fix (jenkins) Fix skip verify value in vault secret

The new pod has label molgenisv2, the legacy one is still labeled molgenis so existing scripts will keep working.

molgenis-httpd/Chart.yaml

@@ -2,4 +2,7 @@ apiVersion: v1
 appVersion: "1.0"
 description: HTTPD for MOLGENIS
 name: molgenis-httpd
-version: 0.1.0
+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-jenkins/Chart.yaml

@@ -1,6 +1,6 @@
 name: molgenis-jenkins
 home: https://jenkins.io/
-version: 0.3.2
+version: 0.7.0
 appVersion: 2.121
 description: Molgenis installation for the jenkins chart.
 sources:

molgenis-jenkins/README.md

@@ -52,6 +52,17 @@ There is one additional group of configuration items specific for this chart, so
    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
+
+   New vault token to be used by the pods to retrieve their tokens from the vault.
+   
+   | Parameter                         | Description                                | Default                                       |
+   | ----------------------------------|--------------------------------------------|-----------------------------------------------|
+   | `PipelineSecrets.Vault.Replace`   | Replace the molgenis-pipeline-vault secret |`true`                                         |
+   | `PipelineSecrets.Vault.Token`     | Token to log into the hashicorp vault      |`xxxx`                                         |
+   | `PipelineSecrets.Vault.Addr`      | Address of the vault                       |`https:vault-operator.vault-operator.svc:8200` |
+   | `PipelineSecrets.Vault.skipVerify`| Skip verification of the https connection  |`1`                                            |
+
 *  Env
    
    Environment variables stored in molgenis-pipeline-env secret, to be added as environment variables
@@ -65,7 +76,9 @@ There is one additional group of configuration items specific for this chart, so
    | `PipelineSecrets.Env.GitHubToken`      | token for GH molgenis-jenkins user        | `xxxx`          |
    | `PipelineSecrets.Env.NexusPassword`    | token for molgenis-jenkins user in NEXUS  | `xxxx`          |
    | `PipelineSecrets.Env.DockerHubPassword`| token for molgenis user in hub.docker.com | `xxxx`          |
-   | `PipelineSecrets.Env.SonarToken`       | token for sonarcloud.io                   | `xxxx`          |                                                            |
+   | `PipelineSecrets.Env.SonarToken`       | token for sonarcloud.io                   | `xxxx`          |
+   | `PipelineSecrets.Env.NpmToken`         | token for npmjs.org                       | `xxxx`          | 
+   | `PipelineSecrets.Env.SauceAccessKey`   | token for saucelabs.com                   | `xxxx`          |
 
 * File
 

molgenis-jenkins/templates/config.tpl

@@ -32,65 +32,6 @@ data:
       <buildsDir>${ITEM_ROOTDIR}/builds</buildsDir>
       <markupFormatter class="hudson.markup.EscapedMarkupFormatter"/>
       <jdks/>
-      <views>
-        <hudson.model.AllView>
-          <owner class="hudson" reference="../../.."/>
-          <name>all</name>
-          <filterExecutors>false</filterExecutors>
-          <filterQueue>false</filterQueue>
-          <properties class="hudson.model.View$PropertyList"/>
-        </hudson.model.AllView>
-        <listView>
-          <owner class="hudson" reference="../../.."/>
-          <name>ops</name>
-          <filterExecutors>false</filterExecutors>
-          <filterQueue>false</filterQueue>
-          <properties class="hudson.model.View$PropertyList"/>
-          <jobNames>
-            <comparator class="hudson.util.CaseInsensitiveComparator"/>
-            <string>molgenis-ops-docker-httpd</string>
-            <string>molgenis-ops-docker-maven</string>
-          </jobNames>
-          <jobFilters/>
-          <columns>
-            <hudson.views.StatusColumn/>
-            <hudson.views.WeatherColumn/>
-            <hudson.views.JobColumn/>
-            <hudson.views.LastSuccessColumn/>
-            <hudson.views.LastFailureColumn/>
-            <hudson.views.LastDurationColumn/>
-            <hudson.views.BuildButtonColumn/>
-            <hudson.plugins.favorite.column.FavoriteColumn plugin="favorite@2.3.2"/>
-          </columns>
-          <recurse>false</recurse>
-        </listView>
-        <listView>
-          <owner class="hudson" reference="../../.."/>
-          <name>dev</name>
-          <filterExecutors>false</filterExecutors>
-          <filterQueue>false</filterQueue>
-          <properties class="hudson.model.View$PropertyList"/>
-          <jobNames>
-            <comparator class="hudson.util.CaseInsensitiveComparator" reference="../../../listView/jobNames/comparator"/>
-            <string>molgenis</string>
-          </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>
-      </views>
-      <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>
@@ -211,18 +152,45 @@ data:
           <readTimeout>0</readTimeout>
         </org.csanchez.jenkins.plugins.kubernetes.KubernetesCloud>
       </clouds>
-      <quietPeriod>5</quietPeriod>
-      <scmCheckoutRetryCount>0</scmCheckoutRetryCount>
       <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>
+      <quietPeriod>5</quietPeriod>
+      <scmCheckoutRetryCount>0</scmCheckoutRetryCount>
       <slaveAgentPort>50000</slaveAgentPort>
       <disabledAgentProtocols>
 {{- range .Values.Master.DisabledAgentProtocols }}

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

@@ -0,0 +1,16 @@
+apiVersion: v1
+kind: Secret
+metadata:
+# this is the jenkins id.
+  name: "molgenis-jenkins-saucelabs-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" : "user to authenticate against Saucelabs (saucelabs.com)"
+  }
+type: Opaque
+data:
+  username: {{ "molgenis-jenkins" | b64enc | quote }}
+  password: {{ .Values.PipelineSecrets.Env.SauceAccessKey | b64enc | quote }}

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

@@ -14,4 +14,5 @@ data:
   codecovToken: {{ .Values.PipelineSecrets.Env.CodecovToken | b64enc | quote }}
   githubToken: {{ .Values.PipelineSecrets.Env.GitHubToken | b64enc | quote }}
   sonarToken: {{ .Values.PipelineSecrets.Env.SonarToken | b64enc | quote }}
+  npmToken: {{ .Values.PipelineSecrets.Env.NpmToken | b64enc | quote }}
 {{- end }}

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

@@ -0,0 +1,16 @@
+{{- if .Values.PipelineSecrets.Vault.Replace }}
+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.PipelineSecrets.Vault.Token | b64enc | quote }}
+  addr: {{ .Values.PipelineSecrets.Vault.Addr | b64enc | quote }}
+  skipVerify: {{ .Values.PipelineSecrets.Vault.SkipVerify | b64enc | quote }}
+{{- end }}

molgenis-jenkins/values.yaml

@@ -3,14 +3,14 @@ jenkins:
     HostName: jenkins.molgenis.org
     ServiceType: ClusterIP
     InstallPlugins:
-      - kubernetes:1.8.4
+      - kubernetes:1.12.3
       - workflow-aggregator:2.5
-      - workflow-job:2.21
+      - workflow-job:2.24
       - credentials-binding:1.16
       - git:3.9.1
       - github-branch-source:2.3.6
       - kubernetes-credentials-provider:0.9
-      - blueocean:1.6.2
+      - blueocean:1.8.2
       - github-oauth:0.29
       - gogs-webhook:1.0.14
     Security:
@@ -18,6 +18,16 @@ jenkins:
       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'?>
@@ -134,11 +144,65 @@ jenkins:
             <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></description>
+          <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>
@@ -186,6 +250,112 @@ jenkins:
             <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
     # Kubernetes secret that contains files to be put in the Jenkins 'secrets' directory,
@@ -197,18 +367,17 @@ jenkins:
     install: true
   Pods:
     molgenis:
-      Label: molgenis
+      Label: molgenisv2
-      NodeUsageMode: NORMAL
+      NodeUsageMode: EXCLUSIVE
       volumes:
         - type: HostPath
           hostPath: "/var/run/docker.sock"
           mountPath: "/var/run/docker.sock"
-        - type: Secret
-          secretName: molgenis-pipeline-file-secret
-          mountPath: "/root/.m2"
       Containers:
         maven:
           Image: "registry.webhosting.rug.nl/molgenis/maven"
+          ImageTag: lts
+          AlwaysPullImage: true
           Command: cat
           WorkingDir: /home/jenkins
           TTY: true
@@ -216,11 +385,46 @@ jenkins:
             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: {}
+    molgenis-legacy:
+      InheritFrom: molgenis
+      Label: molgenis
+      NodeUsageMode: NORMAL
+      volumes:
+        - type: Secret
+          secretName: molgenis-pipeline-file-secret
+          mountPath: "/home/jenkins/.m2"
+      Containers:
       EnvVars:
         - type: Secret
           key: PGP_PASSPHRASE
@@ -228,7 +432,7 @@ jenkins:
           secretKey: pgpPassphrase
         - type: KeyValue
           key: PGP_SECRETKEY
-          value: "keyfile:/root/.m2/key.asc"
+          value: "keyfile:/home.jenkins/.m2/key.asc"
         - type: KeyValue
           key: npm_config_registry
           value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
@@ -250,13 +454,9 @@ jenkins:
       NodeUsageMode: EXCLUSIVE
       Containers:
         node:
-          Image: "node"
+          Image: "registry.webhosting.rug.nl/molgenis/node"
-          ImageTag: carbon
+          ImageTag: lts
-          Command: cat
+          AlwaysPullImage: true
-          WorkingDir: /home/jenkins
-          TTY: true
-        alpine:
-          Image: "spotify/alpine"
           Command: cat
           WorkingDir: /home/jenkins
           TTY: true
@@ -272,6 +472,10 @@ jenkins:
           key: GITHUB_TOKEN
           secretName: molgenis-pipeline-env-secret
           secretKey: githubToken
+        - type: Secret
+          key: NPM_TOKEN
+          secretName: molgenis-pipeline-env-secret
+          secretKey: npmToken
       NodeSelector: {}
     molgenis-it:
       InheritFrom: molgenis
@@ -336,6 +540,11 @@ jenkins:
               memory: "512Mi"
       NodeSelector: {}
 PipelineSecrets:
+  Vault:
+    Replace: true
+    Token: xxxx
+    Addr: "https://vault-operator.vault-operator.svc:8200"
+    SkipVerify: 1
   Env:
     # Set to false to keep existing secret
     Replace: true
@@ -349,10 +558,14 @@ PipelineSecrets:
     GogsToken: xxxx
     # Token for sonarcloud.io
     SonarToken: xxxx
+    # Token for npmjs.org
+    NpmToken: xxxx
     # Password Local NEXUS
     NexusPassword: xxxx
     # Password hub.docker.com
     DockerHubPassword: xxxx
+    # Access key for saucelabs.com
+    SauceAccessKey: xxxx
   File:
     # Set to false to keep existing secret
     Replace: true
@@ -392,5 +605,11 @@ PipelineSecrets:
             <username>admin</username>
             <password>xxxx</password>
           </server>
+          <!-- to authenticate against GOGS for MAVEN release -->
+          <server>
+            <id>gogs</id>
+            <username>xxxx</username>
+            <password>xxxx</password>
+          </server>
         </servers>
       </settings>

molgenis-nexus/Chart.yaml

@@ -2,7 +2,7 @@ apiVersion: v1
 appVersion: "1.0"
 description: Nexus stack for MOLGENIS
 name: molgenis-nexus
-version: 0.2.0
+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-preview/Chart.yaml

@@ -2,4 +2,7 @@ apiVersion: v1
 appVersion: "1.0"
 description: A Helm chart for Kubernetes
 name: molgenis
-version: 0.1.0
+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/questions.yml

@@ -0,0 +1,44 @@
+
+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.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/deployment.yaml

@@ -1,6 +1,10 @@
 apiVersion: apps/v1beta2
 kind: Deployment
 metadata:
+  {{- with .Values.ingress.annotations }}
+  annotations:
+{{ toYaml . | indent 4 }}
+  {{- end }}
   name: {{ template "molgenis.fullname" . }}
   labels:
     app: {{ template "molgenis.name" . }}

molgenis-preview/templates/ingress.yaml

@@ -27,7 +27,7 @@ spec:
 {{- end }}
   rules:
   {{- range .Values.ingress.hosts }}
-    - host: {{ . }}
+    - host: {{ .name }}
       http:
         paths:
           - path: {{ $ingressPath }}

molgenis-preview/values.yaml

@@ -8,12 +8,11 @@ service:
 
 ingress:
   enabled: true
-  annotations: {}
+  annotations:
-    # kubernetes.io/ingress.class: nginx
+    nginx.ingress.kubernetes.io/proxy-body-size: "0"
-    # kubernetes.io/tls-acme: "true"
   path: /
   hosts:
-    - test.molgenis.org
+  - name: test.molgenis.org
   tls: []
 
 molgenis: