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21
README.md
21
README.md
@ -104,6 +104,7 @@ This repository is serves also as a catalogue for Rancher. We have serveral apps
|
||||
- [Jenkins](molgenis-jenkins/README.md)
|
||||
- [NEXUS](molgenis-nexus/README.md)
|
||||
- [HTTPD](molgenis-httpd/README.md)
|
||||
- [MOLGENIS](molgenis/README.md)
|
||||
- [MOLGENIS preview](molgenis-preview/README.md)
|
||||
- [MOLGENIS vault](molgenis-vault/README.md)
|
||||
|
||||
@ -122,6 +123,26 @@ You can you need to know to easily develop and deploy helm-charts
|
||||
|
||||
Do it in the root of the project where the Chart.yaml is located
|
||||
It installs a release of a kubernetes stack. You also store this as an artifact in a kubernetes repository
|
||||
- ```helm package .```
|
||||
|
||||
You can create a package which can be uploaded in the molgenis helm repository
|
||||
|
||||
- ```helm publish```
|
||||
You still have to create an ```index.yaml``` for the chart. You can do this by executing this command: ```helm repo index #directory name of helm chart#```
|
||||
|
||||
Then you can upload it by executing:
|
||||
|
||||
- ```curl -v --user #username#:#password# --upload-file index.yaml https://registry.molgenis.org/repository/helm/#chart name#/index.yml```
|
||||
- ```curl -v --user #username#:#password# --upload-file #chart name#-#version#.tgz https://registry.molgenis.org/repository/helm/#chart name#/#chart name#-#version#.tgz```
|
||||
|
||||
Now you have to add the repository locally to use in your ```requirements.yaml```.
|
||||
|
||||
- ```helm repo add #repository name# https://registry.molgenis.org/repository/helm/molgenis```
|
||||
|
||||
- ```helm dep build```
|
||||
|
||||
You can build your dependencies (create a ```charts``` directory and install the chart in it) of the helm-chart.
|
||||
|
||||
- ```helm list```
|
||||
|
||||
Lists all installed releases
|
||||
|
||||
@ -13,7 +13,7 @@ jenkins:
|
||||
- blueocean:1.6.2
|
||||
- github-oauth:0.29
|
||||
- gogs-webhook:1.0.14
|
||||
- sauce-ondemand:1.176
|
||||
- github-scm-trait-commit-skip:0.1.1
|
||||
Security:
|
||||
UseGitHub: false
|
||||
GitHub:
|
||||
@ -82,6 +82,7 @@ jenkins:
|
||||
<strategyId>1</strategyId>
|
||||
<trust class="org.jenkinsci.plugins.github_branch_source.ForkPullRequestDiscoveryTrait$TrustPermission"/>
|
||||
</org.jenkinsci.plugins.github__branch__source.ForkPullRequestDiscoveryTrait>
|
||||
<org.jenkinsci.plugins.scm__filter.GitHubCommitSkipTrait plugin="github-scm-trait-commit-skip@0.1.1"/>
|
||||
</traits>
|
||||
</org.jenkinsci.plugins.github__branch__source.GitHubSCMNavigator>
|
||||
</navigators>
|
||||
|
||||
@ -8,7 +8,7 @@ questions:
|
||||
description: "Enable ingress"
|
||||
type: boolean
|
||||
required: true
|
||||
group: "Loadbalancing"
|
||||
group: "Load balancing"
|
||||
- variable: opencpu.image.repository
|
||||
label: Registry
|
||||
default: "registry.hub.docker.com"
|
||||
|
||||
@ -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
|
||||
@ -1,8 +0,0 @@
|
||||
apiVersion: v1
|
||||
appVersion: "1.0"
|
||||
description: MOLGENIS - helm stack for testing purposes
|
||||
name: molgenis-preview
|
||||
version: 0.2.0
|
||||
sources:
|
||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis-preview/catalogIcon-molgenis.svg
|
||||
@ -1,16 +0,0 @@
|
||||
# MOLGENIS preview
|
||||
This chart is used for testing purposes. It can be used by data managers or developers to test MOLGENIS (e.g. integration testing).
|
||||
|
||||
## Containers
|
||||
This chart spins up a complete stack to run MOLGENIS. The created containers are:
|
||||
|
||||
- MOLGENIS
|
||||
- PostgreSQL
|
||||
- Elasticsearch
|
||||
- OpenCPU
|
||||
|
||||
## Rancher
|
||||
You can spin up a test instance by navigating to https://rancher.molgenis.org:7777 and login with your LDAP-account.
|
||||
|
||||
Go to the test-environment and click on "Launch". Search for MOLGENIS.
