From b2dbbc029afc3acea06cedd5b2a8848be172cebf Mon Sep 17 00:00:00 2001
From: Fleur Kelpin <f.kelpin@umcg.nl>
Date: Wed, 27 Jun 2018 16:54:50 +0200
Subject: [PATCH] Add molgenis-maven pod template

---
 molgenis-jenkins/templates/config.tpl | 260 ++++++++++++++++++++++++++
 molgenis-jenkins/values.yaml          |   2 +-
 2 files changed, 261 insertions(+), 1 deletion(-)

diff --git a/molgenis-jenkins/templates/config.tpl b/molgenis-jenkins/templates/config.tpl
index e69de29..998a71d 100644
--- a/molgenis-jenkins/templates/config.tpl
+++ b/molgenis-jenkins/templates/config.tpl
@@ -0,0 +1,260 @@
+{{- define "override_config_map" }}
+apiVersion: v1
+kind: ConfigMap
+metadata:
+  name: {{ template "jenkins.fullname" . }}
+data:
+  config.xml: |-
+    <?xml version='1.0' encoding='UTF-8'?>
+    <hudson>
+      <disabledAdministrativeMonitors/>
+      <version>{{ .Values.Master.ImageTag }}</version>
+      <numExecutors>0</numExecutors>
+      <mode>NORMAL</mode>
+      <useSecurity>{{ .Values.Master.UseSecurity }}</useSecurity>
+      <authorizationStrategy class="hudson.security.FullControlOnceLoggedInAuthorizationStrategy">
+        <denyAnonymousReadAccess>true</denyAnonymousReadAccess>
+      </authorizationStrategy>
+      <securityRealm class="hudson.security.LegacySecurityRealm"/>
+      <disableRememberMe>false</disableRememberMe>
+      <projectNamingStrategy class="jenkins.model.ProjectNamingStrategy$DefaultProjectNamingStrategy"/>
+      <workspaceDir>${JENKINS_HOME}/workspace/${ITEM_FULLNAME}</workspaceDir>
+      <buildsDir>${ITEM_ROOTDIR}/builds</buildsDir>
+      <markupFormatter class="hudson.markup.EscapedMarkupFormatter"/>
+      <jdks/>
+      <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>
+          <templates>
+{{- if .Values.Agent.Enabled }}
+            <org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
+              <inheritFrom></inheritFrom>
+              <name>default</name>
+              <instanceCap>2147483647</instanceCap>
+              <idleMinutes>0</idleMinutes>
+              <label>{{ .Release.Name }}-{{ .Values.Agent.Component }}</label>
+              <nodeSelector>
+                {{- $local := dict "first" true }}
+                {{- range $key, $value := .Values.Agent.NodeSelector }}
+                  {{- if not $local.first }},{{- end }}
+                  {{- $key }}={{ $value }}
+                  {{- $_ := set $local "first" false }}
+                {{- end }}</nodeSelector>
+                <nodeUsageMode>NORMAL</nodeUsageMode>
+              <volumes>
+{{- range $index, $volume := .Values.Agent.volumes }}
+                <org.csanchez.jenkins.plugins.kubernetes.volumes.{{ $volume.type }}Volume>
+{{- range $key, $value := $volume }}{{- if not (eq $key "type") }}
+                  <{{ $key }}>{{ $value }}</{{ $key }}>
+{{- end }}{{- end }}
+                </org.csanchez.jenkins.plugins.kubernetes.volumes.{{ $volume.type }}Volume>
+{{- end }}
+              </volumes>
+              <containers>
+                <org.csanchez.jenkins.plugins.kubernetes.ContainerTemplate>
+                  <name>jnlp</name>
+                  <image>{{ .Values.Agent.Image }}:{{ .Values.Agent.ImageTag }}</image>
+{{- if .Values.Agent.Privileged }}
+                  <privileged>true</privileged>
+{{- else }}
+                  <privileged>false</privileged>
+{{- end }}
+                  <alwaysPullImage>{{ .Values.Agent.AlwaysPullImage }}</alwaysPullImage>
+                  <workingDir>/home/jenkins</workingDir>
+                  <command></command>
+                  <args>${computer.jnlpmac} ${computer.name}</args>
+                  <ttyEnabled>false</ttyEnabled>
+                  <resourceRequestCpu>{{.Values.Agent.Cpu}}</resourceRequestCpu>
+                  <resourceRequestMemory>{{.Values.Agent.Memory}}</resourceRequestMemory>
+                  <resourceLimitCpu>{{.Values.Agent.Cpu}}</resourceLimitCpu>
+                  <resourceLimitMemory>{{.Values.Agent.Memory}}</resourceLimitMemory>
+                  <envVars>
+                    <org.csanchez.jenkins.plugins.kubernetes.ContainerEnvVar>
+                      <key>JENKINS_URL</key>
