123 lines
4.6 KiB
Markdown
123 lines
4.6 KiB
Markdown
# MOLGENIS
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This chart is used for acceptance and production use cases.
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## Containers
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This chart spins up a MOLGENIS instance with HTTPD. The created containers are:
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- MOLGENIS
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## Provisioning
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You can choose from which registry you want to pull. There are 2 registries:
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- https://registry.molgenis.org
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- https://hub.docker.com
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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).
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The three properties you need to specify are:
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- ```molgenis.image.repository```
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- ```molgenis.image.name```
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- ```molgenis.image.tag```
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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.
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- ```molgenis.adminPassword```
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## Services
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When you start MOLGENIS you need:
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- an elasticsearch instance (5.5.6)
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- an postgres instance (9.6)
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You can attach additional services like:
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- an opencpu instance
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### Elasticsearch
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You can configure elasticsearch by giving in the cluster location.
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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.
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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.
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- ```molgenis.services.elasticsearch.transportAddresses: localhost:9300```
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To configure the index on a Elasticsearch cluster you can specify the clusterName property.
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- ```molgenis.services.elasticsearch.clusterName: molgenis```
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### Postgres
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You can specify the location of the postgres instance by specify the following property:
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- ```molgenis.services.postgres.host: localhost```
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You can specify the schema by filling out this property:
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- ```molgenis.services.postgres.scheme: molgenis```
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You can specify credentials for the database scheme by specifying the following properties:
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- ```molgenis.services.postgres.user: molgenis```
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- ```molgenis.services.postgres.password: molgenis```
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To test you can use the **PostgreSQL**-helm chart of Kubernetes and specify these answers:
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```bash
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# answers for postgresql chart
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postgresUser=molgenis
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postgresPassword=molgenis
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postgresDatabase=molgenis
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persistence.enabled=false
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```
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### OpenCPU
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You can specify the location of the OpenCPU cluster by specifying this property:
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- ```molgenis.services.opencpu.host: localhost```
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You can test OpenCPU settings using the **OpenCPU**-helm chart of MOLGENIS.
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## Resources
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You can specify resources by resource type. There are 2 resource types.
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- memory of container
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- maximum heap space JVM
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Specify memory usage of container:
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- ```molgenis.resources.limits.memory```
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Specify memory usage for Java JVM:
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- ```molgenis.javaOpts.maxHeapSpace```
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Select the resources you need dependant on the customer you need to serve.
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## Persistence
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You can enable persistence on your MOLGENIS stack by specifying the following property.
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- ```persistence.enabled```
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You can also choose to retain the volume of the NFS.
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- ```persistence.retain```
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The size and claim name can be specified per service. There are now two services that can be persist.
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- MOLGENIS
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- ElasticSearch
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MOLGENIS persistent properties.
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- ```molgenis.persistence.claim```
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- ```molgenis.persistence.size```
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ElasticSearch persistent properties.
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- ```elasticsearch.persistence.claim```
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- ```elasticsearch.persistence.size```
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### Resolve you persistent volume
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You do not know which volume is attached to your MOLGENIS instance. You can resolve this by executing:
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```
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kubectl get pv
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```
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You can now view the persistent volume claims and the attached volumes.
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| NAME | CAPACITY | ACCESS | MODES | RECLAIM | POLICY | STATUS | CLAIM | STORAGECLASS | REASON | AGE |
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| ---- | -------- | ------ | ----- | ------- | ------ | ------ | ----- | ------------ | ------ | --- |
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| pvc-45988f55-900f-11e8-a0b4-005056a51744 | 30G | RWX | | Retain | Bound | molgenis-solverd/molgenis-nfs-claim | nfs-provisioner-retain | | | 33d |
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| pvc-3984723d-220f-14e8-a98a-skjhf88823kk | 30G | RWO | | Delete | Bound | molgenis-test/molgenis-nfs-claim | nfs-provisioner | | | 33d |
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You see the ```molgenis-test/molgenis-nfs-claim``` is bound to the volume: ```pvc-3984723d-220f-14e8-a98a-skjhf88823kk```.
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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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## Firewall
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Is defined at cluster level. This chart does not facilitate firewall configuration.
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