From 2e4e397affc1d906bcb24bbf9e5be3a52b43170c Mon Sep 17 00:00:00 2001 From: Fleur Kelpin Date: Fri, 28 Sep 2018 16:47:47 +0200 Subject: [PATCH] refactor: Move charts to charts directory --- molgenis-httpd/.helmignore | 21 - molgenis-httpd/Chart.yaml | 8 - molgenis-httpd/README.md | 15 - molgenis-httpd/catalogIcon-molgenis-httpd.svg | 1182 ----------- molgenis-httpd/questions.yml | 31 - molgenis-httpd/templates/NOTES.txt | 19 - molgenis-httpd/templates/_helpers.tpl | 32 - molgenis-httpd/templates/deployment.yaml | 57 - molgenis-httpd/templates/ingress.yaml | 36 - molgenis-httpd/templates/service.yaml | 18 - molgenis-httpd/values.yaml | 51 - molgenis-jenkins/Chart.yaml | 8 - molgenis-jenkins/README.md | 111 -- .../catalogIcon-molgenis-jenkins.svg | 1768 ----------------- molgenis-jenkins/charts/jenkins-0.18.0.tgz | Bin 15194 -> 0 bytes molgenis-jenkins/requirements.lock | 6 - molgenis-jenkins/requirements.yaml | 4 - molgenis-jenkins/resources/README.md | 6 - ...nkins-default-tiller-user-rolebinding.yaml | 13 - .../resources/tiller-user-role.yaml | 18 - molgenis-jenkins/templates/config.tpl | 283 --- .../molgenis-jenkins-dockerhub-secret.yaml | 16 - .../molgenis-jenkins-github-secret.yaml | 16 - .../molgenis-jenkins-gogs-secret.yaml | 16 - .../molgenis-jenkins-registry-secret.yaml | 17 - .../molgenis-pipeline-vault-secret.yaml | 14 - molgenis-jenkins/values.yaml | 608 ------ molgenis-nexus/.helmignore | 21 - molgenis-nexus/Chart.yaml | 8 - molgenis-nexus/README.md | 64 - molgenis-nexus/catalogIcon-molgenis-nexus.svg | 551 ----- molgenis-nexus/templates/_helpers.tpl | 32 - .../deployments/nexus-deployment.yaml | 65 - .../deployments/nexusProxy-deployment.yaml | 55 - molgenis-nexus/templates/ingress.yaml | 38 - .../templates/persistence/nexusPVC.yaml | 15 - .../templates/services/nexus-service.yaml | 15 - .../services/nexusProxy-service.yaml | 13 - molgenis-nexus/values.yaml | 65 - molgenis-opencpu/.helmignore | 21 - molgenis-opencpu/Chart.yaml | 8 - molgenis-opencpu/README.md | 38 - molgenis-opencpu/catalog-molgenis-opencpu.svg | 1 - molgenis-opencpu/questions.yml | 28 - molgenis-opencpu/templates/_helpers.tpl | 32 - molgenis-opencpu/templates/deployment.yaml | 35 - molgenis-opencpu/templates/ingress.yaml | 36 - molgenis-opencpu/templates/service.yaml | 20 - molgenis-opencpu/values.yaml | 41 - molgenis-vault/.helmignore | 21 - molgenis-vault/Chart.yaml | 6 - molgenis-vault/README.md | 52 - molgenis-vault/catalogIcon-molgenis-vault.svg | 627 ------ molgenis-vault/charts/etcd-operator-0.8.0.tgz | Bin 7467 -> 0 bytes .../charts/vault-operator-0.1.1.tgz | Bin 11319 -> 0 bytes molgenis-vault/requirements.lock | 9 - molgenis-vault/requirements.yaml | 7 - molgenis-vault/resources/restore.yaml | 15 - molgenis-vault/resources/vault.yaml | 9 - molgenis-vault/templates/NOTES.txt | 13 - molgenis-vault/templates/_helpers.tpl | 54 - molgenis-vault/templates/abs-secret.yaml | 10 - .../templates/backup-configmap.yaml | 18 - molgenis-vault/templates/backup-cronjob.yaml | 30 - molgenis-vault/templates/ui-ingress.yaml | 30 - molgenis-vault/templates/ui-service.yaml | 23 - .../templates/vault-ui-deployment.yaml | 50 - molgenis-vault/values.yaml | 79 - molgenis/Chart.yaml | 8 - molgenis/README.md | 138 -- molgenis/catalogIcon-molgenis.svg | 1024 ---------- molgenis/questions.yml | 167 -- molgenis/templates/NOTES.txt | 19 - molgenis/templates/_helpers.tpl | 32 - molgenis/templates/deployment.yaml | 153 -- molgenis/templates/ingress.yaml | 38 - .../persistence/elasticsearchPVC.yaml | 19 - .../templates/persistence/molgenisPVC.yaml | 19 - .../templates/persistence/postgresPVC.yaml | 21 - molgenis/templates/service.yaml | 29 - molgenis/values.yaml | 103 - 81 files changed, 8399 deletions(-) delete mode 100644 molgenis-httpd/.helmignore delete mode 100644 molgenis-httpd/Chart.yaml delete mode 100644 molgenis-httpd/README.md delete mode 100644 molgenis-httpd/catalogIcon-molgenis-httpd.svg delete mode 100644 molgenis-httpd/questions.yml delete mode 100644 molgenis-httpd/templates/NOTES.txt delete mode 100644 molgenis-httpd/templates/_helpers.tpl delete mode 100644 molgenis-httpd/templates/deployment.yaml delete mode 100644 molgenis-httpd/templates/ingress.yaml delete mode 100644 molgenis-httpd/templates/service.yaml delete mode 100644 molgenis-httpd/values.yaml delete mode 100755 molgenis-jenkins/Chart.yaml delete mode 100644 molgenis-jenkins/README.md delete mode 100644 molgenis-jenkins/catalogIcon-molgenis-jenkins.svg delete mode 100644 molgenis-jenkins/charts/jenkins-0.18.0.tgz delete mode 100644 molgenis-jenkins/requirements.lock delete mode 100644 molgenis-jenkins/requirements.yaml delete mode 100644 molgenis-jenkins/resources/README.md delete mode 100644 molgenis-jenkins/resources/jenkins-default-tiller-user-rolebinding.yaml delete mode 100644 molgenis-jenkins/resources/tiller-user-role.yaml delete mode 100644 molgenis-jenkins/templates/config.tpl delete mode 100644 molgenis-jenkins/templates/molgenis-jenkins-dockerhub-secret.yaml delete mode 100644 molgenis-jenkins/templates/molgenis-jenkins-github-secret.yaml delete mode 100644 molgenis-jenkins/templates/molgenis-jenkins-gogs-secret.yaml delete mode 100644 molgenis-jenkins/templates/molgenis-jenkins-registry-secret.yaml delete mode 100644 molgenis-jenkins/templates/molgenis-pipeline-vault-secret.yaml delete mode 100644 molgenis-jenkins/values.yaml delete mode 100644 molgenis-nexus/.helmignore delete mode 100644 molgenis-nexus/Chart.yaml delete mode 100644 molgenis-nexus/README.md delete mode 100644 molgenis-nexus/catalogIcon-molgenis-nexus.svg delete mode 100644 molgenis-nexus/templates/_helpers.tpl delete mode 100644 molgenis-nexus/templates/deployments/nexus-deployment.yaml delete mode 100644 molgenis-nexus/templates/deployments/nexusProxy-deployment.yaml delete mode 100644 molgenis-nexus/templates/ingress.yaml delete mode 100644 molgenis-nexus/templates/persistence/nexusPVC.yaml delete mode 100644 molgenis-nexus/templates/services/nexus-service.yaml delete mode 100644 molgenis-nexus/templates/services/nexusProxy-service.yaml delete mode 100644 molgenis-nexus/values.yaml delete mode 100644 molgenis-opencpu/.helmignore delete mode 100644 molgenis-opencpu/Chart.yaml delete mode 100644 molgenis-opencpu/README.md delete mode 100644 molgenis-opencpu/catalog-molgenis-opencpu.svg delete mode 100644 molgenis-opencpu/questions.yml delete mode 100644 molgenis-opencpu/templates/_helpers.tpl delete mode 100644 molgenis-opencpu/templates/deployment.yaml delete mode 100644 molgenis-opencpu/templates/ingress.yaml delete mode 100644 molgenis-opencpu/templates/service.yaml delete mode 100644 molgenis-opencpu/values.yaml delete mode 100644 molgenis-vault/.helmignore delete mode 100644 molgenis-vault/Chart.yaml delete mode 100644 molgenis-vault/README.md delete mode 100644 molgenis-vault/catalogIcon-molgenis-vault.svg delete mode 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delete mode 100644 molgenis/questions.yml delete mode 100644 molgenis/templates/NOTES.txt delete mode 100644 molgenis/templates/_helpers.tpl delete mode 100644 molgenis/templates/deployment.yaml delete mode 100644 molgenis/templates/ingress.yaml delete mode 100644 molgenis/templates/persistence/elasticsearchPVC.yaml delete mode 100644 molgenis/templates/persistence/molgenisPVC.yaml delete mode 100644 molgenis/templates/persistence/postgresPVC.yaml delete mode 100644 molgenis/templates/service.yaml delete mode 100644 molgenis/values.yaml diff --git a/molgenis-httpd/.helmignore b/molgenis-httpd/.helmignore deleted file mode 100644 index f0c1319..0000000 --- a/molgenis-httpd/.helmignore +++ /dev/null @@ -1,21 +0,0 @@ -# Patterns to ignore when building packages. -# This supports shell glob matching, relative path matching, and -# negation (prefixed with !). Only one pattern per line. -.DS_Store -# Common VCS dirs -.git/ -.gitignore -.bzr/ -.bzrignore -.hg/ -.hgignore -.svn/ -# Common backup files -*.swp -*.bak -*.tmp -*~ -# Various IDEs -.project -.idea/ -*.tmproj diff --git a/molgenis-httpd/Chart.yaml b/molgenis-httpd/Chart.yaml deleted file mode 100644 index 4fe30f7..0000000 --- a/molgenis-httpd/Chart.yaml +++ /dev/null @@ -1,8 +0,0 @@ -apiVersion: v1 -appVersion: "1.0" -description: HTTPD for MOLGENIS -name: molgenis-httpd -version: 0.1.0 -sources: -- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git -icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-httpd/catalogIcon-molgenis-httpd.svg \ No newline at end of file diff --git a/molgenis-httpd/README.md b/molgenis-httpd/README.md deleted file mode 100644 index 6f7a8df..0000000 --- a/molgenis-httpd/README.md +++ /dev/null @@ -1,15 +0,0 @@ -# MOLGENIS - HTTPD Helm Chart - -HTTPD (web)server for kubernetes to deploy on a kubernetes cluster with NFS-share - -## Chart Details - -This chart will deploy: - -- 1 HTTPD container - -## Installing the Chart - -etc. - - diff --git a/molgenis-httpd/catalogIcon-molgenis-httpd.svg b/molgenis-httpd/catalogIcon-molgenis-httpd.svg deleted file mode 100644 index c1ef350..0000000 --- a/molgenis-httpd/catalogIcon-molgenis-httpd.svg +++ /dev/null @@ -1,1182 +0,0 @@ - - - - diff --git a/molgenis-httpd/questions.yml b/molgenis-httpd/questions.yml deleted file mode 100644 index 623c3cf..0000000 --- a/molgenis-httpd/questions.yml +++ /dev/null @@ -1,31 +0,0 @@ -categories: -- MOLGENIS -questions: -- variable: ingress.hosts[0].name - default: "test.molgenis.org" - description: "Hostname for your stack" - type: hostname - required: true - group: "Services and Load Balancing" - label: Hostname -- variable: httpd.hostname - default: "test.molgenis.org" - description: "Hostname for your services (comma separated, example: [hostname]:[port])" - type: string - required: false - group: "Apache configuration" - label: Hostname -- variable: httpd.proxy - default: "" - description: "Proxy for your services (comma separated, example: [service]:[port]:[path])" - type: string - required: false - group: "Apache configuration" - label: Proxy -- variable: httpd.redirect - default: "" - description: "Redirection urls for your services (comma separated, example: [redirection_url])" - type: string - required: false - group: "Apache configuration" - label: Redirection \ No newline at end of file diff --git a/molgenis-httpd/templates/NOTES.txt b/molgenis-httpd/templates/NOTES.txt deleted file mode 100644 index b486fa5..0000000 --- a/molgenis-httpd/templates/NOTES.txt +++ /dev/null @@ -1,19 +0,0 @@ -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 "httpd.fullname" . }}) - export NODE_IP=$(kubectl get nodes --namespace {{ .Release.Namespace }} -o jsonpath="{.items[0].status.addresses[0].address}") - echo http://$NODE_IP:$NODE_PORT -{{- else if contains "LoadBalancer" .Values.service.type }} - NOTE: It may take a few minutes for the LoadBalancer IP to be available. - You can watch the status of by running 'kubectl get svc -w {{ template "httpd.fullname" . }}' - export SERVICE_IP=$(kubectl get svc --namespace {{ .Release.Namespace }} {{ template "httpd.