Merge pull request #136 from arangodb/feature/pod-finalizers

Feature: finalizers

docs/design/lifecycle_hooks_and_finalizers.md

@@ -0,0 +1,37 @@
+# Lifecycle hooks & Finalizers
+
+The ArangoDB operator expects full control of the `Pods` and `PersistentVolumeClaims` it creates.
+Therefore it takes measures to prevent the removal of those resources
+until it is safe to do so.
+
+To achieve this, the server containers in the `Pods` have
+a `preStop` hook configured and finalizers are added to the `Pods`
+and `PersistentVolumeClaims`.
+
+The `preStop` hook executes a binary that waits until all finalizers of
+the current pod have been removed.
+Until this `preStop` hook terminates, Kubernetes will not send a `TERM` signal
+to the processes inside the container, which ensures that the server remains running
+until it is safe to stop them.
+
+The operator performs all actions needed when a delete of a `Pod` or
+`PersistentVolumeClaims` has been triggered.
+E.g. for a dbserver it cleans out the server if the `Pod` and `PersistentVolumeClaim` are being deleted.
+
+## Lifecycle init-container
+
+Because the binary that is called in the `preStop` hook is not part of a standard
+ArangoDB docker image, it has to be brought into the filesystem of a `Pod`.
+This is done by an initial container that copies the binary to an `emptyDir` volume that
+is shared between the init-container and the server container.
+
+## Finalizers
+
+The ArangoDB operators adds the following finalizers to `Pods`.
+
+- `dbserver.database.arangodb.com/drain`: Added to DBServers, removed only when the dbserver can be restarted or is completely drained
+- `agent.database.arangodb.com/agency-serving`: Added to Agents, removed only when enough agents are left to keep the agency serving
+
+The ArangoDB operators adds the following finalizers to `PersistentVolumeClaims`.
+
+- `pvc.database.arangodb.com/member-exists`: removed only when its member exists no longer exists or can be safely rebuild

