Update K8s support and documentation

- Update docker images to use quay.io/ohsu-comp-bio/funnel

Dockerfile

@@ -1,5 +1,5 @@
 # build stage
-FROM golang:1.21-alpine AS build-env
+FROM golang:1.23-alpine AS build-env
 RUN apk add make git bash build-base
 ENV GOPATH=/go
 ENV PATH="/go/bin:${PATH}"

Dockerfile.dind

@@ -1,13 +1,13 @@
 # build stage
-FROM golang:1.20-alpine AS build-env
+FROM golang:1.23-alpine AS build-env
 RUN apk add make git bash build-base
 ENV GOPATH=/go
 ENV PATH="/go/bin:${PATH}"
 ADD ./ /go/src/github.com/ohsu-comp-bio/funnel
 RUN cd /go/src/github.com/ohsu-comp-bio/funnel && make build
 
 # final stage
-FROM docker:stable-dind
+FROM docker:dind
 WORKDIR /opt/funnel
 VOLUME /opt/funnel/funnel-work-dir
 EXPOSE 8000 9090

Dockerfile.dind-rootless

@@ -1,13 +1,13 @@
 # build stage
-FROM golang:1.20-alpine AS build-env
+FROM golang:1.23-alpine AS build-env
 RUN apk add make git bash build-base
 ENV GOPATH=/go
 ENV PATH="/go/bin:${PATH}"
 ADD ./ /go/src/github.com/ohsu-comp-bio/funnel
 RUN cd /go/src/github.com/ohsu-comp-bio/funnel && make build
 
 # final stage
-FROM docker:stable-dind-rootless
+FROM docker:dind-rootless
 WORKDIR /opt/funnel
 VOLUME /opt/funnel/funnel-work-dir
 EXPOSE 8000 9090

compute/kubernetes/backend.go

@@ -5,6 +5,7 @@ import (
 	"bytes"
 	"context"
 	"encoding/json"
+	"errors"
 	"fmt"
 	"io/ioutil"
 	"text/template"
@@ -82,15 +83,32 @@ func NewBackend(ctx context.Context, conf config.Kubernetes, reader tes.ReadOnly
 
 // Backend represents the local backend.
 type Backend struct {
-	client    batchv1.JobInterface
-	namespace string
-	template  string
-	event     events.Writer
-	database  tes.ReadOnlyServer
-	log       *logger.Logger
+	client            batchv1.JobInterface
+	namespace         string
+	template          string
+	event             events.Writer
+	database          tes.ReadOnlyServer
+	log               *logger.Logger
+	backendParameters map[string]string
 	events.Computer
 }
 
+func (b Backend) CheckBackendParameterSupport(task *tes.Task) error {
+	if !task.Resources.GetBackendParametersStrict() {
+		return nil
+	}
+
+	taskBackendParameters := task.Resources.GetBackendParameters()
+	for k := range taskBackendParameters {
+		_, ok := b.backendParameters[k]
+		if !ok {
+			return errors.New("backend parameters not supported")
+		}
+	}
+
+	return nil
+}
+
 // WriteEvent writes an event to the compute backend.
 // Currently, only TASK_CREATED is handled, which calls Submit.
 func (b *Backend) WriteEvent(ctx context.Context, ev *events.Event) error {
@@ -153,7 +171,8 @@ func (b *Backend) Submit(ctx context.Context, task *tes.Task) error {
 	if err != nil {
 		return fmt.Errorf("creating job spec: %v", err)
 	}
-	_, err = b.client.Create(ctx, job, metav1.CreateOptions{
+	ctx = context.Background()
+	job, err = b.client.Create(ctx, job, metav1.CreateOptions{
 		FieldManager: task.Id,
 	})
 	if err != nil {

compute/kubernetes/backend_test.go

@@ -1,15 +1,62 @@
 package kubernetes
 
 import (
+	"context"
 	"fmt"
 	"io/ioutil"
 	"testing"
 
+	"path/filepath"
+
 	"github.com/ohsu-comp-bio/funnel/config"
 	"github.com/ohsu-comp-bio/funnel/logger"
 	"github.com/ohsu-comp-bio/funnel/tes"
+	"k8s.io/client-go/kubernetes"
+	"k8s.io/client-go/rest"
+	"k8s.io/client-go/tools/clientcmd"
+	"k8s.io/client-go/util/homedir"
 )
 