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 "httpd.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 }} diff --git a/molgenis-httpd/templates/_helpers.tpl b/molgenis-httpd/templates/_helpers.tpl deleted file mode 100644 index 6968597..0000000 --- a/molgenis-httpd/templates/_helpers.tpl +++ /dev/null @@ -1,32 +0,0 @@ -{{/* vim: set filetype=mustache: */}} -{{/* -Expand the name of the chart. -*/}} -{{- define "httpd.name" -}} -{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}} -{{- end -}} - -{{/* -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). -If release name contains chart name it will be used as a full name. -*/}} -{{- define "httpd.fullname" -}} -{{- if .Values.fullnameOverride -}} -{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}} -{{- else -}} -{{- $name := default .Chart.Name .Values.nameOverride -}} -{{- if contains $name .Release.Name -}} -{{- .Release.Name | trunc 63 | trimSuffix "-" -}} -{{- else -}} -{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}} -{{- end -}} -{{- end -}} -{{- end -}} - -{{/* -Create chart name and version as used by the chart label. -*/}} -{{- define "httpd.chart" -}} -{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}} -{{- end -}} diff --git a/molgenis-httpd/templates/deployment.yaml b/molgenis-httpd/templates/deployment.yaml deleted file mode 100644 index a55964a..0000000 --- a/molgenis-httpd/templates/deployment.yaml +++ /dev/null @@ -1,57 +0,0 @@ -apiVersion: apps/v1beta2 -kind: Deployment -metadata: - name: {{ template "httpd.fullname" . }} - labels: - app: {{ template "httpd.name" . }} - chart: {{ template "httpd.chart" . }} - release: {{ .Release.Name }} - heritage: {{ .Release.Service }} -spec: - replicas: {{ .Values.replicaCount }} - selector: - matchLabels: - app: {{ template "httpd.name" . }} - release: {{ .Release.Name }} - template: - metadata: - labels: - app: {{ template "httpd.name" . }} - release: {{ .Release.Name }} - spec: - containers: - - name: {{ .Chart.Name }} - image: "{{ .Values.image.repository }}:{{ .Values.image.tag }}" - imagePullPolicy: {{ .Values.image.pullPolicy }} - ports: - - name: {{ .Values.service.name }} - containerPort: {{ .Values.service.port }} - env: - - name: SERVER_NAME - value: "{{ .Values.httpd.hostname }}" - - name: PROXY_SERVICE - value: "{{ .Values.httpd.proxy }}" - - name: REDIRECT_URL - value: "{{ .Values.httpd.redirect }}" - livenessProbe: - httpGet: - path: / - port: http - readinessProbe: - httpGet: - path: / - port: http - resources: -{{ toYaml .Values.resources | indent 12 }} - {{- with .Values.nodeSelector }} - nodeSelector: -{{ toYaml . | indent 8 }} - {{- end }} - {{- with .Values.affinity }} - affinity: -{{ toYaml . | indent 8 }} - {{- end }} - {{- with .Values.tolerations }} - tolerations: -{{ toYaml . | indent 8 }} - {{- end }} diff --git a/molgenis-httpd/templates/ingress.yaml b/molgenis-httpd/templates/ingress.yaml deleted file mode 100644 index 83a8d70..0000000 --- a/molgenis-httpd/templates/ingress.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{{- if .Values.ingress.enabled }} -{{- range .Values.ingress.hosts }} -apiVersion: extensions/v1beta1 -kind: Ingress -metadata: - name: "{{ $.Release.Name }}-ingress" - labels: - app: {{ template "httpd.fullname" $ }} - 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: {{ template "httpd.fullname" $ }} - servicePort: 80 -{{- if .tls }} - tls: - - hosts: - - {{ .name }} - secretName: {{ .tlsSecret }} -{{- end }} ---- -{{- end }} -{{- end }} \ No newline at end of file diff --git a/molgenis-httpd/templates/service.yaml b/molgenis-httpd/templates/service.yaml deleted file mode 100644 index b3f1374..0000000 --- a/molgenis-httpd/templates/service.yaml +++ /dev/null @@ -1,18 +0,0 @@ -apiVersion: v1 -kind: Service -metadata: - name: {{ template "httpd.fullname" . }} - labels: - app: {{ template "httpd.name" . }} - chart: {{ template "httpd.chart" . }} - release: {{ .Release.Name }} - heritage: {{ .Release.Service }} -spec: - type: {{ .Values.service.type }} - ports: - - name: {{ .Values.service.name }} - port: {{ .Values.service.port }} - - selector: - app: {{ template "httpd.name" . }} - release: {{ .Release.Name }} diff --git a/molgenis-httpd/values.yaml b/molgenis-httpd/values.yaml deleted file mode 100644 index 04fffb6..0000000 --- a/molgenis-httpd/values.yaml +++ /dev/null @@ -1,51 +0,0 @@ -# Default values for jenkins. -# This is a YAML-formatted file. -# Declare variables to be passed into your templates. - -replicaCount: 1 - -image: - repository: registry.webhosting.rug.nl/molgenis/httpd - tag: lts - pullPolicy: Always - -service: - name: httpd - type: ClusterIP - port: 80 - -httpd: - proxy: httpd:80:/ - redirect: redirect.molgenis.local - hostname: test.molgenis.local - -ingress: - enabled: true - annotations: {} - # kubernetes.io/ingress.class: nginx - # kubernetes.io/tls-acme: "true" - path: / - hosts: - - name: test.molgenis.org - tls: [] - # - secretName: chart-example-tls - # hosts: - # - chart-example.local - -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: {} - -tolerations: [] - -affinity: {} \ No newline at end of file diff --git a/molgenis-jenkins/Chart.yaml b/molgenis-jenkins/Chart.yaml deleted file mode 100755 index 855c692..0000000 --- a/molgenis-jenkins/Chart.yaml +++ /dev/null @@ -1,8 +0,0 @@ -name: molgenis-jenkins -home: https://jenkins.io/ -version: 0.7.1 -appVersion: 2.121 -description: Molgenis installation for the jenkins chart. -sources: -- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git -icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-jenkins/catalogIcon-molgenis-jenkins.svg diff --git a/molgenis-jenkins/README.md b/molgenis-jenkins/README.md deleted file mode 100644 index 48c0a53..0000000 --- a/molgenis-jenkins/README.md +++ /dev/null @@ -1,111 +0,0 @@ -# Molgenis Jenkins Helm Chart - -Jenkins master and slave cluster utilizing the Jenkins Kubernetes plugin. -Wraps [the kuberenetes jenkins chart](https://github.com/kubernetes/charts/tree/master/stable/jenkins), see documentation there! - -## Chart Details - -This chart will do the following: - -* 1 x Jenkins Master with port 8080 exposed on an external ClusterIP -* All using Kubernetes Deployments - -## Installing the Chart - -Usually, you'll be deploying this to the molgenis cluster. -In the [Rancher Catalog](https://rancher.molgenis.org:7443/g/catalog), add the latest version of this repository. -In the [molgenis cluster management page](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/apps), choose the -catalog, pick the molgenis-jenkins app from the catalog and deploy it. - -## Configuration - -When deploying, you can paste values into the Rancher Answers to override the defaults in this chart. -Array values can be added as {value, value, value}. -``` -jenkins.Master.HostName=jenkins.molgenis.org -jenkins.Master.AdminPassword=pa$$word -jenkins.Persistence.Enabled=false -jenkins.Master.InstallPlugins={kubernetes:1.8.4, workflow-aggregator:2.5, workflow-job:2.21, credentials-binding:1.16, git:3.9.1, blueocean:1.6.2, github-oauth:0.29} -jenkins.Master.Security.UseGitHub=false -## if UseGitHub=true -jenkins.Master.Security.GitHub.ClientID=id -jenkins.Master.Security.GitHub.ClientSecret=S3cr3t -## end UseGitHub=true -PipelineSecrets.Env.PGPPassphrase=literal:S3cr3t -``` - -You can use [all configuration values of the jenkins subchart](https://github.com/kubernetes/charts/tree/master/stable/jenkins). -> Because we use jenkins as a sub-chart, you should prefix all value keys with `jenkins`! - -### GitHub Authentication delegation -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). - -### Secrets - - When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins. - - You can override the values at deploy time but otherwise also configure them - [in Rancher](https://rancher.molgenis.org:7443/p/c-mhkqb:project-2pf45/secrets) or through kubectl. - -#### Vault - -The vault secret gets mounted in the vault pod so pipeline scripts can retrieve secrets from the vault. - -| Parameter | Description | Default | -| ------------------------- | ------------------------------------------ | ---------------------------------------------- | -| `secret.vault.token` | Token to log into the hashicorp vault | `xxxx` | -| `secret.vault.addr` | Address of the vault | `https:vault-operator.vault-operator.svc:8200` | -| `secret.vault.skipVerify` | Skip verification of the https connection | `1` | - -#### GitHub - -Token used by Jenkins to authenticate on GitHub. - -| Parameter | Description | Default | -| --------------------- | ------------------------ | ------------------ | -| `secret.gitHub.user` | username for the account | `molgenis-jenkins` | -| `secret.gitHub.token` | token for the account | `xxxx` | - -#### Gogs - -Token used by Jenkins to authenticate on the [RuG Webhosting Gogs](https://git.webhosting.rug.nl). - -| Parameter | Description | Default | -| ------------------- | ------------------------ | --------- | -| `secret.gogs.user` | username for the account | `p281392` | -| `secret.gogs.token` | token for the account | `xxxx` | - -#### Legacy: - -##### Docker Hub - -Account used in pipeline builds to push docker images to `hub.docker.com`. -> They should read `secret/gcc/account/dockerhub` from vault instead! - -| Parameter | Description | Default | -| --------------------------- | ------------------------ | --------------- | -| `secret.dockerHub.user` | username for the account | `molgenisci` | -| `secret.dockerHub.password` | password for the account | `xxxx` | - -##### Registry - -Account used in pipeline builds to push docker images to `registry.molgenis.org`. -> They should read `secret/ops/account/nexus` from vault instead! - -| Parameter | Description | Default | -| --------------------------- | ------------------------ | --------- | -| `secret.dockerHub.user` | username for the account | `admin` | -| `secret.dockerHub.password` | password for the account | `xxxx` | - -## Command line use -Specify each parameter using the `--set key=value[,key=value]` argument to `helm install`. - -Alternatively, a YAML file that specifies the values for the parameters can be provided while installing the chart. -For example, - -```bash -$ helm install --name jenkins -f values.yaml molgenis-jenkins -``` - -> **Tip**: You can use the default [values.yaml](values.yaml) - diff --git a/molgenis-jenkins/catalogIcon-molgenis-jenkins.svg b/molgenis-jenkins/catalogIcon-molgenis-jenkins.svg deleted file mode 100644 index 1227303..0000000 --- a/molgenis-jenkins/catalogIcon-molgenis-jenkins.svg +++ /dev/null @@ -1,1768 +0,0 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repository: https://kubernetes-charts.storage.googleapis.com/ - version: 0.18.0 -digest: sha256:39f694515489598fa545c9a5a4f1347749e8f2a8d7fae6ccae3e2acae1564685 -generated: 2018-09-27T11:00:15.795416984+02:00 diff --git a/molgenis-jenkins/requirements.yaml b/molgenis-jenkins/requirements.yaml deleted file mode 100644 index b9331d0..0000000 --- a/molgenis-jenkins/requirements.yaml +++ /dev/null @@ -1,4 +0,0 @@ -dependencies: - - name: jenkins - version: ^0.16 - repository: https://kubernetes-charts.storage.googleapis.com/ \ No newline at end of file diff --git a/molgenis-jenkins/resources/README.md b/molgenis-jenkins/resources/README.md deleted file mode 100644 index 67bf687..0000000 --- a/molgenis-jenkins/resources/README.md +++ /dev/null @@ -1,6 +0,0 @@ -To be able to run helm inside a jenkins pod, you'll need to -* create a role in the namespace where tiller is installed -* bind that role to the user that jenkins pods run as - -This directory contains yaml for these resources. -See also https://github.com/helm/helm/blob/master/docs/rbac.md \ No newline at end of file diff --git a/molgenis-jenkins/resources/jenkins-default-tiller-user-rolebinding.yaml b/molgenis-jenkins/resources/jenkins-default-tiller-user-rolebinding.yaml deleted file mode 100644 index 04aa1f7..0000000 --- a/molgenis-jenkins/resources/jenkins-default-tiller-user-rolebinding.yaml +++ /dev/null @@ -1,13 +0,0 @@ -apiVersion: rbac.authorization.k8s.io/v1beta1 -kind: RoleBinding -metadata: - name: tiller-jenkins-binding - namespace: kube-system -roleRef: - apiGroup: rbac.authorization.k8s.io - kind: Role - name: tiller-user -subjects: -- kind: ServiceAccount - name: default - namespace: molgenis-jenkins \ No newline at end of file diff --git a/molgenis-jenkins/resources/tiller-user-role.yaml b/molgenis-jenkins/resources/tiller-user-role.yaml deleted file mode 100644 index 5555442..0000000 --- a/molgenis-jenkins/resources/tiller-user-role.yaml +++ /dev/null @@ -1,18 +0,0 @@ -apiVersion: rbac.authorization.k8s.io/v1beta1 -kind: Role -metadata: - name: tiller-user - namespace: kube-system -rules: -- apiGroups: - - "" - resources: - - pods/portforward - verbs: - - create -- apiGroups: - - "" - resources: - - pods - verbs: - - list \ No newline at end of file diff --git a/molgenis-jenkins/templates/config.tpl b/molgenis-jenkins/templates/config.tpl deleted file mode 100644 index d899427..0000000 --- a/molgenis-jenkins/templates/config.tpl +++ /dev/null @@ -1,283 +0,0 @@ -{{- define "override_config_map" }} -apiVersion: v1 -kind: ConfigMap -metadata: - name: {{ template "jenkins.fullname" . }} -data: - config.xml: |- - - - - {{ .Values.Master.ImageTag }} - 0 - NORMAL - {{ .Values.Master.UseSecurity }} - - true - -{{- if .Values.Master.Security.UseGitHub }} - - https://github.com - https://api.github.com - {{ .Values.Master.Security.GitHub.ClientID }} - {{ .Values.Master.Security.GitHub.ClientSecret }} - read:org,user:email - -{{- else }} - -{{- end }} - false - - ${JENKINS_HOME}/workspace/${ITEM_FULLNAME} - ${ITEM_ROOTDIR}/builds - - - dev - - - - - kubernetes - -{{- range $podName, $pod := .Values.Pods }} - - {{ $pod.InheritFrom | default "" }} - {{ $podName }} - 2147483647 - 0 - - - {{- $local := dict "first" true }} - {{- range $key, $value := .NodeSelector }} - {{- if not $local.first }},{{- end }} - {{- $key }}={{ $value }} - {{- $_ := set $local "first" false }} - {{- end }} - {{ .NodeUsageMode }} - -{{- range $index, $volume := .volumes }} - -{{- range $key, $value := $volume }}{{- if not (eq $key "type") }} - <{{ $key }}>{{ $value }} -{{- end }}{{- end }} - -{{- end }} - - -{{- range $containerName, $container := .Containers }} - - {{ $containerName }} - {{ .Image }}:{{ .ImageTag | default "latest" }} - -{{- range $index, $envVar := .Ports }} - - {{ .name }} - {{ .containerPort }} - {{ .hostPort }} - -{{- end }} - -{{- if .Privileged }} - true -{{- else }} - false -{{- end }} -{{- if .AlwaysPullImage }} - true -{{- else }} - false -{{- end }} - {{ .WorkingDir | default "" }} - {{ .Command | default "" }} - {{ .Args | default "" }} -{{- if .TTY }} - true -{{- else }} - false -{{- end }} - -{{- range $index, $envVar := .EnvVars }} - -{{- range $key, $value := $envVar }}{{- if not (eq $key "type") }} - <{{ $key }}>{{ $value }} -{{- end }}{{- end }} - -{{- end }} - -{{- if .resources }} -{{- if .resources.requests }} - {{ .resources.requests.cpu | default "" }} - {{ .resources.requests.memory | default "" }} -{{- end }} -{{- if .resources.limits }} - {{ .resources.limits.cpu | default "" }} - {{ .resources.limits.memory | default "" }} -{{- end }} -{{- end }} - -{{- end }} - - - - JENKINS_URL - http://{{ template "jenkins.fullname" $ }}:{{$.Values.Master.ServicePort}}{{ default "" $.Values.Master.JenkinsUriPrefix }} - -{{- range $index, $envVar := .EnvVars }} - -{{- range $key, $value := $envVar }}{{- if not (eq $key "type") }} - <{{ $key }}>{{ $value }} -{{- end }}{{- end }} - -{{- end }} - - -{{- if .ImagePullSecret }} - - - {{ .ImagePullSecret }} - - -{{- else }} - -{{- end }} - - -{{- end }} - - https://kubernetes.default - false - {{ .Release.Namespace }} - http://{{ template "jenkins.fullname" . }}:{{.Values.Master.ServicePort}}{{ default "" .Values.Master.JenkinsUriPrefix }} - {{ template "jenkins.fullname" . }}-agent:50000 - 50 - 5 - 0 - 0 - - - 5 - 0 - - - - all - false - false - - -{{- range $viewName, $view := .Values.Master.Views }} - - - {{ $viewName }} - false - false - - - -{{- range $index, $job := $view }} - {{ $job }} -{{- end }} - - - - - - - - - - - - - false - -{{- end }} - - {{ .Values.Master.DefaultView }} - 50000 - -{{- range .Values.Master.DisabledAgentProtocols }} - {{ . }} -{{- end }} - - -{{- if .Values.Master.CSRF.DefaultCrumbIssuer.Enabled }} - -{{- if .Values.Master.CSRF.DefaultCrumbIssuer.ProxyCompatability }} - true -{{- end }} - -{{- end }} - - - true - -{{- if .Values.Master.ScriptApproval }} - scriptapproval.xml: |- - - - - -{{- range $key, $val := .Values.Master.ScriptApproval }} - {{ $val }} -{{- end }} - - - - - - - -{{- end }} - jenkins.CLI.xml: |- - - -{{- if .Values.Master.CLI }} - true -{{- else }} - false -{{- end }} - - apply_config.sh: |- - mkdir -p /usr/share/jenkins/ref/secrets/; - echo "false" > /usr/share/jenkins/ref/secrets/slave-to-master-security-kill-switch; - cp -n /var/jenkins_config/config.xml /var/jenkins_home; - cp -n /var/jenkins_config/jenkins.CLI.xml /var/jenkins_home; -{{- if .Values.Master.InstallPlugins }} - # Install missing plugins - cp /var/jenkins_config/plugins.txt /var/jenkins_home; - rm -rf /usr/share/jenkins/ref/plugins/*.lock - /usr/local/bin/install-plugins.sh `echo $(cat /var/jenkins_home/plugins.txt)`; - # Copy plugins to shared volume - cp -n /usr/share/jenkins/ref/plugins/* /var/jenkins_plugins; -{{- end }} -{{- if .Values.Master.ScriptApproval }} - cp -n /var/jenkins_config/scriptapproval.xml /var/jenkins_home/scriptApproval.xml; -{{- end }} -{{- if .Values.Master.InitScripts }} - mkdir -p /var/jenkins_home/init.groovy.d/; - cp -n /var/jenkins_config/*.groovy /var/jenkins_home/init.groovy.d/ -{{- end }} -{{- if .Values.Master.CredentialsXmlSecret }} - cp -n /var/jenkins_credentials/credentials.xml /var/jenkins_home; -{{- end }} -{{- if .Values.Master.SecretsFilesSecret }} - cp -n /var/jenkins_secrets/* /usr/share/jenkins/ref/secrets; -{{- end }} -{{- if .Values.Master.Jobs }} - for job in $(ls /var/jenkins_jobs); do - mkdir -p /var/jenkins_home/jobs/$job - cp -n /var/jenkins_jobs/$job /var/jenkins_home/jobs/$job/config.xml - done -{{- end }} -{{- range $key, $val := .Values.Master.InitScripts }} - init{{ $key }}.groovy: |- -{{ $val | indent 4 }} -{{- end }} - plugins.txt: |- -{{- if .Values.Master.InstallPlugins }} -{{- range $index, $val := .Values.Master.InstallPlugins }} -{{ $val | indent 4 }} -{{- end }} -{{- end }} -{{- end }} \ No newline at end of file diff --git a/molgenis-jenkins/templates/molgenis-jenkins-dockerhub-secret.yaml b/molgenis-jenkins/templates/molgenis-jenkins-dockerhub-secret.yaml deleted file mode 100644 index 5c35b46..0000000 --- a/molgenis-jenkins/templates/molgenis-jenkins-dockerhub-secret.yaml +++ /dev/null @@ -1,16 +0,0 @@ -apiVersion: v1 -kind: Secret -metadata: -# this is the jenkins id. - name: "molgenis-jenkins-dockerhub-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" : "(deprecated by vault) Account used in pipeline builds to push docker images to Docker Hub (hub.docker.com)" - } -type: Opaque -data: - username: {{ .Values.secret.registry.user | b64enc | quote }} - password: {{ .Values.secret.registry.password | b64enc | quote }} \ No newline at end of file diff --git a/molgenis-jenkins/templates/molgenis-jenkins-github-secret.yaml b/molgenis-jenkins/templates/molgenis-jenkins-github-secret.yaml deleted file mode 100644 index dc2b8df..0000000 --- a/molgenis-jenkins/templates/molgenis-jenkins-github-secret.yaml +++ /dev/null @@ -1,16 +0,0 @@ -apiVersion: v1 -kind: Secret -metadata: -# this is the jenkins id. - name: "molgenis-jenkins-github-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" : "Oauth token for the {{.Values.secret.gitHub.user}} GitHub user" - } -type: Opaque -data: - username: {{ .Values.secret.gitHub.user | b64enc | quote }} - password: {{ .Values.secret.gitHub.token | b64enc | quote }} \ No newline at end of file diff --git a/molgenis-jenkins/templates/molgenis-jenkins-gogs-secret.yaml b/molgenis-jenkins/templates/molgenis-jenkins-gogs-secret.yaml deleted file mode 100644 index ff6ae17..0000000 --- a/molgenis-jenkins/templates/molgenis-jenkins-gogs-secret.yaml +++ /dev/null @@ -1,16 +0,0 @@ -apiVersion: v1 -kind: Secret -metadata: -# this is the jenkins id. - name: "molgenis-jenkins-gogs-secret" - labels: -# so we know what type it is. - "jenkins.io/credentials-type": "usernamePassword" - annotations: { -# description - can not be a label as spaces are not allowed - "jenkins.io/credentials-description" : "Account used to authenticate against RuG Webhosting Gogs." - } -type: Opaque -data: - username: {{ .Values.secret.gogs.user | b64enc | quote }} - password: {{ .Values.secret.gogs.token | b64enc | quote }} \ No newline at end of file diff --git a/molgenis-jenkins/templates/molgenis-jenkins-registry-secret.yaml b/molgenis-jenkins/templates/molgenis-jenkins-registry-secret.yaml deleted file mode 100644 index b853055..0000000 --- a/molgenis-jenkins/templates/molgenis-jenkins-registry-secret.yaml +++ /dev/null @@ -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 }} \ No newline at end of file diff --git a/molgenis-jenkins/templates/molgenis-pipeline-vault-secret.yaml b/molgenis-jenkins/templates/molgenis-pipeline-vault-secret.yaml deleted file mode 100644 index da4598b..0000000 --- a/molgenis-jenkins/templates/molgenis-pipeline-vault-secret.yaml +++ /dev/null @@ -1,14 +0,0 @@ -apiVersion: v1 -kind: Secret -metadata: - name: molgenis-pipeline-vault-secret - labels: - app: {{ template "jenkins.fullname" . }} - chart: "{{ .Chart.Name }}-{{ .Chart.Version }}" - release: "{{ .Release.Name }}" - heritage: "{{ .Release.Service }}" -type: Opaque -data: - token: {{ .Values.secret.vault.token | b64enc | quote }} - addr: {{ .Values.secret.vault.addr | b64enc | quote }} - skipVerify: {{ .Values.secret.vault.skipVerify | b64enc | quote }} \ No newline at end of file diff --git a/molgenis-jenkins/values.yaml b/molgenis-jenkins/values.yaml deleted file mode 100644 index 9816fee..0000000 --- a/molgenis-jenkins/values.yaml +++ /dev/null @@ -1,608 +0,0 @@ -jenkins: - Master: - HostName: jenkins.molgenis.org - ServiceType: ClusterIP - InstallPlugins: - - kubernetes:1.12.6 - - workflow-aggregator:2.5 - - workflow-job:2.25 - - credentials-binding:1.16 - - git:3.9.1 - - github-branch-source:2.3.6 - - kubernetes-credentials-provider:0.10 - - blueocean:1.8.3 - - github-oauth:0.29 - - gogs-webhook:1.0.14 - - github-scm-trait-commit-skip:0.1.1 - Security: - UseGitHub: false - GitHub: - ClientID: "" - ClienSecret: "" - DefaultView: dev - Views: - dev: - - molgenis - ops: - - molgenis-ops-docker-httpd - - molgenis-ops-docker-maven - - molgenis-ops-docker-node - - molgenis-ops-tools - - molgenis-ops-tomcat - Jobs: |- - molgenis: |- - - - - - - - - - - - .* - - - - - - - - false - - - - - - - true - -1 - -1 - - - - H H * * * - 86400000 - - - false - - - molgenis - molgenis-jenkins-github-secret - - - 1 - - - 1 - - - 1 - - - - - - ** - - - - - MOLGENIS Jenkins - molgenis+ci@gmail.com - - - - - - - - Jenkinsfile - - - - - molgenis-ops-docker-httpd: |- - - - - HTTPD server that can be used for redirection and proxieing - molgenis-ops-docker-httpd - - - - - - - - - - - - false - - - - - - - true - -1 - -1 - - - false - - - - - a756941d-6c9d-4492-bcf9-327041764be6 - https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-httpd.git - molgenis-jenkins-gogs-secret - - - - - ** - - - - - MOLGENIS Jenkins - molgenis+ci@gmail.com - - - - - - - - - - - - - - Jenkinsfile - - - molgenis-ops-docker-node: |- - - - - NodeJS build container with Curl - molgenis-ops-docker-node - - - - - - - - - - - - false - - - - - - - true - -1 - -1 - - - false - - - - - a756941d-6c9d-4492-bcf9-327041764be6 - https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-node.git - molgenis-jenkins-gogs-secret - - - - - ** - - - - - MOLGENIS Jenkins - molgenis+ci@gmail.com - - - - - - - - - - - - - - Jenkinsfile - - - molgenis-ops-docker-maven: |- - - - - MAVEN build container with RPMbuild and Curl - molgenis-ops-docker-maven - - - - - - - - - - - - false - - - - - - - true - -1 - -1 - - - false - - - - - 4702479a-6988-4a85-b4b7-e77fa2d05ffa - https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-maven.git - molgenis-jenkins-gogs-secret - - - - - ** - - - - - MOLGENIS Jenkins - molgenis+ci@gmail.com - - - - - - - - - - - - - - Jenkinsfile - - - molgenis-ops-tomcat: |- - - - - MOLGENIS tomcat package to manage tomcat version on CentOS - molgenis-ops-tomcat - - - - - - - - - - - - false - - - - - - - true - -1 - -1 - - - false - - - - - 4702479a-6988-4a85-b4b7-e77fa2d05ffa - https://git.webhosting.rug.nl/molgenis/molgenis-ops-tomcat.git - molgenis-jenkins-gogs-secret - - - - - ** - - - - - MOLGENIS Jenkins - molgenis+ci@gmail.com - - - - - - - - - - - - - - Jenkinsfile - - - molgenis-ops-tools: |- - - - - MOLGENIS operations tools-package to configure firewall, apache, sudoers, etc. - molgenis-ops-tools - - - - - - - - - - - - false - - - - - - - true - -1 - -1 - - - false - - - - - 4702479a-6988-4a85-b4b7-e77fa2d05ffa - https://git.webhosting.rug.nl/molgenis/molgenis-ops-tools.git - molgenis-jenkins-gogs-secret - - - - - ** - - - - - MOLGENIS Jenkins - molgenis+ci@gmail.com - - - - - - - - - - - - - - Jenkinsfile - - - # Kubernetes secret that contains a 'credentials.xml' for Jenkins - # CredentialsXmlSecret: jenkins-credentials - # Kubernetes secret that contains files to be put in the Jenkins 'secrets' directory, - # useful to manage encryption keys used for credentials.xml for instance (such as - # master.key and hudson.util.Secret) - # SecretsFilesSecret: jenkins-secrets - CustomConfigMap: true - rbac: - install: true - Pods: - molgenis: - Label: molgenis - NodeUsageMode: NORMAL - volumes: - - type: HostPath - hostPath: "/var/run/docker.sock" - mountPath: "/var/run/docker.sock" - Containers: - maven: - Image: "registry.webhosting.rug.nl/molgenis/maven" - ImageTag: lts - AlwaysPullImage: true - Command: cat - WorkingDir: /home/jenkins - TTY: true - resources: - requests: - cpu: "1" - memory: "4Gi" - EnvVars: - - type: KeyValue - key: MAVEN_OPTS - value: "-Duser.home=/home/jenkins" - - type: KeyValue - key: MAVEN_CONFIG - value: "/home/jenkins/.m2" - alpine: - Image: "spotify/alpine" - Command: cat - WorkingDir: /home/jenkins - TTY: true - vault: - Image: "vault" - Command: cat - WorkingDir: /home/jenkins - TTY: true - EnvVars: - - type: Secret - key: VAULT_TOKEN - secretName: molgenis-pipeline-vault-secret - secretKey: token - - type: Secret - key: VAULT_SKIP_VERIFY - secretName: molgenis-pipeline-vault-secret - secretKey: skipVerify - - type: Secret - key: VAULT_ADDR - secretName: molgenis-pipeline-vault-secret - secretKey: addr - helm: - Image: "lachlanevenson/k8s-helm" - ImageTag: "v2.10.0" - Command: cat - WorkingDir: /home/jenkins - TTY: true - NodeSelector: {} - node: - Label: node-carbon - NodeUsageMode: EXCLUSIVE - Containers: - node: - Image: "registry.webhosting.rug.nl/molgenis/node" - ImageTag: lts - AlwaysPullImage: true - Command: cat - WorkingDir: /home/jenkins - TTY: true - vault: - Image: "vault" - Command: cat - WorkingDir: /home/jenkins - TTY: true - EnvVars: - - type: Secret - key: VAULT_TOKEN - secretName: molgenis-pipeline-vault-secret - secretKey: token - - type: Secret - key: VAULT_SKIP_VERIFY - secretName: molgenis-pipeline-vault-secret - secretKey: skipVerify - - type: Secret - key: VAULT_ADDR - secretName: molgenis-pipeline-vault-secret - secretKey: addr - NodeSelector: {} - molgenis-it: - InheritFrom: molgenis - Label: molgenis-it - NodeUsageMode: EXCLUSIVE - Containers: - elasticsearch: - Image: docker.elastic.co/elasticsearch/elasticsearch - ImageTag: 5.5.3 - resources: - requests: - cpu: "100m" - memory: "1Gi" - limits: - cpu: "1" - memory: "1500Mi" - EnvVars: - - type: KeyValue - key: ES_JAVA_OPTS - value: "-Xms512m -Xmx512m" - - type: KeyValue - key: cluster.name - value: molgenis - - type: KeyValue - key: bootstrap.memory_lock - value: "true" - - type: KeyValue - key: xpack.security.enabled - value: "false" - - type: KeyValue - key: discovery.type - value: single-node - postgres: - Image: postgres - ImageTag: 9.6-alpine - resources: - requests: - cpu: "100m" - memory: "250Mi" - limits: - cpu: "1" - memory: "250Mi" - EnvVars: - - type: KeyValue - key: POSTGRES_USER - value: molgenis - - type: KeyValue - key: POSTGRES_PASSWORD - value: molgenis - - type: KeyValue - key: POSTGRES_DB - value: molgenis - opencpu: - Image: molgenis/opencpu - AlwaysPullImage: true - resources: - requests: - cpu: "100m" - memory: "256Mi" - limits: - cpu: "1" - memory: "512Mi" - NodeSelector: {} - -#secret contains configuration for the kubernetes secrets that jenkins can access -secret: - # vault configures the vault secret - vault: - token: xxxx - addr: "https://vault-operator.vault-operator.svc:8200" - skipVerify: "1" - # githubToken contains access token for jenkins bot account on github.com - gitHub: - user: "molgenis-jenkins" - token: xxxx - # gogs contains access token for jenkins bot account on RuG GoGs - gogs: - user: p281392 - token: xxxx - # registry contains credentials for registry.molgenis.org - registry: - user: admin - password: xxxx - # dockerHubPassword contains password for hub.docker.com - dockerHub: - user: molgenisci - password: xxxx \ No newline at end of file diff --git a/molgenis-nexus/.helmignore b/molgenis-nexus/.helmignore deleted file mode 100644 index f0c1319..0000000 --- a/molgenis-nexus/.helmignore +++ /dev/null @@ -1,21 +0,0 @@ -# Patterns to ignore when building packages. -# This supports shell glob matching, relative path matching, and -# negation (prefixed with !). Only one pattern per line. -.DS_Store -# Common VCS dirs -.git/ -.gitignore -.bzr/ -.bzrignore -.hg/ -.hgignore -.svn/ -# Common backup files -*.swp -*.bak -*.tmp -*~ -# Various IDEs -.project -.idea/ -*.tmproj diff --git a/molgenis-nexus/Chart.yaml b/molgenis-nexus/Chart.yaml deleted file mode 100644 index 0ced74d..0000000 --- a/molgenis-nexus/Chart.yaml +++ /dev/null @@ -1,8 +0,0 @@ -apiVersion: v1 -appVersion: "1.0" -description: Nexus stack for MOLGENIS -name: molgenis-nexus -version: 0.4.2 -sources: -- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git -icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-nexus/catalogIcon-molgenis-nexus.svg \ No newline at end of file diff --git a/molgenis-nexus/README.md b/molgenis-nexus/README.md deleted file mode 100644 index b6bda27..0000000 --- a/molgenis-nexus/README.md +++ /dev/null @@ -1,64 +0,0 @@ -# MOLGENIS - NEXUS Helm Chart - -NEXUS repository for kubernetes to deploy on a kubernetes cluster with NFS-share - -## Chart Details - -This chart will deploy: - -- 1 NEXUS-nfs initialization container - - We need this container to avoid permission issues on the NEXUS docker -- 1 NEXUS container -- 1 MOLGENIS-httpd container (to proxy the registry and docker to one domain) - -## Backup restore -There are two steps in restoring the NEXUS. - -- Database -- Blobstore - -### Restore the database -Go to the commandline: - -```bash -kubectl get pv -``` - -```bash -| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE | -| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- | -| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-nexus/molgenis-nfs-claim | nfs-provisioner-retain | | | 33d | -| pvc-3984723d-220f-14e8-a98a-skjhf88823kk | 30G | RWO | | Delete | Bound | molgenis-test/molgenis-nfs-claim | nfs-provisioner | | | 33d | -``` - -The persistent volume is the one in the molgenis-nexus namespace. - -Go to the NFS-provisioner to the path of the persistent volume: - -```bash -ls -t --full-time | head -7 | xargs cp ../restore-from-backup/ -``` - -### Restore the blobstore -You can copy the directory ```blobs``` to the target persistent volume ```/ blobs```. - -You can now bring the NEXUS back up. - -## Installing the Chart - -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. - - diff --git a/molgenis-nexus/catalogIcon-molgenis-nexus.svg b/molgenis-nexus/catalogIcon-molgenis-nexus.svg deleted file mode 100644 index 9c7d611..0000000 --- a/molgenis-nexus/catalogIcon-molgenis-nexus.svg +++ /dev/null @@ -1,551 +0,0 @@ - - - - diff --git a/molgenis-nexus/templates/_helpers.tpl b/molgenis-nexus/templates/_helpers.tpl deleted file mode 100644 index 9f9800c..0000000 --- a/molgenis-nexus/templates/_helpers.tpl +++ /dev/null @@ -1,32 +0,0 @@ -{{/* vim: set filetype=mustache: */}} -{{/* -Expand the name of the chart. -*/}} -{{- define "nexus.name" -}} -{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}} -{{- end -}} - -{{/* -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). -If release name contains chart name it will be used as a full name. -*/}} -{{- define "nexus.fullname" -}} -{{- if .Values.fullnameOverride -}} -{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}} -{{- else -}} -{{- $name := default .Chart.Name .Values.nameOverride -}} -{{- if contains $name .Release.Name -}} -{{- .Release.Name | trunc 63 | trimSuffix "-" -}} -{{- else -}} -{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}} -{{- end -}} -{{- end -}} -{{- end -}} - -{{/* -Create chart name and version as used by the chart label. -*/}} -{{- define "nexus.chart" -}} -{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}} -{{- end -}} diff --git a/molgenis-nexus/templates/deployments/nexus-deployment.yaml b/molgenis-nexus/templates/deployments/nexus-deployment.yaml deleted file mode 100644 index c381aae..0000000 --- a/molgenis-nexus/templates/deployments/nexus-deployment.yaml +++ /dev/null @@ -1,65 +0,0 @@ -apiVersion: extensions/v1beta1 -kind: Deployment -metadata: - creationTimestamp: null - name: {{ .Values.nexus.name }} - labels: - app: {{ .Values.nexus.name }} - environment: {{ .Values.environment }} -spec: - replicas: {{ .Values.replicaCount }} - strategy: - type: {{ .Values.nexus.strategy.type }} - selector: - matchLabels: - app: {{ .Values.nexus.selector }} - template: - metadata: - labels: - app: {{ .Values.nexus.name }} - creationTimestamp: null - spec: - restartPolicy: {{ .Values.nexus.restartPolicy }} - initContainers: - - name: nexus-nfs - image: busybox - command: ["sh", "-c", "chown -R 200:200 /nexus-data"] - volumeMounts: - - name: molgenis-nexus-nfs - mountPath: "/nexus-data" - containers: - - name: {{ .Values.nexus.name }} - image: "{{ .Values.nexus.image.repository }}:{{ .Values.nexus.image.tag }}" - imagePullPolicy: {{ .Values.nexus.image.pullPolicy }} - ports: - - containerPort: {{ .Values.nexus.port.ui }} - - containerPort: {{ .Values.nexus.port.docker }} - volumeMounts: - - name: molgenis-nexus-nfs - mountPath: /nexus-data - livenessProbe: - httpGet: - path: / - port: {{ .Values.nexus.port.ui }} - initialDelaySeconds: 120 - periodSeconds: 20 - failureThreshold: 15 - successThreshold: 1 - readinessProbe: - httpGet: - path: / - port: {{ .Values.nexus.port.ui }} - initialDelaySeconds: 120 - periodSeconds: 20 - failureThreshold: 15 - successThreshold: 1 - - volumes: - - name: molgenis-nexus-nfs - persistentVolumeClaim: - claimName: {{ .Values.persistence.claim }} - - {{- with .Values.nodeSelector }} - nodeSelector: -{{ toYaml . | indent 8 }} - {{- end }} \ No newline at end of file diff --git a/molgenis-nexus/templates/deployments/nexusProxy-deployment.yaml b/molgenis-nexus/templates/deployments/nexusProxy-deployment.yaml deleted file mode 100644 index 2ccc400..0000000 --- a/molgenis-nexus/templates/deployments/nexusProxy-deployment.yaml +++ /dev/null @@ -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 }} \ No newline at end of file diff --git a/molgenis-nexus/templates/ingress.yaml b/molgenis-nexus/templates/ingress.yaml deleted file mode 100644 index 50a4252..0000000 --- a/molgenis-nexus/templates/ingress.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{{- if .Values.ingress.enabled }} -{{- range .Values.ingress.hosts }} -apiVersion: extensions/v1beta1 -kind: Ingress -metadata: - name: "{{ $.Release.Name }}-ingress" - labels: - app: {{ $.Values.nexusProxy.name }} - chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}" - release: "{{ $.Release.Name }}" - heritage: "{{ $.Release.Service }}" - annotations: - kubernetes.io/ingress.class: "nginx" - nginx.ingress.kubernetes.io/proxy-body-size: "0" - {{- 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.nexusProxy.name }} - servicePort: {{ $.Values.nexusProxy.port }} -{{- if .tls }} - tls: - - hosts: - - {{ .name }} - secretName: {{ .tlsSecret }} -{{- end }} ---- -{{- end }} -{{- end }} \ No newline at end of file diff --git a/molgenis-nexus/templates/persistence/nexusPVC.yaml b/molgenis-nexus/templates/persistence/nexusPVC.yaml deleted file mode 100644 index 2e2466f..0000000 --- a/molgenis-nexus/templates/persistence/nexusPVC.yaml +++ /dev/null @@ -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 }} \ No newline at end of file diff --git a/molgenis-nexus/templates/services/nexus-service.yaml b/molgenis-nexus/templates/services/nexus-service.yaml deleted file mode 100644 index dbb9371..0000000 --- a/molgenis-nexus/templates/services/nexus-service.yaml +++ /dev/null @@ -1,15 +0,0 @@ -apiVersion: v1 -kind: Service -metadata: - name: {{ .Values.nexus.name }} - labels: - app: {{ .Values.nexus.name }} -spec: - type: {{ .Values.nexus.service.type }} - ports: - - name: ui - port: {{ .Values.nexus.port.ui }} - - name: docker - port: {{ .Values.nexus.port.docker }} - selector: - app: {{ .Values.nexus.selector }} diff --git a/molgenis-nexus/templates/services/nexusProxy-service.yaml b/molgenis-nexus/templates/services/nexusProxy-service.yaml deleted file mode 100644 index 281ee81..0000000 --- a/molgenis-nexus/templates/services/nexusProxy-service.yaml +++ /dev/null @@ -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 }} diff --git a/molgenis-nexus/values.yaml b/molgenis-nexus/values.yaml deleted file mode 100644 index 3203fa7..0000000 --- a/molgenis-nexus/values.yaml +++ /dev/null @@ -1,65 +0,0 @@ -# Default values for nexus. -# This is a YAML-formatted file. -# Declare variables to be passed into your templates. - -replicaCount: 1 - -environment: production - -nexus: - name: nexus - strategy: - type: Recreate - selector: nexus - restartPolicy: Always - image: - repository: molgenis/nexus3 - tag: latest - pullPolicy: Always - port: - docker: 5000 - ui: 8081 - path: - dockerV2: v2 - service: - type: ClusterIP - -nexusProxy: - name: nexus-proxy - hostname: registry.molgenis.org - strategy: - type: Recreate - selector: nexus-proxy - restartPolicy: Always - image: - repository: molgenis/httpd - tag: latest - pullPolicy: Always - port: 80 - service: - type: LoadBalancer - - -ingress: - enabled: true - annotations: {} - path: / - hosts: - - name: registry.molgenis.org - tls: [] - -persistence: - enabled: true - claim: molgenis-nexus - size: 500Gi - - -resources: {} - -nodeSelector: { - deployPod: "true" -} - -tolerations: [] - -affinity: {} diff --git a/molgenis-opencpu/.helmignore b/molgenis-opencpu/.helmignore deleted file mode 100644 index f0c1319..0000000 --- a/molgenis-opencpu/.helmignore +++ /dev/null @@ -1,21 +0,0 @@ -# Patterns to ignore when building packages. -# This supports shell glob matching, relative path matching, and -# negation (prefixed with !). Only one pattern per line. -.DS_Store -# Common VCS dirs -.git/ -.gitignore -.bzr/ -.bzrignore -.hg/ -.hgignore -.svn/ -# Common backup files -*.swp -*.bak -*.tmp -*~ -# Various IDEs -.project -.idea/ -*.tmproj diff --git a/molgenis-opencpu/Chart.yaml b/molgenis-opencpu/Chart.yaml deleted file mode 100644 index 0ffe477..0000000 --- a/molgenis-opencpu/Chart.yaml +++ /dev/null @@ -1,8 +0,0 @@ -apiVersion: v1 -appVersion: "1.0" -description: Opencpu stack for MOLGENIS -name: molgenis-opencpu -version: 0.1.1 -sources: -- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git -icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-opencpu/catalogIcon-molgenis-opencpu.svg \ No newline at end of file diff --git a/molgenis-opencpu/README.md b/molgenis-opencpu/README.md deleted file mode 100644 index e871170..0000000 --- a/molgenis-opencpu/README.md +++ /dev/null @@ -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. - - diff --git a/molgenis-opencpu/catalog-molgenis-opencpu.svg b/molgenis-opencpu/catalog-molgenis-opencpu.svg deleted file mode 100644 index fc9ca38..0000000 --- a/molgenis-opencpu/catalog-molgenis-opencpu.svg +++ /dev/null @@ -1 +0,0 @@ - \ No newline at end of file diff --git a/molgenis-opencpu/questions.yml b/molgenis-opencpu/questions.yml deleted file mode 100644 index 79f3462..0000000 --- a/molgenis-opencpu/questions.yml +++ /dev/null @@ -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" \ No newline at end of file diff --git a/molgenis-opencpu/templates/_helpers.tpl b/molgenis-opencpu/templates/_helpers.tpl deleted file mode 100644 index a410c46..0000000 --- a/molgenis-opencpu/templates/_helpers.tpl +++ /dev/null @@ -1,32 +0,0 @@ -{{/* vim: set filetype=mustache: */}} -{{/* -Expand the name of the chart. -*/}} -{{- define "opencpu.name" -}} -{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}} -{{- end -}} - -{{/* -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). -If release name contains chart name it will be used as a full name. -*/}} -{{- define "opencpu.fullname" -}} -{{- if .Values.fullnameOverride -}} -{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}} -{{- else -}} -{{- $name := default .Chart.Name .Values.nameOverride -}} -{{- if contains $name .Release.Name -}} -{{- .Release.Name | trunc 63 | trimSuffix "-" -}} -{{- else -}} -{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}} -{{- end -}} -{{- end -}} -{{- end -}} - -{{/* -Create chart name and version as used by the chart label. -*/}} -{{- define "opencpu.chart" -}} -{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}} -{{- end -}} diff --git a/molgenis-opencpu/templates/deployment.yaml b/molgenis-opencpu/templates/deployment.yaml deleted file mode 100644 index ddb57c7..0000000 --- a/molgenis-opencpu/templates/deployment.yaml +++ /dev/null @@ -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 }} - - diff --git a/molgenis-opencpu/templates/ingress.yaml b/molgenis-opencpu/templates/ingress.yaml deleted file mode 100644 index d218231..0000000 --- a/molgenis-opencpu/templates/ingress.yaml +++ /dev/null @@ -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 }} \ No newline at end of file diff --git a/molgenis-opencpu/templates/service.yaml b/molgenis-opencpu/templates/service.yaml deleted file mode 100644 index 4b1cf1e..0000000 --- a/molgenis-opencpu/templates/service.yaml +++ /dev/null @@ -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 }} diff --git a/molgenis-opencpu/values.yaml b/molgenis-opencpu/values.yaml deleted file mode 100644 index c21be14..0000000 --- a/molgenis-opencpu/values.yaml +++ /dev/null @@ -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: {} diff --git a/molgenis-vault/.helmignore b/molgenis-vault/.helmignore deleted file mode 100644 index f0c1319..0000000 --- a/molgenis-vault/.helmignore +++ /dev/null @@ -1,21 +0,0 @@ -# Patterns to ignore when building packages. -# This supports shell glob matching, relative path matching, and -# negation (prefixed with !). Only one pattern per line. -.DS_Store -# Common VCS dirs -.git/ -.gitignore -.bzr/ -.bzrignore -.hg/ -.hgignore -.svn/ -# Common backup files -*.swp -*.bak -*.tmp -*~ -# Various IDEs -.project -.idea/ -*.tmproj diff --git a/molgenis-vault/Chart.yaml b/molgenis-vault/Chart.yaml deleted file mode 100644 index f6b75e4..0000000 --- a/molgenis-vault/Chart.yaml +++ /dev/null @@ -1,6 +0,0 @@ -apiVersion: v1 -appVersion: "1.0" -description: MOLGENIS vault -name: molgenis-vault -version: 0.1.1 -icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-vault/catalogIcon-molgenis-vault.svg diff --git a/molgenis-vault/README.md b/molgenis-vault/README.md deleted file mode 100644 index 5ebac64..0000000 --- a/molgenis-vault/README.md +++ /dev/null @@ -1,52 +0,0 @@ -# MOLGENIS Vault helm chart - -This chart creates a vault operator, but NO vault. -The vault operator defines a new custom resource named `vault` that you can use to create vaults. - -After launching the operator, create the molgenis vault manually: -`kubectl create -f resources/vault.yaml` - -That creates a new vault with two vault pods. - -See https://github.com/coreos/vault-operator/blob/master/doc/user/vault.md - -## Parameters - -### Azure cloud credentials -Define credentials for backup to the Azure Blob Store. -See [etcd-operator documentation](https://github.com/coreos/etcd-operator/blob/master/doc/user/abs_backup.md). - -| Parameter | Description | Default | -| --------------- | ----------------------------- | ------------------ | -| `abs.account` | name of storage account | `fdlkops` | -| `abs.accessKey` | access key of storage account | `xxxx` | -| `abs.cloud` | name of cloud environment | `AzurePublicCloud` | - -### Backup job -Define the schedule of the backup job - -| Parameter | Description | Default | -| -------------------- | ---------------------------- | ------------- | -| `backupJob.enable` | Enable backup cronjob | `true` | -| `backupJob.schedule` | cron schedule for the backup | `0 12 * * 1` | - -### UI - -Parameter | Description | Default ---------- | ----------- | ------- -`ui.replicaCount` | desired number of Vault UI pod | `1` -`ui.image.repository` | Vault UI container image repository | `djenriquez/vault-ui` -`ui.image.tag` | Vault UI container image tag | `latest` -`ui.resources` | Vault UI pod resource requests & limits | `{}` -`ui.nodeSelector` | node labels for Vault UI pod assignment | `{}` -`ui.ingress.enabled` | If true, Vault UI Ingress will be created | `true` -`ui.ingress.annotations` | Vault UI Ingress annotations | `{}` -`ui.ingress.host` | Vault UI Ingress hostname | `vault.molgenis.org` -`ui.ingress.tls` | Vault UI Ingress TLS configuration (YAML) | `[]` -`ui.vault.url` | Vault UI default vault url | `https://vault.vault-operator:8200` -`ui.vault.auth` | Vault UI login method | `GITHUB` -`ui.service.name` | Vault UI service name | `vault-ui` -`ui.service.type` | type of ui service to create | `ClusterIP` -`ui.service.externalPort` | Vault UI service target port | `8000` -`ui.service.internalPort` | Vault UI container port | `8000` -`ui.service.nodePort` | Port to be used as the service NodePort (ignored if `server.service.type` is not `NodePort`) | `0` \ No newline at end of file diff --git a/molgenis-vault/catalogIcon-molgenis-vault.svg b/molgenis-vault/catalogIcon-molgenis-vault.svg deleted file mode 100644 index 61d68a3..0000000 --- a/molgenis-vault/catalogIcon-molgenis-vault.svg +++ /dev/null @@ -1,627 +0,0 @@ - -image/svg+xml \ No newline at end of file diff --git a/molgenis-vault/charts/etcd-operator-0.8.0.tgz b/molgenis-vault/charts/etcd-operator-0.8.0.tgz deleted file mode 100644 index f2c2bc10796cc25aedd91d88492a3ff2efbd7504..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 7467 zcmV+`9n|6Dc zVQyr3R8em|NM&qo0PKDLbKAI*=lhv|ML#)Lo8(MNvf?D8dw%sC+q;+Ad~w;{nVXv0 zvLUi1Vhj-+0+ge~xxal207;P)DN$cyCo@7#O)L^<;wud=`O^KS2D@5SF>n>^H}SV$86t<%|*PPuVE 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https://kubernetes-charts.storage.googleapis.com/ - version: 0.8.0 -digest: sha256:47aa645df7dfce9760905800321599de05995ae50090735d45310936dbaa46de -generated: 2018-09-06T18:59:39.861922543+02:00 diff --git a/molgenis-vault/requirements.yaml b/molgenis-vault/requirements.yaml deleted file mode 100644 index 63b31d4..0000000 --- a/molgenis-vault/requirements.yaml +++ /dev/null @@ -1,7 +0,0 @@ -dependencies: - - name: vault-operator - version: ^0.1.1 - repository: https://kubernetes-charts.storage.googleapis.com/ - - name: etcd-operator - version: ^0.8.0 - repository: https://kubernetes-charts.storage.googleapis.com/ \ No newline at end of file diff --git a/molgenis-vault/resources/restore.yaml b/molgenis-vault/resources/restore.yaml deleted file mode 100644 index c7db422..0000000 --- a/molgenis-vault/resources/restore.yaml +++ /dev/null @@ -1,15 +0,0 @@ -# Use kubectl create -f restore.yaml to manually execute a restore of the vault -apiVersion: "etcd.database.coreos.com/v1beta2" -kind: "EtcdRestore" -metadata: - # The restore CR name must be the same as spec.etcdCluster.name - name: vault-etcd - namespace: vault-operator -spec: - etcdCluster: - # The namespace is the same as this EtcdRestore CR - name: vault-etcd - backupStorageType: ABS - abs: - path: vault/backup- - absSecret: abs \ No newline at end of file diff --git a/molgenis-vault/resources/vault.yaml b/molgenis-vault/resources/vault.yaml deleted file mode 100644 index fa1c83b..0000000 --- a/molgenis-vault/resources/vault.yaml +++ /dev/null @@ -1,9 +0,0 @@ -# Use kubectl create -f vault.yaml to manually create a vault -apiVersion: "vault.security.coreos.com/v1alpha1" -kind: "VaultService" -metadata: - name: "vault" - namespace: "vault-operator" -spec: - nodes: 2 - version: "0.9.1-0" \ No newline at end of file diff --git a/molgenis-vault/templates/NOTES.txt b/molgenis-vault/templates/NOTES.txt deleted file mode 100644 index 5df45af..0000000 --- a/molgenis-vault/templates/NOTES.txt +++ /dev/null @@ -1,13 +0,0 @@ -Vault operator created - -Next steps: - -* Manually create a vault using resources/vault.yaml -* Manually restore a backup using resources/backup.yaml -* Unseal the vault pods - -{{ if .Values.backupJob.enable }} -!! Make sure to check if the backups succeed !! -{{ else }} -!!!!!! NO BACKUPS CONFIGURED !!!!!! -{{ end }} \ No newline at end of file diff --git a/molgenis-vault/templates/_helpers.tpl b/molgenis-vault/templates/_helpers.tpl deleted file mode 100644 index 5c51ec7..0000000 --- a/molgenis-vault/templates/_helpers.tpl +++ /dev/null @@ -1,54 +0,0 @@ -{{/* -Define vault ui fullname -*/}} -{{- define "vault.ui.fullname" -}} -{{- printf "%s-ui" .Release.Name | trunc 63 | trimSuffix "-" -}} -{{- end -}} - -{{/* -Define vault service url for the ui -*/}} -{{- define "vault.service.url" -}} -{{- printf "https://%s:8200" .Release.Name | trunc 63 | trimSuffix "-" -}} -{{- end -}} - -{{/* See https://github.com/helm/helm/issues/4535 */}} -{{- define "call-nested" }} -{{- $dot := index . 0 }} -{{- $subchart := index . 1 }} -{{- $template := index . 2 }} -{{- include $template (dict "Chart" (dict "Name" $subchart) "Values" (index $dot.Values $subchart) "Release" $dot.Release "Capabilities" $dot.Capabilities) }} -{{- end }} - -{{/* vim: set filetype=mustache: */}} -{{/* -Expand the name of the chart. -*/}} -{{- define "molgenis-vault.name" -}} -{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}} -{{- end -}} - -{{/* -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). -If release name contains chart name it will be used as a full name. -*/}} -{{- define "molgenis-vault.fullname" -}} -{{- if .Values.fullnameOverride -}} -{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}} -{{- else -}} -{{- $name := default .Chart.Name .Values.nameOverride -}} -{{- if contains $name .Release.Name -}} -{{- .Release.Name | trunc 63 | trimSuffix "-" -}} -{{- else -}} -{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}} -{{- end -}} -{{- end -}} -{{- end -}} - -{{/* -Create chart name and version as used by the chart label. -*/}} -{{- define "molgenis-vault.chart" -}} -{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}} -{{- end -}} diff --git a/molgenis-vault/templates/abs-secret.yaml b/molgenis-vault/templates/abs-secret.yaml deleted file mode 100644 index 5f31f41..0000000 --- a/molgenis-vault/templates/abs-secret.yaml +++ /dev/null @@ -1,10 +0,0 @@ -# Secret to access microsoft azure blob store -apiVersion: v1 -kind: Secret -metadata: - name: abs -type: Opaque -stringData: - storage-account: {{ .Values.abs.account }} - storage-key: {{ .Values.abs.accessKey }} - cloud: {{ .Values.abs.cloud }} \ No newline at end of file diff --git a/molgenis-vault/templates/backup-configmap.yaml b/molgenis-vault/templates/backup-configmap.yaml deleted file mode 100644 index 8eb22d4..0000000 --- a/molgenis-vault/templates/backup-configmap.yaml +++ /dev/null @@ -1,18 +0,0 @@ -# configmap to use as a template by the backup cronjob to create etcdbackup instances -apiVersion: v1 -kind: ConfigMap -metadata: - name: backup-config -data: - backup_cr.yaml: | - apiVersion: "etcd.database.coreos.com/v1beta2" - kind: "EtcdBackup" - metadata: - generateName: vault-backup- - spec: - etcdEndpoints: ["https://vault-etcd-client:2379"] - storageType: ABS - clientTLSSecret: vault-etcd-client-tls - abs: - path: vault/backup. - absSecret: abs \ No newline at end of file diff --git a/molgenis-vault/templates/backup-cronjob.yaml b/molgenis-vault/templates/backup-cronjob.yaml deleted file mode 100644 index e5687fc..0000000 --- a/molgenis-vault/templates/backup-cronjob.yaml +++ /dev/null @@ -1,30 +0,0 @@ -{{- if .Values.backupJob.enable }} -# cronjob that creates etcdbackups using the etcd backup serviceaccount -apiVersion: batch/v1beta1 -kind: CronJob -metadata: - name: etcd-backup -spec: - schedule: {{ .Values.backupJob.schedule | quote }} - jobTemplate: - spec: - template: - spec: - serviceAccountName: {{ include "call-nested" (list . "etcd-operator" "etcd-operator.serviceAccountName") }} - containers: - - name: etcd-backup - image: lachlanevenson/k8s-kubectl - command: - - /bin/sh - - "-ec" - - | - sed -e "s||$(date '+%Y-%m-%d_%H:%M:%S')|g" /var/etcd_backup/backup_cr.yaml | kubectl create -f - - volumeMounts: - - name: backup-config - mountPath: /var/etcd_backup - restartPolicy: OnFailure - volumes: - - name: backup-config - configMap: - name: backup-config -{{- end }} \ No newline at end of file diff --git a/molgenis-vault/templates/ui-ingress.yaml b/molgenis-vault/templates/ui-ingress.yaml deleted file mode 100644 index d8d8e1f..0000000 --- a/molgenis-vault/templates/ui-ingress.yaml +++ /dev/null @@ -1,30 +0,0 @@ -{{- if .Values.ui.ingress.enabled -}} -{{- $serviceName := include "vault.ui.fullname" . -}} -{{- $servicePort := .Values.ui.service.externalPort -}} -apiVersion: extensions/v1beta1 -kind: Ingress -metadata: - name: {{ template "vault.ui.fullname" . }} - labels: - app: {{ template "molgenis-vault.name" . }} - chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }} - release: {{ .Release.Name }} - heritage: {{ .Release.Service }} - annotations: - {{- range $key, $value := .Values.ui.ingress.annotations }} - {{ $key }}: {{ $value | quote }} - {{- end }} -spec: - rules: - - host: {{ .Values.ui.ingress.host }} - http: - paths: - - path: - backend: - serviceName: {{ $serviceName }} - servicePort: {{ $servicePort }} - {{- if .Values.ui.ingress.tls }} - tls: -{{ toYaml .Values.ui.ingress.tls | indent 4 }} - {{- end -}} -{{- end -}} \ No newline at end of file diff --git a/molgenis-vault/templates/ui-service.yaml b/molgenis-vault/templates/ui-service.yaml deleted file mode 100644 index 0e26d65..0000000 --- a/molgenis-vault/templates/ui-service.yaml +++ /dev/null @@ -1,23 +0,0 @@ -apiVersion: v1 -kind: Service -metadata: - name: {{ template "vault.ui.fullname" . }} - labels: - app: {{ template "vault-operator.name" . }} - chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }} - release: {{ .Release.Name }} - heritage: {{ .Release.Service }} -spec: - type: {{ .Values.ui.service.type }} - ports: - - port: {{ .Values.ui.service.externalPort }} - targetPort: {{ .Values.ui.service.internalPort }} - protocol: TCP - name: {{ .Values.ui.service.name }} - {{- if .Values.ui.service.nodePort }} - nodePort: {{ .Values.ui.service.nodePort }} - {{- end }} - selector: - app: {{ template "vault-operator.name" . }} - release: {{ .Release.Name }} - component: {{ .Values.ui.name }} \ No newline at end of file diff --git a/molgenis-vault/templates/vault-ui-deployment.yaml b/molgenis-vault/templates/vault-ui-deployment.yaml deleted file mode 100644 index d13a154..0000000 --- a/molgenis-vault/templates/vault-ui-deployment.yaml +++ /dev/null @@ -1,50 +0,0 @@ -apiVersion: apps/v1beta1 -kind: Deployment -metadata: - name: {{ template "vault.ui.fullname" . }} - labels: - app: {{ template "vault-operator.name" . }} - chart: {{ .Chart.Name }}-{{ .Chart.Version | replace "+" "_" }} - release: {{ .Release.Name }} - heritage: {{ .Release.Service }} - component: {{ .Values.ui.name }} -spec: - replicas: {{ .Values.ui.replicaCount }} - template: - metadata: - labels: - app: {{ template "vault-operator.name" . }} - release: {{ .Release.Name }} - component: {{ .Values.ui.name }} - spec: - containers: - - name: {{ .Values.ui.name }} - image: "{{ .Values.ui.image.repository }}:{{ .Values.ui.image.tag }}" - imagePullPolicy: {{ .Values.imagePullPolicy }} - env: - - name: VAULT_URL_DEFAULT - {{- if .Values.ui.vault.url }} - value: {{ .Values.ui.vault.url }} - {{ else }} - value: {{ template "vault.service.url" . }} - {{- end }} - - name: VAULT_AUTH_DEFAULT - value: {{ .Values.ui.vault.auth }} - - name: NODE_TLS_REJECT_UNAUTHORIZED - value: '0' - ports: - - containerPort: {{ .Values.ui.service.internalPort }} - livenessProbe: - httpGet: - path: / - port: {{ .Values.ui.service.internalPort }} - readinessProbe: - httpGet: - path: / - port: {{ .Values.ui.service.internalPort }} - resources: -{{ toYaml .Values.ui.resources | indent 12 }} - {{- if .Values.ui.nodeSelector }} - nodeSelector: -{{ toYaml .Values.ui.nodeSelector | indent 8 }} - {{- end }} \ No newline at end of file diff --git a/molgenis-vault/values.yaml b/molgenis-vault/values.yaml deleted file mode 100644 index aaca8f3..0000000 --- a/molgenis-vault/values.yaml +++ /dev/null @@ -1,79 +0,0 @@ -# Default values for molgenis-vault. -# This is a YAML-formatted file. -# Declare variables to be passed into your templates. - -# abs gives details of the credentials to reach the azure backup storage -abs: - # account is the name of the Storage account - account: fdlkops - # access key for the Storage account - accessKey: xxxx - # default cloud - cloud: AzurePublicCloud - -# backupjob describes the backup cronjob -backupJob: - # enable enables the backup job - enable: true - # schedule gives the cron schedule for the backup job - schedule: "0 12 * * 1" - -### -# All of the config variables related to setting up the etcd-operator -# If you want more information about the variables exposed, please visit: -# https://github.com/kubernetes/charts/tree/master/stable/etcd-operator#configuration -### -etcd-operator: - deployments: - etcdOperator: true - backupOperator: true - restoreOperator: true - serviceAccount: - etcdOperatorServiceAccount: - create: true - backupOperatorServiceAccount: - create: true - restoreOperatorServiceAccount: - create: true - etcdOperator: - image: - tag: v0.9.2 - backupOperator: - image: - tag: v0.9.2 - restoreOperator: - image: - tag: v0.9.2 - -ui: - name: "vault-ui" - replicaCount: 1 - image: - repository: djenriquez/vault-ui - tag: latest - service: - name: vault-ui - type: ClusterIP - externalPort: 8000 - internalPort: 8000 - # nodePort: 32001 - ingress: - enabled: true - # Used to create Ingress record (should used with service.type: ClusterIP). - host: vault.molgenis.org - - 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: {} - vault: - auth: GITHUB - url: https://vault.vault-operator:8200 \ No newline at end of file diff --git a/molgenis/Chart.yaml b/molgenis/Chart.yaml deleted file mode 100644 index cde7e05..0000000 --- a/molgenis/Chart.yaml +++ /dev/null @@ -1,8 +0,0 @@ -apiVersion: v1 -appVersion: "1.0" -description: MOLGENIS - helm stack (in BETA) -name: molgenis -version: 0.4.3 -sources: -- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git -icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis/catalogIcon-molgenis.svg \ No newline at end of file diff --git a/molgenis/README.md b/molgenis/README.md deleted file mode 100644 index b45a03d..0000000 --- a/molgenis/README.md +++ /dev/null @@ -1,138 +0,0 @@ -# MOLGENIS -This chart is used for acceptance and production use cases. - -## Containers -This chart spins up a MOLGENIS instance with HTTPD. The created containers are: - -- MOLGENIS -- ElasticSearch -- PostgreSQL **(optional)** - -## Provisioning -You can choose from which registry you want to pull. There are 2 registries: -- https://registry.molgenis.org -- https://hub.docker.com - -The registry.molgenis.org contains the bleeding edge versions (PR's and master merges). The hub.docker.com contains the released artifacts (MOLGENIS releases and release candidates). - -The three properties you need to specify are: -- ```molgenis.image.repository``` -- ```molgenis.image.name``` -- ```molgenis.image.tag``` - -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``` - -### 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 -When you start MOLGENIS you need: -- an elasticsearch instance (5.5.6) -- an postgres instance (9.6) - -You can attach additional services like: -- an opencpu instance - -### Elasticsearch -You can configure elasticsearch by giving in the cluster location. - -To configure the transport address you can address the node communication channel but also the native JAVA API. Which MOLGENIS uses to communicate with Elasticsearch. -From Elasticsearch version 6 and further the JAVA API is not supported anymore. At this moment you can only use Elastic instance till major version 5. -- ```molgenis.services.elasticsearch.transportAddresses: localhost:9300``` - -To configure the index on a Elasticsearch cluster you can specify the clusterName property. -- ```molgenis.services.elasticsearch.clusterName: molgenis``` - -### Postgres -You can specify the location of the postgres instance by specify the following property: -- ```molgenis.services.postgres.host: localhost``` - -You can specify the schema by filling out this property: -- ```molgenis.services.postgres.scheme: molgenis``` - -You can specify credentials for the database scheme by specifying the following properties: -- ```molgenis.services.postgres.user: molgenis``` -- ```molgenis.services.postgres.password: molgenis``` - -To test you can use the **PostgreSQL**-helm chart of Kubernetes and specify these answers: - -```bash -# answers for postgresql chart -postgresUser=molgenis -postgresPassword=molgenis -postgresDatabase=molgenis -persistence.enabled=false -``` - -### OpenCPU -You can specify the location of the OpenCPU cluster by specifying this property: -- ```molgenis.services.opencpu.host: localhost``` - -You can test OpenCPU settings using the **OpenCPU**-helm chart of MOLGENIS. - -## Resources -You can specify resources by resource type. There are 2 resource types. -- memory of container -- maximum heap space JVM - -Specify memory usage of container: -- ```molgenis.resources.limits.memory``` - -Specify memory usage for Java JVM: -- ```molgenis.javaOpts.maxHeapSpace``` - -Select the resources you need dependant on the customer you need to serve. - -## Persistence -You can enable persistence on your MOLGENIS stack by specifying the following property. - -- ```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```. \ No newline at end of file diff --git a/molgenis/catalogIcon-molgenis.svg b/molgenis/catalogIcon-molgenis.svg deleted file mode 100644 index f5e6b5d..0000000 --- a/molgenis/catalogIcon-molgenis.svg +++ /dev/null @@ -1,1024 +0,0 @@ - - - - diff --git a/molgenis/questions.yml b/molgenis/questions.yml deleted file mode 100644 index f62f9a7..0000000 --- a/molgenis/questions.yml +++ /dev/null @@ -1,167 +0,0 @@ - -categories: -- MOLGENIS -questions: -- variable: ingress.hosts[0].name - label: Hostname - default: "test.molgenis.org" - description: "Hostname for your stack" - type: hostname - required: true - group: "Load balancing" -- variable: molgenis.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: molgenis.image.tag - label: Version - default: "" - description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for released tags)" - type: string - required: true - group: "Provisioning" -- variable: molgenis.adminPassword - label: Administrator password - default: "" - description: "Enter an administrator password" - type: password - required: true - 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 - label: OpenCPU cluster - default: "localhost" - description: "Specify the OpenCPU cluster" - type: string - required: true - 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 - label: Postgres cluster location - default: "" - 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)" - type: string - required: true - group: "Services" - - variable: molgenis.services.postgres.scheme - label: Database scheme - default: "molgenis" - description: "Set the database scheme" - type: string - required: true - group: "Services" - - variable: molgenis.services.postgres.user - label: Database username - default: "molgenis" - description: "Set user of the database scheme" - type: string - required: true - group: "Services" - - variable: molgenis.services.postgres.password - label: Database password - default: "molgenis" - description: "Set the password of the database scheme" - type: string - required: true - group: "Services" -- variable: molgenis.resources.limits.memory - label: Container memory limit - default: 1250Mi - description: "Memory limit for this MOLGENIS container" - type: enum - options: - - "1250Mi" - - "2500Mi" - required: true - group: "Resources" -- variable: molgenis.resources.requests.memory - label: Container memory reservation - default: 1250Mi - description: "Memory reservation for this MOLGENIS container (must fit in the selected memory limit for the container)" - type: enum - options: - - "1250Mi" - - "2500Mi" - required: true - group: "Resources" -- variable: molgenis.javaOpts.maxHeapSpace - label: Maximum heap space (JVM) - default: "1g" - description: "Maximum heap space MOLGENIS container JVM. Please not this should fit in your container memory limit" - type: enum - options: - - "1g" - - "2g" - 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 \ No newline at end of file diff --git a/molgenis/templates/NOTES.txt b/molgenis/templates/NOTES.txt deleted file mode 100644 index b5a4d24..0000000 --- a/molgenis/templates/NOTES.txt +++ /dev/null @@ -1,19 +0,0 @@ -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 }} diff --git a/molgenis/templates/_helpers.tpl b/molgenis/templates/_helpers.tpl deleted file mode 100644 index e7cf3ea..0000000 --- a/molgenis/templates/_helpers.tpl +++ /dev/null @@ -1,32 +0,0 @@ -{{/* vim: set filetype=mustache: */}} -{{/* -Expand the name of the chart. -*/}} -{{- define "molgenis.name" -}} -{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}} -{{- end -}} - -{{/* -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). -If release name contains chart name it will be used as a full name. -*/}} -{{- define "molgenis.fullname" -}} -{{- if .Values.fullnameOverride -}} -{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}} -{{- else -}} -{{- $name := default .Chart.Name .Values.nameOverride -}} -{{- if contains $name .Release.Name -}} -{{- .Release.Name | trunc 63 | trimSuffix "-" -}} -{{- else -}} -{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}} -{{- end -}} -{{- end -}} -{{- end -}} - -{{/* -Create chart name and version as used by the chart label. -*/}} -{{- define "molgenis.chart" -}} -{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}} -{{- end -}} diff --git a/molgenis/templates/deployment.yaml b/molgenis/templates/deployment.yaml deleted file mode 100644 index 948f986..0000000 --- a/molgenis/templates/deployment.yaml +++ /dev/null @@ -1,153 +0,0 @@ -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 }} - strategy: - type: Recreate - 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: {{ .services.opencpu.host }} - - name: elasticsearch.transport.addresses - value: {{ .services.elasticsearch.transportAddresses }} - - name: elasticsearch.cluster.name - value: {{ .services.elasticsearch.clusterName }} - - name: db_uri - value: jdbc:postgresql://{{ .services.postgres.host }}/{{ .services.postgres.scheme }} - - name: db_user - value: {{ .services.postgres.user }} - - name: db_password - value: {{ .services.postgres.password }} - - name: admin.password - value: {{ .adminPassword }} - - name: CATALINA_OPTS - value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled" - ports: - - containerPort: 8080 - {{- if $.Values.persistence.enabled }} - volumeMounts: - - name: molgenis-nfs - mountPath: /home/molgenis - {{- end }} - livenessProbe: - httpGet: - path: / - port: 8080 - initialDelaySeconds: 60 - periodSeconds: 5 - failureThreshold: 25 - successThreshold: 1 - readinessProbe: - httpGet: - path: /api/v2/version - port: 8080 - initialDelaySeconds: 120 - periodSeconds: 30 - failureThreshold: 3 - successThreshold: 1 - 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 - {{- if $.Values.persistence.enabled }} - volumeMounts: - - name: elasticsearch-nfs - mountPath: /usr/share/elasticsearch/data - {{- end }} - resources: -{{ toYaml .resources | indent 12 }} - {{- 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 }} - nodeSelector: -{{ toYaml . | indent 8 }} - {{- end }} - {{- with .Values.affinity }} - affinity: -{{ toYaml . | indent 8 }} - {{- end }} - {{- with .Values.tolerations }} - tolerations: -{{ toYaml . | indent 8 }} - {{- end }} diff --git a/molgenis/templates/ingress.yaml b/molgenis/templates/ingress.yaml deleted file mode 100644 index 2434a42..0000000 --- a/molgenis/templates/ingress.yaml +++ /dev/null @@ -1,38 +0,0 @@ -{{- if .Values.ingress.enabled -}} -{{- $fullName := include "molgenis.fullname" . -}} -{{- $ingressPath := .Values.ingress.path -}} -apiVersion: extensions/v1beta1 -kind: Ingress -metadata: - name: "{{ $.Release.Name }}-ingress" - 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: {{ $.Values.service.port }} - {{- end }} -{{- end }} diff --git a/molgenis/templates/persistence/elasticsearchPVC.yaml b/molgenis/templates/persistence/elasticsearchPVC.yaml deleted file mode 100644 index 6c8bef7..0000000 --- a/molgenis/templates/persistence/elasticsearchPVC.yaml +++ /dev/null @@ -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 }} \ No newline at end of file diff --git a/molgenis/templates/persistence/molgenisPVC.yaml b/molgenis/templates/persistence/molgenisPVC.yaml deleted file mode 100644 index 6ec2f93..0000000 --- a/molgenis/templates/persistence/molgenisPVC.yaml +++ /dev/null @@ -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 }} \ No newline at end of file diff --git a/molgenis/templates/persistence/postgresPVC.yaml b/molgenis/templates/persistence/postgresPVC.yaml deleted file mode 100644 index 4e0cfcc..0000000 --- a/molgenis/templates/persistence/postgresPVC.yaml +++ /dev/null @@ -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 }} \ No newline at end of file diff --git a/molgenis/templates/service.yaml b/molgenis/templates/service.yaml deleted file mode 100644 index f9b9d85..0000000 --- a/molgenis/templates/service.yaml +++ /dev/null @@ -1,29 +0,0 @@ -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 }} -{{- 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: - - name: molgenis - port: {{ .Values.service.port }} - selector: - app: {{ template "molgenis.name" . }} - release: {{ .Release.Name }} diff --git a/molgenis/values.yaml b/molgenis/values.yaml deleted file mode 100644 index c9fa30c..0000000 --- a/molgenis/values.yaml +++ /dev/null @@ -1,103 +0,0 @@ -# Default values for molgenis. - -replicaCount: 1 - -service: - type: LoadBalancer - firewall: - enabled: false - kind: "umcg" - umcg: - rules: - - 127.0.0.1/32 - cluster: - rules: - - 127.0.0.1/32 - 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.hub.docker.com - name: molgenis/molgenis-app - tag: stable - pullPolicy: Always - adminPassword: - javaOpts: - maxHeapSpace: "1g" - resources: - limits: - cpu: 1 - memory: 1250Mi - requests: - cpu: 200m - memory: 1250Mi - persistence: - claim: molgenis-nfs-claim - size: 5Gi - services: - opencpu: - host: localhost - elasticsearch: - transportAddresses: localhost:9300 - clusterName: molgenis - postgres: - embedded: false - host: localhost - scheme: molgenis - user: molgenis - password: molgenis - -elasticsearch: - image: - repository: docker.elastic.co/elasticsearch/elasticsearch - tag: 5.5.3 - pullPolicy: IfNotPresent - javaOpts: "-Xms1g -Xmx1g" - clusterName: molgenis - resources: - limits: - cpu: 2 - memory: 3Gi - requests: - cpu: 100m - memory: 1Gi - persistence: - claim: elasticsearch-nfs-claim - size: 5Gi - -postgres: - 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: [] - -affinity: {}