+                      <value>http://{{ template "jenkins.fullname" . }}:{{.Values.Master.ServicePort}}{{ default "" .Values.Master.JenkinsUriPrefix }}</value>
+                    </org.csanchez.jenkins.plugins.kubernetes.ContainerEnvVar>
+                  </envVars>
+                </org.csanchez.jenkins.plugins.kubernetes.ContainerTemplate>
+              </containers>
+              <envVars/>
+              <annotations/>
+{{- if .Values.Agent.ImagePullSecret }}
+              <imagePullSecrets>
+                <org.csanchez.jenkins.plugins.kubernetes.PodImagePullSecret>
+                  <name>{{ .Values.Agent.ImagePullSecret }}</name>
+                </org.csanchez.jenkins.plugins.kubernetes.PodImagePullSecret>
+              </imagePullSecrets>
+{{- else }}
+              <imagePullSecrets/>
+{{- end }}
+              <nodeProperties/>
+            </org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
+            <org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
+              <inheritFrom></inheritFrom>
+              <name></name>
+              <namespace></namespace>
+              <privileged>false</privileged>
+              <capOnlyOnAlivePods>false</capOnlyOnAlivePods>
+              <alwaysPullImage>false</alwaysPullImage>
+              <instanceCap>2147483647</instanceCap>
+              <slaveConnectTimeout>100</slaveConnectTimeout>
+              <idleMinutes>0</idleMinutes>
+              <activeDeadlineSeconds>0</activeDeadlineSeconds>
+              <label>molgenis-maven</label>
+              <nodeSelector></nodeSelector>
+              <nodeUsageMode>EXCLUSIVE</nodeUsageMode>
+              <customWorkspaceVolumeEnabled>false</customWorkspaceVolumeEnabled>
+              <workspaceVolume class="org.csanchez.jenkins.plugins.kubernetes.volumes.workspace.EmptyDirWorkspaceVolume">
+                <memory>false</memory>
+              </workspaceVolume>
+              <volumes>
+                <org.csanchez.jenkins.plugins.kubernetes.volumes.HostPathVolume>
+                  <mountPath>/var/run/docker.sock</mountPath>
+                  <hostPath>/var/run/docker.sock</hostPath>
+                </org.csanchez.jenkins.plugins.kubernetes.volumes.HostPathVolume>
+              </volumes>
+              <containers>
+                <org.csanchez.jenkins.plugins.kubernetes.ContainerTemplate>
+                  <name>maven</name>
+                  <image>webhost12.service.rug.nl/molgenis/molgenis-maven:latest</image>
+                  <privileged>false</privileged>
+                  <alwaysPullImage>true</alwaysPullImage>
+                  <workingDir>/home/jenkins</workingDir>
+                  <command>/bin/sh -c</command>
+                  <args>cat</args>
+                  <ttyEnabled>true</ttyEnabled>
+                  <resourceRequestCpu></resourceRequestCpu>
+                  <resourceRequestMemory></resourceRequestMemory>
+                  <resourceLimitCpu></resourceLimitCpu>
+                  <resourceLimitMemory></resourceLimitMemory>
+                  <envVars/>
+                  <ports/>
+                  <livenessProbe>
+                    <execArgs></execArgs>
+                    <timeoutSeconds>0</timeoutSeconds>
+                    <initialDelaySeconds>0</initialDelaySeconds>
+                    <failureThreshold>0</failureThreshold>
+                    <periodSeconds>0</periodSeconds>
+                    <successThreshold>0</successThreshold>
+                  </livenessProbe>
+                </org.csanchez.jenkins.plugins.kubernetes.ContainerTemplate>
+              </containers>
+              <envVars/>
+              <annotations/>
+              <imagePullSecrets/>
+              <yaml></yaml>
+            </org.csanchez.jenkins.plugins.kubernetes.PodTemplate>
+{{- end -}}
+          </templates>
+          <serverUrl>https://kubernetes.default</serverUrl>
+          <skipTlsVerify>false</skipTlsVerify>
+          <namespace>{{ .Release.Namespace }}</namespace>
+          <jenkinsUrl>http://{{ template "jenkins.fullname" . }}:{{.Values.Master.ServicePort}}{{ default "" .Values.Master.JenkinsUriPrefix }}</jenkinsUrl>
+          <jenkinsTunnel>{{ template "jenkins.fullname" . }}-agent:50000</jenkinsTunnel>
+          <containerCap>10</containerCap>
+          <retentionTimeout>5</retentionTimeout>
+          <connectTimeout>0</connectTimeout>
+          <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>
+          <filterExecutors>false</filterExecutors>
+          <filterQueue>false</filterQueue>
+          <properties class="hudson.model.View$PropertyList"/>
+        </hudson.model.AllView>
+      </views>
+      <primaryView>All</primaryView>
+      <slaveAgentPort>50000</slaveAgentPort>
+      <disabledAgentProtocols>
+{{- range .Values.Master.DisabledAgentProtocols }}
+        <string>{{ . }}</string>
+{{- end }}
+      </disabledAgentProtocols>
+      <label></label>
+{{- if .Values.Master.CSRF.DefaultCrumbIssuer.Enabled }}
+      <crumbIssuer class="hudson.security.csrf.DefaultCrumbIssuer">
+{{- if .Values.Master.CSRF.DefaultCrumbIssuer.ProxyCompatability }}
+        <excludeClientIPFromCrumb>true</excludeClientIPFromCrumb>
+{{- end }}
+      </crumbIssuer>
+{{- end }}
+      <nodeProperties/>
+      <globalNodeProperties/>
+      <noUsageStatistics>true</noUsageStatistics>
+    </hudson>
+{{- if .Values.Master.ScriptApproval }}
+  scriptapproval.xml: |-
+    <?xml version='1.0' encoding='UTF-8'?>
+    <scriptApproval plugin="script-security@1.27">
+      <approvedScriptHashes/>
+      <approvedSignatures>
+{{- range $key, $val := .Values.Master.ScriptApproval }}
+        <string>{{ $val }}</string>
+{{- end }}
+      </approvedSignatures>
+      <aclApprovedSignatures/>
+      <approvedClasspathEntries/>
+      <pendingScripts/>
+      <pendingSignatures/>
+      <pendingClasspathEntries/>
+    </scriptApproval>
+{{- end }}
+  jenkins.CLI.xml: |-
+    <?xml version='1.1' encoding='UTF-8'?>
+    <jenkins.CLI>
+{{- if .Values.Master.CLI }}
+      <enabled>true</enabled>
+{{- else }}
+      <enabled>false</enabled>
+{{- end }}
+    </jenkins.CLI>
+  apply_config.sh: |-
+    mkdir -p /usr/share/jenkins/ref/secrets/;
+    echo "false" > /usr/share/jenkins/ref/secrets/slave-to-master-security-kill-switch;
+    cp -n /var/jenkins_config/config.xml /var/jenkins_home;
+    cp -n /var/jenkins_config/jenkins.CLI.xml /var/jenkins_home;
+{{- if .Values.Master.InstallPlugins }}
+    # Install missing plugins
+    cp /var/jenkins_config/plugins.txt /var/jenkins_home;
+    rm -rf /usr/share/jenkins/ref/plugins/*.lock
+    /usr/local/bin/install-plugins.sh `echo $(cat /var/jenkins_home/plugins.txt)`;
+    # Copy plugins to shared volume
+    cp -n /usr/share/jenkins/ref/plugins/* /var/jenkins_plugins;
+{{- end }}
+{{- if .Values.Master.ScriptApproval }}
+    cp -n /var/jenkins_config/scriptapproval.xml /var/jenkins_home/scriptApproval.xml;
+{{- end }}
+{{- if .Values.Master.InitScripts }}
+    mkdir -p /var/jenkins_home/init.groovy.d/;
+    cp -n /var/jenkins_config/*.groovy /var/jenkins_home/init.groovy.d/
+{{- end }}
+{{- if .Values.Master.CredentialsXmlSecret }}
+    cp -n /var/jenkins_credentials/credentials.xml /var/jenkins_home;
+{{- end }}
+{{- if .Values.Master.SecretsFilesSecret }}
+    cp -n /var/jenkins_secrets/* /usr/share/jenkins/ref/secrets;
+{{- end }}
+{{- if .Values.Master.Jobs }}
+    for job in $(ls /var/jenkins_jobs); do
+      mkdir -p /var/jenkins_home/jobs/$job
+      cp -n /var/jenkins_jobs/$job /var/jenkins_home/jobs/$job/config.xml
+    done
+{{- end }}
+{{- range $key, $val := .Values.Master.InitScripts }}
+  init{{ $key }}.groovy: |-
+{{ $val | indent 4 }}
+{{- end }}
+  plugins.txt: |-
+{{- if .Values.Master.InstallPlugins }}
+{{- range $index, $val := .Values.Master.InstallPlugins }}
+{{ $val | indent 4 }}
+{{- end }}
+{{- end }}
+{{- end }}
\ No newline at end of file
diff --git a/molgenis-jenkins/values.yaml b/molgenis-jenkins/values.yaml
index cd770cc..02af41a 100644
--- a/molgenis-jenkins/values.yaml
+++ b/molgenis-jenkins/values.yaml
@@ -67,6 +67,6 @@ jenkins:
     # useful to manage encryption keys used for credentials.xml for instance (such as
     # master.key and hudson.util.Secret)
     # SecretsFilesSecret: jenkins-secrets
-    CustomConfigMap: false
+    CustomConfigMap: true
   rbac:
     install: true
\ No newline at end of file