gen3-helm

Helm charts for deploying Gen3 on any kubernetes cluster.

Deploying gen3 with helm

TL;DR

helm repo add gen3 https://helm.gen3.org
helm repo update
helm upgrade --install gen3 gen3/gen3 -f ./values.yaml

Assuming you already have the prerequisites installed and configured, you can deploy Gen3 with the helm command.

Warning The default Helm chart configuration is not intended for production. The default chart creates a proof of concept (PoC) implementation where all Gen3 services are deployed in the cluster, including postgres and elasticsearch. For production deployments, you must follow the Production/Cloud Native/Hybrid architecture

For a production deployment, you should have strong working knowledge of Kubernetes. This method of deployment has different management, observability, and concepts than traditional deployments.

In a production deployment:

The stateful components, like PostgreSQL or Elasticsearch, must run outside the cluster on PaaS or compute instances. This configuration is required to scale and reliably service the variety of workloads found in production Gen3 environments.
You should use Cloud PaaS for PostgreSQL, Elasticsearch, and object storage.

Configuration

For a full set of configuration options see the CONFIGURATION.md for a more in depth instructions on how to configure each service.

There's also an auto-generated table of basic configuration options here:

README.md for gen3 chart (auto-generated documentation) or

To see documentation around setting up gen3 developer environments see gen3_developer_environments.md

Use the following as a template for your values.yaml file for a minimum deployment of gen3 using these helm charts.

global:
  hostname: example-commons.com

fence: 
  FENCE_CONFIG:
    # Any fence-config overrides here.

Selective deployments

All gen3 services are sub-charts of the gen3 chart (which acts as an umbrella chart).

For your specific installation of gen3, you may not require all our services.

To enable or disable a service you can use this pattern in your values.yaml

fence:
  enabled: true

wts:
  enabled: false

Gen3 Login Options

Gen3 does not have any IDP, but can integrate with many. We will cover Google login here, but refer to the fence documentation for additional options.

TL/DR: At minimum to have google logins working you need to set these settings in your values.yaml file

fence: 
  FENCE_CONFIG:
    OPENID_CONNECT:
      google:
        client_id: "insert.google.client_id.here"
        client_secret: "insert.google.client_secret.here"

Google login generation

You need to set up a google credential for google login as that's the default enabled option in fence.

The following steps explain how to create credentials for your gen3

Go to the Credentials page.

Click Create credentials > OAuth client ID.

Select the Web application application type. Name your OAuth 2.0 client and click Create.

For Authorized Javascript Origins add https://<hostname>

For "Authorized redirect URIs" add https://<hostname>/user/login/google/login/

After configuration is complete, take note of the client ID that was created. You will need the client ID and client secret to complete the next steps.

Production deployments

Please read this for more details on production deployments.

NOTE: Gen3 helm charts are currently not used in production by CTDS, but we are aiming to do that soon and will have additional documentation on that.

Local Development

For local development you must be connected to a kubernetes cluster. As referenced above in the section Kubernetes cluster we recommend using Rancher Desktop as Kubernetes on your local machine, especially on M1 Mac's. You also get ingress and other benefits out of the box.

For MacOS users, Minikube equipped with the ingress addon serves as a viable alternative to Rancher Desktop. On Linux, we've observed that using Kind with an NGINX ingress installed often provides a more seamless experience compared to both Rancher Desktop and Minikube. Essentially, Helm requires access to a Kubernetes cluster with ingress capabilities, facilitating the loading of the portal in your browser for an optimal development workflow.

To install the NGINX ingress:

  helm repo add nginx-stable https://helm.nginx.com/stable
  helm repo update
  kubectl create ns nginx-ingress
  helm install nginx-ingress nginx-stable/nginx-ingress --namespace nginx-ingress

Warning If you are using Rancher Desktop you need to increase the vm.max_map_count as outlined here If you are using Minikube you will need to enabled the ingress addon as outlined here

Clone the repository
Navigate to the gen3-helm/helm/gen3 directory and run helm dependency update
Navigate to the back to the gen3-helm directory and create your values.yaml file. See the TL;DR section for a minimal example.
Run helm upgrade --install gen3 ./helm/gen3 -f ./values.yaml

Using Skaffold

Skaffold is a tool for local development that can be used to automatically rebuild and redeploy your application when changes are detected. A minimal skaffold.yaml configuration file has been provided in the gen3-helm directory. Update the values of this file to match your needs.

Follow the steps above, but instead of doing the helm upgrade --install step, use skaffold dev to start the development process. Skaffold will automatically build and deploy your application to your kubernetes cluster.

Troubleshooting

Sanity checks

If deploying from the local repo, make sure you followed the steps for helm dependency update. If you make any changes, this must be repeated for those changes to propagate.

Debugging helm chart issues

Sometimes there are cryptic errors that occur during use of the helm chart, such as duplicate env vars or other items. Try rendering the resources to a file, in debug mode, and it will help determine where the issues may be taking place

helm template --debug gen3 ./helm/gen3 -f ./values.yaml > test.yaml

uc-cdis/gen3-helm