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revert/nod
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33d8a30c69
| Author | SHA1 | Date | |
|---|---|---|---|
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33d8a30c69 |
21
README.md
21
README.md
@@ -104,7 +104,6 @@ This repository is serves also as a catalogue for Rancher. We have serveral apps
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- [Jenkins](molgenis-jenkins/README.md)
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- [Jenkins](molgenis-jenkins/README.md)
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- [NEXUS](molgenis-nexus/README.md)
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- [NEXUS](molgenis-nexus/README.md)
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- [HTTPD](molgenis-httpd/README.md)
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- [HTTPD](molgenis-httpd/README.md)
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- [MOLGENIS](molgenis/README.md)
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- [MOLGENIS preview](molgenis-preview/README.md)
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- [MOLGENIS preview](molgenis-preview/README.md)
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- [MOLGENIS vault](molgenis-vault/README.md)
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- [MOLGENIS vault](molgenis-vault/README.md)
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@@ -123,26 +122,6 @@ You can you need to know to easily develop and deploy helm-charts
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Do it in the root of the project where the Chart.yaml is located
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Do it in the root of the project where the Chart.yaml is located
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It installs a release of a kubernetes stack. You also store this as an artifact in a kubernetes repository
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It installs a release of a kubernetes stack. You also store this as an artifact in a kubernetes repository
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- ```helm package .```
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You can create a package which can be uploaded in the molgenis helm repository
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- ```helm publish```
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You still have to create an ```index.yaml``` for the chart. You can do this by executing this command: ```helm repo index #directory name of helm chart#```
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Then you can upload it by executing:
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- ```curl -v --user #username#:#password# --upload-file index.yaml https://registry.molgenis.org/repository/helm/#chart name#/index.yml```
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- ```curl -v --user #username#:#password# --upload-file #chart name#-#version#.tgz https://registry.molgenis.org/repository/helm/#chart name#/#chart name#-#version#.tgz```
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Now you have to add the repository locally to use in your ```requirements.yaml```.
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- ```helm repo add #repository name# https://registry.molgenis.org/repository/helm/molgenis```
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- ```helm dep build```
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You can build your dependencies (create a ```charts``` directory and install the chart in it) of the helm-chart.
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- ```helm list```
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- ```helm list```
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Lists all installed releases
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Lists all installed releases
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16
charts/index.yaml
Executable file
16
charts/index.yaml
Executable file
@@ -0,0 +1,16 @@
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apiVersion: v1
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entries:
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molgenis-preview:
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- apiVersion: v1
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appVersion: "1.0"
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created: 2018-09-11T16:11:49.165533266+02:00
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description: MOLGENIS - helm stack for testing purposes
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digest: e1174bd0d8a71bf4d23f5463521cf4dbcac39dc93f16cd842c92cda1a963f6b2
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icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-preview/catalogIcon-molgenis.svg
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name: molgenis-preview
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sources:
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- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
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urls:
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- molgenis-preview-0.2.0.tgz
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version: 0.2.0
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generated: 2018-09-11T16:11:49.158086031+02:00
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BIN
charts/molgenis-preview-0.2.0.tgz
Normal file
BIN
charts/molgenis-preview-0.2.0.tgz
Normal file
Binary file not shown.
@@ -1,6 +1,6 @@
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name: molgenis-jenkins
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name: molgenis-jenkins
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home: https://jenkins.io/
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home: https://jenkins.io/
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version: 0.8.0
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version: 0.7.0
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appVersion: 2.121
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appVersion: 2.121
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description: Molgenis installation for the jenkins chart.
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description: Molgenis installation for the jenkins chart.
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sources:
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sources:
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@@ -40,66 +40,57 @@ You can use [all configuration values of the jenkins subchart](https://github.co
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### GitHub Authentication delegation
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### GitHub Authentication delegation
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You need to setup a MOLGENIS - Jenkins GitHub OAuth App. You can do this by accessing this url: [add new OAuth app](https://github.com/settings/applications/new).
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You need to setup a MOLGENIS - Jenkins GitHub OAuth App. You can do this by accessing this url: [add new OAuth app](https://github.com/settings/applications/new).
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### Secrets
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### Additional configuration
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There is one additional group of configuration items specific for this chart, so not prefixed with `jenkins`:
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When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins.
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* PipelineSecrets
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When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins and mounted in the jenkins
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build pods. The secrets, like the rest of the deployment, is namespaced so multiple instances can run beside
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each other with their own secrets.
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You can override the values at deploy time but otherwise also configure them
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You can override the values at deploy time but otherwise also configure them
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[in Rancher](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/secrets) or through kubectl.
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[in Rancher](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/secrets) or through kubectl.
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#### Vault
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* Vault
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The vault secret gets mounted in the vault pod so pipeline scripts can retrieve secrets from the vault.
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New vault token to be used by the pods to retrieve their tokens from the vault.
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| Parameter | Description | Default |
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| Parameter | Description | Default |
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| ------------------------- | ------------------------------------------ | ---------------------------------------------- |
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| ---------------------------------- | ------------------------------------------ | ---------------------------------------------- |
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| `secret.vault.token` | Token to log into the hashicorp vault | `xxxx` |
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| `PipelineSecrets.Vault.Replace` | Replace the molgenis-pipeline-vault secret | `true` |
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| `secret.vault.addr` | Address of the vault | `https:vault-operator.vault-operator.svc:8200` |
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| `PipelineSecrets.Vault.Token` | Token to log into the hashicorp vault | `xxxx` |
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| `secret.vault.skipVerify` | Skip verification of the https connection | `1` |
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| `PipelineSecrets.Vault.Addr` | Address of the vault | `https:vault-operator.vault-operator.svc:8200` |
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| `PipelineSecrets.Vault.SkipVerify` | Skip verification of the https connection | `1` |
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#### GitHub
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* Env
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Token used by Jenkins to authenticate on GitHub.
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Environment variables stored in molgenis-pipeline-env secret, to be added as environment variables
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in the slave pods.
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| Parameter | Description | Default |
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| Parameter | Description | Default |
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| --------------------- | ------------------------ | ------------------ |
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| --------------------------------------- | ----------------------------------------- | --------------- |
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| `secret.gitHub.user` | username for the account | `molgenis-jenkins` |
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| `PipelineSecrets.Env.Replace` | Replace molgenis-pipeline-env secret | `true` |
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| `secret.gitHub.token` | token for the account | `xxxx` |
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| `PipelineSecrets.Env.PGPPassphrase` | passphrase for the pgp signing key | `literal:xxxx` |
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| `PipelineSecrets.Env.CodecovToken` | token for codecov.io | `xxxx` |
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| `PipelineSecrets.Env.GitHubToken` | token for GH molgenis-jenkins user | `xxxx` |
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| `PipelineSecrets.Env.NexusPassword` | token for molgenis-jenkins user in NEXUS | `xxxx` |
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| `PipelineSecrets.Env.DockerHubPassword` | token for molgenis user in hub.docker.com | `xxxx` |
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| `PipelineSecrets.Env.SonarToken` | token for sonarcloud.io | `xxxx` |
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| `PipelineSecrets.Env.NpmToken` | token for npmjs.org | `xxxx` |
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| `PipelineSecrets.Env.SauceAccessKey` | token for saucelabs.com | `xxxx` |
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#### Gogs
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* File
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Token used by Jenkins to authenticate on the [RuG Webhosting Gogs](https://git.webhosting.rug.nl).
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Environment variables stored in molgenis-pipeline-file secret, to be mounted as files
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in the `/root/.m2` directory of the slave pods.
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> The settings.xml file references the
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| Parameter | Description | Default |
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| Parameter | Description | Default |
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| ------------------- | ------------------------ | --------- |
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| -------------------------------------- | ------------------------------------- | ------------------------------------------------------------------------------- |
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| `secret.gogs.user` | username for the account | `p281392` |
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| `PipelineSecrets.File.Replace` | Replace molgenis-pipeline-file secret | `true` |
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| `secret.gogs.token` | token for the account | `xxxx` |
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| `PipelineSecrets.File.PGPPrivateKeyAsc`| pgp signing key in ascii form | `-----BEGIN PGP PRIVATE KEY BLOCK-----xxxxx-----END PGP PRIVATE KEY BLOCK-----` |
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| `PipelineSecrets.File.MavenSettingsXML`| Maven settings.xml file | `<settings>[...]</settings>` (see actual [values.yaml](values.yaml)) |
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#### Slack
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The Slack integration is done mostly in the Jenkinsfile of each project. It is sufficient to only add the plugin to the Jenkins configuration in Helm.
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#### Legacy:
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##### Docker Hub
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Account used in pipeline builds to push docker images to `hub.docker.com`.
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> They should read `secret/gcc/account/dockerhub` from vault instead!
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| Parameter | Description | Default |
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| --------------------------- | ------------------------ | --------------- |
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| `secret.dockerHub.user` | username for the account | `molgenisci` |
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| `secret.dockerHub.password` | password for the account | `xxxx` |
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##### Registry
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Account used in pipeline builds to push docker images to `registry.molgenis.org`.
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> They should read `secret/ops/account/nexus` from vault instead!
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| Parameter | Description | Default |
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| --------------------------- | ------------------------ | --------- |
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| `secret.dockerHub.user` | username for the account | `admin` |
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| `secret.dockerHub.password` | password for the account | `xxxx` |
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## Command line use
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## Command line use
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Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`.
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Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`.
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BIN
molgenis-jenkins/charts/jenkins-0.16.4.tgz
Normal file
BIN
molgenis-jenkins/charts/jenkins-0.16.4.tgz
Normal file
Binary file not shown.
Binary file not shown.
@@ -1,6 +1,6 @@
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dependencies:
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dependencies:
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- name: jenkins
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- name: jenkins
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repository: https://kubernetes-charts.storage.googleapis.com/
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repository: https://kubernetes-charts.storage.googleapis.com/
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version: 0.18.0
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version: 0.16.4
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digest: sha256:39f694515489598fa545c9a5a4f1347749e8f2a8d7fae6ccae3e2acae1564685
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digest: sha256:39f694515489598fa545c9a5a4f1347749e8f2a8d7fae6ccae3e2acae1564685
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||||||
generated: 2018-09-27T11:00:15.795416984+02:00
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generated: 2018-06-27T14:36:23.172954738+02:00
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@@ -1,8 +0,0 @@
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# Helm in Jenkins
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To be able to run helm inside a jenkins pod, you'll need to
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* create a role in the namespace where tiller is installed
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* bind that role to the user that jenkins pods run as
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This directory contains yaml for these resources.
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See also https://github.com/helm/helm/blob/master/docs/rbac.md
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@@ -1,13 +0,0 @@
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apiVersion: rbac.authorization.k8s.io/v1beta1
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kind: RoleBinding
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metadata:
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name: tiller-jenkins-binding
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namespace: kube-system
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roleRef:
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apiGroup: rbac.authorization.k8s.io
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kind: Role
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|
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name: tiller-user
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subjects:
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- kind: ServiceAccount
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|
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name: default
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namespace: molgenis-jenkins
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@@ -1,18 +0,0 @@
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apiVersion: rbac.authorization.k8s.io/v1beta1
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|
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kind: Role
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metadata:
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|
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name: tiller-user
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namespace: kube-system
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|
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rules:
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|
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- apiGroups:
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|
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- ""
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|
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resources:
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|
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- pods/portforward
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|
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verbs:
|
|
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- create
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|
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- apiGroups:
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|
||||||
- ""
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resources:
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- pods
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verbs:
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|
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- list
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@@ -8,9 +8,9 @@ metadata:
|
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"jenkins.io/credentials-type": "usernamePassword"
|
"jenkins.io/credentials-type": "usernamePassword"
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annotations: {
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annotations: {
|
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# description - can not be a label as spaces are not allowed
|
# description - can not be a label as spaces are not allowed
|
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"jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to Docker Hub (hub.docker.com)"
|
"jenkins.io/credentials-description" : "user to authenticate against Docker Hub (hub.docker.com)"
|
||||||
}
|
}
|
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type: Opaque
|
type: Opaque
|
||||||
data:
|
data:
|
||||||
username: {{ .Values.secret.registry.user | b64enc | quote }}
|
username: {{ "molgenisci" | b64enc | quote }}
|
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password: {{ .Values.secret.registry.password | b64enc | quote }}
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password: {{ .Values.PipelineSecrets.Env.DockerHubPassword | b64enc | quote }}
|
||||||
@@ -8,9 +8,9 @@ metadata:
|
|||||||
"jenkins.io/credentials-type": "usernamePassword"
|
"jenkins.io/credentials-type": "usernamePassword"
|
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annotations: {
|
annotations: {
|
||||||
# description - can not be a label as spaces are not allowed
|
# description - can not be a label as spaces are not allowed
|
||||||
"jenkins.io/credentials-description" : "Oauth token for the {{.Values.secret.gitHub.user}} GitHub user"
|
"jenkins.io/credentials-description" : "oauth token for the molgenis-jenkins github user"
|
||||||
}
|
}
|
||||||
type: Opaque
|
type: Opaque
|
||||||
data:
|
data:
|
||||||
username: {{ .Values.secret.gitHub.user | b64enc | quote }}
|
username: {{ "molgenis-jenkins" | b64enc | quote }}
|
||||||
password: {{ .Values.secret.gitHub.token | b64enc | quote }}
|
password: {{ .Values.PipelineSecrets.Env.GitHubToken | b64enc | quote }}
|
||||||
@@ -8,9 +8,9 @@ metadata:
|
|||||||
"jenkins.io/credentials-type": "usernamePassword"
|
"jenkins.io/credentials-type": "usernamePassword"
|
||||||
annotations: {
|
annotations: {
|
||||||
# description - can not be a label as spaces are not allowed
|
# description - can not be a label as spaces are not allowed
|
||||||
"jenkins.io/credentials-description" : "Account used to authenticate against RuG Webhosting Gogs."
|
"jenkins.io/credentials-description" : "user to authenticate against GOGS (git.webhosting.rug.nl)"
|
||||||
}
|
}
|
||||||
type: Opaque
|
type: Opaque
|
||||||
data:
|
data:
|
||||||
username: {{ .Values.secret.gogs.user | b64enc | quote }}
|
username: {{ "p281392" | b64enc | quote }}
|
||||||
password: {{ .Values.secret.gogs.token | b64enc | quote }}
|
password: {{ .Values.PipelineSecrets.Env.GogsToken | b64enc | quote }}
|
||||||
@@ -0,0 +1,16 @@
|
|||||||
|
apiVersion: v1
|
||||||
|
kind: Secret
|
||||||
|
metadata:
|
||||||
|
# this is the jenkins id.
|
||||||
|
name: "molgenis-jenkins-nexus-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 NEXUS"
|
||||||
|
}
|
||||||
|
type: Opaque
|
||||||
|
data:
|
||||||
|
username: {{ "admin" | b64enc | quote }}
|
||||||
|
password: {{ .Values.PipelineSecrets.Env.NexusPassword | b64enc | quote }}
|
||||||
@@ -1,17 +0,0 @@
|
|||||||
apiVersion: v1
|
|
||||||
kind: Secret
|
|
||||||
metadata:
|
|
||||||
name: molgenis-jenkins-registry-secret
|
|
||||||
labels:
|
|
||||||
app: {{ template "jenkins.fullname" . }}
|
|
||||||
chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
|
|
||||||
release: "{{ .Release.Name }}"
|
|
||||||
heritage: "{{ .Release.Service }}"
|
|
||||||
annotations: {
|
|
||||||
# description - can not be a label as spaces are not allowed
|
|
||||||
"jenkins.io/credentials-description" : "(deprecated by vault) Account used in pipeline builds to push docker images to registry.molgenis.org."
|
|
||||||
}
|
|
||||||
type: Opaque
|
|
||||||
data:
|
|
||||||
username: {{ .Values.secret.registry.user | b64enc | quote }}
|
|
||||||
password: {{ .Values.secret.registry.password | b64enc | quote }}
|
|
||||||
@@ -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 }}
|
||||||
18
molgenis-jenkins/templates/molgenis-pipeline-env-secret.yaml
Normal file
18
molgenis-jenkins/templates/molgenis-pipeline-env-secret.yaml
Normal file
@@ -0,0 +1,18 @@
|
|||||||
|
{{- if .Values.PipelineSecrets.Env.Replace }}
|
||||||
|
apiVersion: v1
|
||||||
|
kind: Secret
|
||||||
|
metadata:
|
||||||
|
name: molgenis-pipeline-env-secret
|
||||||
|
labels:
|
||||||
|
app: {{ template "jenkins.fullname" . }}
|
||||||
|
chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
|
||||||
|
release: "{{ .Release.Name }}"
|
||||||
|
heritage: "{{ .Release.Service }}"
|
||||||
|
type: Opaque
|
||||||
|
data:
|
||||||
|
pgpPassphrase: {{ .Values.PipelineSecrets.Env.PGPPassphrase | b64enc | quote }}
|
||||||
|
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 }}
|
||||||
@@ -0,0 +1,15 @@
|
|||||||
|
{{- if .Values.PipelineSecrets.File.Replace }}
|
||||||
|
apiVersion: v1
|
||||||
|
kind: Secret
|
||||||
|
metadata:
|
||||||
|
name: molgenis-pipeline-file-secret
|
||||||
|
labels:
|
||||||
|
app: {{ template "jenkins.fullname" . }}
|
||||||
|
chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
|
||||||
|
release: "{{ .Release.Name }}"
|
||||||
|
heritage: "{{ .Release.Service }}"
|
||||||
|
type: Opaque
|
||||||
|
data:
|
||||||
|
key.asc: {{ .Values.PipelineSecrets.File.PGPPrivateKeyAsc | b64enc | quote }}
|
||||||
|
settings.xml: {{ .Values.PipelineSecrets.File.MavenSettingsXML | b64enc | quote }}
|
||||||
|
{{- end }}
|
||||||
@@ -1,3 +1,4 @@
|
|||||||
|
{{- if .Values.PipelineSecrets.Vault.Replace }}
|
||||||
apiVersion: v1
|
apiVersion: v1
|
||||||
kind: Secret
|
kind: Secret
|
||||||
metadata:
|
metadata:
|
||||||
@@ -9,6 +10,7 @@ metadata:
|
|||||||
heritage: "{{ .Release.Service }}"
|
heritage: "{{ .Release.Service }}"
|
||||||
type: Opaque
|
type: Opaque
|
||||||
data:
|
data:
|
||||||
token: {{ .Values.secret.vault.token | b64enc | quote }}
|
token: {{ .Values.PipelineSecrets.Vault.Token | b64enc | quote }}
|
||||||
addr: {{ .Values.secret.vault.addr | b64enc | quote }}
|
addr: {{ .Values.PipelineSecrets.Vault.Addr | b64enc | quote }}
|
||||||
skipVerify: {{ .Values.secret.vault.skipVerify | b64enc | quote }}
|
skipVerify: {{ .Values.PipelineSecrets.Vault.SkipVerify | b64enc | quote }}
|
||||||
|
{{- end }}
|
||||||
@@ -3,18 +3,17 @@ jenkins:
|
|||||||
HostName: jenkins.molgenis.org
|
HostName: jenkins.molgenis.org
|
||||||
ServiceType: ClusterIP
|
ServiceType: ClusterIP
|
||||||
InstallPlugins:
|
InstallPlugins:
|
||||||
- kubernetes:1.12.6
|
- kubernetes:1.12.0
|
||||||
- workflow-aggregator:2.5
|
- workflow-aggregator:2.5
|
||||||
- workflow-job:2.25
|
- workflow-job:2.21
|
||||||
- credentials-binding:1.16
|
- credentials-binding:1.16
|
||||||
- git:3.9.1
|
- git:3.9.1
|
||||||
- github-branch-source:2.3.6
|
- github-branch-source:2.3.6
|
||||||
- kubernetes-credentials-provider:0.10
|
- kubernetes-credentials-provider:0.9
|
||||||
- blueocean:1.8.3
|
- blueocean:1.6.2
|
||||||
- github-oauth:0.29
|
- github-oauth:0.29
|
||||||
- gogs-webhook:1.0.14
|
- gogs-webhook:1.0.14
|
||||||
- github-scm-trait-commit-skip:0.1.1
|
- sauce-ondemand:1.176
|
||||||
- slack:2.3
|
|
||||||
Security:
|
Security:
|
||||||
UseGitHub: false
|
UseGitHub: false
|
||||||
GitHub:
|
GitHub:
|
||||||
@@ -83,18 +82,6 @@ jenkins:
|
|||||||
<strategyId>1</strategyId>
|
<strategyId>1</strategyId>
|
||||||
<trust class="org.jenkinsci.plugins.github_branch_source.ForkPullRequestDiscoveryTrait$TrustPermission"/>
|
<trust class="org.jenkinsci.plugins.github_branch_source.ForkPullRequestDiscoveryTrait$TrustPermission"/>
|
||||||
</org.jenkinsci.plugins.github__branch__source.ForkPullRequestDiscoveryTrait>
|
</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>
|
</traits>
|
||||||
</org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator>
|
