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cxg_on_k8

Proof of concept about deploying cellxgene instances on a kubernetes cluster;

->Technical presentation

python3 -m pip install kubernetes kopf[uvloop]
  • Namespace: Instances are deployed in a dedicated cellxgene namespace.
kubectl apply -f manifests/namespace_cellxgene.yaml
  • Tests: Conversely for unit tests instances:
kubectl apply -f manifests/namespace_testing.yaml

Docker images

Kubernetes runs containerized applications.

minikube For minikube you should preface building phase with the following command so that build happens inside. Else you'd have to make your images available through a registry.

eval $(minikube docker-env)

For the demo, size optimized alpine images are used. To build them:

  • cellxgene alpine - warning: takes 1000+ seconds
docker build . -f docker/Dockerfile_cellxgene_alpine -t cellxgene:1.1.2-python3.11-alpine3.19

OR alternatively

  • cellxgene slim
docker build . -f docker/Dockerfile_cellxgene_slim -t cellxgene:1.1.2-python3.11-slim-bookworm

Note: You may set the PYTHON__V and ALPINE__V variables in the corresponding dockerfiles to build for different versions.

  • cellxgene VIP - warning: 3x heavier than cellxgene - Supports only python3.8
docker build . -f docker/Dockerfile_cellxgene_VIP_slim -t cellxgene:1.1.2-VIP-python3.8-slim-bookworm
  • aws-cli
docker build . -f docker/Dockerfile_aws-cli -t aws_cli:xsmall
  • sui-operator
docker build . -f docker/Dockerfile_operator -t sui_operator:v1

Authentication

Kubernetes

To be able to query the kubernetes api, a serviceaccount needs to exist with the proper RBAC permissions.

In our example, the file manifests/serviceaccount_omicsdm.yaml contains the definition of this service account.

Note: At the moment, for development purposes, permissions have been set loosely. For production we will need to restrict the rights of the user according to minimum permissions principle.

kubectl apply -f manifests/serviceaccount_omicsdm.yaml

Now to retrieve the token you may use the following

kubectl describe secrets omicsdm-token

Related script variables SERVICE_ACCOUNT and ACCOUNT_TOKEN

OpenID-Connect client

For the connection between our OIDC provider (I.e. keycloak) and oauth2-proxy, we configure a client like this:

  • Keycloak v18
  1. Client -> Create -> enter ClientID
  2. Set Client protocol openid-connect -> save
  3. Set Access Type confidential -> save
  4. http://* and https://* in Valid Redirect URIs
  5. Mappers -> Create -> Audience -> name audience -> select Client in Included Client Audience
  6. (for groups: optional) Mappers -> Create -> Group Membership -> Group Membership -> name groups -> Token Claim Name groups -> Turn off full group path
  7. Credentials -> Secret lets you set OAUTH2_CLIENT_ID and OAUTH2_CLIENT_SECRET variables in deployment script.
  8. Populate with users (for groups: create group and add your users to it group)
  1. Client -> Create -> enter ClientID -> Next
  2. Client authentication On, tick everything except OIDC -> Next
  3. http://* and https://* in Valid Redirect URIs -> Save
  4. Client Scopes (realm) -> Create -> cellxgene-audience + Type Default -> Save
  5. Tab Mapper of Client Scope -> Configure a new mapper -> Audience
  6. name: cellxgene-audience, set ClientID in Included client audience -> Save
  7. Back to your Client -> Client Scopes tab (client) -> add client scope -> cellxgene-audience -> add Default

AWS

For containers to access s3 bucket you need to populate the variables within manifests/secret_aws-cred.yaml (Note: values must be encoded in base64). Then add it to the cluster. Secrets are defined per namespace, so the entries of this file are duplicated for cellxgene and testing namespaces.

kubectl apply -f manifests/secret_aws-cred.yaml

### Minikube

For the authentication chain to work, you have to add those entries to your /etc/hosts of host machine. Replacing those IPs with your configuration.

192.168.49.2    minikube.local
10.10.0.3       keycloak.local host.minikube.internal

Moreover, you should set frontend url=http://host.minikube.internal:8080 in your realms settings.

Operator and SingleUserInstances

This proof of concept is leveraging a custom Kubernetes Operator developped with kopf. Combined with a custom resource it allows us to joinly create the Deployment, Service and Ingress that constitute an instance. Moreover, it handles the lifecycle through the lifespan field and flushes the instance after some time the user quits cellxgene - i.e. closes the tab/browser.

User termination of the instance is detected by querying the ingress-nginx-controller's metrics server, thus we need a service that exposes the metrics server cluster-wide. In particular nginx_ingress_controller_ingress_upstream_latency_seconds monitors per instance the latency of the connection with the browser.

This operator needs to run inside the cluster and is essentially a Deployment. We make it monitor the events on the namespace and it also needs a service account with proper proper RBAC permissions.

To deploy:

kubectl apply -f manifests/crd_single-user-instance.yaml
kubectl apply -f manifests/serviceaccount_sui-operator.yaml
kubectl apply -f manifests/service_ingress-nginx-controller_metrics.yaml
kubectl apply -f manifests/deployment_sui_operator.yaml

You may then check that the operator successfuly launched by querying the status. E.g.

kubectl -n cellxgene get pods

NAME                            READY   STATUS    RESTARTS      AGE
sui-operator-57666b6944-q4lqt   1/1     Running   2 (40m ago)   10d

Then the logs should look like this:

kubectl -n cellxgene logs pod/sui-operator-57666b6944-q4lqt

[2023-11-06 13:32:22,644] kopf._core.reactor.r [DEBUG   ] Starting Kopf 1.36.2.
[2023-11-06 13:32:22,644] kopf._core.engines.a [INFO    ] Initial authentication has been initiated.
[2023-11-06 13:32:22,644] kopf.activities.auth [DEBUG   ] Activity 'login_via_client' is invoked.
[2023-11-06 13:32:22,661] kopf.activities.auth [DEBUG   ] Client is configured in cluster with service account.
[2023-11-06 13:32:22,661] kopf.activities.auth [INFO    ] Activity 'login_via_client' succeeded.
[2023-11-06 13:32:22,662] kopf._core.engines.a [INFO    ] Initial authentication has finished.
[2023-11-06 13:32:22,710] kopf._cogs.clients.w [DEBUG   ] Starting the watch-stream for customresourcedefinitions.v1.apiextensions.k8s.io cluster-wide.
[2023-11-06 13:32:22,713] kopf._cogs.clients.w [DEBUG   ] Starting the watch-stream for namespaces.v1 cluster-wide.
[2023-11-06 13:32:22,715] kopf._cogs.clients.w [DEBUG   ] Starting the watch-stream for singleuserinstances.v1.cnag.eu in 'cellxgene'.

Once the operator is running you may submit manifests of kind SingleUserInstance with apiVersion cnag.eu/v1. If the operator is not running you might run into problems to create and especially delete resources of that type.

Dev: run operator outside the cluster

You can also run the operator outside the cluster.

In that case you will also need to expose the metrics server in a different terminal.

kubectl -n ingress-nginx port-forward svc/metrics 10254:80

Then

kopf run -n {namespace} operator/operator_single-user-instances.py --debug

Note: If an operator is running within the cluster already, then it will have priority over the operator your are running through the command line.

Testing

Dependencies:

python3 -m pip install pytest pytest-cov

Assuming you have deployed testing namespace and populated it with the AWS credentials you are now able to run the Operator unit tests.

pytest -k 'test_operator'

Furthermore, If you want the code coverage:

pytest --cov-report [html | term] --cov=. tests/

API Handler

The api handler is a layer over the kubernetes python client API to abstract some of the complexity.

E.g. the functions to create deployments, services and ingresses are respectively part of the AppsV1Api, CoreV1Api, NetworkingV1Api objects

One can instanciate it like this

kah = K8ApiHandler(
    host=f"https://{K8_IP}:{K8_PORT}",
    oidc_client=(SERVICE_ACCOUNT, TOKEN),
    cert=CLUSTER_ROOT_CERTIFICATE
)

The command kubectl cluster-info gives K8_IP and K8_PORT, and HOST_NAME can be set freely.

On a minikube install the CLUSTER_ROOT_CERTIFICATE is located at ~/.minikube/ca.crt and see authentication section for the oidc client.

One may use the methods such as:

kah.create_deployment(manifest)

Or

kah.list_pods()

Scripts

yaml_to_py

This small script is a helper to turn the yaml kubernetes manifests into python dicts to query the api.

E.g.

python3 yaml_to_py.py manifests/templates/service_cxg.yaml

It also includes a py_to_yaml function that does the inverse transformation. You may import and use it like this:

from yaml_to_py import py_to_yaml

d = {'a': 1, 'b': {'c': [2, 3, 4]}}
py_to_yaml(d)

Demo: deploy_cellxgene

This script uses the api handler described above to create a cellxgene instance composed of a joined deployment, service and ingress that will expose the container and give an url to access it from your browser.

This also includes an oauth2-proxy instance that will be fired if not present on the cluster to handle authentication with keycloak.

python3 deploy_cellxgene.py

Output should be similar as:

[ No oauth2-proxy instance found in the cluster: creating it
Deployment oauth2-proxy up.
Service oauth2-proxy up.
Ingress oauth2-proxy setup.
oauth2-proxy deployed.
| An oauth2-proxy instance was found in the cluster ]

Custom object: SingleUserInstance with name: cellxgene-90afa5bf-823b-40df-a5b6-51c36827033b up.
Done.
The instance is now accessible at: http://minikube.local/cellxgene-90afa5bf-823b-40df-a5b6-51c36827033b/

Clean after demo

All ressources are tagged using the metadata.labels.app = cellxgene label. Then we then can peform some operations on all objects at once such as

kubectl delete all,ing,sui -l app=cellxgene

Ressources tied to an instance are also tagged using the metadata.labels.instance = cellxgene-90afa5bf-823b-40df-a5b6-51c36827033b label.

You may similarly delete like this

kubectl delete all,ing,sui -l instance=cellxgene-90afa5bf-823b-40df-a5b6-51c36827033b

Debugging

You can adjoin an image to a running pod

kubectl debug -it <pod> --image=python:debug --target <pod> -- sh

Minikube

This section provides some minikube specific details.

Docker images

minikube runs its own docker. In consequence it cannot see local images.

The easiest solution is to use the following command to make your local images accessibles inside the cluster

minikube image load <local-image>:<tag>

then you may check if the image is present like this

minikube image ls --format table