+// getKubernetesClient creates a Kubernetes clientset for communication with the Kubernetes API
+func getKubernetesClient() (*kubernetes.Clientset, error) {
+	var config *rest.Config
+	var err error
+	var contextName string
+
+	// Try to create an in-cluster client
+	config, err = rest.InClusterConfig()
+	if err != nil {
+		// If in-cluster config fails, fallback to kubeconfig file for out-of-cluster
+		kubeconfig := filepath.Join(homedir.HomeDir(), ".kube", "config")
+		kubeConfig, err := clientcmd.LoadFromFile(kubeconfig)
+		if err != nil {
+			return nil, fmt.Errorf("failed to load kubeconfig: %v", err)
+		}
+
+		// Get the current context name
+		contextName = kubeConfig.CurrentContext
+
+		// Build config from flags or kubeconfig
+		config, err = clientcmd.BuildConfigFromFlags("", kubeconfig)
+		if err != nil {
+			return nil, fmt.Errorf("failed to create kubernetes config: %v", err)
+		}
+	} else {
+		contextName = "in-cluster"
+	}
+
+	// Create the clientset
+	clientset, err := kubernetes.NewForConfig(config)
+	if err != nil {
+		return nil, fmt.Errorf("failed to create kubernetes clientset: %v", err)
+	}
+
+	// Log or print the current context being used
+	fmt.Printf("Using Kubernetes context: %s\n", contextName)
+
+	return clientset, nil
+}
+
 func TestCreateJobc(t *testing.T) {
 	conf := config.DefaultConfig().Kubernetes
 	content, err := ioutil.ReadFile("../../config/kubernetes-template.yaml")
@@ -18,8 +65,15 @@ func TestCreateJobc(t *testing.T) {
 	}
 	conf.Template = string(content)
 	log := logger.NewLogger("test", logger.DefaultConfig())
+
+	// Create Kubernetes client
+	clientset, err := getKubernetesClient()
+	if err != nil {
+		t.Fatal(fmt.Errorf("creating kubernetes client: %v", err))
+	}
+
 	b := &Backend{
-		client:    nil,
+		client:    clientset.BatchV1().Jobs(conf.Namespace),
 		namespace: conf.Namespace,
 		template:  conf.Template,
 		event:     nil,
@@ -42,4 +96,9 @@ func TestCreateJobc(t *testing.T) {
 		t.Fatal(err)
 	}
 	t.Logf("%+v", job)
+
+	err = b.Submit(context.Background(), task)
+	if err != nil {
+		t.Fatal(err)
+	}
 }

deployments/kubernetes/README.md

@@ -1,3 +1,6 @@
+> [!NOTE]
+> Kubernetes support is in active development and may involve frequent updates
+
 # Using Funnel with Kubernetes
 
 Examples can be found here: https://github.com/ohsu-comp-bio/funnel/tree/master/deployments/kubernetes
@@ -6,7 +9,7 @@ Examples can be found here: https://github.com/ohsu-comp-bio/funnel/tree/master/
 
 *funnel-service.yml*
 
-```
+```yaml
 apiVersion: v1
 kind: Service
 metadata:
@@ -23,32 +26,35 @@ spec:
       protocol: TCP
       port: 9090
       targetPort: 9090
-
 ```
 
 Deploy it:
 
-```
+```sh
 kubectl apply -f funnel-service.yml
 ```
 
 Get the clusterIP:
 
-```
+```sh
 kubectl get services funnel --output=yaml | grep clusterIP
 ```
 
 Use this value to configure the server hostname of the worker config. 
 
 #### Create Funnel config files
 
-*Note*: The configures job template uses the image, `ohsucompbio/funnel-dind:latest`, which is built on docker's official [docker-in-docker image (dind)](https://hub.docker.com/_/docker). You can also use the experimental [rootless dind variant](https://docs.docker.com/engine/security/rootless/) by changing the image to `ohsucompbio/funnel-dind-rootless:latest`.
+> [!TIP]
+> The configures job template uses the image, `ohsucompbio/funnel-dind:latest`, which is built on docker's official [docker-in-docker image (dind)](https://hub.docker.com/_/docker). You can also use the experimental [rootless dind variant](https://docs.docker.com/engine/security/rootless/) by changing the image to `quay.io/ohsu-comp-bio/funnel-dind-rootless:latest`
 
 *funnel-server-config.yml*
 
-```
+```yaml
 Database: boltdb
 
+BoltDB:
+  Path: /opt/funnel/funnel-work-dir/funnel.bolt.db
+
 Compute: kubernetes
 
 Logger:
@@ -74,7 +80,7 @@ Kubernetes:
           restartPolicy: Never
           containers: 
             - name: {{printf "funnel-worker-%s" .TaskId}}
-              image: ohsucompbio/funnel-kube-dind:latest
+              image: quay.io/ohsu-comp-bio/funnel-dind:latest
               imagePullPolicy: IfNotPresent
               args:
                 - "funnel"
@@ -87,8 +93,8 @@ Kubernetes:
               resources:
                   requests:
                     cpu: {{if ne .Cpus 0 -}}{{.Cpus}}{{ else }}{{"100m"}}{{end}}
-                    memory: {{if ne .RamGb 0.0 -}}{{printf "%.0fG" .RamGb}}{{else}}{{"16M"}}{{end}}
-                    ephemeral-storage: {{if ne .DiskGb 0.0 -}}{{printf "%.0fG" .DiskGb}}{{else}}{{"100M"}}{{end}}
+                    memory: {{if ne .RamGb 0.0 -}}{{printf "%.0fG" .RamGb}}{{else}}{{"16Mi"}}{{end}}
+                    ephemeral-storage: {{if ne .DiskGb 0.0 -}}{{printf "%.0fG" .DiskGb}}{{else}}{{"100Mi"}}{{end}}
               volumeMounts:
                 - name: {{printf "funnel-storage-%s" .TaskId}}
                   mountPath: {{printf "/opt/funnel/funnel-work-dir/%s" .TaskId}}
@@ -112,7 +118,7 @@ I recommend setting `DisableJobCleanup` to `true` for debugging - otherwise fail
 
 ***Remember to modify the template below to have the actual server hostname.***
 
-```
+```yaml
 Database: boltdb
 
 BoltDB:
@@ -138,7 +144,7 @@ Server:
 
 #### Create a ConfigMap
 
-```
+```sh
 kubectl create configmap funnel-config --from-file=funnel-server-config.yml --from-file=funnel-worker-config.yml
 ```
 
@@ -148,7 +154,7 @@ Define a Role and RoleBinding:
 
 *role.yml*
 
-```
+```yaml
 kind: Role
 apiVersion: rbac.authorization.k8s.io/v1
 metadata:
@@ -168,7 +174,7 @@ rules:
 
 *role_binding.yml*
 
-```
+```yaml
 kind: RoleBinding
 apiVersion: rbac.authorization.k8s.io/v1
 metadata:
@@ -195,7 +201,7 @@ kubectl create -f role_binding.yml
 
 *funnel-deployment.yml*
 
-```
+```yaml
 apiVersion: apps/v1
 kind: Deployment
 metadata:
@@ -215,7 +221,7 @@ spec:
       serviceAccountName: funnel-sa
       containers:
         - name: funnel
-          image: ohsucompbio/funnel:latest
+          image: quay.io/ohsu-comp-bio/funnel:latest
           imagePullPolicy: IfNotPresent
           command: 
             - 'funnel'
@@ -225,9 +231,13 @@ spec:
             - '/etc/config/funnel-server-config.yml'
           resources: 
             requests: 
-              cpu: 2 
+              cpu: 500m
+              memory: 1G
+              ephemeral-storage: 25G
+            limits:
+              cpu: 2000m
               memory: 4G
-              ephemeral-storage: 25G # needed since we are using boltdb
+              ephemeral-storage: 25G
           volumeMounts:
             - name: funnel-deployment-storage
               mountPath: /opt/funnel/funnel-work-dir
@@ -247,25 +257,25 @@ spec:
 
 Deploy it:
 
-```
+```sh
 kubectl apply -f funnel-deployment.yml
 ```
 
 #### Proxy the Service for local testing
 
-```
+```sh
 kubectl port-forward service/funnel 8000:8000
 ```
 
 Now you can access the funnel server locally. Verify by running:
 
-```
+```sh
 funnel task list
 ```
 
 Now try running a task:
 
-```
+```sh
 funnel examples hello-world > hello.json
 funnel task create hello.json
 ```