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molgenis-ops-docker-helm
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base: P129679:2a1e9eacbb88c7dfbfafe920e5dbbfa4b8584d47
Branches Tags
P129679:master
P129679:fix/links
P129679:chore/pipeline
P129679:revert/nodeSelector
P129679:chore/nodeSelector
P129679:chore/jenkins-gitsource
P129679:fix/75
P129679:chore/upgrade-jenkins
P129679:feature/molgenis-it
P129679:feat/helm-in-jenkins
P129679:doc/helm-role
P129679:feature/helm-role
P129679:feature/s3
P129679:chore/remove-secrets
P129679:feature/vault
P129679:deploy-test
..
compare: P129679:5760171c4bd25487c016602aac07b8b62a875dab
Branches Tags
P129679:fix/links
P129679:master
P129679:chore/pipeline
P129679:revert/nodeSelector
P129679:chore/nodeSelector
P129679:chore/jenkins-gitsource
P129679:fix/75
P129679:chore/upgrade-jenkins
P129679:feature/molgenis-it
P129679:feat/helm-in-jenkins
P129679:doc/helm-role
P129679:feature/helm-role
P129679:feature/s3
P129679:chore/remove-secrets
P129679:feature/vault
P129679:deploy-test

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13 changed files with 45 additions and 156 deletions
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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: 0.7.1
version: 0.7.0
appVersion: 2.121
description: Molgenis installation for the jenkins chart.
sources:

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4
molgenis-jenkins/requirements.lock
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@ -1,6 +1,6 @@
dependencies:
- name: jenkins
repository: https://kubernetes-charts.storage.googleapis.com/
version: 0.18.0
version: 0.16.4
digest: sha256:39f694515489598fa545c9a5a4f1347749e8f2a8d7fae6ccae3e2acae1564685
generated: 2018-09-27T11:00:15.795416984+02:00
generated: 2018-06-27T14:36:23.172954738+02:00

76
molgenis-jenkins/values.yaml
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@ -3,17 +3,17 @@ jenkins:
HostName: jenkins.molgenis.org
ServiceType: ClusterIP
InstallPlugins:
- kubernetes:1.12.6
- kubernetes:1.12.0
- workflow-aggregator:2.5
- workflow-job:2.25
- workflow-job:2.21
- credentials-binding:1.16
- git:3.9.1
- github-branch-source:2.3.6
- kubernetes-credentials-provider:0.10
- blueocean:1.8.3
- kubernetes-credentials-provider:0.9
- blueocean:1.6.2
- github-oauth:0.29
- gogs-webhook:1.0.14
- github-scm-trait-commit-skip:0.1.1
- github-scm-trait-commit-skip:0.1.1
Security:
UseGitHub: false
GitHub:
@ -83,17 +83,6 @@ jenkins:
<trust class="org.jenkinsci.plugins.github_branch_source.ForkPullRequestDiscoveryTrait$TrustPermission"/>
</org.jenkinsci.plugins.github__branch__source.ForkPullRequestDiscoveryTrait>
<org.jenkinsci.plugins.scm__filter.GitHubCommitSkipTrait plugin="github-scm-trait-commit-skip@0.1.1"/>
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
<localBranch>**</localBranch>
</extension>
</jenkins.plugins.git.traits.LocalBranchTrait>
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
<name>MOLGENIS Jenkins</name>
<email>molgenis+ci@gmail.com</email>
</extension>
</jenkins.plugins.git.traits.UserIdentityTrait>
</traits>
</org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator>
</navigators>
@ -143,17 +132,6 @@ jenkins:
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
<traits>
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
<localBranch>**</localBranch>
</extension>
</jenkins.plugins.git.traits.LocalBranchTrait>
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
<name>MOLGENIS Jenkins</name>
<email>molgenis+ci@gmail.com</email>
</extension>
</jenkins.plugins.git.traits.UserIdentityTrait>
</traits>
</source>
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@ -207,17 +185,6 @@ jenkins:
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
<traits>
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
<localBranch>**</localBranch>
</extension>
</jenkins.plugins.git.traits.LocalBranchTrait>
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
<name>MOLGENIS Jenkins</name>
<email>molgenis+ci@gmail.com</email>
</extension>
</jenkins.plugins.git.traits.UserIdentityTrait>
</traits>
</source>
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@ -271,17 +238,6 @@ jenkins:
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
<traits>
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
<localBranch>**</localBranch>
</extension>
</jenkins.plugins.git.traits.LocalBranchTrait>
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
<name>MOLGENIS Jenkins</name>
<email>molgenis+ci@gmail.com</email>
</extension>
</jenkins.plugins.git.traits.UserIdentityTrait>
</traits>
</source>
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@ -335,17 +291,6 @@ jenkins:
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
<traits>
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
<localBranch>**</localBranch>
</extension>
</jenkins.plugins.git.traits.LocalBranchTrait>
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
<name>MOLGENIS Jenkins</name>
<email>molgenis+ci@gmail.com</email>
</extension>
</jenkins.plugins.git.traits.UserIdentityTrait>
</traits>
</source>
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
@ -399,17 +344,6 @@ jenkins:
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
<traits>
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
<jenkins.plugins.git.traits.LocalBranchTrait plugin="git@3.9.1">
<extension class="hudson.plugins.git.extensions.impl.LocalBranch">
<localBranch>**</localBranch>
</extension>
</jenkins.plugins.git.traits.LocalBranchTrait>
<jenkins.plugins.git.traits.UserIdentityTrait plugin="git@3.9.1">
<extension class="hudson.plugins.git.extensions.impl.UserIdentity">
<name>MOLGENIS Jenkins</name>
<email>molgenis+ci@gmail.com</email>
</extension>
</jenkins.plugins.git.traits.UserIdentityTrait>
</traits>
</source>
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">

