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15 changed files with 77 additions and 2509 deletions

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

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

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@ -65,9 +65,7 @@ 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.NpmToken` | token for npmjs.org | `xxxx` |
| `PipelineSecrets.Env.SauceAccessKey` | token for saucelabs.com | `xxxx` |
| `PipelineSecrets.Env.SonarToken` | token for sonarcloud.io | `xxxx` | |
* File

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@ -32,6 +32,62 @@ 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"/>
@ -160,40 +216,13 @@ data:
<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>{{ .Values.Master.DefaultView }}</primaryView>
<primaryView>All</primaryView>
<slaveAgentPort>50000</slaveAgentPort>
<disabledAgentProtocols>
{{- range .Values.Master.DisabledAgentProtocols }}

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@ -1,16 +0,0 @@
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 }}

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@ -14,5 +14,4 @@ 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 }}

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@ -3,7 +3,7 @@ jenkins:
HostName: jenkins.molgenis.org
ServiceType: ClusterIP
InstallPlugins:
- kubernetes:1.12.0
- kubernetes:1.8.4
- workflow-aggregator:2.5
- workflow-job:2.21
- credentials-binding:1.16
@ -13,22 +13,11 @@ jenkins:
- blueocean:1.6.2
- github-oauth:0.29
- gogs-webhook:1.0.14
- sauce-ondemand:1.176
Security:
UseGitHub: false
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'?>
@ -145,65 +134,11 @@ 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>MAVEN build container with RPMbuild and Curl</description>
<displayName>molgenis-ops-docker-maven</displayName>
<description></description>
<properties>
<org.jenkinsci.plugins.pipeline.modeldefinition.config.FolderConfig plugin="pipeline-model-definition@1.3.1">
<dockerLabel></dockerLabel>
@ -251,112 +186,6 @@ 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,
@ -380,8 +209,6 @@ jenkins:
Containers:
maven:
Image: "registry.webhosting.rug.nl/molgenis/maven"
ImageTag: lts
AlwaysPullImage: true
Command: cat
WorkingDir: /home/jenkins
TTY: true
@ -423,9 +250,13 @@ jenkins:
NodeUsageMode: EXCLUSIVE
Containers:
node:
Image: "registry.webhosting.rug.nl/molgenis/node"
ImageTag: lts
AlwaysPullImage: true
Image: "node"
ImageTag: carbon
Command: cat
WorkingDir: /home/jenkins
TTY: true
alpine:
Image: "spotify/alpine"
Command: cat
WorkingDir: /home/jenkins
TTY: true
@ -441,10 +272,6 @@ 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
@ -522,14 +349,10 @@ 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
@ -569,11 +392,5 @@ 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>

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@ -2,7 +2,7 @@ apiVersion: v1
appVersion: "1.0"
description: Nexus stack for MOLGENIS
name: molgenis-nexus
version: 0.3.0
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-nexus/catalogIcon-molgenis-nexus.svg

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

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@ -1,44 +0,0 @@
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

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

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

View File

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