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
|
Before Width: | Height: | Size: 77 KiB |
@ -1,61 +0,0 @@
|
||||
|
||||
categories:
|
||||
- MOLGENIS
|
||||
questions:
|
||||
- variable: ingress.hosts[0].name
|
||||
default: "test.molgenis.org"
|
||||
description: "Hostname for your stack"
|
||||
type: hostname
|
||||
required: true
|
||||
group: "Services and Load Balancing"
|
||||
label: Hostname
|
||||
- variable: molgenis.image.repository
|
||||
default: "registry.hub.docker.com"
|
||||
description: "Select a registry to pull from"
|
||||
type: enum
|
||||
options:
|
||||
- "registry.hub.docker.com"
|
||||
- "registry.molgenis.org"
|
||||
required: true
|
||||
group: "MOLGENIS - Version"
|
||||
label: Registry
|
||||
- variable: molgenis.image.tag
|
||||
default: "stable"
|
||||
description: "Select a MOLGENIS version (check the registry.molgenis.org or hub.docker.com for other tags)"
|
||||
type: string
|
||||
required: true
|
||||
group: "MOLGENIS - Version"
|
||||
label: Version
|
||||
- variable: molgenis.resources.limits.cpu
|
||||
default: 1
|
||||
description: "CPU limit for this MOLGENIS instance"
|
||||
type: enum
|
||||
options:
|
||||
- "1"
|
||||
- "2"
|
||||
- "3"
|
||||
- "4"
|
||||
required: true
|
||||
group: "MOLGENIS - Resource limits"
|
||||
label: CPU limit
|
||||
- variable: molgenis.resources.limits.memory
|
||||
default: 1250Mi
|
||||
description: "Memory limit for this MOLGENIS instance"
|
||||
type: enum
|
||||
options:
|
||||
- "1250Mi"
|
||||
- "1500Mi"
|
||||
- "2000Mi"
|
||||
- "2500Mi"
|
||||
required: true
|
||||
group: "MOLGENIS - Resource limits"
|
||||
label: Memory limit
|
||||
- variable: molgenis.javaOpts
|
||||
default: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||
description: "Java runtime options for the MOLGENIS instance"
|
||||
type: enum
|
||||
options:
|
||||
- "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||
- "-Xmx2g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||
group: "MOLGENIS - Resource limits"
|
||||
label: Java memory options
|
||||
@ -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 }}
|
||||
@ -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 -}}
|
||||
@ -1,124 +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 }}
|
||||
template:
|
||||
metadata:
|
||||
labels:
|
||||
app: {{ template "molgenis.name" . }}
|
||||
release: {{ .Release.Name }}
|
||||
spec:
|
||||
containers:
|
||||
- name: molgenis
|
||||
{{- with .Values.molgenis }}
|
||||
image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
|
||||
imagePullPolicy: {{ .image.pullPolicy }}
|
||||
env:
|
||||
- name: molgenis.home
|
||||
value: /home/molgenis
|
||||
- name: opencpu.uri.host
|
||||
value: localhost
|
||||
- name: elasticsearch.transport.addresses
|
||||
value: localhost:9300
|
||||
- name: elasticsearch.cluster.name
|
||||
value: {{ $.Values.elasticsearch.clusterName }}
|
||||
- name: db_uri
|
||||
value: "jdbc:postgresql://localhost/{{ $.Values.postgres.db }}"
|
||||
- name: db_user
|
||||
value: {{ $.Values.postgres.user }}
|
||||
- name: db_password
|
||||
value: {{ $.Values.postgres.password }}
|
||||
- name: admin.password
|
||||
value: {{ .adminPassword }}
|
||||
- name: CATALINA_OPTS
|
||||
value: "{{ .javaOpts }}"
|
||||
ports:
|
||||
- containerPort: 8080
|
||||
# livenessProbe:
|
||||
# httpGet:
|
||||
# path: /
|
||||
# port: 8080
|
||||
# readinessProbe:
|
||||
# httpGet:
|
||||
# path: /api/v2/version
|
||||
# port: 8080
|
||||
resources:
|
||||
{{ toYaml .resources | indent 12 }}
|
||||
{{- end }}
|
||||
|
||||
- name: elasticsearch
|
||||
{{- with .Values.elasticsearch }}
|
||||
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||
imagePullPolicy: {{ .image.pullPolicy }}
|
||||
env:
|
||||
- name: cluster.name
|
||||
value: {{ .clusterName }}
|
||||
- name: bootstrap.memory_lock
|
||||
value: "true"
|
||||
- name: ES_JAVA_OPTS
|
||||
value: "{{ .javaOpts }}"
|
||||
- name: xpack.security.enabled
|
||||
value: "false"
|
||||
- name: discovery.type
|
||||
value: single-node
|
||||
ports:
|
||||
- containerPort: 9200
|
||||
- containerPort: 9300
|
||||
resources:
|
||||
{{ toYaml .resources | indent 12 }}
|
||||
{{- end }}
|
||||
|
||||
- name: postgres
|
||||
{{- with .Values.postgres }}
|
||||
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||
imagePullPolicy: {{ .image.pullPolicy }}
|
||||
env:
|
||||
- name: POSTGRES_USER
|
||||
value: {{ .user }}
|
||||
- name: POSTGRES_PASSWORD
|
||||
value: {{ .password }}
|
||||
- name: POSTGRES_DB
|
||||
value: {{ .db }}
|
||||
ports:
|
||||
- containerPort: 5432
|
||||
resources:
|
||||
{{ toYaml .resources | indent 12 }}
|
||||
{{- end }}
|
||||
|
||||
- name: opencpu
|
||||
{{- with .Values.opencpu }}
|
||||
image: "{{ .image.repository }}:{{ .image.tag }}"
|
||||
imagePullPolicy: {{ .image.pullPolicy }}
|
||||
ports:
|
||||
- containerPort: 8004
|
||||
resources:
|
||||
{{ toYaml .resources | indent 12 }}
|
||||
{{- end }}
|
||||
|
||||
{{- with .Values.nodeSelector }}
|
||||
nodeSelector:
|
||||
{{ toYaml . | indent 8 }}
|
||||
{{- end }}
|
||||
{{- with .Values.affinity }}
|
||||
affinity:
|
||||
{{ toYaml . | indent 8 }}
|
||||
{{- end }}
|
||||
{{- with .Values.tolerations }}
|
||||
tolerations:
|
||||
{{ toYaml . | indent 8 }}
|
||||
{{- end }}
|
||||
@ -1,38 +0,0 @@
|
||||
{{- if .Values.ingress.enabled -}}
|
||||
{{- $fullName := include "molgenis.fullname" . -}}
|
||||
{{- $ingressPath := .Values.ingress.path -}}
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: Ingress
|
||||
metadata:
|
||||
name: {{ $fullName }}
|
||||
labels:
|
||||
app: {{ template "molgenis.name" . }}
|
||||
chart: {{ template "molgenis.chart" . }}
|
||||
release: {{ .Release.Name }}
|
||||
heritage: {{ .Release.Service }}
|
||||
{{- with .Values.ingress.annotations }}
|
||||
annotations:
|
||||
{{ toYaml . | indent 4 }}
|
||||
{{- end }}
|
||||
spec:
|
||||
{{- if .Values.ingress.tls }}
|
||||
tls:
|
||||
{{- range .Values.ingress.tls }}
|
||||
- hosts:
|
||||
{{- range .hosts }}
|
||||
- {{ . }}
|
||||
{{- end }}
|
||||
secretName: {{ .secretName }}
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
rules:
|
||||
{{- range .Values.ingress.hosts }}
|
||||
- host: {{ .name }}
|
||||
http:
|
||||
paths:
|
||||
- path: {{ $ingressPath }}
|
||||
backend:
|
||||
serviceName: {{ $fullName }}
|
||||
servicePort: 8080
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
@ -1,17 +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 }}
|
||||
ports:
|
||||
- name: molgenis
|
||||
port: {{ .Values.service.port }}
|
||||
selector:
|
||||
app: {{ template "molgenis.name" . }}
|
||||
release: {{ .Release.Name }}
|
||||
@ -1,82 +0,0 @@
|
||||
# Default values for molgenis.
|
||||
|
||||
replicaCount: 1
|
||||
|
||||
service:
|
||||
type: LoadBalancer
|
||||
port: 8080
|
||||
|
||||
ingress:
|
||||
enabled: true
|
||||
annotations:
|
||||
nginx.ingress.kubernetes.io/proxy-body-size: "0"
|
||||
path: /
|
||||
hosts:
|
||||
- name: test.molgenis.org
|
||||
tls: []
|
||||
|
||||
molgenis:
|
||||
image:
|
||||
repository: registry.molgenis.org
|
||||
name: molgenis/molgenis-app
|
||||
tag: 7.0.0-SNAPSHOT
|
||||
pullPolicy: Always
|
||||
adminPassword: admin
|
||||
javaOpts: "-Xmx1g -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
|
||||
resources:
|
||||
limits:
|
||||
cpu: 1
|
||||
memory: 1250Mi
|
||||
requests:
|
||||
cpu: 200m
|
||||
memory: 1Gi
|
||||
|
||||
postgres:
|
||||
image:
|
||||
repository: postgres
|
||||
tag: 9.6-alpine
|
||||
pullPolicy: IfNotPresent
|
||||
user: molgenis
|
||||
password: molgenis
|
||||
db: molgenis
|
||||
resources:
|
||||
limits:
|
||||
cpu: 1
|
||||
memory: 250Mi
|
||||
requests:
|
||||
cpu: 100m
|
||||
memory: 250Mi
|
||||
|
||||
elasticsearch:
|
||||
image:
|
||||
repository: docker.elastic.co/elasticsearch/elasticsearch
|
||||
tag: 5.5.3
|
||||
pullPolicy: IfNotPresent
|
||||
javaOpts: "-Xms512m -Xmx512m"
|
||||
clusterName: molgenis
|
||||
resources:
|
||||
limits:
|
||||
cpu: 1
|
||||
memory: 1500Mi
|
||||
requests:
|
||||
cpu: 100m
|
||||
memory: 1Gi
|
||||
|
||||
opencpu:
|
||||
image:
|
||||
repository: molgenis/opencpu
|
||||
tag: latest
|
||||
pullPolicy: Always
|
||||
resources:
|
||||
limits:
|
||||
cpu: 1
|
||||
memory: 512Mi
|
||||
requests:
|
||||
cpu: 100m
|
||||
memory: 256Mi
|
||||
|
||||
nodeSelector: {}
|
||||
|
||||
tolerations: []
|
||||
|
||||
affinity: {}
|
||||
@ -1,8 +1,8 @@
|
||||
apiVersion: v1
|
||||
appVersion: "1.0"
|
||||
description: MOLGENIS - helm stack (in BETA)
|
||||
name: molgenis-beta
|
||||
version: 0.3.0
|
||||
name: molgenis
|
||||
version: 0.4.2
|
||||
sources:
|
||||
- https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm.git
|
||||
icon: https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm/raw/master/molgenis/catalogIcon-molgenis.svg
|
||||
@ -5,6 +5,8 @@ This chart is used for acceptance and production use cases.
|
||||
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:
|
||||
@ -21,6 +23,19 @@ The three properties you need to specify are:
|
||||
Besides determining which image you want to pull, you also have to set an administrator password. You can do this by specifying the following property.
|
||||
- ```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)
|
||||
@ -82,15 +97,16 @@ 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```
|
||||
- ```persistence.enabled``` default 'true'
|
||||
|
||||
You can also choose to retain the volume of the NFS.
|
||||
- ```persistence.retain```
|
||||
- ```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```
|
||||
@ -100,6 +116,9 @@ 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:
|
||||
@ -116,7 +135,4 @@ You can now view the persistent volume claims and the attached volumes.
|
||||
| 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```.
|
||||
|
||||
## Firewall
|
||||
Is defined at cluster level. This chart does not facilitate firewall configuration.
|
||||
When you want to view the data in the this volume you can go to the nfs-provisioning pod and execute the shell. Go to the directory ```export``` and lookup the directory ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
|
||||
@ -8,7 +8,7 @@ questions:
|
||||
description: "Hostname for your stack"
|
||||
type: hostname
|
||||
required: true
|
||||
group: "Load Balancing"
|
||||
group: "Load balancing"
|
||||
- variable: molgenis.image.repository
|
||||
label: Registry
|
||||
default: "registry.hub.docker.com"
|
||||
@ -33,6 +33,24 @@ questions:
|
||||
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"
|
||||
@ -40,34 +58,43 @@ questions:
|
||||
type: string
|
||||
required: true
|
||||
group: "Services"
|
||||
- variable: molgenis.services.postgres.host
|
||||
label: Postgres cluster location
|
||||
default: "postgresql.molgenis-postgresql.svc"
|
||||
description: "Set the location of the postgres cluster"
|
||||
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
|
||||
- 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
|
||||
@ -98,7 +125,7 @@ questions:
|
||||
- "2g"
|
||||
group: "Resources"
|
||||
- variable: persistence.enabled
|
||||
default: false
|
||||
default: true
|
||||
description: "Do you want to use persistence"
|
||||
type: boolean
|
||||
required: true
|
||||
@ -112,20 +139,29 @@ questions:
|
||||
type: boolean
|
||||
label: Retain volume
|
||||
- variable: molgenis.persistence.size
|
||||
default: "30Gi"
|
||||
default: "5Gi"
|
||||
description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
|
||||
type: enum
|
||||
options:
|
||||
- "30Gi"
|
||||
- "50Gi"
|
||||
- "100Gi"
|
||||
- "5Gi"
|
||||
- "10Gi"
|
||||
- "20Gi"
|
||||
label: Size MOLGENIS filestore
|
||||
- variable: elasticsearch.persistence.size
|
||||
default: "50Gi"
|
||||
default: "5Gi"
|
||||
description: "Size of ElasticSearch data (directory that is persist: /usr/share/elasticsearch/data)"
|
||||
type: enum
|
||||
options:
|
||||
- "5Gi"
|
||||
- "10Gi"
|
||||
- "50Gi"
|
||||
- "100Gi"
|
||||
- "200Gi"
|
||||
label: Size for ElasticSearch data
|
||||
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
|
||||
@ -97,11 +97,33 @@ spec:
|
||||
- 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
|
||||
@ -110,6 +132,9 @@ spec:
|
||||
- name: elasticsearch-nfs
|
||||
persistentVolumeClaim:
|
||||
claimName: {{ .Values.elasticsearch.persistence.claim }}
|
||||
- name: postgres-nfs
|
||||
persistentVolumeClaim:
|
||||
claimName: {{ .Values.postgres.persistence.claim }}
|
||||
{{- end }}
|
||||
|
||||
{{- with .Values.nodeSelector }}
|
||||
|
||||
@ -4,7 +4,7 @@
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: Ingress
|
||||
metadata:
|
||||
name: {{ $fullName }}
|
||||
name: "{{ $.Release.Name }}-ingress"
|
||||
labels:
|
||||
app: {{ template "molgenis.name" . }}
|
||||
chart: {{ template "molgenis.chart" . }}
|
||||
@ -33,6 +33,6 @@ spec:
|
||||
- path: {{ $ingressPath }}
|
||||
backend:
|
||||
serviceName: {{ $fullName }}
|
||||
servicePort: 8080
|
||||
servicePort: {{ $.Values.service.port }}
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
|
||||
21
molgenis/templates/persistence/postgresPVC.yaml
Normal file
21
molgenis/templates/persistence/postgresPVC.yaml
Normal file
@ -0,0 +1,21 @@
|
||||
{{- if .Values.molgenis.services.postgres.embedded }}
|
||||
{{- if .Values.persistence.enabled }}
|
||||
apiVersion: extensions/v1beta1
|
||||
kind: PersistentVolumeClaim
|
||||
apiVersion: v1
|
||||
metadata:
|
||||
name: {{ .Values.postgres.persistence.claim }}
|
||||
annotations:
|
||||
{{- if .Values.persistence.retain }}
|
||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner-retain"
|
||||
{{- else }}
|
||||
volume.beta.kubernetes.io/storage-class: "nfs-provisioner"
|
||||
{{- end }}
|
||||
spec:
|
||||
accessModes:
|
||||
- ReadWriteMany
|
||||
resources:
|
||||
requests:
|
||||
storage: {{ .Values.postgres.persistence.size }}
|
||||
{{- end }}
|
||||
{{- end }}
|
||||
@ -9,6 +9,18 @@ metadata:
|
||||
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 }}
|
||||
|
||||
@ -4,6 +4,15 @@ 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:
|
||||
@ -33,7 +42,7 @@ molgenis:
|
||||
memory: 1250Mi
|
||||
persistence:
|
||||
claim: molgenis-nfs-claim
|
||||
size: 30Gi
|
||||
size: 5Gi
|
||||
services:
|
||||
opencpu:
|
||||
host: localhost
|
||||
@ -41,6 +50,7 @@ molgenis:
|
||||
transportAddresses: localhost:9300
|
||||
clusterName: molgenis
|
||||
postgres:
|
||||
embedded: false
|
||||
host: localhost
|
||||
scheme: molgenis
|
||||
user: molgenis
|
||||
@ -62,10 +72,26 @@ elasticsearch:
|
||||
memory: 1Gi
|
||||
persistence:
|
||||
claim: elasticsearch-nfs-claim
|
||||
size: 50Gi
|
||||
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: false
|
||||
enabled: true
|
||||
retain: false
|
||||
|
||||
nodeSelector: {
|
||||
|
||||
Loading…
Reference in New Issue
Block a user