</org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator>
|
||||||
</navigators>
|
</navigators>
|
||||||
@@ -144,17 +131,6 @@ jenkins:
|
|||||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||||
<traits>
|
<traits>
|
||||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
<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>
|
</traits>
|
||||||
</source>
|
</source>
|
||||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||||
@@ -208,17 +184,6 @@ jenkins:
|
|||||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||||
<traits>
|
<traits>
|
||||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
<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>
|
</traits>
|
||||||
</source>
|
</source>
|
||||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||||
@@ -272,17 +237,6 @@ jenkins:
|
|||||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||||
<traits>
|
<traits>
|
||||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
<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>
|
</traits>
|
||||||
</source>
|
</source>
|
||||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||||
@@ -336,17 +290,6 @@ jenkins:
|
|||||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||||
<traits>
|
<traits>
|
||||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
<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>
|
</traits>
|
||||||
</source>
|
</source>
|
||||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||||
@@ -400,17 +343,6 @@ jenkins:
|
|||||||
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
<credentialsId>molgenis-jenkins-gogs-secret</credentialsId>
|
||||||
<traits>
|
<traits>
|
||||||
<jenkins.plugins.git.traits.BranchDiscoveryTrait/>
|
<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>
|
</traits>
|
||||||
</source>
|
</source>
|
||||||
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
<strategy class="jenkins.branch.DefaultBranchPropertyStrategy">
|
||||||
@@ -436,8 +368,8 @@ jenkins:
|
|||||||
install: true
|
install: true
|
||||||
Pods:
|
Pods:
|
||||||
molgenis:
|
molgenis:
|
||||||
Label: molgenis
|
Label: molgenisv2
|
||||||
NodeUsageMode: NORMAL
|
NodeUsageMode: EXCLUSIVE
|
||||||
volumes:
|
volumes:
|
||||||
- type: HostPath
|
- type: HostPath
|
||||||
hostPath: "/var/run/docker.sock"
|
hostPath: "/var/run/docker.sock"
|
||||||
@@ -484,12 +416,39 @@ jenkins:
|
|||||||
key: VAULT_ADDR
|
key: VAULT_ADDR
|
||||||
secretName: molgenis-pipeline-vault-secret
|
secretName: molgenis-pipeline-vault-secret
|
||||||
secretKey: addr
|
secretKey: addr
|
||||||
helm:
|
NodeSelector: {}
|
||||||
Image: "lachlanevenson/k8s-helm"
|
molgenis-legacy:
|
||||||
ImageTag: "v2.10.0"
|
InheritFrom: molgenis
|
||||||
Command: cat
|
Label: molgenis
|
||||||
WorkingDir: /home/jenkins
|
NodeUsageMode: NORMAL
|
||||||
TTY: true
|
volumes:
|
||||||
|
- type: Secret
|
||||||
|
secretName: molgenis-pipeline-file-secret
|
||||||
|
mountPath: "/home/jenkins/.m2"
|
||||||
|
Containers:
|
||||||
|
EnvVars:
|
||||||
|
- type: Secret
|
||||||
|
key: PGP_PASSPHRASE
|
||||||
|
secretName: molgenis-pipeline-env-secret
|
||||||
|
secretKey: pgpPassphrase
|
||||||
|
- type: KeyValue
|
||||||
|
key: PGP_SECRETKEY
|
||||||
|
value: "keyfile:/home.jenkins/.m2/key.asc"
|
||||||
|
- type: KeyValue
|
||||||
|
key: npm_config_registry
|
||||||
|
value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
|
||||||
|
- type: Secret
|
||||||
|
key: SONAR_TOKEN
|
||||||
|
secretName: molgenis-pipeline-env-secret
|
||||||
|
secretKey: sonarToken
|
||||||
|
- type: Secret
|
||||||
|
key: CODECOV_TOKEN
|
||||||
|
secretName: molgenis-pipeline-env-secret
|
||||||
|
secretKey: codecovToken
|
||||||
|
- type: Secret
|
||||||
|
key: GITHUB_TOKEN
|
||||||
|
secretName: molgenis-pipeline-env-secret
|
||||||
|
secretKey: githubToken
|
||||||
NodeSelector: {}
|
NodeSelector: {}
|
||||||
node:
|
node:
|
||||||
Label: node-carbon
|
Label: node-carbon
|
||||||
@@ -502,24 +461,22 @@ jenkins:
|
|||||||
Command: cat
|
Command: cat
|
||||||
WorkingDir: /home/jenkins
|
WorkingDir: /home/jenkins
|
||||||
TTY: true
|
TTY: true
|
||||||
vault:
|
|
||||||
Image: "vault"
|
|
||||||
Command: cat
|
|
||||||
WorkingDir: /home/jenkins
|
|
||||||
TTY: true
|
|
||||||
EnvVars:
|
EnvVars:
|
||||||
|
- type: KeyValue
|
||||||
|
key: npm_config_registry
|
||||||
|
value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
|
||||||
- type: Secret
|
- type: Secret
|
||||||
key: VAULT_TOKEN
|
key: CODECOV_TOKEN
|
||||||
secretName: molgenis-pipeline-vault-secret
|
secretName: molgenis-pipeline-env-secret
|
||||||
secretKey: token
|
secretKey: codecovToken
|
||||||
- type: Secret
|
- type: Secret
|
||||||
key: VAULT_SKIP_VERIFY
|
key: GITHUB_TOKEN
|
||||||
secretName: molgenis-pipeline-vault-secret
|
secretName: molgenis-pipeline-env-secret
|
||||||
secretKey: skipVerify
|
secretKey: githubToken
|
||||||
- type: Secret
|
- type: Secret
|
||||||
key: VAULT_ADDR
|
key: NPM_TOKEN
|
||||||
secretName: molgenis-pipeline-vault-secret
|
secretName: molgenis-pipeline-env-secret
|
||||||
secretKey: addr
|
secretKey: npmToken
|
||||||
NodeSelector: {}
|
NodeSelector: {}
|
||||||
molgenis-it:
|
molgenis-it:
|
||||||
InheritFrom: molgenis
|
InheritFrom: molgenis
|
||||||
@@ -583,27 +540,76 @@ jenkins:
|
|||||||
cpu: "1"
|
cpu: "1"
|
||||||
memory: "512Mi"
|
memory: "512Mi"
|
||||||
NodeSelector: {}
|
NodeSelector: {}
|
||||||
|
PipelineSecrets:
|
||||||
#secret contains configuration for the kubernetes secrets that jenkins can access
|
Vault:
|
||||||
secret:
|
Replace: true
|
||||||
# vault configures the vault secret
|
Token: xxxx
|
||||||
vault:
|
Addr: "https://vault-operator.vault-operator.svc:8200"
|
||||||
token: xxxx
|
SkipVerify: 1
|
||||||
addr: "https://vault-operator.vault-operator.svc:8200"
|
Env:
|
||||||
skipVerify: "1"
|
# Set to false to keep existing secret
|
||||||
# githubToken contains access token for jenkins bot account on github.com
|
Replace: true
|
||||||
gitHub:
|
# Passphrase for the pgp private key file, prefixed with literal:
|
||||||
user: "molgenis-jenkins"
|
PGPPassphrase: literal:xxxx
|
||||||
token: xxxx
|
# Token for codecov.io service
|
||||||
# gogs contains access token for jenkins bot account on RuG GoGs
|
CodecovToken: xxxx
|
||||||
gogs:
|
# Token for github bot account
|
||||||
user: p281392
|
GitHubToken: xxxx
|
||||||
token: xxxx
|
# Token for github bot account
|
||||||
# registry contains credentials for registry.molgenis.org
|
GogsToken: xxxx
|
||||||
registry:
|
# Token for sonarcloud.io
|
||||||
user: admin
|
SonarToken: xxxx
|
||||||
password: xxxx
|
# Token for npmjs.org
|
||||||
# dockerHubPassword contains password for hub.docker.com
|
NpmToken: xxxx
|
||||||
dockerHub:
|
# Password Local NEXUS
|
||||||
user: molgenisci
|
NexusPassword: xxxx
|
||||||
password: xxxx
|
# Password hub.docker.com
|
||||||
|
DockerHubPassword: xxxx
|
||||||
|
# Access key for saucelabs.com
|
||||||
|
SauceAccessKey: xxxx
|
||||||
|
File:
|
||||||
|
# Set to false to keep existing secret
|
||||||
|
Replace: true
|
||||||
|
# PGP Private key in ascii format used to sign artifacts
|
||||||
|
PGPPrivateKeyAsc: |-
|
||||||
|
-----BEGIN PGP PRIVATE KEY BLOCK-----
|
||||||
|
xxxxx
|
||||||
|
-----END PGP PRIVATE KEY BLOCK-----
|
||||||
|
# maven.settings file
|
||||||
|
MavenSettingsXML: |-
|
||||||
|
<settings>
|
||||||
|
<localRepository>${user.home}/.mvnrepository</localRepository>
|
||||||
|
<interactiveMode>false</interactiveMode>
|
||||||
|
<mirrors>
|
||||||
|
<mirror>
|
||||||
|
<id>nexus</id>
|
||||||
|
<mirrorOf>external:*</mirrorOf>
|
||||||
|
<url>http://nexus.molgenis-nexus:8081/repository/maven-central/</url>
|
||||||
|
</mirror>
|
||||||
|
</mirrors>
|
||||||
|
<servers>
|
||||||
|
<!-- for snapshot builds of the master -->
|
||||||
|
<server>
|
||||||
|
<id>sonatype-nexus-staging</id>
|
||||||
|
<username>molgenis</username>
|
||||||
|
<password>xxxx</password>
|
||||||
|
</server>
|
||||||
|
<server>
|
||||||
|
<id>local-nexus</id>
|
||||||
|
<url>http://nexus.molgenis-nexus:8081/repository/maven-snapshots/</url>
|
||||||
|
<username>admin</username>
|
||||||
|
<password>xxxxx</password>
|
||||||
|
</server>
|
||||||
|
<!-- for docker images-->
|
||||||
|
<server>
|
||||||
|
<id>registry.molgenis.org</id>
|
||||||
|
<username>admin</username>
|
||||||
|
<password>xxxx</password>
|
||||||
|
</server>
|
||||||
|
<server>
|
||||||
|
<id>registry.hub.docker.com</id>
|
||||||
|
<username>molgenisci</username>
|
||||||
|
<password>xxxx</password>
|
||||||
|
</server>
|
||||||
|
</servers>
|
||||||
|
</settings>
|
||||||
@@ -2,7 +2,7 @@ apiVersion: v1
|
|||||||
appVersion: "1.0"
|
appVersion: "1.0"
|
||||||
description: Nexus stack for MOLGENIS
|
description: Nexus stack for MOLGENIS
|
||||||
name: molgenis-nexus
|
name: molgenis-nexus
|
||||||
version: 0.4.2
|
version: 0.3.0
|
||||||
sources:
|
sources:
|
||||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
- 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
|
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-nexus/catalogIcon-molgenis-nexus.svg
|
||||||
@@ -6,44 +6,8 @@ NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
|
|||||||
|
|
||||||
This chart will deploy:
|
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 NEXUS container
|
||||||
- 1 MOLGENIS-httpd container (to proxy the registry and docker to one domain)
|
- 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.
|
|
||||||
|
|
||||||
## Installing the Chart
|
## Installing the Chart
|
||||||
|
|
||||||
@@ -61,9 +25,4 @@ To test if your hem chart works and:
|
|||||||
|
|
||||||
To deploy it on the cluster.
|
To deploy it on the cluster.
|
||||||
|
|
||||||
```curl -L -u xxxx:xxxx http://registry.molgenis.org/repository/helm/ --upload-file molgenis-x.x.x.tgz```
|
|
||||||
|
|
||||||
To push it to the registry
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|||||||
34
molgenis-nexus/templates/deployments/httpd-deployment.yaml
Normal file
34
molgenis-nexus/templates/deployments/httpd-deployment.yaml
Normal file
@@ -0,0 +1,34 @@
|
|||||||
|
apiVersion: extensions/v1beta1
|
||||||
|
kind: Deployment
|
||||||
|
metadata:
|
||||||
|
creationTimestamp: null
|
||||||
|
name: {{ .Values.httpd.name }}
|
||||||
|
labels:
|
||||||
|
app: {{ .Values.httpd.name }}
|
||||||
|
environment: {{ .Values.environment }}
|
||||||
|
spec:
|
||||||
|
replicas: {{ .Values.replicaCount }}
|
||||||
|
strategy:
|
||||||
|
type: {{ .Values.httpd.strategy.type }}
|
||||||
|
selector:
|
||||||
|
matchLabels:
|
||||||
|
app: {{ .Values.httpd.selector }}
|
||||||
|
template:
|
||||||
|
metadata:
|
||||||
|
labels:
|
||||||
|
app: {{ .Values.httpd.name }}
|
||||||
|
creationTimestamp: null
|
||||||
|
spec:
|
||||||
|
restartPolicy: {{ .Values.httpd.restartPolicy }}
|
||||||
|
containers:
|
||||||
|
- name: {{ .Values.httpd.name }}
|
||||||
|
image: "{{ .Values.httpd.image.repository }}:{{ .Values.httpd.image.tag }}"
|
||||||
|
imagePullPolicy: {{ .Values.httpd.image.pullPolicy }}
|
||||||
|
env:
|
||||||
|
- name: PROXY_SERVICE
|
||||||
|
value: "{{ .Values.nexus.name }}:{{ .Values.nexus.port.ui }},{{ .Values.nexus.name }}:{{ .Values.nexus.port.docker }}:{{ .Values.nexus.path.dockerV2 }}"
|
||||||
|
- name: SERVER_NAME
|
||||||
|
value: {{ .Values.httpd.hostname }}
|
||||||
|
ports:
|
||||||
|
- containerPort: {{ .Values.httpd.port }}
|
||||||
|
resources: {}
|
||||||
@@ -19,14 +19,18 @@ spec:
|
|||||||
app: {{ .Values.nexus.name }}
|
app: {{ .Values.nexus.name }}
|
||||||
creationTimestamp: null
|
creationTimestamp: null
|
||||||
spec:
|
spec:
|
||||||
|
volumes:
|
||||||
|
- name: {{ .Values.persistence.name }}
|
||||||
|
persistentVolumeClaim:
|
||||||
|
claimName: {{ .Values.persistence.name }}
|
||||||
restartPolicy: {{ .Values.nexus.restartPolicy }}
|
restartPolicy: {{ .Values.nexus.restartPolicy }}
|
||||||
initContainers:
|
initContainers:
|
||||||
- name: nexus-nfs
|
- name: volume-mount-nexus
|
||||||
image: busybox
|
image: busybox
|
||||||
command: ["sh", "-c", "chown -R 200:200 /nexus-data"]
|
command: ["sh", "-c", "chown -R 200:200 {{ .Values.persistence.mountPath }}"]
|
||||||
volumeMounts:
|
volumeMounts:
|
||||||
- name: molgenis-nexus-nfs
|
- name: {{ .Values.persistence.name }}
|
||||||
mountPath: "/nexus-data"
|
mountPath: "{{ .Values.persistence.mountPath }}"
|
||||||
containers:
|
containers:
|
||||||
- name: {{ .Values.nexus.name }}
|
- name: {{ .Values.nexus.name }}
|
||||||
image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
|
image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}"
|
||||||
@@ -35,31 +39,6 @@ spec:
|
|||||||
- containerPort: {{ .Values.nexus.port.ui }}
|
- containerPort: {{ .Values.nexus.port.ui }}
|
||||||
- containerPort: {{ .Values.nexus.port.docker }}
|
- containerPort: {{ .Values.nexus.port.docker }}
|
||||||
volumeMounts:
|
volumeMounts:
|
||||||
- name: molgenis-nexus-nfs
|
- name: {{ .Values.persistence.name }}
|
||||||
mountPath: /nexus-data
|
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
|
|
||||||
|
|
||||||
volumes:
|
|
||||||
- name: molgenis-nexus-nfs
|
|
||||||
persistentVolumeClaim:
|
|
||||||
claimName: {{ .Values.persistence.claim }}
|
|
||||||
|
|
||||||
{{- with .Values.nodeSelector }}
|
|
||||||
nodeSelector:
|
|
||||||
{{ toYaml . | indent 8 }}
|
|
||||||
{{- end }}
|
|
||||||
@@ -1,55 +0,0 @@
|
|||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: Deployment
|
|
||||||
metadata:
|
|
||||||
creationTimestamp: null
|
|
||||||
name: {{ .Values.nexusProxy.name }}
|
|
||||||
labels:
|
|
||||||
app: {{ .Values.nexusProxy.name }}
|
|
||||||
environment: {{ .Values.environment }}
|
|
||||||
spec:
|
|
||||||
replicas: {{ .Values.replicaCount }}
|
|
||||||
strategy:
|
|
||||||
type: {{ .Values.nexusProxy.strategy.type }}
|
|
||||||
selector:
|
|
||||||
matchLabels:
|
|
||||||
app: {{ .Values.nexusProxy.selector }}
|
|
||||||
template:
|
|
||||||
metadata:
|
|
||||||
labels:
|
|
||||||
app: {{ .Values.nexusProxy.name }}
|
|
||||||
creationTimestamp: null
|
|
||||||
spec:
|
|
||||||
restartPolicy: {{ .Values.nexusProxy.restartPolicy }}
|
|
||||||
containers:
|
|
||||||
- name: {{ .Values.nexusProxy.name }}
|
|
||||||
image: "{{ .Values.nexusProxy.image.repository }}:{{ .Values.nexusProxy.image.tag }}"
|
|
||||||
imagePullPolicy: {{ .Values.nexusProxy.image.pullPolicy }}
|
|
||||||
env:
|
|
||||||
- name: PROXY_SERVICE
|
|
||||||
value: "{{ .Values.nexus.name }}:{{ .Values.nexus.port.ui }},{{ .Values.nexus.name }}:{{ .Values.nexus.port.docker }}:{{ .Values.nexus.path.dockerV2 }}"
|
|
||||||
- name: SERVER_NAME
|
|
||||||
value: {{ .Values.nexusProxy.hostname }}
|
|
||||||
ports:
|
|
||||||
- containerPort: {{ .Values.nexusProxy.port }}
|
|
||||||
resources: {}
|
|
||||||
livenessProbe:
|
|
||||||
httpGet:
|
|
||||||
path: /
|
|
||||||
port: {{ .Values.nexusProxy.port }}
|
|
||||||
initialDelaySeconds: 1500
|
|
||||||
periodSeconds: 20
|
|
||||||
failureThreshold: 5
|
|
||||||
successThreshold: 1
|
|
||||||
readinessProbe:
|
|
||||||
httpGet:
|
|
||||||
path: /
|
|
||||||
port: {{ .Values.nexusProxy.port }}
|
|
||||||
initialDelaySeconds: 150
|
|
||||||
periodSeconds: 20
|
|
||||||
failureThreshold: 15
|
|
||||||
successThreshold: 1
|
|
||||||
|
|
||||||
{{- with .Values.nodeSelector }}
|
|
||||||
nodeSelector:
|
|
||||||
{{ toYaml . | indent 8 }}
|
|
||||||
{{- end }}
|
|
||||||
@@ -5,7 +5,7 @@ kind: Ingress
|
|||||||
metadata:
|
metadata:
|
||||||
name: "{{ $.Release.Name }}-ingress"
|
name: "{{ $.Release.Name }}-ingress"
|
||||||
labels:
|
labels:
|
||||||
app: {{ $.Values.nexusProxy.name }}
|
app: httpd
|
||||||
chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
|
chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
|
||||||
release: "{{ $.Release.Name }}"
|
release: "{{ $.Release.Name }}"
|
||||||
heritage: "{{ $.Release.Service }}"
|
heritage: "{{ $.Release.Service }}"
|
||||||
@@ -25,8 +25,8 @@ spec:
|
|||||||
paths:
|
paths:
|
||||||
- path: {{ default "/" .path }}
|
- path: {{ default "/" .path }}
|
||||||
backend:
|
backend:
|
||||||
serviceName: {{ $.Values.nexusProxy.name }}
|
serviceName: httpd
|
||||||
servicePort: {{ $.Values.nexusProxy.port }}
|
servicePort: 80
|
||||||
{{- if .tls }}
|
{{- if .tls }}
|
||||||
tls:
|
tls:
|
||||||
- hosts:
|
- hosts:
|
||||||
|
|||||||
@@ -1,15 +0,0 @@
|
|||||||
{{- if .Values.persistence.enabled -}}
|
|
||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: PersistentVolumeClaim
|
|
||||||
apiVersion: v1
|
|
||||||
metadata:
|
|
||||||
name: {{ .Values.persistence.claim }}
|
|
||||||
annotations:
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
|
||||||
spec:
|
|
||||||
accessModes:
|
|
||||||
- ReadWriteMany
|
|
||||||
resources:
|
|
||||||
requests:
|
|
||||||
storage: {{ .Values.persistence.size }}
|
|
||||||
{{- end }}
|
|
||||||
13
molgenis-nexus/templates/services/httpd-service.yaml
Normal file
13
molgenis-nexus/templates/services/httpd-service.yaml
Normal file
@@ -0,0 +1,13 @@
|
|||||||
|
apiVersion: v1
|
||||||
|
kind: Service
|
||||||
|
metadata:
|
||||||
|
name: {{ .Values.httpd.name }}
|
||||||
|
labels:
|
||||||
|
app: {{ .Values.httpd.name }}
|
||||||
|
spec:
|
||||||
|
type: {{ .Values.httpd.service.type }}
|
||||||
|
ports:
|
||||||
|
- name: {{ .Values.httpd.name }}
|
||||||
|
port: {{ .Values.httpd.port }}
|
||||||
|
selector:
|
||||||
|
app: {{ .Values.httpd.selector }}
|
||||||
@@ -1,13 +0,0 @@
|
|||||||
apiVersion: v1
|
|
||||||
kind: Service
|
|
||||||
metadata:
|
|
||||||
name: {{ .Values.nexusProxy.name }}
|
|
||||||
labels:
|
|
||||||
app: {{ .Values.nexusProxy.name }}
|
|
||||||
spec:
|
|
||||||
type: {{ .Values.nexusProxy.service.type }}
|
|
||||||
ports:
|
|
||||||
- name: {{ .Values.nexusProxy.name }}
|
|
||||||
port: {{ .Values.nexusProxy.port }}
|
|
||||||
selector:
|
|
||||||
app: {{ .Values.nexusProxy.selector }}
|
|
||||||
16
molgenis-nexus/templates/volumes/nexus-pv.yaml
Normal file
16
molgenis-nexus/templates/volumes/nexus-pv.yaml
Normal file
@@ -0,0 +1,16 @@
|
|||||||
|
apiVersion: v1
|
||||||
|
kind: PersistentVolume
|
||||||
|
metadata:
|
||||||
|
name: {{ .Values.persistence.name }}
|
||||||
|
labels:
|
||||||
|
name: nfs2
|
||||||
|
spec:
|
||||||
|
storageClassName: {{ .Values.persistence.storageClass }}
|
||||||
|
capacity:
|
||||||
|
storage: {{ .Values.persistence.size }}
|
||||||
|
accessModes:
|
||||||
|
- {{ .Values.persistence.accessMode }}
|
||||||
|
persistentVolumeReclaimPolicy: {{ .Values.persistence.reclaimPolicy }}
|
||||||
|
nfs:
|
||||||
|
server: {{ .Values.persistence.server }}
|
||||||
|
path: {{ .Values.persistence.mountPath }}
|
||||||
11
molgenis-nexus/templates/volumes/nexus-pvc.yaml
Normal file
11
molgenis-nexus/templates/volumes/nexus-pvc.yaml
Normal file
@@ -0,0 +1,11 @@
|
|||||||
|
kind: PersistentVolumeClaim
|
||||||
|
apiVersion: v1
|
||||||
|
metadata:
|
||||||
|
name: {{ .Values.persistence.name }}
|
||||||
|
spec:
|
||||||
|
storageClassName: {{ .Values.persistence.storageClass }}
|
||||||
|
accessModes:
|
||||||
|
- {{ .Values.persistence.accessMode }}
|
||||||
|
resources:
|
||||||
|
requests:
|
||||||
|
storage: {{ .Values.persistence.size }}
|
||||||
@@ -13,7 +13,7 @@ nexus:
|
|||||||
selector: nexus
|
selector: nexus
|
||||||
restartPolicy: Always
|
restartPolicy: Always
|
||||||
image:
|
image:
|
||||||
repository: molgenis/nexus3
|
repository: sonatype/nexus3
|
||||||
tag: latest
|
tag: latest
|
||||||
pullPolicy: Always
|
pullPolicy: Always
|
||||||
port:
|
port:
|
||||||
@@ -24,16 +24,16 @@ nexus:
|
|||||||
service:
|
service:
|
||||||
type: ClusterIP
|
type: ClusterIP
|
||||||
|
|
||||||
nexusProxy:
|
httpd:
|
||||||
name: nexus-proxy
|
name: httpd
|
||||||
hostname: registry.molgenis.org
|
hostname: registry.molgenis.org
|
||||||
strategy:
|
strategy:
|
||||||
type: Recreate
|
type: Recreate
|
||||||
selector: nexus-proxy
|
selector: httpd
|
||||||
restartPolicy: Always
|
restartPolicy: Always
|
||||||
image:
|
image:
|
||||||
repository: molgenis/httpd
|
repository: registry.webhosting.rug.nl/molgenis/httpd
|
||||||
tag: latest
|
tag: lts
|
||||||
pullPolicy: Always
|
pullPolicy: Always
|
||||||
port: 80
|
port: 80
|
||||||
service:
|
service:
|
||||||
@@ -43,22 +43,39 @@ nexusProxy:
|
|||||||
ingress:
|
ingress:
|
||||||
enabled: true
|
enabled: true
|
||||||
annotations: {}
|
annotations: {}
|
||||||
|
# kubernetes.io/ingress.class: nginx
|
||||||
|
# kubernetes.io/tls-acme: "true"
|
||||||
path: /
|
path: /
|
||||||
hosts:
|
hosts:
|
||||||
- name: registry.molgenis.org
|
- name: registry.molgenis.org
|
||||||
tls: []
|
tls: []
|
||||||
|
# - secretName: chart-example-tls
|
||||||
|
# hosts:
|
||||||
|
# - chart-example.local
|
||||||
|
|
||||||
persistence:
|
persistence:
|
||||||
enabled: true
|
name: molgenis-nexus-data
|
||||||
claim: molgenis-nexus
|
storageClass: nfs-class
|
||||||
size: 500Gi
|
size: 30G
|
||||||
|
reclaimPolicy: Retain
|
||||||
|
server: 192.168.64.12
|
||||||
|
accessMode: ReadWriteMany
|
||||||
|
mountPath: /gcc/molgenis/nexus
|
||||||
|
|
||||||
|
|
||||||
resources: {}
|
resources: {}
|
||||||
|
# We usually recommend not to specify default resources and to leave this as a conscious
|
||||||
|
# choice for the user. This also increases chances charts run on environments with little
|
||||||
|
# resources, such as Minikube. If you do want to specify resources, uncomment the following
|
||||||
|
# lines, adjust them as necessary, and remove the curly braces after 'resources:'.
|
||||||
|
# limits:
|
||||||
|
# cpu: 100m
|
||||||
|
# memory: 128Mi
|
||||||
|
# requests:
|
||||||
|
# cpu: 100m
|
||||||
|
# memory: 128Mi
|
||||||
|
|
||||||
nodeSelector: {
|
nodeSelector: {}
|
||||||
deployPod: "true"
|
|
||||||
}
|
|
||||||
|
|
||||||
tolerations: []
|
tolerations: []
|
||||||
|
|
||||||
|
|||||||
@@ -1,38 +0,0 @@
|
|||||||
# MOLGENIS - OpenCPU Helm Chart
|
|
||||||
|
|
||||||
NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share
|
|
||||||
|
|
||||||
## Containers
|
|
||||||
|
|
||||||
This chart will deploy the following containers:
|
|
||||||
|
|
||||||
- OpenCPU
|
|
||||||
- MOLGENIS-httpd (to proxy the registry and docker to one domain)
|
|
||||||
|
|
||||||
## Provisioning
|
|
||||||
You can choose for the OpenCPU image from which repository you want to pull. Experimental builds are pushed to registry.molgenis.org and the stable builds to hub.docker.com.
|
|
||||||
You need to fill out 2 properties to determine which repository you are going to use.
|
|
||||||
|
|
||||||
- ```opencpu.image.repository```
|
|
||||||
- ```opencpu.image.tag```
|
|
||||||
|
|
||||||
You can do this in the questions in Rancher or in the ```values.yaml```.
