Merge branch 'master' of https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm into add-npm-token

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: 0.6.5
+version: 0.7.0
 appVersion: 2.121
 description: Molgenis installation for the jenkins chart.
 sources:

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/values.yaml

@@ -3,7 +3,7 @@ jenkins:
     HostName: jenkins.molgenis.org
     ServiceType: ClusterIP
     InstallPlugins:
-      - kubernetes:1.8.4
+      - kubernetes:1.12.0
       - workflow-aggregator:2.5
       - workflow-job:2.21
       - credentials-binding:1.16
@@ -13,6 +13,7 @@ jenkins:
       - blueocean:1.6.2
       - github-oauth:0.29
       - gogs-webhook:1.0.14
+      - sauce-ondemand:1.176
     Security:
       UseGitHub: false
       GitHub:
@@ -25,6 +26,9 @@ jenkins:
       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'?>
@@ -141,11 +145,65 @@ 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>
@@ -193,6 +251,112 @@ 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,
@@ -359,6 +523,8 @@ PipelineSecrets:
     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
@@ -398,5 +564,11 @@ 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-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: