P129679/molgenis-ops-docker-helm
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Merge branch 'master' of https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm into add-npm-token

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sido 2018-08-06 20:39:13 +02:00
commit f19b014446
11 changed files with 2457 additions and 10 deletions
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5
molgenis-httpd/Chart.yaml
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@ -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

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2
molgenis-jenkins/Chart.yaml
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@ -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:

16
molgenis-jenkins/templates/molgenis-jenkins-saucelabs-secret.yaml Normal file
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@ -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 }}

176
molgenis-jenkins/values.yaml
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@ -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>

5
molgenis-preview/Chart.yaml
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@ -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

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molgenis-preview/questions.yml Normal file
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@ -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

4
molgenis-preview/templates/deployment.yaml
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@ -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" . }}

2
molgenis-preview/templates/ingress.yaml
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@ -27,7 +27,7 @@ spec:
{{- end }}
rules:
{{- range .Values.ingress.hosts }}
- host: {{ . }}
- host: {{ .name }}
http:
paths:
- path: {{ $ingressPath }}

7
molgenis-preview/values.yaml
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@ -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: