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Chart](https://github.com/MaastrichtU-IDS/fairscape-helm/workflows/Lint%20and%20Test%20Charts/badge.svg)](https://github.com/MaastrichtU-IDS/fairscape-helm/actions?query=workflow%3A%22Test+Fairscape+Helm+Chart%22) [![Validate Helm chart](https://github.com/MaastrichtU-IDS/fairscape-helm/workflows/Validate%20Helm%20chart/badge.svg)](https://github.com/MaastrichtU-IDS/fairscape-helm/actions?query=workflow%3A%22Validate+Helm+chart%22)\n\nSome links:\n\n* FAIRscape publication: https://www.biorxiv.org/content/10.1101/2020.08.10.244947v3.full.pdf\n* FAIRscape GitHub repositories: https://github.com/fairscape\n* Data Science Research Infrastructure (DSRI, OpenShift cluster) documentation: https://maastrichtu-ids.github.io/dsri-documentation/\n\n## Defining a Helm chart\n\nTo redeploy easily FAIRscape on any Kubernetes cluster.\n\nCheck the documentation to create a [Helm](https://helm.sh/) chart:\n\n* `Helm create` docs: https://helm.sh/docs/helm/helm_create/\n* Create Helm chart (Bitnami): https://docs.bitnami.com/tutorials/create-your-first-helm-chart/\n* Helm tips and trick: https://helm.sh/docs/howto/charts_tips_and_tricks/\n\n### How to build the Helm chart\n\n* Define parameters go to `values.yaml` (variables and their values to be used by the templates)\n* Then the deployment is defined in `templates/deployment.yaml` and can use variables defined in `values.yaml`\n* `Charts/` folder is for external charts dependencies (if we want to define FAIRscape using multiple charts for modularity)\n\nAdded: defined OpenShift Route in the Helm chart (alongside Ingress)\n\n* cf. https://www.ibm.com/cloud/blog/deploying-helm-charts-on-openshift\n* https://artifacthub.io/packages/helm/appuio/openshift-route\n* Example `openshift-route` chart: https://github.com/appuio/charts/tree/master/openshift-route\n\n### Test run the chart\n\nCheck if the Helm chart is properly defined:\n\n```bash\nhelm lint fairscape\n```\n\nTo run the chart in dry-run mode:\n\n```bash\nhelm install --dry-run --debug ./fairscape --set service.internalPort=8080 --generate-name\n```\n\n### Deploy the chart\n\nCheck the [`fairscape/values.yaml`](https://github.com/MaastrichtU-IDS/fairscape-helm/blob/main/fairscape/values.yaml) file to see the parameters of the chart.\n\n* Deploy the chart on **OpenShift DSRI**:\n\n```bash\nhelm install fairscape ./fairscape --set service.type=NodePort,serviceAccount.name=anyuid,openshiftRoute.enabled=true\n```\n\n\u003e We override `service.type` and `serviceAccount.name` from the `values.yaml` file\n\n* Or deploy on **Kubernetes** with Ingress routes:\n\n```bash\nhelm install fairscape ./fairscape --set service.type=NodePort,ingress.enabled=true\n```\n\n### Update the chart\n\nUpgrade the deployed chart using local source code:\n\n```bash\nhelm upgrade fairscape ./fairscape --set service.type=NodePort,serviceAccount.name=anyuid,openshiftRoute.enabled=true\n```\n\n### Uninstall the chart\n\n```bash\nhelm uninstall fairscape\n```\n\n### Known issues\n\nHelm Swagger API validation reject when we provide an empty string as host `\"\"`\n\n* cf. deploying OpenShift Route: https://bugzilla.redhat.com/show_bug.cgi?id=1773682\n* cf issue: https://github.com/openshift/origin/issues/24060\n\nCurrent fix: `host` is hardcoded as `\"\"` in the template instead of using value from `values.yaml`\n\nIt was previously (in `templates/openshiftRoute.yaml`):\n\n```yaml\nspec:\n  host: {{ .Values.openshiftRoute.host }}\n```\n\n## Setup the triplestore\n\nRecommended to use [Stardog](https://www.stardog.com/) (licensed triplestore) for its path explanation feature\n\n* Academic trial (1 year): https://www.stardog.com/academic-trial/\n  * Request academic trial: https://community.stardog.com/t/academic-license/1883/7 (use an academic email)\n* Setup instructions: 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