2
molgenis-nexus/Chart.yaml
View File

@ -2,7 +2,7 @@ apiVersion: v1
appVersion: "1.0"
description: Nexus stack for MOLGENIS
name: molgenis-nexus
version: 0.4.2
version: 0.3.0
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

38
molgenis-nexus/README.md
View File

@ -6,44 +6,8 @@ NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
This chart will deploy:
- 1 NEXUS-nfs initialization container
We need this container to avoid permission issues on the NEXUS docker
- 1 NEXUS container
- 1 MOLGENIS-httpd container (to proxy the registry and docker to one domain)
## Backup restore
There are two steps in restoring the NEXUS.
- Database
- Blobstore
### Restore the database
Go to the commandline:
```bash
kubectl get pv
```
```bash
| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-nexus/molgenis-nfs-claim | nfs-provisioner-retain | | | 33d |
| pvc-3984723d-220f-14e8-a98a-skjhf88823kk | 30G | RWO | | Delete | Bound | molgenis-test/molgenis-nfs-claim | nfs-provisioner | | | 33d |
```
The persistent volume is the one in the molgenis-nexus namespace.
Go to the NFS-provisioner to the path of the persistent volume:
```bash
ls -t --full-time | head -7 | xargs cp ../restore-from-backup/
```
### Restore the blobstore
You can copy the directory ```blobs``` to the target persistent volume ```/ blobs```.
You can now bring the NEXUS back up.
- 1 MOLGENIS-httpd container ()to proxy the registry and docker to one domain)
## Installing the Chart

57
molgenis-nexus/templates/deployments/nexus-deployment.yaml
View File

@ -20,39 +20,32 @@ spec:
creationTimestamp: null
spec:
restartPolicy: {{ .Values.nexus.restartPolicy }}
initContainers:
- name: nexus-nfs
image: busybox
command: ["sh", "-c", "chown -R 200:200 /nexus-data"]
volumeMounts:
- name: molgenis-nexus-nfs
mountPath: "/nexus-data"
containers:
- name: {{ .Values.nexus.name }}
image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
imagePullPolicy: {{ .Values.nexus.image.pullPolicy }}
ports:
- containerPort: {{ .Values.nexus.port.ui }}
- containerPort: {{ .Values.nexus.port.docker }}
volumeMounts:
- name: molgenis-nexus-nfs
mountPath: /nexus-data
livenessProbe:
httpGet:
path: /
port: {{ .Values.nexus.port.ui }}
initialDelaySeconds: 120
periodSeconds: 20
failureThreshold: 15
successThreshold: 1
readinessProbe:
httpGet:
path: /
port: {{ .Values.nexus.port.ui }}
initialDelaySeconds: 120
periodSeconds: 20
failureThreshold: 15
successThreshold: 1
- name: {{ .Values.nexus.name }}
image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
imagePullPolicy: {{ .Values.nexus.image.pullPolicy }}
ports:
- containerPort: {{ .Values.nexus.port.ui }}
- containerPort: {{ .Values.nexus.port.docker }}
volumeMounts:
- name: molgenis-nexus-nfs
mountPath: "/nexus-data"
livenessProbe:
httpGet:
path: /
port: {{ .Values.nexus.port.ui }}
initialDelaySeconds: 90
periodSeconds: 20
failureThreshold: 5
successThreshold: 1
readinessProbe:
httpGet:
path: /
port: {{ .Values.nexus.port.ui }}
initialDelaySeconds: 90
periodSeconds: 5
failureThreshold: 5
successThreshold: 1
volumes:
- name: molgenis-nexus-nfs

10
molgenis-nexus/templates/deployments/nexusProxy-deployment.yaml
View File

@ -36,17 +36,17 @@ spec:
httpGet:
path: /
port: {{ .Values.nexusProxy.port }}
initialDelaySeconds: 1500
periodSeconds: 20
initialDelaySeconds: 90
periodSeconds: 5
failureThreshold: 5
successThreshold: 1
readinessProbe:
httpGet:
path: /
port: {{ .Values.nexusProxy.port }}
initialDelaySeconds: 150
periodSeconds: 20
failureThreshold: 15
initialDelaySeconds: 90
periodSeconds: 5
failureThreshold: 5
successThreshold: 1
{{- with .Values.nodeSelector }}

2
molgenis-nexus/templates/ingress.yaml
View File

@ -5,7 +5,7 @@ kind: Ingress
metadata:
name: "{{ $.Release.Name }}-ingress"
labels:
app: {{ $.Values.nexusProxy.name }}
app: httpd
chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
release: "{{ $.Release.Name }}"
heritage: "{{ $.Release.Service }}"

6
molgenis-nexus/values.yaml
View File

@ -13,7 +13,7 @@ nexus:
selector: nexus
restartPolicy: Always
image:
repository: molgenis/nexus3
repository: sonatype/nexus3
tag: latest
pullPolicy: Always
port:
@ -32,8 +32,8 @@ nexusProxy:
selector: nexus-proxy
restartPolicy: Always
image:
repository: molgenis/httpd
tag: latest
repository: registry.webhosting.rug.nl/molgenis/httpd
tag: lts
pullPolicy: Always
port: 80
service:

2
molgenis/Chart.yaml
View File

@ -2,7 +2,7 @@ apiVersion: v1
appVersion: "1.0"
description: MOLGENIS - helm stack (in BETA)
name: molgenis
version: 0.4.3
version: 0.4.2
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/catalogIcon-molgenis.svg

2
molgenis/templates/deployment.yaml
View File

@ -17,8 +17,6 @@ spec:
matchLabels:
app: {{ template "molgenis.name" . }}
release: {{ .Release.Name }}
strategy:
type: Recreate
template:
metadata:
labels: