fix (jenkins) Fix skip verify value in vault secret

Merge branch 'fix-views' of https://git.webhosting.rug.nl/p281392/molgenis-ops-docker-helm into deploy-test
fix (jenkins): Move maven's user.home dir to /home/jenkins so that it gets shared between containers in the molgenis pod
2018-08-19 23:05:53 +02:00 · 2018-08-19 22:40:09 +02:00 · 2018-08-19 13:46:18 +02:00 · 2018-08-18 23:47:57 +02:00 · 2018-08-18 23:40:57 +02:00 · 2018-08-18 23:18:10 +02:00
16 changed files with 2582 additions and 90 deletions
@@ -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
@@ -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:
@@ -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

@@ -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 }}
@@ -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 }}
@@ -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 }}
@@ -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 }}
@@ -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
-      NodeUsageMode: NORMAL
+      Label: molgenisv2
+      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"
-          ImageTag: carbon
-          Command: cat
-          WorkingDir: /home/jenkins
-          TTY: true
-        alpine:
-          Image: "spotify/alpine"
+          Image: "registry.webhosting.rug.nl/molgenis/node"
+          ImageTag: lts
+          AlwaysPullImage: true
          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>
@@ -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
@@ -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
@@ -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
@@ -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" . }}
@@ -27,7 +27,7 @@ spec:
 {{- end }}
  rules:
  {{- range .Values.ingress.hosts }}
-    - host: {{ . }}
+    - host: {{ .name }}
      http:
        paths:
          - path: {{ $ingressPath }}
@@ -8,12 +8,11 @@ service:

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

 molgenis:
Author	SHA1	Message	Date
Fleur Kelpin	f8de505ed6	fix (jenkins) Fix skip verify value in vault secret	2018-08-19 23:05:53 +02:00
Fleur Kelpin	af00229be0	Merge branch 'fix-views' of https://git.webhosting.rug.nl/p281392/molgenis-ops-docker-helm into deploy-test	2018-08-19 22:40:09 +02:00
Fleur Kelpin	e088ad8942	fix (jenkins): Move maven's user.home dir to /home/jenkins so that it gets shared between containers in the molgenis pod	2018-08-19 13:46:18 +02:00
Fleur Kelpin	2fae637eee	feat (jenkins): Create new molgenis pod with vault container and without the secrets. The new pod has label molgenisv2, the legacy one is still labeled molgenis so existing scripts will keep working.	2018-08-18 23:47:57 +02:00
Fleur Kelpin	3a720a8a85	feat (jenkins): Add vault secret	2018-08-18 23:40:57 +02:00
sido	d5ed6e979b	updated views	2018-08-18 23:18:10 +02:00
sido	2d84fb08a8	updated views	2018-08-18 23:12:54 +02:00
sido	44044b59aa	updated views	2018-08-18 23:12:02 +02:00
sido	acbd380a0c	updated plugins	2018-08-18 22:36:05 +02:00
sido	e54f958add	fix views by reorder the views	2018-08-18 22:16:13 +02:00
Fleur Kelpin	764cda4064	Merge branch 'fix/npm-integration' of p281392/molgenis-ops-docker-helm into master	2018-08-18 21:34:23 +02:00
sido	b36759fab2	updated docs and fixed npm integration	2018-08-06 21:44:00 +02:00
S. Haakma	83e9a428d7	Merge branch 'add-npm-token' of p281392/molgenis-ops-docker-helm into master	2018-08-06 20:41:57 +02:00
sido	1215e3edbe	added alpine container	2018-08-06 20:40:51 +02:00
sido	f19b014446	Merge branch 'master' of https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm into add-npm-token	2018-08-06 20:39:13 +02:00
S. Haakma	9443f9a0bb	Merge branch 'add-ops-jobs' of p281392/molgenis-ops-docker-helm into master	2018-08-06 20:38:44 +02:00
S. Haakma	c43bf50180	Merge branch 'master' of p281392/molgenis-ops-docker-helm into master	2018-08-06 20:36:48 +02:00
sido	d76aced730	update version	2018-08-06 20:31:10 +02:00
S. Haakma	4fe58b496b	Merge branch 'feature/add-gogs-settings' of p281392/molgenis-ops-docker-helm into master	2018-08-06 17:13:19 +02:00
S. Haakma	7a54c88da1	Merge branch 'feat/add-saucelabs' of p281392/molgenis-ops-docker-helm into master	2018-08-06 16:55:51 +02:00
sido	01b8893d5b	updated saucelabs user	2018-08-02 22:31:57 +02:00
sido	9c6865336f	added saucelabs cred	2018-08-02 07:49:15 +02:00
sido	59e42a3048	updated node container and removed alpine containers	2018-08-01 22:36:02 +02:00
sido	87951be9c4	added ops jobs for building releases	2018-08-01 22:27:41 +02:00
S. Haakma	b5128bc253	Merge branch 'add-icons' of p281392/molgenis-ops-docker-helm into master	2018-07-30 22:17:28 +02:00
sido	592e93b40d	fixed uppercase	2018-07-30 22:15:37 +02:00
sido	a8a895248b	updated icons for httpd and molgenis preview	2018-07-30 22:13:26 +02:00
S. Haakma	65023d9f2d	Merge branch 'updated-questions' of p281392/molgenis-ops-docker-helm into master	2018-07-30 21:29:28 +02:00
sido	521c92f379	added group	2018-07-30 21:28:51 +02:00
sido	91e38eab6b	merge with blessed	2018-07-30 21:27:46 +02:00
sido	936e1252fd	added Java runtime question	2018-07-30 21:23:13 +02:00
S. Haakma	ec42841aac	Merge branch 'master' of p281392/molgenis-ops-docker-helm into master	2018-07-30 21:09:34 +02:00
sido	c269997fd0	added MOLGENIS resources to questions	2018-07-30 21:08:40 +02:00
sido	a0e11833d2	updated structure	2018-07-30 21:06:03 +02:00
sido	557bcf5354	updated options	2018-07-30 21:05:16 +02:00
sido	f35e8c62c1	updated helm cahrt	2018-07-30 20:56:28 +02:00
sido	c10544c47e	updated questions	2018-07-30 17:52:07 +02:00
S. Haakma	e725951f04	Merge branch 'add-questions' of p281392/molgenis-ops-docker-helm into master	2018-07-30 17:32:40 +02:00
sido	adfd742ecb	add questions and updated post body	2018-07-30 17:23:58 +02:00
S. Haakma	4b2a3a01d9	Merge branch 'fix/max-upload-size' of p281392/molgenis-ops-docker-helm into master	2018-07-30 15:35:19 +02:00
sido	7ff04e01d3	updated proxy body size to nginx	2018-07-30 15:34:10 +02:00
S. Haakma	05708f3885	Merge branch 'fix/max-upload-size' of p281392/molgenis-ops-docker-helm into master	2018-07-30 15:10:47 +02:00
sido	114b0acbfa	set max size to zero	2018-07-30 15:10:07 +02:00
sido	91af7787b0	fix upload large files	2018-07-30 15:08:11 +02:00
sido	6a77c1e688	added sonar token	2018-07-25 08:45:37 +02:00
sido	63a99c2c00	add gogs settings	2018-07-23 22:21:11 +02:00
S. Haakma	37de4f870f	Merge branch 'master' of p281392/molgenis-ops-docker-helm into master	2018-07-20 00:29:09 +02:00
sido	44f0962857	version bump to 0.6.5	2018-07-20 00:27:13 +02:00
Fleur Kelpin	5f04d3d505	Merge branch 'master' of p281392/molgenis-ops-docker-helm into master	2018-07-20 00:20:07 +02:00
sido	dcf6d3d137	make default view configurable	2018-07-20 00:14:25 +02:00
S. Haakma	0afd014bf6	Merge branch 'master' of p281392/molgenis-ops-docker-helm into master	2018-07-20 00:05:41 +02:00
sido	e6523827e3	added keys to jobs	2018-07-20 00:04:46 +02:00
S. Haakma	e436bd27b1	Merge branch 'master' of p281392/molgenis-ops-docker-helm into master	2018-07-19 23:53:17 +02:00
sido	4ebdf6e66a	fix(views): missed curly braces	2018-07-19 23:51:58 +02:00
S. Haakma	60be819212	Merge branch 'master' of p281392/molgenis-ops-docker-helm into master	2018-07-19 23:44:33 +02:00
sido	4482ebef4b	forgot dollar sign	2018-07-19 23:42:39 +02:00
sido	0a85053e15	fix(views): added key and index to loop through array	2018-07-19 23:40:57 +02:00
Fleur Kelpin	4d357aa1d5	Merge branch 'master' of p281392/molgenis-ops-docker-helm into master	2018-07-19 23:30:16 +02:00
sido	b31082c4f4	fix(views): get other key from values to create views	2018-07-19 23:27:38 +02:00
Fleur Kelpin	bc83a4f224	Merge branch 'master' of p281392/molgenis-ops-docker-helm into master	2018-07-19 23:20:59 +02:00
sido	7a262b88c0	bumped version to 0.6.0 (configurable views)	2018-07-19 23:20:10 +02:00
Fleur Kelpin	614b578ecd	Merge branch 'make-views-configurable' of p281392/molgenis-ops-docker-helm into master	2018-07-19 23:18:26 +02:00
sido	586e777f77	Merge branch 'master' of https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm into make-views-configurable	2018-07-19 23:17:33 +02:00
Fleur Kelpin	ef59e83d5c	Merge branch 'master' of p281392/molgenis-ops-docker-helm into master	2018-07-19 23:17:01 +02:00
sido	3499710765	make views confiogurable	2018-07-19 23:15:28 +02:00
S. Haakma	7bcfb04822	Merge branch 'master' of P129679/molgenis-ops-docker-helm into master	2018-07-19 22:53:34 +02:00
sido	4667af0968	updated version to 0.3.0	2018-07-19 22:51:02 +02:00
S. Haakma	0cf23a8d47	Merge branch 'master' of p281392/molgenis-ops-docker-helm into master	2018-07-19 22:46:21 +02:00
sido	2430354e98	bumped version to 0.5.0	2018-07-19 22:40:51 +02:00
S. Haakma	4ad7d69169	Merge branch 'master' of P129679/molgenis-ops-docker-helm into master	2018-07-19 22:40:00 +02:00
S. Haakma	85a46c5196	Merge branch 'version-bump-to-04.0' of p281392/molgenis-ops-docker-helm into master	2018-07-19 22:36:54 +02:00
sido	bc33f83b07	updated version to 0.4.0	2018-07-19 22:25:15 +02:00