Backup and Restore MongoDB ReplicaSet Clusters using Stash

Stash supports taking backup and restores MongoDB ReplicaSet clusters in “idiomatic” way. This guide will show you how you can backup and restore your MongoDB ReplicaSet clusters with Stash.

Before You Begin

At first, you need to have a Kubernetes cluster, and the kubectl command-line tool must be configured to communicate with your cluster. If you do not already have a cluster, you can create one by using Minikube.
Install KubeDB in your cluster following the steps here.
Install Stash in your cluster following the steps here.
Install Stash kubectl plugin following the steps here.
If you are not familiar with how Stash backup and restore MongoDB databases, please check the following guide here.

You have to be familiar with following custom resources:

To keep things isolated, we are going to use a separate namespace called demo throughout this tutorial. Create demo namespace if you haven’t created yet.

$ kubectl create ns demo
namespace/demo created

Backup MongoDB ReplicaSet using Stash

This section will demonstrate how to backup MongoDB ReplicaSet cluster. Here, we are going to deploy a MongoDB ReplicaSet using KubeDB. Then, we are going to backup this database into a GCS bucket. Finally, we are going to restore the backed up data into another MongoDB ReplicaSet.

Deploy Sample MongoDB ReplicaSet

Let’s deploy a sample MongoDB ReplicaSet database and insert some data into it.

Create MongoDB CRD:

Below is the YAML of a sample MongoDB crd that we are going to create for this tutorial:

apiVersion: kubedb.com/v1alpha2
kind: MongoDB
metadata:
  name: sample-mgo-rs
  namespace: demo
spec:
  version: "4.4.26"
  replicas: 3
  replicaSet:
    name: rs0
  storage:
    storageClassName: "standard"
    accessModes:
    - ReadWriteOnce
    resources:
      requests:
        storage: 1Gi
  terminationPolicy: WipeOut

Create the above MongoDB crd,

$ kubectl apply -f https://github.com/kubedb/docs/raw/v2024.1.26-rc.0/docs/guides/mongodb/backup/logical/replicaset/examples/mongodb-replicaset.yaml
mongodb.kubedb.com/sample-mgo-rs created

KubeDB will deploy a MongoDB database according to the above specification. It will also create the necessary secrets and services to access the database.

Let’s check if the database is ready to use,

$ kubectl get mg -n demo sample-mgo-rs
NAME            VERSION     STATUS  AGE
sample-mgo-rs   4.4.26       Ready   1m

The database is Running. Verify that KubeDB has created a Secret and a Service for this database using the following commands,

$ kubectl get secret -n demo -l=app.kubernetes.io/instance=sample-mgo-rs
NAME                 TYPE     DATA   AGE
sample-mgo-rs-auth   Opaque   2      117s
sample-mgo-rs-cert   Opaque   4      116s

$ kubectl get service -n demo -l=app.kubernetes.io/instance=sample-mgo-rs
NAME                TYPE        CLUSTER-IP     EXTERNAL-IP   PORT(S)     AGE
sample-mgo-rs       ClusterIP   10.107.13.16   <none>        27017/TCP   2m14s
sample-mgo-rs-gvr   ClusterIP   None           <none>        27017/TCP   2m14s

KubeDB creates an AppBinding crd that holds the necessary information to connect with the database.

Verify AppBinding:

Verify that the AppBinding has been created successfully using the following command,

$ kubectl get appbindings -n demo
NAME            AGE
sample-mgo-rs   58s

Let’s check the YAML of the above AppBinding,

$ kubectl get appbindings -n demo sample-mgo-rs -o yaml

apiVersion: appcatalog.appscode.com/v1alpha1
kind: AppBinding
metadata:
  annotations:
    kubectl.kubernetes.io/last-applied-configuration: |
      {"apiVersion":"kubedb.com/v1alpha2","kind":"MongoDB","metadata":{"annotations":{},"name":"sample-mgo-rs","namespace":"demo"},"spec":{"replicaSet":{"name":"rs0"},"replicas":3,"storage":{"accessModes":["ReadWriteOnce"],"resources":{"requests":{"storage":"1Gi"}},"storageClassName":"standard"},"terminationPolicy":"WipeOut","version":"4.4.26"}}      
  creationTimestamp: "2022-10-26T04:42:05Z"
  generation: 1
  labels:
    app.kubernetes.io/component: database
    app.kubernetes.io/instance: sample-mgo-rs
    app.kubernetes.io/managed-by: kubedb.com
    app.kubernetes.io/name: mongodbs.kubedb.com
  name: sample-mgo-rs
  namespace: demo
  ownerReferences:
    - apiVersion: kubedb.com/v1alpha2
      blockOwnerDeletion: true
      controller: true
      kind: MongoDB
      name: sample-mgo-rs
      uid: 658bf7d1-3772-4c89-84db-5ac74a6c5851
  resourceVersion: "577375"
  uid: b0cd9885-53d9-4a2b-93a9-cf9fa90594fd
spec:
  appRef:
    apiGroup: kubedb.com
    kind: MongoDB
    name: sample-mgo-rs
    namespace: demo
  clientConfig:
    service:
      name: sample-mgo-rs
      port: 27017
      scheme: mongodb
  parameters:
    apiVersion: config.kubedb.com/v1alpha1
    kind: MongoConfiguration
    replicaSets:
      host-0: rs0/sample-mgo-rs-0.sample-mgo-rs-pods.demo.svc:27017,sample-mgo-rs-1.sample-mgo-rs-pods.demo.svc:27017,sample-mgo-rs-2.sample-mgo-rs-pods.demo.svc:27017
    stash:
      addon:
        backupTask:
          name: mongodb-backup-4.4.6
        restoreTask:
          name: mongodb-restore-4.4.6
  secret:
    name: sample-mgo-rs-auth
  type: kubedb.com/mongodb
  version: 4.4.26

Stash uses the AppBinding crd to connect with the target database. It requires the following two fields to set in AppBinding’s Spec section.

spec.appRef refers to the underlying application.
spec.clientConfig defines how to communicate with the application.
spec.clientConfig.service.name specifies the name of the service that connects to the database.
spec.secret specifies the name of the secret that holds necessary credentials to access the database.
spec.parameters.replicaSets contains the dsn of replicaset. The DSNs are in key-value pair. If there is only one replicaset (replicaset can be multiple, because of sharding), then ReplicaSets field contains only one key-value pair where the key is host-0 and the value is dsn of that replicaset.
spec.parameters.stash section specifies the Stash Addons that will be used to backup and restore this MongoDB.
spec.type specifies the types of the app that this AppBinding is pointing to. KubeDB generated AppBinding follows the following format: <app group>/<app resource type>.

Insert Sample Data:

Now, we are going to exec into the database pod and create some sample data. At first, find out the database pod using the following command,

$ kubectl get pods -n demo --selector="app.kubernetes.io/instance=sample-mgo-rs"
NAME              READY   STATUS    RESTARTS   AGE
sample-mgo-rs-0   1/1     Running   0          16m
sample-mgo-rs-1   1/1     Running   0          15m
sample-mgo-rs-2   1/1     Running   0          15m

Now, let’s exec into the pod and create a table,

$ export USER=$(kubectl get secrets -n demo sample-mgo-rs-auth -o jsonpath='{.data.\username}' | base64 -d)

$ export PASSWORD=$(kubectl get secrets -n demo sample-mgo-rs-auth -o jsonpath='{.data.\password}' | base64 -d)

$ kubectl exec -it -n demo sample-mgo-rs-0 -- mongo admin -u $USER -p $PASSWORD

rs0:PRIMARY> rs.isMaster().primary
sample-mgo-rs-0.sample-mgo-rs-gvr.demo.svc.cluster.local:27017

rs0:PRIMARY> show dbs
admin   0.000GB
config  0.000GB
local   0.000GB

rs0:PRIMARY> show users
{
	"_id" : "admin.root",
	"userId" : UUID("0e9345cc-27ea-4175-acc4-295c987ac06b"),
	"user" : "root",
	"db" : "admin",
	"roles" : [
		{
			"role" : "root",
			"db" : "admin"
		}
	]
}

rs0:PRIMARY> use newdb
switched to db newdb

rs0:PRIMARY> db.movie.insert({"name":"batman"});
WriteResult({ "Inserted" : 1 })

rs0:PRIMARY> db.movie.find().pretty()
{ "_id" : ObjectId("5d31b9d44db670db130d7a5c"), "name" : "batman" }

rs0:PRIMARY> exit
bye

Now, we are ready to backup this sample database.

Prepare Backend

We are going to store our backed up data into a GCS bucket. At first, we need to create a secret with GCS credentials then we need to create a Repository crd. If you want to use a different backend, please read the respective backend configuration doc from here.

Create Storage Secret:

Let’s create a secret called gcs-secret with access credentials to our desired GCS bucket,

$ echo -n 'changeit' > RESTIC_PASSWORD
$ echo -n '<your-project-id>' > GOOGLE_PROJECT_ID
$ cat downloaded-sa-key.json > GOOGLE_SERVICE_ACCOUNT_JSON_KEY
$ kubectl create secret generic -n demo gcs-secret \
    --from-file=./RESTIC_PASSWORD \
    --from-file=./GOOGLE_PROJECT_ID \
    --from-file=./GOOGLE_SERVICE_ACCOUNT_JSON_KEY
secret/gcs-secret created

Create Repository:

Now, crete a Repository using this secret. Below is the YAML of Repository crd we are going to create,

apiVersion: stash.appscode.com/v1alpha1
kind: Repository
metadata:
  name: gcs-repo-replicaset
  namespace: demo
spec:
  backend:
    gcs:
      bucket: appscode-qa
      prefix: demo/mongodb/sample-mgo-rs
    storageSecretName: gcs-secret

Let’s create the Repository we have shown above,

$ kubectl apply -f https://github.com/kubedb/docs/raw/v2024.1.26-rc.0/docs/guides/mongodb/backup/logical/replicaset/examples/repository-replicaset.yaml
repository.stash.appscode.com/gcs-repo-replicaset created

Now, we are ready to backup our database to our desired backend.

Backup MongoDB ReplicaSet

We have to create a BackupConfiguration targeting respective AppBinding crd of our desired database. Then Stash will create a CronJob to periodically backup the database.

Create BackupConfiguration:

Below is the YAML for BackupConfiguration crd to backup the sample-mgo-rs database we have deployed earlier.,

apiVersion: stash.appscode.com/v1beta1
kind: BackupConfiguration
metadata:
  name: sample-mgo-rs-backup
  namespace: demo
spec:
  schedule: "*/5 * * * *"
  repository:
    name: gcs-repo-replicaset
  target:
    ref:
      apiVersion: appcatalog.appscode.com/v1alpha1
      kind: AppBinding
      name: sample-mgo-rs
  retentionPolicy:
    name: keep-last-5
    keepLast: 5
    prune: true

Here,

spec.schedule specifies that we want to backup the database at 5 minutes interval.
spec.target.ref refers to the AppBinding crd that was created for sample-mgo-rs database.

Let’s create the BackupConfiguration crd we have shown above,

$ kubectl apply -f https://github.com/kubedb/docs/raw/v2024.1.26-rc.0/docs/guides/mongodb/backup/logical/replicaset/examples/backupconfiguration-replicaset.yaml
backupconfiguration.stash.appscode.com/sample-mgo-rs-backup created

Verify Backup Setup Successful:

If everything goes well, the phase of the BackupConfiguration should be Ready. The Ready phase indicates that the backup setup is successful. Let’s verify the Phase of the BackupConfiguration,

$ kubectl get backupconfiguration -n demo
NAME                    TASK                    SCHEDULE      PAUSED   PHASE      AGE
sample-mgo-rs-backup    mongodb-backup-4.4.6    */5 * * * *            Ready      11s

Verify CronJob:

Stash will create a CronJob with the schedule specified in spec.schedule field of BackupConfiguration crd.

