Merge pull request #642 from Vafilor/fix/jupyterlab.migrations

feat: added convenience method to update workspace template manifest

.github/workflows/push_tag.yaml

@@ -0,0 +1,29 @@
+name: Publish docker image on tag push
+on:
+  push:
+    tags:
+      - '*'
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - uses: olegtarasov/get-tag@v2
+        id: tagName
+      - name: Publish to Registry
+        uses: elgohr/Publish-Docker-Github-Action@master
+        with:
+          name: onepanel/core
+          username: ${{ secrets.DOCKER_HUB_USERNAME }}
+          password: ${{ secrets.DOCKER_HUB_TOKEN }}
+          tags: "${{ env.GIT_TAG_NAME }}"
+      - name: Set Slack Message
+        run: echo "::set-env name=SLACK_MESSAGE::Tag $GIT_TAG_NAME. Docker Tag onepanel/core:$GIT_TAG_NAME"
+      - name: Notify Slack Channels
+        uses: rtCamp/action-slack-notify@v2.0.0
+        env:
+          SLACK_CHANNEL: dev
+          SLACK_ICON: https://avatars1.githubusercontent.com/u/30390575?s=48&v=4
+          SLACK_TITLE: New Core Version
+          SLACK_USERNAME: opBot
+          SLACK_WEBHOOK: ${{ secrets.SLACK_WEBHOOK }}

cmd/gen-release-md/gen-release-md.go

@@ -155,6 +155,10 @@ func printMarkDown(issues []*issue, version *string) {
 	fmt.Println("# Contributors")
 	contributors := make([]user, 0)
 	for _, contributor := range contributorsMap {
+		// Sorry, no bots.
+		if contributor.Login == "dependabot[bot]" {
+			continue
+		}
 		contributors = append(contributors, contributor)
 	}
 	sort.Slice(contributors, func(i, j int) bool { return contributors[i].ContributionsCount > contributors[j].ContributionsCount })

db/go/20200821162630_update_jupyter_workspace_template.go

@@ -105,13 +105,14 @@ func Up20200821162630(tx *sql.Tx) error {
 	if err != nil {
 		return err
 	}
-	workspaceTemplate := &v1.WorkspaceTemplate{
-		UID:      uid,
-		Name:     jupyterLabTemplateName,
-		Manifest: jupyterWorkspaceTemplate2,
-	}
 
 	for _, namespace := range namespaces {
+		workspaceTemplate := &v1.WorkspaceTemplate{
+			UID:      uid,
+			Name:     jupyterLabTemplateName,
+			Manifest: jupyterWorkspaceTemplate2,
+		}
+
 		if _, err := client.UpdateWorkspaceTemplate(namespace.Name, workspaceTemplate); err != nil {
 			return err
 		}

db/go/20200929153931_update_jupyter_lab_workspace_command.go

@@ -2,7 +2,6 @@ package migration
 
 import (
 	"database/sql"
-	v1 "github.com/onepanelio/core/pkg"
 	uid2 "github.com/onepanelio/core/pkg/util/uid"
 	"github.com/pressly/goose"
 )
@@ -102,14 +101,8 @@ func Up20200929153931(tx *sql.Tx) error {
 	if err != nil {
 		return err
 	}
-	workspaceTemplate := &v1.WorkspaceTemplate{
-		UID:      uid,
-		Name:     jupyterLabTemplateName,
-		Manifest: jupyterWorkspaceTemplate3,
-	}
-
 	for _, namespace := range namespaces {
-		if _, err := client.UpdateWorkspaceTemplate(namespace.Name, workspaceTemplate); err != nil {
+		if _, err := client.UpdateWorkspaceTemplateManifest(namespace.Name, uid, jupyterWorkspaceTemplate3); err != nil {
 			return err
 		}
 	}
@@ -144,14 +137,9 @@ func Down20200929153931(tx *sql.Tx) error {
 	if err != nil {
 		return err
 	}
-	workspaceTemplate := &v1.WorkspaceTemplate{
-		UID:      uid,
-		Name:     jupyterLabTemplateName,
-		Manifest: jupyterWorkspaceTemplate2,
-	}
 
 	for _, namespace := range namespaces {
-		if _, err := client.UpdateWorkspaceTemplate(namespace.Name, workspaceTemplate); err != nil {
+		if _, err := client.UpdateWorkspaceTemplateManifest(namespace.Name, uid, jupyterWorkspaceTemplate2); err != nil {
 			return err
 		}
 	}

pkg/workflow_execution.go

@@ -18,7 +18,6 @@ import (
 	"gopkg.in/yaml.v2"
 	"io"
 	"io/ioutil"
-	"k8s.io/apimachinery/pkg/api/resource"
 	"k8s.io/apimachinery/pkg/watch"
 	"net/http"
 	"strconv"
@@ -197,93 +196,21 @@ func injectArtifactRepositoryConfig(artifact *wfv1.Artifact, namespaceConfig *Na
 	}
 }
 
-// injectContainerResourceQuotas adds resource requests and limits if they exist
+// injectHostPortToContainer adds a hostPort to the template container, if a nodeSelector is present.
-// Code grabs the resource request information from the nodeSelector, compared against running nodes.
+// Kubernetes will ensure that multiple containers with the same hostPort do not share the same node.
-// If the running node is not present, no resource information is retrieved.
+func (c *Client) injectHostPortToContainer(template *wfv1.Template) error {
-func (c *Client) injectContainerResourceQuotas(wf *wfv1.Workflow, template *wfv1.Template, systemConfig SystemConfig) error {
 	if template.NodeSelector == nil {
 		return nil
 	}
 
-	supportedNodePoolLabels := []string{"beta.kubernetes.io/instance-type", "node.kubernetes.io/instance-type"}
+	ports := []corev1.ContainerPort{
-	nodePoolLabel := ""
+		{Name: "node-capturer", HostPort: 80, ContainerPort: 80},
-	var value string
-	for k, v := range template.NodeSelector {
-		for _, supportedNodePoolLabel := range supportedNodePoolLabels {
-			if k == supportedNodePoolLabel {
-				nodePoolLabel = k
-				value = v
-				break
-			}
-		}
 	}
-	if value == "" {
+	if template.Container != nil {
-		return nil
+		template.Container.Ports = ports
 	}
-	if strings.Contains(value, "{{workflow.") {
+	if template.Script != nil {
-		parts := strings.Split(strings.Replace(value, "}}", "", -1), ".")
+		template.Script.Container.Ports = ports
-		paramName := parts[len(parts)-1]
-		for _, param := range wf.Spec.Arguments.Parameters {
-			if param.Name == paramName && param.Value != nil {
-				value = *param.Value
-				break
-			}
-		}
-	}
-
-	runningNodes, err := c.Interface.CoreV1().Nodes().List(ListOptions{})
-	if err != nil {
-		return err
-	}
-	var cpu string
-	var memory string
-	var gpu int64
-	gpuManufacturer := ""
-	for _, node := range runningNodes.Items {
-		if node.Labels[nodePoolLabel] == value {
-			cpuInt := node.Status.Allocatable.Cpu().MilliValue()
-			cpu = strconv.FormatFloat(float64(cpuInt)*.9, 'f', 0, 64) + "m"
-			memoryInt := node.Status.Allocatable.Memory().MilliValue()
-			kiBase := 1024.0
-			ninetyPerc := float64(memoryInt) * .9
-			toKi := ninetyPerc / kiBase / kiBase
-			memory = strconv.FormatFloat(toKi, 'f', 0, 64) + "Ki"
-			//Check for Nvidia
-			gpuQuantity := node.Status.Allocatable["nvidia.com/gpu"]
-			if gpuQuantity.IsZero() == false {
-				gpu = gpuQuantity.Value()
-				gpuManufacturer = "nvidia.com/gpu"
-			}
-
-			//Check for AMD
-			//Source: https://github.com/RadeonOpenCompute/k8s-device-plugin/blob/master/example/pod/alexnet-gpu.yaml
-			gpuQuantity = node.Status.Allocatable["amd.com/gpu"]
-			if gpuQuantity.IsZero() == false {
-				gpu = gpuQuantity.Value()
-				gpuManufacturer = "amd.com/gpu"
-			}
-		}
-	}
-
-	if cpu != "" && memory != "" {
-		resourceList := corev1.ResourceRequirements{
-			Limits: nil,
-			Requests: map[corev1.ResourceName]resource.Quantity{
-				corev1.ResourceCPU:    resource.MustParse(cpu),
-				corev1.ResourceMemory: resource.MustParse(memory),
-			},
-		}
-		if gpu > 0 {
-			stringGpu := strconv.FormatInt(gpu, 10)
-			resourceList.Limits = make(map[corev1.ResourceName]resource.Quantity)
-			resourceList.Limits[corev1.ResourceName(gpuManufacturer)] = resource.MustParse(stringGpu)
-		}
-		if template.Container != nil {
-			template.Container.Resources = resourceList
-		}
-		if template.Script != nil {
-			template.Script.Container.Resources = resourceList
-		}
 	}
 	return nil
 }
@@ -355,7 +282,7 @@ func (c *Client) injectAutomatedFields(namespace string, wf *wfv1.Workflow, opts
 				Name:      "sys-dshm",
 				MountPath: "/dev/shm",
 			})
-			err = c.injectContainerResourceQuotas(wf, template, systemConfig)
+			err = c.injectHostPortToContainer(template)
 			if err != nil {
 				return err
 			}
@@ -363,7 +290,7 @@ func (c *Client) injectAutomatedFields(namespace string, wf *wfv1.Workflow, opts
 		}
 
 		if template.Script != nil {
-			err = c.injectContainerResourceQuotas(wf, template, systemConfig)
+			err = c.injectHostPortToContainer(template)
 			if err != nil {
 				return err
 			}

pkg/workspace.go

@@ -15,7 +15,6 @@ import (
 	"github.com/onepanelio/core/pkg/util/request"
 	log "github.com/sirupsen/logrus"
 	"google.golang.org/grpc/codes"
-	"strconv"
 	"strings"
 	"time"
 )
@@ -286,32 +285,15 @@ func (c *Client) addResourceRequestsAndLimitsToWorkspaceTemplate(t wfv1.Template
 	if !ok {
 		return nil, errors.New("unable to type check statefulset manifest")
 	}
-	//Get node selected
+	extraContainer := generateExtraContainerWithHostPortToSequesterNode()
-	labelKey := "sys-node-pool-label"
+	if extraContainer != nil {
-	labelKeyVal := ""
+		containers, ok := templateSpec["containers"].([]interface{})
-	for _, parameter := range argoTemplate.Spec.Arguments.Parameters {
+		if !ok {
-		if parameter.Name == labelKey {
+			return nil, errors.New("unable to type check statefulset manifest")
-			labelKeyVal = *parameter.Value
 		}
-	}
 
-	nodePoolKey := "sys-node-pool"
+		templateSpec["containers"] = append([]interface{}{extraContainer}, containers...)
-	nodePoolVal := ""
-	for _, parameter := range workspace.Parameters {
-		if parameter.Name == nodePoolKey {
-			nodePoolVal = *parameter.Value
-		}
 	}
-	extraContainer, err := generateExtraContainerWithResources(c, labelKeyVal, nodePoolVal)
-	if err != nil {
-		return nil, err
-	}
-	containers, ok := templateSpec["containers"].([]interface{})
-	if !ok {
-		return nil, errors.New("unable to type check statefulset manifest")
-	}
-
-	templateSpec["containers"] = append([]interface{}{extraContainer}, containers...)
 	resultManifest, err := yaml.Marshal(statefulSet)
 	if err != nil {
 		return nil, err
@@ -319,78 +301,25 @@ func (c *Client) addResourceRequestsAndLimitsToWorkspaceTemplate(t wfv1.Template
 	return resultManifest, nil
 }
 
-// generateExtraContainerWithResources will add an extra container to a workspace.
+// generateExtraContainerWithHostPortToSequesterNode will add an extra container to a workspace.
-// The extra container will have the calculated resource request for the node selected by the workspace.
+// The extra container have a hostPort set. Kubernetes will ensure the hostPort does not get conflict
+// between containers, scheduling a new node as needed.
 // The container will sleep once started, and generally consume negligible resources.
-//
+func generateExtraContainerWithHostPortToSequesterNode() map[string]interface{} {
-// The node that was selected has to be already running, in order to get the resource request correct.
-func generateExtraContainerWithResources(c *Client, labelKeyVal string, nodePoolVal string) (map[string]interface{}, error) {
-	runningNodes, err := c.Interface.CoreV1().Nodes().List(ListOptions{})
-	if err != nil {
-		return nil, err
-	}
-	var cpu string
-	var memory string
-	var gpu int64
-	gpuManufacturer := ""
-	for _, node := range runningNodes.Items {
-		if node.Labels[labelKeyVal] == nodePoolVal {
-			cpuInt := node.Status.Allocatable.Cpu().MilliValue()
-			cpu = strconv.FormatFloat(float64(cpuInt)*.9, 'f', 0, 64) + "m"
-			memoryInt := node.Status.Allocatable.Memory().MilliValue()
-			kiBase := 1024.0
-			ninetyPerc := float64(memoryInt) * .9
-			toKi := ninetyPerc / kiBase / kiBase
-			memory = strconv.FormatFloat(toKi, 'f', 0, 64) + "Ki"
-			//Check for Nvidia
-			gpuQuantity := node.Status.Allocatable["nvidia.com/gpu"]
-			if gpuQuantity.IsZero() == false {
-				gpu = gpuQuantity.Value()
-				gpuManufacturer = "nvidia.com/gpu"
-			}
-
-			//Check for AMD
-			//Source: https://github.com/RadeonOpenCompute/k8s-device-plugin/blob/master/example/pod/alexnet-gpu.yaml
-			gpuQuantity = node.Status.Allocatable["amd.com/gpu"]
-			if gpuQuantity.IsZero() == false {
-				gpu = gpuQuantity.Value()
-				gpuManufacturer = "amd.com/gpu"
-			}
-		}
-	}
 	extraContainer := map[string]interface{}{
 		"image":   "alpine:latest",
-		"name":    "resource-requester",
+		"name":    "node-capturer",
 		"command": []interface{}{"/bin/sh"},
 		"args":    []interface{}{"-c", "while :; do sleep 2073600; done"},
-		"resources": map[string]interface{}{
+		"ports": []interface{}{
-			"requests": map[string]interface{}{
+			map[string]interface{}{
-				"cpu":    cpu,
+				"name":          "node-capturer",
-				"memory": memory,
+				"hostPort":      80,
+				"containerPort": 80,
 			},
-			"limits": map[string]interface{}{},
 		},
 	}
-
+	return extraContainer
-	if gpu > 0 {
-		res, ok := extraContainer["resources"].(map[string]interface{})
-		if !ok {
-			return nil, errors.New("unable to type check extraContainer")
-		}
-		reqs, ok := res["requests"].(map[string]interface{})
-		if !ok {
-			return nil, errors.New("unable to type check extraContainer")
-		}
-		reqs[gpuManufacturer] = gpu
-
-		limits, ok := res["limits"].(map[string]interface{})
-		if !ok {
-			return nil, errors.New("unable to type check extraContainer")
-		}
-		limits[gpuManufacturer] = gpu
-
-	}
-	return extraContainer, err
 }
 
 // startWorkspace starts a workspace and related resources. It assumes a DB record already exists
@@ -441,6 +370,17 @@ func (c *Client) startWorkspace(namespace string, parameters []byte, workspace *
 		}
 	}
 
+	templates := argoTemplate.Spec.Templates
+	for i, t := range templates {
+		if t.Name == WorkspaceStatefulSetResource {
+			resultManifest, err := c.addResourceRequestsAndLimitsToWorkspaceTemplate(t, argoTemplate, workspace)
+			if err != nil {
+				return nil, err
+			}
+			templates[i].Resource.Manifest = string(resultManifest)
+		}
+	}
+
 	_, err = c.CreateWorkflowExecution(namespace, &WorkflowExecution{
 		Parameters: workspace.Parameters,
 	}, workflowTemplate)

pkg/workspace_template.go

@@ -1158,6 +1158,19 @@ func (c *Client) UpdateWorkspaceTemplate(namespace string, workspaceTemplate *Wo
 	return workspaceTemplate, nil
 }
 
+// UpdateWorkspaceTemplateManifest updates a workspace template by creating a new version where the only difference is the manifest
+func (c *Client) UpdateWorkspaceTemplateManifest(namespace, uid string, manifest string) (*WorkspaceTemplate, error) {
+	existingTemplate, err := c.GetWorkspaceTemplate(namespace, uid, 0)
+	if err != nil {
+		return nil, err
+	}
+
+	existingTemplate.UID = uid
+	existingTemplate.Manifest = manifest
+
+	return c.UpdateWorkspaceTemplate(namespace, existingTemplate)
+}
+
 // ListWorkspaceTemplates returns a list of workspace templates that are not archived, sorted by most recent created first
 func (c *Client) ListWorkspaceTemplates(namespace string, request *request.Request) (workspaceTemplates []*WorkspaceTemplate, err error) {
 	sb := c.workspaceTemplatesSelectBuilder(namespace).