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working opal

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sido 2018-11-06 12:09:12 +00:00
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commit c225d71968
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133
charts/opal/README.md
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@ -4,135 +4,10 @@ This chart is used for acceptance and production use cases.
## Containers
The created containers are:
- MOLGENIS
- ElasticSearch
- PostgreSQL **(optional)**
- Opal
- MongoDB
- RServer
## Provisioning
You can choose from which registry you want to pull. There are 2 registries:
- https://registry.molgenis.org
You can choose from which registry you want to pull. There is 1 one registry:
- 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```.

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8
charts/opal/requirements.lock
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@ -1,6 +1,6 @@
dependencies:
- name: mysql
- name: mongodb
repository: https://kubernetes-charts.storage.googleapis.com/
version: 0.10.2
digest: sha256:77710fe100fb005d51e006d2e19643f9af2b1aadd1c2249c67ffc5be6a095f30
generated: 2018-10-24T22:38:04.939630519+02:00
version: 4.8.1
digest: sha256:14ec2719c92a969b8dcac0de0deea31154c4dc135710f43acb7f0dc209faa9ea
generated: 2018-11-06T10:03:54.890729161Z

4
charts/opal/requirements.yaml
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@ -1,4 +1,4 @@
dependencies:
- name: mysql
version: ^0.10.2
- name: mongodb
version: ^4.8.1
repository: https://kubernetes-charts.storage.googleapis.com/

34
charts/opal/templates/deployment.yaml
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@ -31,20 +31,10 @@ spec:
image: {{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}
imagePullPolicy: {{ .image.pullPolicy }}
env:
- name: opal.home
value: /home/opal
- name: db_uri
value: jdbc:postgresql://localhost/opal
- name: db_user
value: opal
- name: db_password
value: opal
- name: admin.password
- name: OPAL_ADMINISTRATOR_PASSWORD
value: "{{ .adminPassword }}"
- name: CATALINA_OPTS
value: "-Xmx{{ .javaOpts.maxHeapSpace }} -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled"
ports:
- containerPort: 8080
- containerPort: {{ $.Values.service.port }}
{{- if $.Values.persistence.enabled }}
volumeMounts:
- name: opal-nfs
@ -53,19 +43,21 @@ spec:
livenessProbe:
httpGet:
path: /
port: 8080
port: {{ $.Values.service.port }}
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: rserver
{{- with .Values.rserver }}
image: {{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}
imagePullPolicy: {{ .image.pullPolicy }}
ports:
- containerPort: 6612
- containerPort: 6311
resources:
{{ toYaml .resources | indent 12 }}
{{- end }}

10
charts/opal/templates/ingress.yaml
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@ -6,10 +6,10 @@ kind: Ingress
metadata:
name: "{{ $.Release.Name }}-ingress"
labels:
app: {{ template "opal.name" . }}
chart: {{ template "opal.chart" . }}
release: {{ .Release.Name }}
heritage: {{ .Release.Service }}
app: {{ $.Values.service.name }}
chart: "{{ $.Chart.Name }}-{{ $.Chart.Version }}"
release: "{{ .Release.Name }}"
heritage: "{{ .Release.Service }}"
{{- with .Values.ingress.annotations }}
annotations:
{{ toYaml . | indent 4 }}
@ -33,7 +33,7 @@ spec:
paths:
- path: {{ $ingressPath }}
backend:
serviceName: {{ $fullName }}
serviceName: {{ $.Values.service.name }}
servicePort: {{ $.Values.service.port }}
{{- end }}
{{- end }}

6
charts/opal/templates/service.yaml
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@ -1,16 +1,16 @@
apiVersion: v1
kind: Service
metadata:
name: {{ template "opal.fullname" . }}
name: {{ .Values.service.name }}
labels:
app: {{ template "opal.name" . }}
app: {{ .Values.service.name }}
chart: {{ template "opal.chart" . }}
release: {{ .Release.Name }}
heritage: {{ .Release.Service }}
spec:
type: {{ .Values.service.type }}
ports:
- name: opal
- name: {{ .Values.service.name }}
port: {{ .Values.service.port }}
selector:
app: {{ template "opal.name" . }}

28
charts/opal/values.yaml
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@ -3,6 +3,7 @@
replicaCount: 1
service:
name: opal
type: ClusterIP
port: 8080
@ -21,8 +22,8 @@ opal:
maxHeapSpace: "4g"
resources:
limits:
cpu: 4
memory: 4Gi
cpu: 1
memory: 2Gi
requests:
cpu: 200m
memory: 4Gi
@ -33,21 +34,30 @@ opal:
name: obiba/opal
tag: latest
pullPolicy: Always
adminPassword:
adminPassword: admin
persistence:
claim: pvc-opal
size: 10Gi
services:
rserver:
host: localhost
mysql:
host: localhost
containerPorts:
- 8080
rserver:
image:
repository: obiba/opal-rserver
repository: registry.hub.docker.com
name: obiba/opal-rserver
tag: latest
pullPolicy: IfNotPresent
resources:
limits:
cpu: 1
memory: 2Gi
containerPorts:
- 6612
- 6311
mongodb:
persistence:
enabled: false
persistence:
enabled: false

11
charts/rstudio/templates/deployment.yaml
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@ -28,8 +28,19 @@ spec:
- name: {{ .name }}
image: "{{ .image.repository }}/{{ .image.name }}:{{ .image.tag }}"
imagePullPolicy: {{ .image.pullPolicy }}
env:
- name: PASSWORD
value: "{{ .adminPassword }}"
ports:
- containerPort: {{ .service.port }}
livenessProbe:
httpGet:
path: /
port: {{ .service.port }}
initialDelaySeconds: 60
periodSeconds: 5
failureThreshold: 25
successThreshold: 1
{{- end }}

4
charts/rstudio/templates/service.yaml
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@ -8,10 +8,6 @@ metadata:
heritage: {{ .Release.Service }}
spec:
type: {{ .Values.rstudio.service.type }}
loadBalancerSourceRanges:
{{- range $index, $rule := .Values.rstudio.service.firewall }}
- {{ $rule }}
{{- end }}
ports:
- name: {{ .Values.rstudio.service.name }}
port: {{ .Values.rstudio.service.port }}

5
charts/rstudio/values.yaml
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@ -11,14 +11,15 @@ rstudio:
strategy:
type: Recreate
restartPolicy: Always
adminPassword: ?01LifeCycle!
image:
repository: registry.hub.docker.com
name: molgenis/rstudio
tag: latest
tag: beta
pullPolicy: Always
service:
name: rstudio
type: LoadBalancer
type: ClusterIP
port: 8787
ingress: