FAIRscape Helm chart

Some links:

• FAIRscape publication: https://www.biorxiv.org/content/10.1101/2020.08.10.244947v3.full.pdf
• FAIRscape GitHub repositories: https://github.com/fairscape
• Data Science Research Infrastructure (DSRI, OpenShift cluster) documentation: https://maastrichtu-ids.github.io/dsri-documentation/

Defining a Helm chart

To redeploy easily FAIRscape on any Kubernetes cluster.

Check the documentation to create a Helm chart:

• Helm create docs: https://helm.sh/docs/helm/helm_create/
• Create Helm chart (Bitnami): https://docs.bitnami.com/tutorials/create-your-first-helm-chart/
• Helm tips and trick: https://helm.sh/docs/howto/charts_tips_and_tricks/

How to build the Helm chart

• Define parameters go to values.yaml (variables and their values to be used by the templates)
• Then the deployment is defined in templates/deployment.yaml and can use variables defined in values.yaml
• Charts/ folder is for external charts dependencies (if we want to define FAIRscape using multiple charts for modularity)

Added: defined OpenShift Route in the Helm chart (alongside Ingress)

• cf. https://www.ibm.com/cloud/blog/deploying-helm-charts-on-openshift
• https://artifacthub.io/packages/helm/appuio/openshift-route
• Example openshift-route chart: https://github.com/appuio/charts/tree/master/openshift-route

Test run the chart

Check if the Helm chart is properly defined:

helm lint fairscape

To run the chart in dry-run mode:

helm install --dry-run --debug ./fairscape --set service.internalPort=8080 --generate-name

Deploy the chart

Check the fairscape/values.yaml file to see the parameters of the chart.

• Deploy the chart on OpenShift DSRI:

helm install fairscape ./fairscape --set service.type=NodePort,serviceAccount.name=anyuid,openshiftRoute.enabled=true

We override service.type and serviceAccount.name from the values.yaml file

• Or deploy on Kubernetes with Ingress routes:

helm install fairscape ./fairscape --set service.type=NodePort,ingress.enabled=true

Update the chart

Upgrade the deployed chart using local source code:

helm upgrade fairscape ./fairscape --set service.type=NodePort,serviceAccount.name=anyuid,openshiftRoute.enabled=true

Uninstall the chart

helm uninstall fairscape

Known issues

Helm Swagger API validation reject when we provide an empty string as host ""

• cf. deploying OpenShift Route: https://bugzilla.redhat.com/show_bug.cgi?id=1773682
• cf issue: openshift/origin#24060

Current fix: host is hardcoded as "" in the template instead of using value from values.yaml

It was previously (in templates/openshiftRoute.yaml):

spec:
  host: {{ .Values.openshiftRoute.host }}

Setup the triplestore

Recommended to use Stardog (licensed triplestore) for its path explanation feature

• Academic trial (1 year): https://www.stardog.com/academic-trial/
  • Request academic trial: https://community.stardog.com/t/academic-license/1883/7 (use an academic email)
• Setup instructions: https://www.stardog.com/docs/#_starting_stardog