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Author SHA1 Message Date
Fleur Kelpin 7127914de2 Merge branch 'master' of https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm 2018-09-21 13:50:26 +02:00
Fleur Kelpin 16f2701fd2 Merge branch 'add-pvs-to-molgenis' of p281392/molgenis-ops-docker-helm into master 2018-09-12 09:50:34 +02:00
sido 501982ca53 removed redunant volume entry in deployment 2018-09-12 08:19:48 +02:00
sido 7305d54630 updated volume name 2018-09-12 08:17:34 +02:00
sido c28f08bedd one end to much 2018-09-12 08:15:38 +02:00
sido 321af8f2f2 updated labels and desc 2018-09-12 08:13:33 +02:00
sido d17c137dd5 added elasticsearch persistence 2018-09-12 08:04:59 +02:00
Sido Haakma 6f0262d2d9 Merge branch 'chore/remove-secrets' of P129679/molgenis-ops-docker-helm into master 2018-09-11 17:10:10 +02:00
sido 34c8f048b9 also upgraded the default value in values.yaml 2018-09-11 17:08:44 +02:00
sido d7ccab34c4 version bump and enumerized values for sizing volumes 2018-09-11 17:07:14 +02:00
sido 5fd05f505a updated docs 2018-09-11 16:59:40 +02:00
sido 61d5505126 updated persistence README.md 2018-09-11 16:56:27 +02:00
sido e5cbcdf933 added retainability for pv's 2018-09-11 15:48:56 +02:00
sido 04bd9cd653 added persistence to questions and bumped chart 2018-09-11 13:51:58 +02:00
sido 88134dbccb Merge branch 'master' of https://git.webhosting.rug.nl/molgenis/molgenis-ops-docker-helm into add-pvs-to-molgenis 2018-09-11 13:46:37 +02:00
sido 947e389b92 moved volumes down below in deployment 2018-09-10 22:06:20 +02:00
sido ed948c40aa referred to right config values.yaml 2018-09-10 22:02:18 +02:00
sido bfb2e45877 added volumes 2018-09-10 22:00:51 +02:00
sido 59d99deab5 restrcuture deployment 2018-09-10 21:57:39 +02:00
sido a660aff355 udpated structure 2018-09-10 21:53:29 +02:00
sido 846df81522 udpated structure 2018-09-10 21:49:12 +02:00
sido a2922c4d49 persistence keys in deploymeny 2018-09-10 21:47:12 +02:00
sido 0c9548069c add subquestion heading 2018-09-10 21:44:34 +02:00
sido 5a98e35273 added persistence properties to values and deployment 2018-09-10 21:41:54 +02:00
sido d9053b656c updated volume claims 2018-09-10 17:37:50 +02:00
Fleur Kelpin a836ab4e6e chore (molgenis-jenkins): Retrieve pipeline secrets from vault when possible. 2018-09-10 17:28:42 +02:00
sido 14b27fc043 updated persistence configuration 2018-09-10 17:05:10 +02:00
sido cf47b432e2 added persistence to questions 2018-09-10 16:59:14 +02:00
sido 11b25a5df6 added initialDelay 2018-09-10 16:53:58 +02:00
18 changed files with 268 additions and 315 deletions

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@ -40,57 +40,62 @@ You can use [all configuration values of the jenkins subchart](https://github.co
### 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).
### Additional configuration
There is one additional group of configuration items specific for this chart, so not prefixed with `jenkins`:
### Secrets
* PipelineSecrets
When deployed, the chart creates a couple of kubernetes secrets that get used by jenkins and mounted in the jenkins
build pods. The secrets, like the rest of the deployment, is namespaced so multiple instances can run beside
each other with their own 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
#### Vault
New vault token to be used by the pods to retrieve their tokens from the 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
| Parameter | Description | Default |
| ---------------------------------- | ------------------------------------------ | ---------------------------------------------- |
| `PipelineSecrets.Vault.Replace` | Replace the molgenis-pipeline-vault secret | `true` |
| `PipelineSecrets.Vault.Token` | Token to log into the hashicorp vault | `xxxx` |
| `PipelineSecrets.Vault.Addr` | Address of the vault | `https:vault-operator.vault-operator.svc:8200` |
| `PipelineSecrets.Vault.SkipVerify` | Skip verification of the https connection | `1` |
Account used in pipeline builds to push docker images to `hub.docker.com`.
> They should read `secret/gcc/account/dockerhub` from vault instead!
* Env
| Parameter | Description | Default |
| --------------------------- | ------------------------ | --------------- |
| `secret.dockerHub.user` | username for the account | `molgenisci` |
| `secret.dockerHub.password` | password for the account | `xxxx` |
##### Registry
Environment variables stored in molgenis-pipeline-env secret, to be added as environment variables
in the slave pods.
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 |
| --------------------------------------- | ----------------------------------------- | --------------- |
| `PipelineSecrets.Env.Replace` | Replace molgenis-pipeline-env secret | `true` |
| `PipelineSecrets.Env.PGPPassphrase` | passphrase for the pgp signing key | `literal:xxxx` |
| `PipelineSecrets.Env.CodecovToken` | token for codecov.io | `xxxx` |
| `PipelineSecrets.Env.GitHubToken` | token for GH molgenis-jenkins user | `xxxx` |
| `PipelineSecrets.Env.NexusPassword` | token for molgenis-jenkins user in NEXUS | `xxxx` |
| `PipelineSecrets.Env.DockerHubPassword` | token for molgenis user in hub.docker.com | `xxxx` |
| `PipelineSecrets.Env.SonarToken` | token for sonarcloud.io | `xxxx` |
| `PipelineSecrets.Env.NpmToken` | token for npmjs.org | `xxxx` |
| `PipelineSecrets.Env.SauceAccessKey` | token for saucelabs.com | `xxxx` |
* File
Environment variables stored in molgenis-pipeline-file secret, to be mounted as files
in the `/root/.m2` directory of the slave pods.
> The settings.xml file references the
| Parameter | Description | Default |
| -------------------------------------- | ------------------------------------- | ------------------------------------------------------------------------------- |
| `PipelineSecrets.File.Replace` | Replace molgenis-pipeline-file secret | `true` |
| `PipelineSecrets.File.PGPPrivateKeyAsc`| pgp signing key in ascii form | `-----BEGIN PGP PRIVATE KEY BLOCK-----xxxxx-----END PGP PRIVATE KEY BLOCK-----` |
| `PipelineSecrets.File.MavenSettingsXML`| Maven settings.xml file | `<settings>[...]</settings>` (see actual [values.yaml](values.yaml)) |
| 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`.

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@ -8,9 +8,9 @@ metadata:
"jenkins.io/credentials-type": "usernamePassword"
annotations: {
# description - can not be a label as spaces are not allowed
"jenkins.io/credentials-description" : "user to authenticate against Docker Hub (hub.docker.com)"
"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: {{ "molgenisci" | b64enc | quote }}
password: {{ .Values.PipelineSecrets.Env.DockerHubPassword | b64enc | quote }}
username: {{ .Values.secret.registry.user | b64enc | quote }}
password: {{ .Values.secret.registry.password | b64enc | quote }}

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@ -8,9 +8,9 @@ metadata:
"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 molgenis-jenkins github user"
"jenkins.io/credentials-description" : "Oauth token for the {{.Values.secret.gitHub.user}} GitHub user"
}
type: Opaque
data:
username: {{ "molgenis-jenkins" | b64enc | quote }}
password: {{ .Values.PipelineSecrets.Env.GitHubToken | b64enc | quote }}
username: {{ .Values.secret.gitHub.user | b64enc | quote }}
password: {{ .Values.secret.gitHub.token | b64enc | quote }}

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@ -8,9 +8,9 @@ metadata:
"jenkins.io/credentials-type": "usernamePassword"
annotations: {
# description - can not be a label as spaces are not allowed
"jenkins.io/credentials-description" : "user to authenticate against GOGS (git.webhosting.rug.nl)"
"jenkins.io/credentials-description" : "Account used to authenticate against RuG Webhosting Gogs."
}
type: Opaque
data:
username: {{ "p281392" | b64enc | quote }}
password: {{ .Values.PipelineSecrets.Env.GogsToken | b64enc | quote }}
username: {{ .Values.secret.gogs.user | b64enc | quote }}
password: {{ .Values.secret.gogs.token | b64enc | quote }}

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@ -1,16 +0,0 @@
apiVersion: v1
kind: Secret
metadata:
# this is the jenkins id.
name: "molgenis-jenkins-nexus-secret"
labels:
# so we know what type it is.
"jenkins.io/credentials-type": "usernamePassword"
annotations: {
# description - can not be a label as spaces are not allowed
"jenkins.io/credentials-description" : "user to authenticate against NEXUS"
}
type: Opaque
data:
username: {{ "admin" | b64enc | quote }}
password: {{ .Values.PipelineSecrets.Env.NexusPassword | b64enc | quote }}

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@ -0,0 +1,17 @@
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 }}

View File

@ -1,16 +0,0 @@
apiVersion: v1
kind: Secret
metadata:
# this is the jenkins id.
name: "molgenis-jenkins-saucelabs-secret"
labels:
# so we know what type it is.
"jenkins.io/credentials-type": "usernamePassword"
annotations: {
# description - can not be a label as spaces are not allowed
"jenkins.io/credentials-description" : "user to authenticate against Saucelabs (saucelabs.com)"
}
type: Opaque
data:
username: {{ "molgenis-jenkins" | b64enc | quote }}
password: {{ .Values.PipelineSecrets.Env.SauceAccessKey | b64enc | quote }}

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@ -1,18 +0,0 @@
{{- if .Values.PipelineSecrets.Env.Replace }}
apiVersion: v1
kind: Secret
metadata:
name: molgenis-pipeline-env-secret
labels:
app: {{ template "jenkins.fullname" . }}
chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
release: "{{ .Release.Name }}"
heritage: "{{ .Release.Service }}"
type: Opaque
data:
pgpPassphrase: {{ .Values.PipelineSecrets.Env.PGPPassphrase | b64enc | quote }}
codecovToken: {{ .Values.PipelineSecrets.Env.CodecovToken | b64enc | quote }}
githubToken: {{ .Values.PipelineSecrets.Env.GitHubToken | b64enc | quote }}
sonarToken: {{ .Values.PipelineSecrets.Env.SonarToken | b64enc | quote }}
npmToken: {{ .Values.PipelineSecrets.Env.NpmToken | b64enc | quote }}
{{- end }}

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@ -1,15 +0,0 @@
{{- if .Values.PipelineSecrets.File.Replace }}
apiVersion: v1
kind: Secret
metadata:
name: molgenis-pipeline-file-secret
labels:
app: {{ template "jenkins.fullname" . }}
chart: "{{ .Chart.Name }}-{{ .Chart.Version }}"
release: "{{ .Release.Name }}"
heritage: "{{ .Release.Service }}"
type: Opaque
data:
key.asc: {{ .Values.PipelineSecrets.File.PGPPrivateKeyAsc | b64enc | quote }}
settings.xml: {{ .Values.PipelineSecrets.File.MavenSettingsXML | b64enc | quote }}
{{- end }}

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@ -1,4 +1,3 @@
{{- if .Values.PipelineSecrets.Vault.Replace }}
apiVersion: v1
kind: Secret
metadata:
@ -10,7 +9,6 @@ metadata:
heritage: "{{ .Release.Service }}"
type: Opaque
data:
token: {{ .Values.PipelineSecrets.Vault.Token | b64enc | quote }}
addr: {{ .Values.PipelineSecrets.Vault.Addr | b64enc | quote }}
skipVerify: {{ .Values.PipelineSecrets.Vault.SkipVerify | b64enc | quote }}
{{- end }}
token: {{ .Values.secret.vault.token | b64enc | quote }}
addr: {{ .Values.secret.vault.addr | b64enc | quote }}
skipVerify: {{ .Values.secret.vault.skipVerify | b64enc | quote }}

View File

@ -368,8 +368,8 @@ jenkins:
install: true
Pods:
molgenis:
Label: molgenisv2
NodeUsageMode: EXCLUSIVE
Label: molgenis
NodeUsageMode: NORMAL
volumes:
- type: HostPath
hostPath: "/var/run/docker.sock"
@ -417,39 +417,6 @@ jenkins:
secretName: molgenis-pipeline-vault-secret
secretKey: addr
NodeSelector: {}
molgenis-legacy:
InheritFrom: molgenis
Label: molgenis
NodeUsageMode: NORMAL
volumes:
- type: Secret
secretName: molgenis-pipeline-file-secret
mountPath: "/home/jenkins/.m2"
Containers:
EnvVars:
- type: Secret
key: PGP_PASSPHRASE
secretName: molgenis-pipeline-env-secret
secretKey: pgpPassphrase
- type: KeyValue
key: PGP_SECRETKEY
value: "keyfile:/home.jenkins/.m2/key.asc"
- type: KeyValue
key: npm_config_registry
value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
- type: Secret
key: SONAR_TOKEN
secretName: molgenis-pipeline-env-secret
secretKey: sonarToken
- type: Secret
key: CODECOV_TOKEN
secretName: molgenis-pipeline-env-secret
secretKey: codecovToken
- type: Secret
key: GITHUB_TOKEN
secretName: molgenis-pipeline-env-secret
secretKey: githubToken
NodeSelector: {}
node:
Label: node-carbon
NodeUsageMode: EXCLUSIVE
@ -461,155 +428,45 @@ jenkins:
Command: cat
WorkingDir: /home/jenkins
TTY: true
EnvVars:
- type: KeyValue
key: npm_config_registry
value: "http://nexus.molgenis-nexus:8081/repository/npm-central/"
- type: Secret
key: CODECOV_TOKEN
secretName: molgenis-pipeline-env-secret
secretKey: codecovToken
- type: Secret
key: GITHUB_TOKEN
secretName: molgenis-pipeline-env-secret
secretKey: githubToken
- type: Secret
key: NPM_TOKEN
secretName: molgenis-pipeline-env-secret
secretKey: npmToken
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"
vault:
Image: "vault"
Command: cat
WorkingDir: /home/jenkins
TTY: true
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"
- 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: {}
PipelineSecrets:
Vault:
Replace: true
Token: xxxx
Addr: "https://vault-operator.vault-operator.svc:8200"
SkipVerify: 1
Env:
# Set to false to keep existing secret
Replace: true
# Passphrase for the pgp private key file, prefixed with literal:
PGPPassphrase: literal:xxxx
# Token for codecov.io service
CodecovToken: xxxx
# Token for github bot account
GitHubToken: xxxx
# Token for github bot account
GogsToken: xxxx
# Token for sonarcloud.io
SonarToken: xxxx
# Token for npmjs.org
NpmToken: xxxx
# Password Local NEXUS
NexusPassword: xxxx
# Password hub.docker.com
DockerHubPassword: xxxx
# Access key for saucelabs.com
SauceAccessKey: xxxx
File:
# Set to false to keep existing secret
Replace: true
# PGP Private key in ascii format used to sign artifacts
PGPPrivateKeyAsc: |-
-----BEGIN PGP PRIVATE KEY BLOCK-----
xxxxx
-----END PGP PRIVATE KEY BLOCK-----
# maven.settings file
MavenSettingsXML: |-
<settings>
<localRepository>${user.home}/.mvnrepository</localRepository>
<interactiveMode>false</interactiveMode>
<mirrors>
<mirror>
<id>nexus</id>
<mirrorOf>external:*</mirrorOf>
<url>http://nexus.molgenis-nexus:8081/repository/maven-central/</url>
</mirror>
</mirrors>
<servers>
<!-- for snapshot builds of the master -->
<server>
<id>sonatype-nexus-staging</id>
<username>molgenis</username>
<password>xxxx</password>
</server>
<server>
<id>local-nexus</id>
<url>http://nexus.molgenis-nexus:8081/repository/maven-snapshots/</url>
<username>admin</username>
<password>xxxxx</password>
</server>
<!-- for docker images-->
<server>
<id>registry.molgenis.org</id>
<username>admin</username>
<password>xxxx</password>
</server>
<server>
<id>registry.hub.docker.com</id>
<username>molgenisci</username>
<password>xxxx</password>
</server>
</servers>
</settings>
#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

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@ -2,7 +2,7 @@ apiVersion: v1
appVersion: "1.0"
description: MOLGENIS - helm stack (in BETA)
name: molgenis-beta
version: 0.1.0
version: 0.3.0
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

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@ -79,5 +79,44 @@ Specify memory usage for Java JVM:
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```
You can also choose to retain the volume of the NFS.
- ```persistence.retain```
The size and claim name can be specified per service. There are now two services that can be persist.
- MOLGENIS
- ElasticSearch
MOLGENIS persistent properties.
- ```molgenis.persistence.claim```
- ```molgenis.persistence.size```
ElasticSearch persistent properties.
- ```elasticsearch.persistence.claim```
- ```elasticsearch.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```.
## Firewall
Is defined at cluster level. This chart does not facilitate firewall configuration.

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@ -81,7 +81,7 @@ questions:
- variable: molgenis.resources.requests.memory
label: Container memory reservation
default: 1250Mi
description: "Memory reservation for this MOLGENIS container"
description: "Memory reservation for this MOLGENIS container (must fit in the selected memory limit for the container)"
type: enum
options:
- "1250Mi"
@ -96,4 +96,36 @@ questions:
options:
- "1g"
- "2g"
group: "Resources"
group: "Resources"
- variable: persistence.enabled
default: false
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: "30Gi"
description: "Size of MOLGENIS filestore (PostgreSQL and ElasticSearch excluded)"
type: enum
options:
- "30Gi"
- "50Gi"
- "100Gi"
label: Size MOLGENIS filestore
- variable: elasticsearch.persistence.size
default: "50Gi"
description: "Size of ElasticSearch data (directory that is persist: /usr/share/elasticsearch/data)"
type: enum
options:
- "50Gi"
- "100Gi"
- "200Gi"
label: Size for ElasticSearch data

View File

@ -49,6 +49,11 @@ spec:
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: /
@ -87,10 +92,25 @@ spec:
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 }}
{{- if .Values.persistence.enabled }}
volumes:
- name: molgenis-nfs
persistentVolumeClaim:
claimName: {{ .Values.molgenis.persistence.claim }}
- name: elasticsearch-nfs
persistentVolumeClaim:
claimName: {{ .Values.elasticsearch.persistence.claim }}
{{- end }}
{{- with .Values.nodeSelector }}
nodeSelector:

View File

@ -0,0 +1,19 @@
{{- 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 }}

View File

@ -0,0 +1,19 @@
{{- 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 }}

View File

@ -25,12 +25,15 @@ molgenis:
javaOpts:
maxHeapSpace: "1g"
resources:
limits:
cpu: 1
memory: 1250Mi
requests:
cpu: 200m
memory: 1250Mi
limits:
cpu: 1
memory: 1250Mi
requests:
cpu: 200m
memory: 1250Mi
persistence:
claim: molgenis-nfs-claim
size: 30Gi
services:
opencpu:
host: localhost
@ -57,8 +60,17 @@ elasticsearch:
requests:
cpu: 100m
memory: 1Gi
persistence:
claim: elasticsearch-nfs-claim
size: 50Gi
nodeSelector: {}
persistence:
enabled: false
retain: false
nodeSelector: {
deployPod: "true"
}
tolerations: []