lifecycle.go

@@ -0,0 +1,150 @@
+//
+// DISCLAIMER
+//
+// Copyright 2018 ArangoDB GmbH, Cologne, Germany
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+// Copyright holder is ArangoDB GmbH, Cologne, Germany
+//
+// Author Ewout Prangsma
+//
+
+package main
+
+import (
+	"io"
+	"os"
+	"path/filepath"
+	"time"
+
+	"github.com/spf13/cobra"
+	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
+
+	"github.com/arangodb/kube-arangodb/pkg/util/constants"
+	"github.com/arangodb/kube-arangodb/pkg/util/k8sutil"
+)
+
+var (
+	cmdLifecycle = &cobra.Command{
+		Use:    "lifecycle",
+		Run:    cmdUsage,
+		Hidden: true,
+	}
+
+	cmdLifecyclePreStop = &cobra.Command{
+		Use:    "preStop",
+		Run:    cmdLifecyclePreStopRun,
+		Hidden: true,
+	}
+	cmdLifecycleCopy = &cobra.Command{
+		Use:    "copy",
+		Run:    cmdLifecycleCopyRun,
+		Hidden: true,
+	}
+
+	lifecycleCopyOptions struct {
+		TargetDir string
+	}
+)
+
+func init() {
+	cmdMain.AddCommand(cmdLifecycle)
+	cmdLifecycle.AddCommand(cmdLifecyclePreStop)
+	cmdLifecycle.AddCommand(cmdLifecycleCopy)
+
+	cmdLifecycleCopy.Flags().StringVar(&lifecycleCopyOptions.TargetDir, "target", "", "Target directory to copy the executable to")
+}
+
+// Wait until all finalizers of the current pod have been removed.
+func cmdLifecyclePreStopRun(cmd *cobra.Command, args []string) {
+	cliLog.Info().Msgf("Starting arangodb-operator, lifecycle preStop, version %s build %s", projectVersion, projectBuild)
+
+	// Get environment
+	namespace := os.Getenv(constants.EnvOperatorPodNamespace)
+	if len(namespace) == 0 {
+		cliLog.Fatal().Msgf("%s environment variable missing", constants.EnvOperatorPodNamespace)
+	}
+	name := os.Getenv(constants.EnvOperatorPodName)
+	if len(name) == 0 {
+		cliLog.Fatal().Msgf("%s environment variable missing", constants.EnvOperatorPodName)
+	}
+
+	// Create kubernetes client
+	kubecli, err := k8sutil.NewKubeClient()
+	if err != nil {
+		cliLog.Fatal().Err(err).Msg("Failed to create Kubernetes client")
+	}
+
+	pods := kubecli.CoreV1().Pods(namespace)
+	recentErrors := 0
+	for {
+		p, err := pods.Get(name, metav1.GetOptions{})
+		if k8sutil.IsNotFound(err) {
+			cliLog.Warn().Msg("Pod not found")
+			return
+		} else if err != nil {
+			recentErrors++
+			cliLog.Error().Err(err).Msg("Failed to get pod")
+			if recentErrors > 20 {
+				cliLog.Fatal().Err(err).Msg("Too many recent errors")
+				return
+			}
+		} else {
+			// We got our pod
+			finalizerCount := len(p.GetFinalizers())
+			if finalizerCount == 0 {
+				// No more finalizers, we're done
+				cliLog.Info().Msg("All finalizers gone, we can stop now")
+				return
+			}
+			cliLog.Info().Msgf("Waiting for %d more finalizers to be removed", finalizerCount)
+		}
+		// Wait a bit
+		time.Sleep(time.Second)
+	}
+}
+
+// Copy the executable to a given place.
+func cmdLifecycleCopyRun(cmd *cobra.Command, args []string) {
+	cliLog.Info().Msgf("Starting arangodb-operator, lifecycle copy, version %s build %s", projectVersion, projectBuild)
+
+	exePath, err := os.Executable()
+	if err != nil {
+		cliLog.Fatal().Err(err).Msg("Failed to get executable path")
+	}
+
+	// Open source
+	rd, err := os.Open(exePath)
+	if err != nil {
+		cliLog.Fatal().Err(err).Msg("Failed to open executable file")
+	}
+	defer rd.Close()
+
+	// Open target
+	targetPath := filepath.Join(lifecycleCopyOptions.TargetDir, filepath.Base(exePath))
+	wr, err := os.Create(targetPath)
+	if err != nil {
+		cliLog.Fatal().Err(err).Msg("Failed to create target file")
+	}
+	defer wr.Close()
+
+	if _, err := io.Copy(wr, rd); err != nil {
+		cliLog.Fatal().Err(err).Msg("Failed to copy")
+	}
+
+	// Set file mode
+	if err := os.Chmod(targetPath, 0755); err != nil {
+		cliLog.Fatal().Err(err).Msg("Failed to chmod")
+	}
+}

main.go

@@ -193,7 +193,7 @@ func newOperatorConfigAndDeps(id, namespace, name string) (operator.Config, oper
 		return operator.Config{}, operator.Dependencies{}, maskAny(err)
 	}
 
-	serviceAccount, err := getMyPodServiceAccount(kubecli, namespace, name)
+	image, serviceAccount, err := getMyPodInfo(kubecli, namespace, name)
 	if err != nil {
 		return operator.Config{}, operator.Dependencies{}, maskAny(fmt.Errorf("Failed to get my pod's service account: %s", err))
 	}
@@ -213,6 +213,7 @@ func newOperatorConfigAndDeps(id, namespace, name string) (operator.Config, oper
 		Namespace:        namespace,
 		PodName:          name,
 		ServiceAccount:   serviceAccount,
+		LifecycleImage:   image,
 		EnableDeployment: operatorOptions.enableDeployment,
 		EnableStorage:    operatorOptions.enableStorage,
 		AllowChaos:       chaosOptions.allowed,
@@ -231,9 +232,10 @@ func newOperatorConfigAndDeps(id, namespace, name string) (operator.Config, oper
 	return cfg, deps, nil
 }
 
-// getMyPodServiceAccount looks up the service account of the pod with given name in given namespace
-func getMyPodServiceAccount(kubecli kubernetes.Interface, namespace, name string) (string, error) {
-	var sa string
+// getMyPodInfo looks up the image & service account of the pod with given name in given namespace
+// Returns image, serviceAccount, error.
+func getMyPodInfo(kubecli kubernetes.Interface, namespace, name string) (string, string, error) {
+	var image, sa string
 	op := func() error {
 		pod, err := kubecli.CoreV1().Pods(namespace).Get(name, metav1.GetOptions{})
 		if err != nil {
@@ -244,12 +246,17 @@ func getMyPodServiceAccount(kubecli kubernetes.Interface, namespace, name string
 			return maskAny(err)
 		}
 		sa = pod.Spec.ServiceAccountName
+		image = k8sutil.ConvertImageID2Image(pod.Status.ContainerStatuses[0].ImageID)
+		if image == "" {
+			// Fallback in case we don't know the id.
+			image = pod.Spec.Containers[0].Image
+		}
 		return nil
 	}
 	if err := retry.Retry(op, time.Minute*5); err != nil {
-		return "", maskAny(err)
+		return "", "", maskAny(err)
 	}
-	return sa, nil
+	return image, sa, nil
 }
 
 func createRecorder(log zerolog.Logger, kubecli kubernetes.Interface, name, namespace string) record.EventRecorder {

pkg/apis/deployment/v1alpha/conditions.go

@@ -37,6 +37,9 @@ const (
 	ConditionTypeTerminated ConditionType = "Terminated"
 	// ConditionTypeAutoUpgrade indicates that the member has to be started with `--database.auto-upgrade` once.
 	ConditionTypeAutoUpgrade ConditionType = "AutoUpgrade"
+	// ConditionTypeCleanedOut indicates that the member (dbserver) has been cleaned out.
+	// Always check in combination with ConditionTypeTerminated.
+	ConditionTypeCleanedOut ConditionType = "CleanedOut"
 	// ConditionTypePodSchedulingFailure indicates that one or more pods belonging to the deployment cannot be schedule.
 	ConditionTypePodSchedulingFailure ConditionType = "PodSchedulingFailure"
 	// ConditionTypeSecretsChanged indicates that the value of one of more secrets used by

pkg/apis/deployment/v1alpha/deployment.go

@@ -50,11 +50,14 @@ type ArangoDeployment struct {
 
 // AsOwner creates an OwnerReference for the given deployment
 func (d *ArangoDeployment) AsOwner() metav1.OwnerReference {
+	trueVar := true
 	return metav1.OwnerReference{
-		APIVersion: SchemeGroupVersion.String(),
-		Kind:       ArangoDeploymentResourceKind,
-		Name:       d.Name,
-		UID:        d.UID,
+		APIVersion:         SchemeGroupVersion.String(),
+		Kind:               ArangoDeploymentResourceKind,
+		Name:               d.Name,
+		UID:                d.UID,
+		Controller:         &trueVar,
+		BlockOwnerDeletion: &trueVar,
 	}
 }
 

pkg/apis/deployment/v1alpha/deployment_status_members.go

@@ -121,6 +121,22 @@ func (ds DeploymentStatusMembers) MemberStatusByPodName(podName string) (MemberS
 	return MemberStatus{}, 0, false
 }
 
+// MemberStatusByPVCName returns a reference to the element in the given set of lists that has the given PVC name.
+// If no such element exists, nil is returned.
+func (ds DeploymentStatusMembers) MemberStatusByPVCName(pvcName string) (MemberStatus, ServerGroup, bool) {
+	if result, found := ds.Single.ElementByPVCName(pvcName); found {
+		return result, ServerGroupSingle, true
+	}
+	if result, found := ds.Agents.ElementByPVCName(pvcName); found {
+		return result, ServerGroupAgents, true
+	}
+	if result, found := ds.DBServers.ElementByPVCName(pvcName); found {
+		return result, ServerGroupDBServers, true
+	}
+	// Note: Other server groups do not have PVC's so we can skip them.
+	return MemberStatus{}, 0, false
+}
+
 // UpdateMemberStatus updates the given status in the given group.
 func (ds *DeploymentStatusMembers) UpdateMemberStatus(status MemberStatus, group ServerGroup) error {
 	var err error

pkg/apis/deployment/v1alpha/member_status_list.go

@@ -63,6 +63,17 @@ func (l MemberStatusList) ElementByPodName(podName string) (MemberStatus, bool)
 	return MemberStatus{}, false
 }
 
+// ElementByPVCName returns the element in the given list that has the given PVC name and true.
+// If no such element exists, an empty element and false is returned.
+func (l MemberStatusList) ElementByPVCName(pvcName string) (MemberStatus, bool) {
+	for i, x := range l {
+		if x.PersistentVolumeClaimName == pvcName {
+			return l[i], true
+		}
+	}
+	return MemberStatus{}, false
+}
+
 // Add a member to the list.
 // Returns an AlreadyExistsError if the ID of the given member already exists.
 func (l *MemberStatusList) Add(m MemberStatus) error {

pkg/apis/deployment/v1alpha/server_group.go

@@ -22,6 +22,8 @@
 
 package v1alpha
 
+import time "time"
+
 type ServerGroup int
 
 const (
@@ -85,6 +87,20 @@ func (g ServerGroup) AsRoleAbbreviated() string {
 	}
 }
 
+// DefaultTerminationGracePeriod returns the default period between SIGTERM & SIGKILL for a server in the given group.
+func (g ServerGroup) DefaultTerminationGracePeriod() time.Duration {
+	switch g {
+	case ServerGroupSingle:
+		return time.Minute
+	case ServerGroupAgents:
+		return time.Minute
+	case ServerGroupDBServers:
+		return time.Hour
+	default:
+		return time.Second * 30
+	}
+}
+
 // IsArangod returns true when the groups runs servers of type `arangod`.
 func (g ServerGroup) IsArangod() bool {
 	switch g {

pkg/deployment/cleanup.go

@@ -0,0 +1,59 @@
+//
+// DISCLAIMER
+//
+// Copyright 2018 ArangoDB GmbH, Cologne, Germany
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+// http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+// Copyright holder is ArangoDB GmbH, Cologne, Germany
+//
+// Author Ewout Prangsma
+//
+
+package deployment
+
+import (
+	"github.com/arangodb/kube-arangodb/pkg/util/k8sutil"
+)
+
+// removePodFinalizers removes all finalizers from all pods owned by us.
+func (d *Deployment) removePodFinalizers() error {
+	log := d.deps.Log
+	kubecli := d.GetKubeCli()
+	pods, err := d.GetOwnedPods()
+	if err != nil {
+		return maskAny(err)
+	}
+	for _, p := range pods {
+		if err := k8sutil.RemovePodFinalizers(log, kubecli, &p, p.GetFinalizers()); err != nil {
+			log.Warn().Err(err).Msg("Failed to remove pod finalizers")
+		}
+	}
+	return nil
+}
+
+// removePVCFinalizers removes all finalizers from all PVCs owned by us.
+func (d *Deployment) removePVCFinalizers() error {
+	log := d.deps.Log
+	kubecli := d.GetKubeCli()
+	pvcs, err := d.GetOwnedPVCs()
+	if err != nil {
+		return maskAny(err)
+	}
+	for _, p := range pvcs {
+		if err := k8sutil.RemovePVCFinalizers(log, kubecli, &p, p.GetFinalizers()); err != nil {
+			log.Warn().Err(err).Msg("Failed to remove PVC finalizers")
+		}
+	}
+	return nil
+}