From 28efad8cb83edbb382e3536a0ad6ed927f26ed54 Mon Sep 17 00:00:00 2001
From: sido <sido@haakma.org>
Date: Fri, 29 Jun 2018 23:30:38 +0200
Subject: [PATCH 1/7] add gogs secrets

---
 .../templates/molgenis-jenkins-gogs-secret.yaml  | 16 ++++++++++++++++
 molgenis-jenkins/values.yaml                     |  2 ++
 2 files changed, 18 insertions(+)
 create mode 100644 molgenis-jenkins/templates/molgenis-jenkins-gogs-secret.yaml

diff --git a/molgenis-jenkins/templates/molgenis-jenkins-gogs-secret.yaml b/molgenis-jenkins/templates/molgenis-jenkins-gogs-secret.yaml
new file mode 100644
index 0000000..a16303d
--- /dev/null
+++ b/molgenis-jenkins/templates/molgenis-jenkins-gogs-secret.yaml
@@ -0,0 +1,16 @@
+apiVersion: v1
+kind: Secret
+metadata:
+# this is the jenkins id.
+  name: "molgenis-jenkins-gogs-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 GOGS (git.webhosting.rug.nl)"
+  }
+type: Opaque
+data:
+  username: {{ "p281392" | b64enc | quote }}
+  password: {{ .Values.PipelineSecrets.Env.GogsToken | b64enc | quote }}
\ No newline at end of file
diff --git a/molgenis-jenkins/values.yaml b/molgenis-jenkins/values.yaml
index 7d054ad..fb08713 100644
--- a/molgenis-jenkins/values.yaml
+++ b/molgenis-jenkins/values.yaml
@@ -164,6 +164,8 @@ PipelineSecrets:
     CodecovToken: xxxx
     # Token for github bot account
     GitHubToken: xxxx
+    # Token for github bot account
+    GogsToken: xxxx
     # Token for sonarcloud.io
     SonarToken: xxxx
   File:

From 62114aecc42578f19db8b9907d89f51bef2f25a4 Mon Sep 17 00:00:00 2001
From: Fleur Kelpin <f.kelpin@umcg.nl>
Date: Fri, 29 Jun 2018 23:31:08 +0200
Subject: [PATCH 2/7] Increase container cap

---
 molgenis-jenkins/templates/config.tpl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/molgenis-jenkins/templates/config.tpl b/molgenis-jenkins/templates/config.tpl
index dd504b8..162cff5 100644
--- a/molgenis-jenkins/templates/config.tpl
+++ b/molgenis-jenkins/templates/config.tpl
@@ -129,7 +129,7 @@ data:
           <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>
+          <containerCap>50</containerCap>
           <retentionTimeout>5</retentionTimeout>
           <connectTimeout>0</connectTimeout>
           <readTimeout>0</readTimeout>

From 633863e7f7b4e5a091552b037067723fc979d476 Mon Sep 17 00:00:00 2001
From: Fleur Kelpin <f.kelpin@umcg.nl>
Date: Fri, 29 Jun 2018 23:37:47 +0200
Subject: [PATCH 3/7] Fix cat and tty

---
 molgenis-jenkins/templates/config.tpl | 2 +-
 molgenis-jenkins/values.yaml          | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/molgenis-jenkins/templates/config.tpl b/molgenis-jenkins/templates/config.tpl
index 162cff5..570ce05 100644
--- a/molgenis-jenkins/templates/config.tpl
+++ b/molgenis-jenkins/templates/config.tpl
@@ -77,7 +77,7 @@ data:
                   <alwaysPullImage>false</alwaysPullImage>
 {{- end }}
                   <workingDir>/home/jenkins</workingDir>
-                  <command>{{ .Command | default "cat" }}</command>
+                  <command>{{ .Command | default "" }}</command>
                   <args>{{ .Args | default "" }}</args>
 {{- if .TTY }}
                   <ttyEnabled>true</ttyEnabled>
diff --git a/molgenis-jenkins/values.yaml b/molgenis-jenkins/values.yaml
index 7d054ad..19699bc 100644
--- a/molgenis-jenkins/values.yaml
+++ b/molgenis-jenkins/values.yaml
@@ -97,6 +97,7 @@ jenkins:
       Containers:
         maven:
           Image: "registry.webhosting.rug.nl/molgenis/maven"
+          Command: cat
           TTY: true
           resources:
             requests:
@@ -105,11 +106,11 @@ jenkins:
               memory: "1Gi"
         alpine:
           Image: "spotify/alpine"
+          Command: cat
           TTY: true
         elasticsearch:
           Image: "elasticsearch"
           ImageTag: "5.5.1"
-          TTY: true
           Ports:
             - name: rest
               containerPort: "9200"
@@ -120,7 +121,6 @@ jenkins:
         postgres:
           Image: "postgres"
           ImageTag: "9.6-alpine"
-          TTY: true
           Ports:
             - name: postgres
               containerPort: "5432"

From 52c64e6d293c9d1d5d350dd44d6cf05079a48043 Mon Sep 17 00:00:00 2001
From: Fleur Kelpin <f.kelpin@umcg.nl>
Date: Fri, 29 Jun 2018 23:44:50 +0200
Subject: [PATCH 4/7] Fine tune the jenkins config

---
 molgenis-jenkins/values.yaml | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/molgenis-jenkins/values.yaml b/molgenis-jenkins/values.yaml
index 19699bc..5147465 100644
--- a/molgenis-jenkins/values.yaml
+++ b/molgenis-jenkins/values.yaml
@@ -99,11 +99,6 @@ jenkins:
           Image: "registry.webhosting.rug.nl/molgenis/maven"
           Command: cat
           TTY: true
-          resources:
-            requests:
-              cpu: "1000m"
-            limits:
-              memory: "1Gi"
         alpine:
           Image: "spotify/alpine"
           Command: cat

From 00a2032aea6dfd539c023e4b301525c43c9a3983 Mon Sep 17 00:00:00 2001
From: Fleur Kelpin <f.kelpin@umcg.nl>
Date: Sat, 30 Jun 2018 17:14:20 +0200
Subject: [PATCH 5/7] Add operations jobs

---
 molgenis-jenkins/values.yaml | 105 +++++++++++++++++++++++++++++++++++
 1 file changed, 105 insertions(+)

diff --git a/molgenis-jenkins/values.yaml b/molgenis-jenkins/values.yaml
index 27d3cd8..ad480f3 100644
--- a/molgenis-jenkins/values.yaml
+++ b/molgenis-jenkins/values.yaml
@@ -74,6 +74,111 @@ jenkins:
           </projectFactories>
           <buildStrategies/>
         </jenkins.branch.OrganizationFolder>
+      molgenis-operations: |-
+        <?xml version='1.1' encoding='UTF-8'?>
+        <org.jenkinsci.plugins.workflow.multibranch.WorkflowMultiBranchProject plugin="workflow-multibranch@2.19">
+          <actions/>
+          <description>HTTPD server that can be used for redirection and proxieing</description>
+          <displayName>molgenis-ops-docker-httpd</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-httpd.git</remote>
+                  <credentialsId>molgenis-jenkins-github-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>
+          <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-docker-maven.git</remote>
+                  <credentialsId></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,

From 4cfb7d9d26a609679c49d94f4cc129072fefc24c Mon Sep 17 00:00:00 2001
From: Fleur Kelpin <f.kelpin@umcg.nl>
Date: Sat, 30 Jun 2018 21:25:49 +0200
Subject: [PATCH 6/7] Fix nexus yarn/npm config.

---
 molgenis-jenkins/values.yaml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/molgenis-jenkins/values.yaml b/molgenis-jenkins/values.yaml
index ad480f3..ab308b9 100644
--- a/molgenis-jenkins/values.yaml
+++ b/molgenis-jenkins/values.yaml
@@ -235,10 +235,7 @@ jenkins:
           value: "keyfile:/root/.m2/key.asc"
         - type: KeyValue
           key: npm_config_registry
-          value: "http://nexus.molgenis-nexus:8081/repository/npm-central"
-        - type: KeyValue
-          key: yarn_proxy
-          value: "http://nexus.molgenis-nexus:8081/repository/npm-central"
+          value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
         - type: Secret
           key: SONAR_TOKEN
           secretName: molgenis-pipeline-env-secret

From 9711660fc4298c27fcc25e3225c4685956a1436f Mon Sep 17 00:00:00 2001
From: Fleur Kelpin <f.kelpin@umcg.nl>
Date: Sun, 1 Jul 2018 00:32:47 +0200
Subject: [PATCH 7/7] containerPort alone is enough, hostPort makes it exposed
 on the host node

---
 molgenis-jenkins/values.yaml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/molgenis-jenkins/values.yaml b/molgenis-jenkins/values.yaml
index ab308b9..8704f5d 100644
--- a/molgenis-jenkins/values.yaml
+++ b/molgenis-jenkins/values.yaml
@@ -214,17 +214,14 @@ jenkins:
           Ports:
             - name: rest
               containerPort: "9200"
-              hostPort: "9200"
             - name: api
               containerPort: "9300"
-              hostPort: "9300"
         postgres:
           Image: "postgres"
           ImageTag: "9.6-alpine"
           Ports:
             - name: postgres
               containerPort: "5432"
-              hostPort: "5432"
       EnvVars:
         - type: Secret
           key: PGP_PASSPHRASE