Update command string handling in K8s templates

config/kubernetes-pv.yaml

@@ -0,0 +1,27 @@
+# Worker/Executor PV
+apiVersion: v1
+kind: PersistentVolume
+metadata:
+  name: funnel-pv-{{.TaskId}}
+  labels:
+    app: funnel
+    taskId: {{.TaskId}}
+spec:
+  capacity:
+    storage: 1Gi
+  accessModes:
+    - ReadWriteMany
+  persistentVolumeReclaimPolicy: Retain
+  mountOptions:
+    - allow-delete
+    - allow-overwrite
+    - region={{.Region}}
+    - file-mode=0755
+  csi:
+    driver: s3.csi.aws.com
+    volumeHandle: s3-csi-{{.TaskId}}
+    volumeAttributes:
+      bucketName: {{.Bucket}}
+  claimRef:
+    namespace: {{.Namespace}}
+    name: funnel-pvc-{{.TaskId}}

config/kubernetes-pvc.yaml

@@ -0,0 +1,16 @@
+# Worker/Executor PVC
+apiVersion: v1
+kind: PersistentVolumeClaim
+metadata:
+  name: funnel-pvc-{{.TaskId}}
+  namespace: {{ .Namespace }}
+  labels:
+    app: funnel
+    taskId: {{.TaskId}}
+spec:
+  accessModes:
+    - ReadWriteMany
+  resources:
+    requests:
+      storage: 1Gi
+  volumeName: funnel-pv-{{.TaskId}}

go.mod

@@ -170,6 +170,7 @@ require (
 	golang.org/x/term v0.26.0 // indirect
 	golang.org/x/text v0.20.0 // indirect
 	google.golang.org/genproto/googleapis/rpc v0.0.0-20241021214115-324edc3d5d38 // indirect
+	gopkg.in/evanphx/json-patch.v4 v4.12.0 // indirect
 	gopkg.in/inf.v0 v0.9.1 // indirect
 	gopkg.in/yaml.v2 v2.4.0 // indirect
 	gopkg.in/yaml.v3 v3.0.1 // indirect

go.sum

@@ -614,6 +614,8 @@ gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8
 gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c h1:Hei/4ADfdWqJk1ZMxUNpqntNwaWcugrBjAiHlqqRiVk=
 gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c/go.mod h1:JHkPIbrfpd72SG/EVd6muEfDQjcINNoR0C8j2r3qZ4Q=
+gopkg.in/evanphx/json-patch.v4 v4.12.0 h1:n6jtcsulIzXPJaxegRbvFNNrZDjbij7ny3gmSPG+6V4=
+gopkg.in/evanphx/json-patch.v4 v4.12.0/go.mod h1:p8EYWUEYMpynmqDbY58zCKCFZw8pRWMG4EsWvDvM72M=
 gopkg.in/inf.v0 v0.9.1 h1:73M5CoZyi3ZLMOyDlQh031Cx6N9NDJ2Vvfl76EDAgDc=
 gopkg.in/inf.v0 v0.9.1/go.mod h1:cWUDdTG/fYaXco+Dcufb5Vnc6Gp2YChqWtbxRZE0mXw=
 gopkg.in/olivere/elastic.v5 v5.0.86 h1:xFy6qRCGAmo5Wjx96srho9BitLhZl2fcnpuidPwduXM=

website/content/docs/compute/kubernetes.md

@@ -104,7 +104,9 @@ funnel task create hello-world.json
 
 # Storage Architecture
 
-![K8s Storage](/img/k8s-pvc.png)
+<a href="https://www.figma.com/board/bzgv8kVL2QKESU3Sqn7S1a/Funnel-%2B-Gen3?node-id=2-1059&t=9bcuG0bMAcxBLcRD-1">
+  <img title="K8s Storage" src="/img/k8s-pvc.png" />
+</a>
 
 # Additional Resources 📚
 

worker/kubernetes.go

@@ -5,6 +5,7 @@ import (
 	"context"
 	"fmt"
 	"io"
+	"strings"
 	"text/template"
 
 	"github.com/ohsu-comp-bio/funnel/tes"
@@ -26,6 +27,7 @@ type KubernetesCommand struct {
 	Namespace      string
 	Resources      *tes.Resources
 	ServiceAccount string
+	Clientset      kubernetes.Interface
 	Command
 }
 
@@ -43,6 +45,11 @@ func (kcmd KubernetesCommand) Run(ctx context.Context) error {
 	if kcmd.StdinFile != "" {
 		command = append(command, "<", kcmd.StdinFile)
 	}
+	for i, v := range command {
+		if strings.Contains(v, " ") {
+			command[i] = fmt.Sprintf("'%s'", v)
+		}
+	}
 
 	var buf bytes.Buffer
 	err = tpl.Execute(&buf, map[string]interface{}{
@@ -74,9 +81,13 @@ func (kcmd KubernetesCommand) Run(ctx context.Context) error {
 		return err
 	}
 
-	clientset, err := getKubernetesClientset()
-	if err != nil {
-		return err
+	clientset := kcmd.Clientset
+	if clientset == nil {
+		var err error
+		clientset, err = getKubernetesClientset()
+		if err != nil {
+			return err
+		}
 	}
 
 	var client = clientset.BatchV1().Jobs(kcmd.Namespace)