chore (Jenkinsfile): Only deploy if branch is master

This reverts commit f94e6da6e3, reversing
changes made to b73fd578ea.

.gitignore

@@ -1,2 +1,3 @@
 .idea
 *.iml
+target

Jenkinsfile

@@ -0,0 +1,40 @@
+pipeline {
+    agent {
+        kubernetes {
+            label 'helm'
+        }
+    }
+    stages {
+        stage('Test') {
+            steps {
+                container('chart-testing') {
+                    sh "chart_test.sh --no-install --all"
+                }
+            }
+        }
+        stage('Package') {
+            steps {
+                container('chart-testing'){
+                    sh 'mkdir target'
+                    sh 'for dir in charts/*; do helm package --destination target "$dir"; done'
+                }
+            }
+        }
+        stage('Deploy') {
+            when {
+                branch 'master'
+            }
+            steps {
+                container('vault') {
+                    script {
+                        env.NEXUS_USER = sh(script: 'vault read -field=username secret/ops/account/nexus', returnStdout: true)
+                        env.NEXUS_PWD = sh(script: 'vault read -field=password secret/ops/account/nexus', returnStdout: true)
+                    }
+                }
+                container('alpine') {
+                    sh 'set +x; for chart in target/*; do curl -L -u $NEXUS_USER:$NEXUS_PWD http://registry.molgenis.org/repository/helm/ --upload-file "$chart"; done'
+                }
+            }
+        }
+    }
+}

charts/molgenis-httpd/Chart.yaml

@@ -6,3 +6,7 @@ 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
+home: http://httpd.apache.org
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/molgenis-jenkins/Chart.yaml

@@ -1,8 +1,11 @@
 name: molgenis-jenkins
 home: https://jenkins.io/
-version: 0.7.0
-appVersion: 2.121
+version: 0.8.1
+appVersion: 2.138.1
 description: Molgenis installation for the jenkins chart.
 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-jenkins/catalogIcon-molgenis-jenkins.svg
+maintainers:
+- name: fdlk
+- name: sidohaakma

charts/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

charts/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

charts/molgenis-jenkins/resources/README.md

@@ -1,3 +1,5 @@
+# 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

charts/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
-      - blueocean:1.6.2
+      - kubernetes-credentials-provider:0.10
+      - blueocean:1.8.3
       - github-oauth:0.29
       - gogs-webhook:1.0.14
       - github-scm-trait-commit-skip:0.1.1
+      - slack:2.3
     Security:
       UseGitHub: false
       GitHub:
@@ -83,6 +84,17 @@ jenkins:
                   <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>
@@ -132,6 +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">
@@ -185,6 +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">
@@ -238,6 +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">
@@ -291,6 +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">
@@ -344,6 +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">
@@ -516,8 +583,42 @@ jenkins:
               cpu: "1"
               memory: "512Mi"
       NodeSelector: {}
+    helm:
+      Label: helm
+      NodeUsageMode: EXCLUSIVE
+      Containers:
+        chart-testing:
+          Image: "quay.io/helmpack/chart-testing"
+          ImageTag: v1.1.0
+          Command: cat
+          WorkingDir: /home/jenkins
+          TTY: true
+        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: {}
 
-#secret contains configuration for the kubernetes secrets that jenkins can access
+# secret contains configuration for the kubernetes secrets that jenkins can access
 secret:
   # vault configures the vault secret
   vault:

charts/molgenis-nexus/Chart.yaml

@@ -2,7 +2,11 @@ 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
+home: https://www.sonatype.com/nexus-repository-oss
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/molgenis-nexus/README.md

@@ -0,0 +1,69 @@
+# 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-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)
+
+## 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
+
+You can test in install the chart by executing:
+
+```helm lint .```
+
+To test if your helm chart-syntax is right and:
+
+```helm install . --dry-run --debug```
+
+To test if your hem chart works and:
+
+```helm install .```
+
+To deploy it on the cluster.
+
+```curl -L -u xxxx:xxxx http://registry.molgenis.org/repository/helm/ --upload-file molgenis-x.x.x.tgz```
+
+To push it to the registry
+
+
+

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

@@ -0,0 +1,65 @@
+apiVersion: extensions/v1beta1
+kind: Deployment
+metadata:
+  creationTimestamp: null
+  name: {{ .Values.nexus.name }}
+  labels:
+    app: {{ .Values.nexus.name }}
+    environment: {{ .Values.environment }}
+spec:
+  replicas: {{ .Values.replicaCount }}
+  strategy:
+    type: {{ .Values.nexus.strategy.type }}
+  selector:
+    matchLabels:
+      app: {{ .Values.nexus.selector }}
+  template:
+    metadata:
+      labels:
+        app: {{ .Values.nexus.name }}
+      creationTimestamp: null
+    spec:
+      restartPolicy: {{ .Values.nexus.restartPolicy }}
+      initContainers:
+      - name: nexus-nfs
+        image: busybox
+        command: ["sh", "-c", "chown -R 200:200 /nexus-data"]
+        volumeMounts:
+        - name: molgenis-nexus-nfs
+          mountPath: "/nexus-data"
+      containers:
+      - name: {{ .Values.nexus.name }}
+        image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
+        imagePullPolicy: {{ .Values.nexus.image.pullPolicy }}
+        ports:
+        - containerPort: {{ .Values.nexus.port.ui }}
+        - containerPort: {{ .Values.nexus.port.docker }}
+        volumeMounts:
+        - name: molgenis-nexus-nfs
+          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 }}

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

@@ -36,17 +36,17 @@ spec:
           httpGet:
             path: /
             port: {{ .Values.nexusProxy.port }}
-          initialDelaySeconds: 90
-          periodSeconds: 5
+          initialDelaySeconds: 1500
+          periodSeconds: 20
           failureThreshold: 5
           successThreshold: 1
         readinessProbe:
           httpGet:
             path: /
             port: {{ .Values.nexusProxy.port }}
-          initialDelaySeconds: 90
-          periodSeconds: 5
-          failureThreshold: 5
+          initialDelaySeconds: 150
+          periodSeconds: 20
+          failureThreshold: 15
           successThreshold: 1
 
     {{- with .Values.nodeSelector }}

charts/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 }}"

charts/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:
@@ -32,8 +32,8 @@ nexusProxy:
   selector: nexus-proxy
   restartPolicy: Always
   image:
-    repository: registry.webhosting.rug.nl/molgenis/httpd
-    tag: lts
+    repository: molgenis/httpd
+    tag: latest
     pullPolicy: Always
   port: 80
   service:

charts/molgenis-opencpu/Chart.yaml

@@ -6,3 +6,7 @@ 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-opencpu/catalogIcon-molgenis-opencpu.svg
+home: https://www.opencpu.org
+maintainers:
+- name: sidohaakma
+- name: fdlk

charts/molgenis-vault/Chart.yaml

@@ -4,3 +4,7 @@ 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
+home: https://github.com/coreos/vault-operator
+maintainers:
+- name: fdlk
+- name: sidohaakma

charts/molgenis-vault/values.yaml

@@ -70,7 +70,7 @@ ui:
     # limits:
     #  cpu: 100m
     #  memory: 128Mi
-    #requests:
+    # requests:
     #  cpu: 100m
     #  memory: 128Mi
   nodeSelector: {}

charts/molgenis/Chart.yaml

@@ -6,3 +6,7 @@ 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
+home: http://molgenis.org
+maintainers:
+- name: sidohaakma
+- name: fdlk

molgenis-nexus/README.md

@@ -1,28 +0,0 @@
-# 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

@@ -1,58 +0,0 @@
-apiVersion: extensions/v1beta1
-kind: Deployment
-metadata:
-  creationTimestamp: null
-  name: {{ .Values.nexus.name }}
-  labels:
-    app: {{ .Values.nexus.name }}
-    environment: {{ .Values.environment }}
-spec:
-  replicas: {{ .Values.replicaCount }}
-  strategy:
-    type: {{ .Values.nexus.strategy.type }}
-  selector:
-    matchLabels:
-      app: {{ .Values.nexus.selector }}
-  template:
-    metadata:
-      labels:
-        app: {{ .Values.nexus.name }}
-      creationTimestamp: null
-    spec:
-      restartPolicy: {{ .Values.nexus.restartPolicy }}
-      containers:
-        - name: {{ .Values.nexus.name }}
-          image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
-          imagePullPolicy: {{ .Values.nexus.image.pullPolicy }}
-          ports:
-          - containerPort: {{ .Values.nexus.port.ui }}
-          - containerPort: {{ .Values.nexus.port.docker }}
-          volumeMounts:
-          - name: molgenis-nexus-nfs
-            mountPath: "/nexus-data"
-          livenessProbe:
-            httpGet:
-              path: /
-              port: {{ .Values.nexus.port.ui }}
-            initialDelaySeconds: 90
-            periodSeconds: 20
-            failureThreshold: 5
-            successThreshold: 1
-          readinessProbe:
-            httpGet:
-              path: /
-              port: {{ .Values.nexus.port.ui }}
-            initialDelaySeconds: 90
-            periodSeconds: 5
-            failureThreshold: 5
-            successThreshold: 1
-
-      volumes:
-        - name: molgenis-nexus-nfs
-          persistentVolumeClaim:
-            claimName: {{ .Values.persistence.claim }}
-
-    {{- with .Values.nodeSelector }}
-      nodeSelector:
-{{ toYaml . | indent 8 }}
-    {{- end }}