVolumeClaim:
+            claimName: {{ .Values.postgres.persistence.claim }}
 {{- end }}
 
     {{- with .Values.nodeSelector }}

molgenis/templates/ingress.yaml

@@ -4,7 +4,7 @@
 apiVersion: extensions/v1beta1
 kind: Ingress
 metadata:
-  name: {{ $fullName }}
+  name: "{{ $.Release.Name }}-ingress"
   labels:
     app: {{ template "molgenis.name" . }}
     chart: {{ template "molgenis.chart" . }}
@@ -33,6 +33,6 @@ spec:
           - path: {{ $ingressPath }}
             backend:
               serviceName: {{ $fullName }}
-              servicePort: 8080
+              servicePort: {{ $.Values.service.port }}
   {{- end }}
 {{- end }}

molgenis/templates/persistence/postgresPVC.yaml

@@ -0,0 +1,21 @@
+{{- if .Values.molgenis.services.postgres.embedded }}
+{{- if .Values.persistence.enabled }}
+apiVersion: extensions/v1beta1
+kind: PersistentVolumeClaim
+apiVersion: v1
+metadata:
+  name: {{ .Values.postgres.persistence.claim }}
+  annotations:
+    {{- if .Values.persistence.retain }}
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
+    {{- else }}
+    volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
+    {{- end }}
+spec:
+  accessModes:
+    - ReadWriteMany
+  resources:
+    requests:
+      storage: {{ .Values.postgres.persistence.size }}
+{{- end }}
+{{- end }}

molgenis/templates/service.yaml

@@ -9,6 +9,18 @@ metadata:
     heritage: {{ .Release.Service }}
 spec:
   type: {{ .Values.service.type }}
+{{- if .Values.service.firewall.enabled }}
+  loadBalancerSourceRanges:
+{{- if .Values.service.firewall.kind eq "umcg" }}
+    {{- range $index, $rule := .Values.service.firewall.umcg.rules }}
+    - {{ $rule }}
+    {{- end }}
+{{- else }}
+    {{- range $index, $rule := .Values.service.firewall.cluster.rules }}
+    - {{ $rule }}
+    {{- end }}
+{{- end }}
+{{- end }}
   ports:
     - name: molgenis
       port: {{ .Values.service.port }}

molgenis/values.yaml

@@ -4,6 +4,15 @@ replicaCount: 1
 
 service:
   type: LoadBalancer
+  firewall:
+    enabled: false
+    kind: "umcg"
+    umcg:
+      rules:
+      - 127.0.0.1/32
+    cluster:
+      rules:
+      - 127.0.0.1/32
   port: 8080
 
 ingress:
@@ -33,7 +42,7 @@ molgenis:
       memory: 1250Mi
   persistence:
     claim: molgenis-nfs-claim
-    size: 30Gi
+    size: 5Gi
   services:
     opencpu:
       host: localhost
@@ -41,6 +50,7 @@ molgenis:
       transportAddresses: localhost:9300
       clusterName: molgenis
     postgres:
+      embedded: false
       host: localhost
       scheme: molgenis
       user: molgenis
@@ -62,10 +72,26 @@ elasticsearch:
     memory: 1Gi
   persistence:
     claim: elasticsearch-nfs-claim
-    size: 50Gi
+    size: 5Gi
+
+postgres:
+  image:
+    repository: postgres
+    tag: 9.6-alpine
+    pullPolicy: IfNotPresent
+  resources:
+    limits:
+      cpu: 1
+      memory: 250Mi
+    requests:
+      cpu: 100m
+      memory: 250Mi
+  persistence:
+    claim: postgres-nfs-claim
+    size: 5Gi
 
 persistence:
-  enabled: false
+  enabled: true
   retain: false
 
 nodeSelector: {