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
## Development
|
|
||||||
You can test in install the chart by executing:
|
|
||||||
|
|
||||||
```helm lint .```
|
|
||||||
|
|
||||||
To test if your helm chart-syntax is right and:
|
|
||||||
|
|
||||||
```helm install . --dry-run --debug```
|
|
||||||
|
|
||||||
To test if your hem chart works and:
|
|
||||||
|
|
||||||
```helm install .```
|
|
||||||
|
|
||||||
To deploy it on the cluster.
|
|
||||||
|
|
||||||
|
|
||||||
File diff suppressed because one or more lines are too long
|
Before Width: | Height: | Size: 245 KiB |
@@ -1,28 +0,0 @@
|
|||||||
|
|
||||||
categories:
|
|
||||||
- MOLGENIS
|
|
||||||
questions:
|
|
||||||
- variable: ingress.enabled
|
|
||||||
label: Enable ingress
|
|
||||||
default: false
|
|
||||||
description: "Enable ingress"
|
|
||||||
type: boolean
|
|
||||||
required: true
|
|
||||||
group: "Load balancing"
|
|
||||||
- variable: opencpu.image.repository
|
|
||||||
label: Registry
|
|
||||||
default: "registry.hub.docker.com"
|
|
||||||
description: "Select a registry to pull from"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "registry.hub.docker.com"
|
|
||||||
- "registry.molgenis.org"
|
|
||||||
required: true
|
|
||||||
group: "Provisioning"
|
|
||||||
- variable: opencpu.image.tag
|
|
||||||
label: Version
|
|
||||||
default: ""
|
|
||||||
description: "Select a OpenCPU version (check the registry.molgenis.org or hub.docker.com for released tags)"
|
|
||||||
type: string
|
|
||||||
required: true
|
|
||||||
group: "Provisioning"
|
|
||||||
@@ -1,35 +0,0 @@
|
|||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: Deployment
|
|
||||||
metadata:
|
|
||||||
{{- with .Values.ingress.annotations }}
|
|
||||||
annotations:
|
|
||||||
{{ toYaml . | indent 4 }}
|
|
||||||
{{- end }}
|
|
||||||
name: {{ template "opencpu.fullname" . }}
|
|
||||||
labels:
|
|
||||||
app: {{ template "opencpu.name" . }}
|
|
||||||
chart: {{ template "opencpu.chart" . }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
heritage: {{ .Release.Service }}
|
|
||||||
spec:
|
|
||||||
replicas: {{ .Values.replicaCount }}
|
|
||||||
selector:
|
|
||||||
matchLabels:
|
|
||||||
app: {{ template "opencpu.name" . }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
template:
|
|
||||||
metadata:
|
|
||||||
labels:
|
|
||||||
app: {{ template "opencpu.name" . }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
spec:
|
|
||||||
containers:
|
|
||||||
{{- with .Values.opencpu }}
|
|
||||||
- name: {{ .name }}
|
|
||||||
image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
|
|
||||||
imagePullPolicy: {{ .image.pullPolicy }}
|
|
||||||
ports:
|
|
||||||
- containerPort: {{ .service.port }}
|
|
||||||
{{- end }}
|
|
||||||
|
|
||||||
|
|
||||||
@@ -1,36 +0,0 @@
|
|||||||
{{- if .Values.ingress.enabled }}
|
|
||||||
{{- range .Values.ingress.hosts }}
|
|
||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: Ingress
|
|
||||||
metadata:
|
|
||||||
name: "{{ $.Release.Name }}-ingress"
|
|
||||||
labels:
|
|
||||||
app: {{ $.Values.opencpu.name }}
|
|
||||||
chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
|
|
||||||
release: "{{ $.Release.Name }}"
|
|
||||||
heritage: "{{ $.Release.Service }}"
|
|
||||||
annotations:
|
|
||||||
{{- if .tls }}
|
|
||||||
ingress.kubernetes.io/secure-backends: "true"
|
|
||||||
{{- end }}
|
|
||||||
{{- range $key, $value := .annotations }}
|
|
||||||
{{ $key }}: {{ $value | quote }}
|
|
||||||
{{- end }}
|
|
||||||
spec:
|
|
||||||
rules:
|
|
||||||
- host: {{ .name }}
|
|
||||||
http:
|
|
||||||
paths:
|
|
||||||
- path: {{ default "/" .path }}
|
|
||||||
backend:
|
|
||||||
serviceName: {{ $.Values.opencpu.service.name }}
|
|
||||||
servicePort: {{ $.Values.opencpu.service.port }}
|
|
||||||
{{- if .tls }}
|
|
||||||
tls:
|
|
||||||
- hosts:
|
|
||||||
- {{ .name }}
|
|
||||||
secretName: {{ .tlsSecret }}
|
|
||||||
{{- end }}
|
|
||||||
---
|
|
||||||
{{- end }}
|
|
||||||
{{- end }}
|
|
||||||
@@ -1,20 +0,0 @@
|
|||||||
apiVersion: v1
|
|
||||||
kind: Service
|
|
||||||
metadata:
|
|
||||||
name: {{ .Values.opencpu.service.name }}
|
|
||||||
labels:
|
|
||||||
app: {{ .Values.opencpu.service.name }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
heritage: {{ .Release.Service }}
|
|
||||||
spec:
|
|
||||||
type: {{ .Values.opencpu.service.type }}
|
|
||||||
loadBalancerSourceRanges:
|
|
||||||
{{- range $index, $rule := .Values.opencpu.service.firewall }}
|
|
||||||
- {{ $rule }}
|
|
||||||
{{- end }}
|
|
||||||
ports:
|
|
||||||
- name: {{ .Values.opencpu.service.name }}
|
|
||||||
port: {{ .Values.opencpu.service.port }}
|
|
||||||
selector:
|
|
||||||
app: {{ template "opencpu.name" . }}
|
|
||||||
release: {{ .Release.Name }}
|
|
||||||
@@ -1,41 +0,0 @@
|
|||||||
# Default values for nexus.
|
|
||||||
# This is a YAML-formatted file.
|
|
||||||
# Declare variables to be passed into your templates.
|
|
||||||
|
|
||||||
replicaCount: 1
|
|
||||||
|
|
||||||
environment: production
|
|
||||||
|
|
||||||
opencpu:
|
|
||||||
name: opencpu
|
|
||||||
strategy:
|
|
||||||
type: Recreate
|
|
||||||
restartPolicy: Always
|
|
||||||
image:
|
|
||||||
repository: registry.hub.docker.com
|
|
||||||
name: molgenis/opencpu
|
|
||||||
tag: stable
|
|
||||||
pullPolicy: Always
|
|
||||||
service:
|
|
||||||
name: opencpu
|
|
||||||
type: LoadBalancer
|
|
||||||
port: 8004
|
|
||||||
firewall:
|
|
||||||
- 145.100.224.1/24
|
|
||||||
|
|
||||||
ingress:
|
|
||||||
enabled: false
|
|
||||||
annotations: {
|
|
||||||
kubernetes.io/ingress.class: "nginx",
|
|
||||||
nginx.ingress.kubernetes.io/proxy-body-size: "0"
|
|
||||||
}
|
|
||||||
path: /
|
|
||||||
hosts:
|
|
||||||
- name: opencpu.molgenis.org
|
|
||||||
tls: []
|
|
||||||
|
|
||||||
nodeSelector: {}
|
|
||||||
|
|
||||||
tolerations: []
|
|
||||||
|
|
||||||
affinity: {}
|
|
||||||
@@ -1,8 +1,8 @@
|
|||||||
apiVersion: v1
|
apiVersion: v1
|
||||||
appVersion: "1.0"
|
appVersion: "1.0"
|
||||||
description: Opencpu stack for MOLGENIS
|
description: MOLGENIS - helm stack for testing purposes
|
||||||
name: molgenis-opencpu
|
name: molgenis-preview
|
||||||
version: 0.1.1
|
version: 0.2.0
|
||||||
sources:
|
sources:
|
||||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
- 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-opencpu/catalogIcon-molgenis-opencpu.svg
|
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-preview/catalogIcon-molgenis.svg
|
||||||
16
molgenis-preview/README.md
Normal file
16
molgenis-preview/README.md
Normal file
@@ -0,0 +1,16 @@
|
|||||||
|
# MOLGENIS preview
|
||||||
|
This chart is used for testing purposes. It can be used by data managers or developers to test MOLGENIS (e.g. integration testing).
|
||||||
|
|
||||||
|
## Containers
|
||||||
|
This chart spins up a complete stack to run MOLGENIS. The created containers are:
|
||||||
|
|
||||||
|
- MOLGENIS
|
||||||
|
- PostgreSQL
|
||||||
|
- Elasticsearch
|
||||||
|
- OpenCPU
|
||||||
|
|
||||||
|
## Rancher
|
||||||
|
You can spin up a test instance by navigating to https://rancher.molgenis.org:7777 and login with your LDAP-account.
|
||||||
|
|
||||||
|
Go to the test-environment and click on "Launch". Search for MOLGENIS.
|
||||||
|
|
||||||
1024
molgenis-preview/catalogIcon-molgenis.svg
Normal file
1024
molgenis-preview/catalogIcon-molgenis.svg
Normal file
File diff suppressed because it is too large
Load Diff
|
After Width: | Height: | Size: 77 KiB |
61
molgenis-preview/questions.yml
Normal file
61
molgenis-preview/questions.yml
Normal file
@@ -0,0 +1,61 @@
|
|||||||
|
|
||||||
|
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.image.repository
|
||||||
|
default: "registry.hub.docker.com"
|
||||||
|
description: "Select a registry to pull from"
|
||||||
|
type: enum
|
||||||
|
options:
|
||||||
|
- "registry.hub.docker.com"
|
||||||
|
- "registry.molgenis.org"
|
||||||
|
required: true
|
||||||
|
group: "MOLGENIS - Version"
|
||||||
|
label: Registry
|
||||||
|
- variable: molgenis.image.tag
|
||||||
|
default: "stable"
|
||||||
|
description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for other tags)"
|
||||||
|
type: string
|
||||||
|
required: true
|
||||||
|
group: "MOLGENIS - Version"
|
||||||
|
label: Version
|
||||||
|
- 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
|
||||||
19
molgenis-preview/templates/NOTES.txt
Normal file
19
molgenis-preview/templates/NOTES.txt
Normal file
@@ -0,0 +1,19 @@
|
|||||||
|
1. Get the application URL by running these commands:
|
||||||
|
{{- if .Values.ingress.enabled }}
|
||||||
|
{{- range .Values.ingress.hosts }}
|
||||||
|
http{{ if $.Values.ingress.tls }}s{{ end }}://{{ . }}{{ $.Values.ingress.path }}
|
||||||
|
{{- end }}
|
||||||
|
{{- else if contains "NodePort" .Values.service.type }}
|
||||||
|
export NODE_PORT=$(kubectl get --namespace {{ .Release.Namespace }} -o jsonpath="{.spec.ports[0].nodePort}" services {{ template "molgenis.fullname" . }})
|
||||||
|
export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}")
|
||||||
|
echo http://$NODE_IP:$NODE_PORT
|
||||||
|
{{- else if contains "LoadBalancer" .Values.service.type }}
|
||||||
|
NOTE: It may take a few minutes for the LoadBalancer IP to be available.
|
||||||
|
You can watch the status of by running 'kubectl get svc -w {{ template "molgenis.fullname" . }}'
|
||||||
|
export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ template "molgenis.fullname" . }} -o jsonpath='{.status.loadBalancer.ingress[0].ip}')
|
||||||
|
echo http://$SERVICE_IP:{{ .Values.service.port }}
|
||||||
|
{{- else if contains "ClusterIP" .Values.service.type }}
|
||||||
|
export POD_NAME=$(kubectl get pods --namespace {{ .Release.Namespace }} -l "app={{ template "molgenis.name" . }},release={{ .Release.Name }}" -o jsonpath="{.items[0].metadata.name}")
|
||||||
|
echo "Visit http://127.0.0.1:8080 to use your application"
|
||||||
|
kubectl port-forward $POD_NAME 8080:80
|
||||||
|
{{- end }}
|
||||||
@@ -2,7 +2,7 @@
|
|||||||
{{/*
|
{{/*
|
||||||
Expand the name of the chart.
|
Expand the name of the chart.
|
||||||
*/}}
|
*/}}
|
||||||
{{- define "opencpu.name" -}}
|
{{- define "molgenis.name" -}}
|
||||||
{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
|
{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}}
|
||||||
{{- end -}}
|
{{- end -}}
|
||||||
|
|
||||||
@@ -11,7 +11,7 @@ Create a default fully qualified app name.
|
|||||||
We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
|
We truncate at 63 chars because some Kubernetes name fields are limited to this (by the DNS naming spec).
|
||||||
If release name contains chart name it will be used as a full name.
|
If release name contains chart name it will be used as a full name.
|
||||||
*/}}
|
*/}}
|
||||||
{{- define "opencpu.fullname" -}}
|
{{- define "molgenis.fullname" -}}
|
||||||
{{- if .Values.fullnameOverride -}}
|
{{- if .Values.fullnameOverride -}}
|
||||||
{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
|
{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}}
|
||||||
{{- else -}}
|
{{- else -}}
|
||||||
@@ -27,6 +27,6 @@ If release name contains chart name it will be used as a full name.
|
|||||||
{{/*
|
{{/*
|
||||||
Create chart name and version as used by the chart label.
|
Create chart name and version as used by the chart label.
|
||||||
*/}}
|
*/}}
|
||||||
{{- define "opencpu.chart" -}}
|
{{- define "molgenis.chart" -}}
|
||||||
{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
|
{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}}
|
||||||
{{- end -}}
|
{{- end -}}
|
||||||
124
molgenis-preview/templates/deployment.yaml
Normal file
124
molgenis-preview/templates/deployment.yaml
Normal file
@@ -0,0 +1,124 @@
|
|||||||
|
apiVersion: apps/v1beta2
|
||||||
|
kind: Deployment
|
||||||
|
metadata:
|
||||||
|
{{- with .Values.ingress.annotations }}
|
||||||
|
annotations:
|
||||||
|
{{ toYaml . | indent 4 }}
|
||||||
|
{{- end }}
|
||||||
|
name: {{ template "molgenis.fullname" . }}
|
||||||
|
labels:
|
||||||
|
app: {{ template "molgenis.name" . }}
|
||||||
|
chart: {{ template "molgenis.chart" . }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
heritage: {{ .Release.Service }}
|
||||||
|
spec:
|
||||||
|
replicas: {{ .Values.replicaCount }}
|
||||||
|
selector:
|
||||||
|
matchLabels:
|
||||||
|
app: {{ template "molgenis.name" . }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
template:
|
||||||
|
metadata:
|
||||||
|
labels:
|
||||||
|
app: {{ template "molgenis.name" . }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
spec:
|
||||||
|
containers:
|
||||||
|
- name: molgenis
|
||||||
|
{{- with .Values.molgenis }}
|
||||||
|
image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
|
||||||
|
imagePullPolicy: {{ .image.pullPolicy }}
|
||||||
|
env:
|
||||||
|
- name: molgenis.home
|
||||||
|
value: /home/molgenis
|
||||||
|
- name: opencpu.uri.host
|
||||||
|
value: localhost
|
||||||
|
- name: elasticsearch.transport.addresses
|
||||||
|
value: localhost:9300
|
||||||
|
- name: elasticsearch.cluster.name
|
||||||
|
value: {{ $.Values.elasticsearch.clusterName }}
|
||||||
|
- name: db_uri
|
||||||
|
value: "jdbc:postgresql://localhost/{{ $.Values.postgres.db }}"
|
||||||
|
- name: db_user
|
||||||
|
value: {{ $.Values.postgres.user }}
|
||||||
|
- name: db_password
|
||||||
|
value: {{ $.Values.postgres.password }}
|
||||||
|
- name: admin.password
|
||||||
|
value: {{ .adminPassword }}
|
||||||
|
- name: CATALINA_OPTS
|
||||||
|
value: "{{ .javaOpts }}"
|
||||||
|
ports:
|
||||||
|
- containerPort: 8080
|
||||||
|
# livenessProbe:
|
||||||
|
# httpGet:
|
||||||
|
# path: /
|
||||||
|
# port: 8080
|
||||||
|
# readinessProbe:
|
||||||
|
# httpGet:
|
||||||
|
# path: /api/v2/version
|
||||||
|
# port: 8080
|
||||||
|
resources:
|
||||||
|
{{ toYaml .resources | indent 12 }}
|
||||||
|
{{- end }}
|
||||||
|
|
||||||
|
- name: elasticsearch
|
||||||
|
{{- with .Values.elasticsearch }}
|
||||||
|
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||||
|
imagePullPolicy: {{ .image.pullPolicy }}
|
||||||
|
env:
|
||||||
|
- name: cluster.name
|
||||||
|
value: {{ .clusterName }}
|
||||||
|
- name: bootstrap.memory_lock
|
||||||
|
value: "true"
|
||||||
|
- name: ES_JAVA_OPTS
|
||||||
|
value: "{{ .javaOpts }}"
|
||||||
|
- name: xpack.security.enabled
|
||||||
|
value: "false"
|
||||||
|
- name: discovery.type
|
||||||
|
value: single-node
|
||||||
|
ports:
|
||||||
|
- containerPort: 9200
|
||||||
|
- containerPort: 9300
|
||||||
|
resources:
|
||||||
|
{{ toYaml .resources | indent 12 }}
|
||||||
|
{{- end }}
|
||||||
|
|
||||||
|
- name: postgres
|
||||||
|
{{- with .Values.postgres }}
|
||||||
|
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||||
|
imagePullPolicy: {{ .image.pullPolicy }}
|
||||||
|
env:
|
||||||
|
- name: POSTGRES_USER
|
||||||
|
value: {{ .user }}
|
||||||
|
- name: POSTGRES_PASSWORD
|
||||||
|
value: {{ .password }}
|
||||||
|
- name: POSTGRES_DB
|
||||||
|
value: {{ .db }}
|
||||||
|
ports:
|
||||||
|
- containerPort: 5432
|
||||||
|
resources:
|
||||||
|
{{ toYaml .resources | indent 12 }}
|
||||||
|
{{- end }}
|
||||||
|
|
||||||
|
- name: opencpu
|
||||||
|
{{- with .Values.opencpu }}
|
||||||
|
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||||
|
imagePullPolicy: {{ .image.pullPolicy }}
|
||||||
|
ports:
|
||||||
|
- containerPort: 8004
|
||||||
|
resources:
|
||||||
|
{{ toYaml .resources | indent 12 }}
|
||||||
|
{{- end }}
|
||||||
|
|
||||||
|
{{- with .Values.nodeSelector }}
|
||||||
|
nodeSelector:
|
||||||
|
{{ toYaml . | indent 8 }}
|
||||||
|
{{- end }}
|
||||||
|
{{- with .Values.affinity }}
|
||||||
|
affinity:
|
||||||
|
{{ toYaml . | indent 8 }}
|
||||||
|
{{- end }}
|
||||||
|
{{- with .Values.tolerations }}
|
||||||
|
tolerations:
|
||||||
|
{{ toYaml . | indent 8 }}
|
||||||
|
{{- end }}
|
||||||
38
molgenis-preview/templates/ingress.yaml
Normal file
38
molgenis-preview/templates/ingress.yaml
Normal file
@@ -0,0 +1,38 @@
|
|||||||
|
{{- if .Values.ingress.enabled -}}
|
||||||
|
{{- $fullName := include "molgenis.fullname" . -}}
|
||||||
|
{{- $ingressPath := .Values.ingress.path -}}
|
||||||
|
apiVersion: extensions/v1beta1
|
||||||
|
kind: Ingress
|
||||||
|
metadata:
|
||||||
|
name: {{ $fullName }}
|
||||||
|
labels:
|
||||||
|
app: {{ template "molgenis.name" . }}
|
||||||
|
chart: {{ template "molgenis.chart" . }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
heritage: {{ .Release.Service }}
|
||||||
|
{{- with .Values.ingress.annotations }}
|
||||||
|
annotations:
|
||||||
|
{{ toYaml . | indent 4 }}
|
||||||
|
{{- end }}
|
||||||
|
spec:
|
||||||
|
{{- if .Values.ingress.tls }}
|
||||||
|
tls:
|
||||||
|
{{- range .Values.ingress.tls }}
|
||||||
|
- hosts:
|
||||||
|
{{- range .hosts }}
|
||||||
|
- {{ . }}
|
||||||
|
{{- end }}
|
||||||
|
secretName: {{ .secretName }}
|
||||||
|
{{- end }}
|
||||||
|
{{- end }}
|
||||||
|
rules:
|
||||||
|
{{- range .Values.ingress.hosts }}
|
||||||
|
- host: {{ .name }}
|
||||||
|
http:
|
||||||
|
paths:
|
||||||
|
- path: {{ $ingressPath }}
|
||||||
|
backend:
|
||||||
|
serviceName: {{ $fullName }}
|
||||||
|
servicePort: 8080
|
||||||
|
{{- end }}
|
||||||
|
{{- end }}
|
||||||
17
molgenis-preview/templates/service.yaml
Normal file
17
molgenis-preview/templates/service.yaml
Normal file
@@ -0,0 +1,17 @@
|
|||||||
|
apiVersion: v1
|
||||||
|
kind: Service
|
||||||
|
metadata:
|
||||||
|
name: {{ template "molgenis.fullname" . }}
|
||||||
|
labels:
|
||||||
|
app: {{ template "molgenis.name" . }}
|
||||||
|
chart: {{ template "molgenis.chart" . }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
|
heritage: {{ .Release.Service }}
|
||||||
|
spec:
|
||||||
|
type: {{ .Values.service.type }}
|
||||||
|
ports:
|
||||||
|
- name: molgenis
|
||||||
|
port: {{ .Values.service.port }}
|
||||||
|
selector:
|
||||||
|
app: {{ template "molgenis.name" . }}
|
||||||
|
release: {{ .Release.Name }}
|
||||||
82
molgenis-preview/values.yaml
Normal file
82
molgenis-preview/values.yaml
Normal file
@@ -0,0 +1,82 @@
|
|||||||
|
# Default values for molgenis.
|
||||||
|
|
||||||
|
replicaCount: 1
|
||||||
|
|
||||||
|
service:
|
||||||
|
type: LoadBalancer
|
||||||
|
port: 8080
|
||||||
|
|
||||||
|
ingress:
|
||||||
|
enabled: true
|
||||||
|
annotations:
|
||||||
|
nginx.ingress.kubernetes.io/proxy-body-size: "0"
|
||||||
|
path: /
|
||||||
|
hosts:
|
||||||
|
- name: test.molgenis.org
|
||||||
|
tls: []
|
||||||
|
|
||||||
|
molgenis:
|
||||||
|
image:
|
||||||
|
repository: registry.molgenis.org
|
||||||
|
name: molgenis/molgenis-app
|
||||||
|
tag: 7.0.0-SNAPSHOT
|
||||||
|
pullPolicy: Always
|
||||||
|
adminPassword: admin
|
||||||
|
javaOpts: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||||
|
resources:
|
||||||
|
limits:
|
||||||
|
cpu: 1
|
||||||
|
memory: 1250Mi
|
||||||
|
requests:
|
||||||
|
cpu: 200m
|
||||||
|
memory: 1Gi
|
||||||
|
|
||||||
|
postgres:
|
||||||
|
image:
|
||||||
|
repository: postgres
|
||||||
|
tag: 9.6-alpine
|
||||||
|
pullPolicy: IfNotPresent
|
||||||
|
user: molgenis
|
||||||
|
password: molgenis
|
||||||
|
db: molgenis
|
||||||
|
resources:
|
||||||
|
limits:
|
||||||
|
cpu: 1
|
||||||
|
memory: 250Mi
|
||||||
|
requests:
|
||||||
|
cpu: 100m
|
||||||
|
memory: 250Mi
|
||||||
|
|
||||||
|
elasticsearch:
|
||||||
|
image:
|
||||||
|
repository: docker.elastic.co/elasticsearch/elasticsearch
|
||||||
|
tag: 5.5.3
|
||||||
|
pullPolicy: IfNotPresent
|
||||||
|
javaOpts: "-Xms512m -Xmx512m"
|
||||||
|
clusterName: molgenis
|
||||||
|
resources:
|
||||||
|
limits:
|
||||||
|
cpu: 1
|
||||||
|
memory: 1500Mi
|
||||||
|
requests:
|
||||||
|
cpu: 100m
|
||||||
|
memory: 1Gi
|
||||||
|
|
||||||
|
opencpu:
|
||||||
|
image:
|
||||||
|
repository: molgenis/opencpu
|
||||||
|
tag: latest
|
||||||
|
pullPolicy: Always
|
||||||
|
resources:
|
||||||
|
limits:
|
||||||
|
cpu: 1
|
||||||
|
memory: 512Mi
|
||||||
|
requests:
|
||||||
|
cpu: 100m
|
||||||
|
memory: 256Mi
|
||||||
|
|
||||||
|
nodeSelector: {}
|
||||||
|
|
||||||
|
tolerations: []
|
||||||
|
|
||||||
|
affinity: {}
|
||||||
@@ -1,8 +1,8 @@
|
|||||||
apiVersion: v1
|
apiVersion: v1
|
||||||
appVersion: "1.0"
|
appVersion: "1.0"
|
||||||
description: MOLGENIS - helm stack (in BETA)
|
description: MOLGENIS - helm stack (in BETA)
|
||||||
name: molgenis
|
name: molgenis-beta
|
||||||
version: 0.4.3
|
version: 0.1.0
|
||||||
sources:
|
sources:
|
||||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
- 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
|
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis/catalogIcon-molgenis.svg
|
||||||
@@ -5,8 +5,6 @@ This chart is used for acceptance and production use cases.
|
|||||||
This chart spins up a MOLGENIS instance with HTTPD. The created containers are:
|
This chart spins up a MOLGENIS instance with HTTPD. The created containers are:
|
||||||
|
|
||||||
- MOLGENIS
|
- MOLGENIS
|
||||||
- ElasticSearch
|
|
||||||
- PostgreSQL **(optional)**
|
|
||||||
|
|
||||||
## Provisioning
|
## Provisioning
|
||||||
You can choose from which registry you want to pull. There are 2 registries:
|
You can choose from which registry you want to pull. There are 2 registries:
|
||||||
@@ -23,19 +21,6 @@ The three properties you need to specify are:
|
|||||||
Besides determining which image you want to pull, you also have to set an administrator password. You can do this by specifying the following property.
|
Besides determining which image you want to pull, you also have to set an administrator password. You can do this by specifying the following property.
|
||||||
- ```molgenis.adminPassword```
|
- ```molgenis.adminPassword```
|
||||||
|
|
||||||
### Firewall
|
|
||||||
Is defined at service level you can specify this attribute in the values:
|
|
||||||
|
|
||||||
- ```molgenis.firewall.enabled``` default 'false'
|
|
||||||
|
|
||||||
If set to 'true' the following options are available. One of the options below has to be set.
|
|
||||||
|
|
||||||
- ```molgenis.firewall.umcg.enabled``` default 'false'
|
|
||||||
- ```molgenis.firewall.cluster.enabled``` default 'false'
|
|
||||||
|
|
||||||
UMCG = only available within the UMCG.
|
|
||||||
Cluster = only available within the GCC cluster environment.
|
|
||||||
|
|
||||||
## Services
|
## Services
|
||||||
When you start MOLGENIS you need:
|
When you start MOLGENIS you need:
|
||||||
- an elasticsearch instance (5.5.6)
|
- an elasticsearch instance (5.5.6)
|
||||||
@@ -94,45 +79,5 @@ Specify memory usage for Java JVM:
|
|||||||
|
|
||||||
Select the resources you need dependant on the customer you need to serve.
|
Select the resources you need dependant on the customer you need to serve.
|
||||||
|
|
||||||
## Persistence
|
## Firewall
|
||||||
You can enable persistence on your MOLGENIS stack by specifying the following property.
|
Is defined at cluster level. This chart does not facilitate firewall configuration.
|
||||||
|
|
||||||
- ```persistence.enabled``` default 'true'
|
|
||||||
|
|
||||||
You can also choose to retain the volume of the NFS.
|
|
||||||
- ```persistence.retain``` default 'false'
|
|
||||||
|
|
||||||
The size and claim name can be specified per service. There are now two services that can be persist.
|
|
||||||
|
|
||||||
- MOLGENIS
|
|
||||||
- ElasticSearch
|
|
||||||
- PostgreSQL **(optional)**
|
|
||||||
|
|
||||||
MOLGENIS persistent properties.
|
|
||||||
- ```molgenis.persistence.claim```
|
|
||||||
- ```molgenis.persistence.size```
|
|
||||||
|
|
||||||
ElasticSearch persistent properties.
|
|
||||||
- ```elasticsearch.persistence.claim```
|
|
||||||
- ```elasticsearch.persistence.size```
|
|
||||||
|
|
||||||
PostgreSQL persistent properties.
|
|
||||||
- ```postgres.persistence.claim```
|
|
||||||
- ```postgres.persistence.size```
|
|
||||||
|
|
||||||
### Resolve you persistent volume
|
|
||||||
You do not know which volume is attached to your MOLGENIS instance. You can resolve this by executing:
|
|
||||||
|
|
||||||
```
|
|
||||||
kubectl get pv
|
|
||||||
```
|
|
||||||
|
|
||||||
You can now view the persistent volume claims and the attached volumes.
|
|
||||||
|
|
||||||
| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
|
|
||||||
| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
|
|
||||||
| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-solverd/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 |
|
|
||||||
|
|
||||||
You see the ```molgenis-test/molgenis-nfs-claim``` is bound to the volume: ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
|
|
||||||
When you want to view the data in the this volume you can go to the nfs-provisioning pod and execute the shell. Go to the directory ```export``` and lookup the directory ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
|
|
||||||
|
|||||||
@@ -8,7 +8,7 @@ questions:
|
|||||||
description: "Hostname for your stack"
|
description: "Hostname for your stack"
|
||||||
type: hostname
|
type: hostname
|
||||||
required: true
|
required: true
|
||||||
group: "Load balancing"
|
group: "Load Balancing"
|
||||||
- variable: molgenis.image.repository
|
- variable: molgenis.image.repository
|
||||||
label: Registry
|
label: Registry
|
||||||
default: "registry.hub.docker.com"
|
default: "registry.hub.docker.com"
|
||||||
@@ -33,24 +33,6 @@ questions:
|
|||||||
type: password
|
type: password
|
||||||
required: true
|
required: true
|
||||||
group: "Provisioning"
|
group: "Provisioning"
|
||||||
- variable: service.firewall.enabled
|
|
||||||
label: Firewall enabled
|
|
||||||
default: false
|
|
||||||
description: "Firewall enabled (can be cluster or UMCG scoped)"
|
|
||||||
type: boolean
|
|
||||||
required: true
|
|
||||||
group: "Provisioning"
|
|
||||||
show_subquestion_if: true
|
|
||||||
subquestions:
|
|
||||||
- variable: service.firewall.kind
|
|
||||||
default: "umcg"
|
|
||||||
description: "Firewall kind. This can be 'umcg' or 'cluster' environment"
|
|
||||||
type: enum
|
|
||||||
required: true
|
|
||||||
options:
|
|
||||||
- umcg
|
|
||||||
- cluster
|
|
||||||
label: Firewall kind
|
|
||||||
- variable: molgenis.services.opencpu.host
|
- variable: molgenis.services.opencpu.host
|
||||||
label: OpenCPU cluster
|
label: OpenCPU cluster
|
||||||
default: "localhost"
|
default: "localhost"
|
||||||
@@ -58,19 +40,10 @@ questions:
|
|||||||
type: string
|
type: string
|
||||||
required: true
|
required: true
|
||||||
group: "Services"
|
group: "Services"
|
||||||
- variable: molgenis.services.postgres.embedded
|
|
||||||
label: Postgres embedded
|
|
||||||
default: false
|
|
||||||
description: "Do you want an embedded postgres"
|
|
||||||
type: boolean
|
|
||||||
required: true
|
|
||||||
group: "Services"
|
|
||||||
show_subquestion_if: false
|
|
||||||
subquestions:
|
|
||||||
- variable: molgenis.services.postgres.host
|
- variable: molgenis.services.postgres.host
|
||||||
label: Postgres cluster location
|
label: Postgres cluster location
|
||||||
default: ""
|
default: "postgresql.molgenis-postgresql.svc"
|
||||||
description: "Set the location of the postgres cluster. This can be localhost when the postgres is enabled else you need to specify a cluster location if you do not want a embedded postgres instance)"
|
description: "Set the location of the postgres cluster"
|
||||||
type: string
|
type: string
|
||||||
required: true
|
required: true
|
||||||
group: "Services"
|
group: "Services"
|
||||||
@@ -108,7 +81,7 @@ questions:
|
|||||||
- variable: molgenis.resources.requests.memory
|
- variable: molgenis.resources.requests.memory
|
||||||
label: Container memory reservation
|
label: Container memory reservation
|
||||||
default: 1250Mi
|
default: 1250Mi
|
||||||
description: "Memory reservation for this MOLGENIS container (must fit in the selected memory limit for the container)"
|
description: "Memory reservation for this MOLGENIS container"
|
||||||
type: enum
|
type: enum
|
||||||
options:
|
options:
|
||||||
- "1250Mi"
|
- "1250Mi"
|
||||||
@@ -124,44 +97,3 @@ questions:
|
|||||||
- "1g"
|
- "1g"
|
||||||
- "2g"
|
- "2g"
|
||||||
group: "Resources"
|
group: "Resources"
|
||||||
- variable: persistence.enabled
|
|
||||||
default: true
|
|
||||||
description: "Do you want to use persistence"
|
|
||||||
type: boolean
|
|
||||||
required: true
|
|
||||||
group: "Persistence"
|
|
||||||
label: Persistence
|
|
||||||
show_subquestion_if: true
|
|
||||||
subquestions:
|
|
||||||
- variable: persistence.retain
|
|
||||||
default: false
|
|
||||||
description: "Do you want to retain the persistent volume"
|
|
||||||
type: boolean
|
|
||||||
label: Retain volume
|
|
||||||
- variable: molgenis.persistence.size
|
|
||||||
default: "5Gi"
|
|
||||||
description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "5Gi"
|
|
||||||
- "10Gi"
|
|
||||||
- "20Gi"
|
|
||||||
label: Size MOLGENIS filestore
|
|
||||||
- variable: elasticsearch.persistence.size
|
|
||||||
default: "5Gi"
|
|
||||||
description: "Size of ElasticSearch data (directory that is persist: /usr/share/elasticsearch/data)"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "5Gi"
|
|
||||||
- "10Gi"
|
|
||||||
- "50Gi"
|
|
||||||
label: Size for ElasticSearch data
|
|
||||||
- variable: postgres.persistence.size
|
|
||||||
default: "5Gi"
|
|
||||||
description: "Size of PostgreSQL data (directory that is persist: /var/lib/postgresql/data/pgdata)"
|
|
||||||
type: enum
|
|
||||||
options:
|
|
||||||
- "5Gi"
|
|
||||||
- "10Gi"
|
|
||||||
- "50Gi"
|
|
||||||
label: Size for PostgreSQL data
|
|
||||||
@@ -17,8 +17,6 @@ spec:
|
|||||||
matchLabels:
|
matchLabels:
|
||||||
app: {{ template "molgenis.name" . }}
|
app: {{ template "molgenis.name" . }}
|
||||||
release: {{ .Release.Name }}
|
release: {{ .Release.Name }}
|
||||||
strategy:
|
|
||||||
type: Recreate
|
|
||||||
template:
|
template:
|
||||||
metadata:
|
metadata:
|
||||||
labels:
|
labels:
|
||||||
@@ -51,11 +49,6 @@ spec:
|
|||||||
value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||||
ports:
|
ports:
|
||||||
- containerPort: 8080
|
- containerPort: 8080
|
||||||
{{- if $.Values.persistence.enabled }}
|
|
||||||
volumeMounts:
|
|
||||||
- name: molgenis-nfs
|
|
||||||
mountPath: /home/molgenis
|
|
||||||
{{- end }}
|
|
||||||
livenessProbe:
|
livenessProbe:
|
||||||
httpGet:
|
httpGet:
|
||||||
path: /
|
path: /
|
||||||
@@ -94,50 +87,10 @@ spec:
|
|||||||
ports:
|
ports:
|
||||||
- containerPort: 9200
|
- containerPort: 9200
|
||||||
- containerPort: 9300
|
- containerPort: 9300
|
||||||
{{- if $.Values.persistence.enabled }}
|
|
||||||
volumeMounts:
|
|
||||||
- name: elasticsearch-nfs
|
|
||||||
mountPath: /usr/share/elasticsearch/data
|
|
||||||
{{- end }}
|
|
||||||
resources:
|
resources:
|
||||||
{{ toYaml .resources | indent 12 }}
|
{{ toYaml .resources | indent 12 }}
|
||||||
{{- end }}
|
{{- end }}
|
||||||
|
|
||||||
- name: postgres
|
|
||||||
{{- with .Values.postgres }}
|
|
||||||
image: "{{ .image.repository }}:{{ .image.tag }}"
|
|
||||||
imagePullPolicy: {{ .image.pullPolicy }}
|
|
||||||
env:
|
|
||||||
- name: POSTGRES_USER
|
|
||||||
value: {{ $.Values.molgenis.services.postgres.user }}
|
|
||||||
- name: POSTGRES_PASSWORD
|
|
||||||
value: {{ $.Values.molgenis.services.postgres.password }}
|
|
||||||
- name: POSTGRES_DB
|
|
||||||
value: {{ $.Values.molgenis.services.postgres.scheme }}
|
|
||||||
ports:
|
|
||||||
- containerPort: 5432
|
|
||||||
resources:
|
|
||||||
{{ toYaml .resources | indent 12 }}
|
|
||||||
{{- if $.Values.persistence.enabled }}
|
|
||||||
volumeMounts:
|
|
||||||
- name: postgres-nfs
|
|
||||||
mountPath: /var/lib/postgresql/data
|
|
||||||
{{- end }}
|
|
||||||
{{- end }}
|
|
||||||
|
|
||||||
|
|
||||||
{{- if .Values.persistence.enabled }}
|
|
||||||
volumes:
|
|
||||||
- name: molgenis-nfs
|
|
||||||
persistentVolumeClaim:
|
|
||||||
claimName: {{ .Values.molgenis.persistence.claim }}
|
|
||||||
- name: elasticsearch-nfs
|
|
||||||
persistentVolumeClaim:
|
|
||||||
claimName: {{ .Values.elasticsearch.persistence.claim }}
|
|
||||||
- name: postgres-nfs
|
|
||||||
persistentVolumeClaim:
|
|
||||||
claimName: {{ .Values.postgres.persistence.claim }}
|
|
||||||
{{- end }}
|
|
||||||
|
|
||||||
{{- with .Values.nodeSelector }}
|
{{- with .Values.nodeSelector }}
|
||||||
nodeSelector:
|
nodeSelector:
|
||||||
|
|||||||
@@ -4,7 +4,7 @@
|
|||||||
apiVersion: extensions/v1beta1
|
apiVersion: extensions/v1beta1
|
||||||
kind: Ingress
|
kind: Ingress
|
||||||
metadata:
|
metadata:
|
||||||
name: "{{ $.Release.Name }}-ingress"
|
name: {{ $fullName }}
|
||||||
labels:
|
labels:
|
||||||
app: {{ template "molgenis.name" . }}
|
app: {{ template "molgenis.name" . }}
|
||||||
chart: {{ template "molgenis.chart" . }}
|
chart: {{ template "molgenis.chart" . }}
|
||||||
@@ -33,6 +33,6 @@ spec:
|
|||||||
- path: {{ $ingressPath }}
|
- path: {{ $ingressPath }}
|
||||||
backend:
|
backend:
|
||||||
serviceName: {{ $fullName }}
|
serviceName: {{ $fullName }}
|
||||||
servicePort: {{ $.Values.service.port }}
|
servicePort: 8080
|
||||||
{{- end }}
|
{{- end }}
|
||||||
{{- end }}
|
{{- end }}
|
||||||
|
|||||||
@@ -1,19 +0,0 @@
|
|||||||
{{- if .Values.persistence.enabled -}}
|
|
||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: PersistentVolumeClaim
|
|
||||||
apiVersion: v1
|
|
||||||
metadata:
|
|
||||||
name: {{ .Values.elasticsearch.persistence.claim }}
|
|
||||||
annotations:
|
|
||||||
{{- if .Values.persistence.retain }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
|
||||||
{{- else }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
|
|
||||||
{{- end }}
|
|
||||||
spec:
|
|
||||||
accessModes:
|
|
||||||
- ReadWriteMany
|
|
||||||
resources:
|
|
||||||
requests:
|
|
||||||
storage: {{ .Values.elasticsearch.persistence.size }}
|
|
||||||
{{- end }}
|
|
||||||
@@ -1,19 +0,0 @@
|
|||||||
{{- if .Values.persistence.enabled -}}
|
|
||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: PersistentVolumeClaim
|
|
||||||
apiVersion: v1
|
|
||||||
metadata:
|
|
||||||
name: {{ .Values.molgenis.persistence.claim }}
|
|
||||||
annotations:
|
|
||||||
{{- if .Values.persistence.retain }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
|
||||||
{{- else }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
|
|
||||||
{{- end }}
|
|
||||||
spec:
|
|
||||||
accessModes:
|
|
||||||
- ReadWriteMany
|
|
||||||
resources:
|
|
||||||
requests:
|
|
||||||
storage: {{ .Values.molgenis.persistence.size }}
|
|
||||||
{{- end }}
|
|
||||||
@@ -1,21 +0,0 @@
|
|||||||
{{- if .Values.molgenis.services.postgres.embedded }}
|
|
||||||
{{- if .Values.persistence.enabled }}
|
|
||||||
apiVersion: extensions/v1beta1
|
|
||||||
kind: PersistentVolumeClaim
|
|
||||||
apiVersion: v1
|
|
||||||
metadata:
|
|
||||||
name: {{ .Values.postgres.persistence.claim }}
|
|
||||||
annotations:
|
|
||||||
{{- if .Values.persistence.retain }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
|
||||||
{{- else }}
|
|
||||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
|
|
||||||
{{- end }}
|
|
||||||
spec:
|
|
||||||
accessModes:
|
|
||||||
- ReadWriteMany
|
|
||||||
resources:
|
|
||||||
requests:
|
|
||||||
storage: {{ .Values.postgres.persistence.size }}
|
|
||||||
{{- end }}
|
|
||||||
{{- end }}
|
|
||||||
@@ -9,18 +9,6 @@ metadata:
|
|||||||
heritage: {{ .Release.Service }}
|
heritage: {{ .Release.Service }}
|
||||||
spec:
|
spec:
|
||||||
type: {{ .Values.service.type }}
|
type: {{ .Values.service.type }}
|
||||||
{{- if .Values.service.firewall.enabled }}
|
|
||||||
loadBalancerSourceRanges:
|
|
||||||
{{- if .Values.service.firewall.kind eq "umcg" }}
|
|
||||||
{{- range $index, $rule := .Values.service.firewall.umcg.rules }}
|
|
||||||
- {{ $rule }}
|
|
||||||
{{- end }}
|
|
||||||
{{- else }}
|
|
||||||
{{- range $index, $rule := .Values.service.firewall.cluster.rules }}
|
|
||||||
- {{ $rule }}
|
|
||||||
{{- end }}
|
|
||||||
{{- end }}
|
|
||||||
{{- end }}
|
|
||||||
ports:
|
ports:
|
||||||
- name: molgenis
|
- name: molgenis
|
||||||
port: {{ .Values.service.port }}
|
port: {{ .Values.service.port }}
|
||||||
|
|||||||
@@ -4,15 +4,6 @@ replicaCount: 1
|
|||||||
|
|
||||||
service:
|
service:
|
||||||
type: LoadBalancer
|
type: LoadBalancer
|
||||||
firewall:
|
|
||||||
enabled: false
|
|
||||||
kind: "umcg"
|
|
||||||
umcg:
|
|
||||||
rules:
|
|
||||||
- 127.0.0.1/32
|
|
||||||
cluster:
|
|
||||||
rules:
|
|
||||||
- 127.0.0.1/32
|
|
||||||
port: 8080
|
port: 8080
|
||||||
|
|
||||||
ingress:
|
ingress:
|
||||||
@@ -40,9 +31,6 @@ molgenis:
|
|||||||
requests:
|
requests:
|
||||||
cpu: 200m
|
cpu: 200m
|
||||||
memory: 1250Mi
|
memory: 1250Mi
|
||||||
persistence:
|
|
||||||
claim: molgenis-nfs-claim
|
|
||||||
size: 5Gi
|
|
||||||
services:
|
services:
|
||||||
opencpu:
|
opencpu:
|
||||||
host: localhost
|
host: localhost
|
||||||
@@ -50,7 +38,6 @@ molgenis:
|
|||||||
transportAddresses: localhost:9300
|
transportAddresses: localhost:9300
|
||||||
clusterName: molgenis
|
clusterName: molgenis
|
||||||
postgres:
|
postgres:
|
||||||
embedded: false
|
|
||||||
host: localhost
|
host: localhost
|
||||||
scheme: molgenis
|
scheme: molgenis
|
||||||
user: molgenis
|
user: molgenis
|
||||||
@@ -70,33 +57,8 @@ elasticsearch:
|
|||||||
requests:
|
requests:
|
||||||
cpu: 100m
|
cpu: 100m
|
||||||
memory: 1Gi
|
memory: 1Gi
|
||||||
persistence:
|
|
||||||
claim: elasticsearch-nfs-claim
|
|
||||||
size: 5Gi
|
|
||||||
|
|
||||||
postgres:
|
nodeSelector: {}
|
||||||
image:
|
|
||||||
repository: postgres
|
|
||||||
tag: 9.6-alpine
|
|
||||||
pullPolicy: IfNotPresent
|
|
||||||
resources:
|
|
||||||
limits:
|
|
||||||
cpu: 1
|
|
||||||
memory: 250Mi
|
|
||||||
requests:
|
|
||||||
cpu: 100m
|
|
||||||
memory: 250Mi
|
|
||||||
persistence:
|
|
||||||
claim: postgres-nfs-claim
|
|
||||||
size: 5Gi
|
|
||||||
|
|
||||||
persistence:
|
|
||||||
enabled: true
|
|
||||||
retain: false
|
|
||||||
|
|
||||||
nodeSelector: {
|
|
||||||
deployPod: "true"
|
|
||||||
}
|
|
||||||
|
|
||||||
tolerations: []
|
tolerations: []
|
||||||
|
|
||||||
|
|||||||
Reference in New Issue
Block a user