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updated production chart and removed preview chart

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sido
2018-09-26 16:04:22 +02:00
parent 95dc0acabd
commit f10b8d7ea8
21 changed files with 205 additions and 1493 deletions
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4
molgenis/Chart.yaml
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@ -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: 0.4.0
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/catalogIcon-molgenis.svg

26
molgenis/README.md
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@ -21,6 +21,19 @@ 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 +95,16 @@ 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 +114,9 @@ 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 +133,4 @@ 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```.

109
molgenis/questions.yml
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@ -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 +33,25 @@ 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.umcg.enabled
default: false
description: "Firewall within the UMCG environment"
type: boolean
label: Firewall UMCG enabled
- variable: service.firewall.cluster.enabled
default: false
description: "Firewall within the cluster environment"
type: boolean
label: Firewall cluster enabled
- variable: molgenis.services.opencpu.host
label: OpenCPU cluster
default: "localhost"
@ -40,34 +59,43 @@ 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 +126,7 @@ questions:
- "2g"
group: "Resources"
- variable: persistence.enabled
default: false
default: true
description: "Do you want to use persistence"
type: boolean
required: true
@ -112,20 +140,29 @@ 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

25
molgenis/templates/deployment.yaml
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@ -97,11 +97,31 @@ 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 }}
volumeMounts:
- name: postgres-nfs
mountPath: /var/lib/postgresql/data
{{- end }}
{{- if .Values.persistence.enabled }}
volumes:
- name: molgenis-nfs
@ -110,6 +130,9 @@ spec:
- name: elasticsearch-nfs
persistentVolumeClaim:
claimName: {{ .Values.elasticsearch.persistence.claim }}
- name: postgres-nfs
persistentVolumeClaim:
claimName: {{ .Values.postgres.persistence.claim }}
{{- end }}
{{- with .Values.nodeSelector }}

4
molgenis/templates/ingress.yaml
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@ -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 }}

19
molgenis/templates/persistence/postgresPVC.yaml Normal file
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@ -0,0 +1,19 @@
{{- if .Values.molgenis.services.postgres.embedded -}}
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 }}

13
molgenis/templates/service.yaml
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@ -9,6 +9,19 @@ metadata:
heritage: {{ .Release.Service }}
spec:
type: {{ .Values.service.type }}
{{- if .Values.service.firewall.enabled }}
loadBalancerSourceRanges:
{{- if .Values.service.firewall.umcg.enabled }}
{{- range $index, $rule := .Values.service.firewall.umcg.rules }}
- {{ $rule }}
{{- end }}
{{- if .Values.service.firewall.cluster.enabled }}
{{- range $index, $rule := .Values.service.firewall.cluster.rules }}
- {{ $rule }}
{{- end }}
{{- end }}
{{- end }}
{{- end }}
ports:
- name: molgenis
port: {{ .Values.service.port }}

33
molgenis/values.yaml
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@ -4,6 +4,16 @@ replicaCount: 1
service:
type: LoadBalancer
firewall:
enabled: false
umcg:
enabled: false
rules:
- 127.0.0.1/32
cluster:
enabled: false
rules:
- 127.0.0.1/32
port: 8080
ingress:
@ -33,7 +43,7 @@ molgenis:
memory: 1250Mi
persistence:
claim: molgenis-nfs-claim
size: 30Gi
size: 5Gi
services:
opencpu:
host: localhost
@ -41,6 +51,7 @@ molgenis:
transportAddresses: localhost:9300
clusterName: molgenis
postgres:
embedded: false
host: localhost
scheme: molgenis
user: molgenis
@ -62,10 +73,26 @@ 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: {