Verify that the CronJob has been created using the following command,

$ kubectl get cronjob -n demo
NAME                   SCHEDULE      SUSPEND   ACTIVE   LAST SCHEDULE   AGE
sample-mgo-rs-backup   */5 * * * *   False     0        <none>          62s

Wait for BackupSession:

The sample-mgo-rs-backup CronJob will trigger a backup on each schedule by creating a BackupSession crd.

Wait for the next schedule. Run the following command to watch BackupSession crd,

$ kubectl get backupsession -n demo -w
NAME                              INVOKER-TYPE          INVOKER-NAME           PHASE       AGE
sample-mgo-rs-backup-1563540308   BackupConfiguration   sample-mgo-rs-backup   Running     5m19s
sample-mgo-rs-backup-1563540308   BackupConfiguration   sample-mgo-rs-backup   Succeeded   5m45s

We can see above that the backup session has succeeded. Now, we are going to verify that the backed up data has been stored in the backend.

Verify Backup:

Once a backup is complete, Stash will update the respective Repository crd to reflect the backup. Check that the repository gcs-repo-replicaset has been updated by the following command,

$ kubectl get repository -n demo gcs-repo-replicaset
NAME                  INTEGRITY   SIZE        SNAPSHOT-COUNT   LAST-SUCCESSFUL-BACKUP   AGE
gcs-repo-replicaset   true        3.844 KiB   2                14s                      10m

Now, if we navigate to the GCS bucket, we are going to see backed up data has been stored in demo/mongodb/sample-mgo-rs directory as specified by spec.backend.gcs.prefix field of Repository crd.

Note: Stash keeps all the backed up data encrypted. So, data in the backend will not make any sense until they are decrypted.

Restore MongoDB ReplicaSet

You can restore your data into the same database you have backed up from or into a different database in the same cluster or a different cluster. In this section, we are going to show you how to restore in the same database which may be necessary when you have accidentally deleted any data from the running database.

Temporarily Pause Backup

At first, let’s stop taking any further backup of the old database so that no backup is taken during restore process. We are going to pause the BackupConfiguration crd that we had created to backup the sample-mgo-rs database. Then, Stash will stop taking any further backup for this database.

Let’s pause the sample-mgo-rs-backup BackupConfiguration,

$ kubectl patch backupconfiguration -n demo sample-mgo-rs-backup --type="merge" --patch='{"spec": {"paused": true}}'
backupconfiguration.stash.appscode.com/sample-mgo-rs-backup patched

Or you can use the Stash kubectl plugin to pause the BackupConfiguration,

$ kubectl stash pause backup -n demo --backupconfig=sample-mgo-rs-backup
BackupConfiguration demo/sample-mgo-rs-backup has been paused successfu

Now, wait for a moment. Stash will pause the BackupConfiguration. Verify that the BackupConfiguration has been paused,

$ kubectl get backupconfiguration -n demo sample-mgo-rs-backup
NAME                  TASK                      SCHEDULE      PAUSED   PHASE   AGE
sample-mgo-rs-backup  mongodb-backup-4.4.6      */5 * * * *   true     Ready   26m

Notice the PAUSED column. Value true for this field means that the BackupConfiguration has been paused.

Simulate Disaster

Now, let’s simulate an accidental deletion scenario. Here, we are going to exec into the database pod and delete the newdb database we had created earlier.

$ kubectl exec -it -n demo sample-mgo-rs-0 -- mongo admin -u $USER -p $PASSWORD

rs0:PRIMARY> rs.isMaster().primary
sample-mgo-rs-0.sample-mgo-rs-gvr.demo.svc.cluster.local:27017

rs0:PRIMARY> use newdb
switched to db newdb

rs0:PRIMARY> db.dropDatabase()
{ "dropped" : "newdb", "ok" : 1 }

rs0:PRIMARY> show dbs
admin   0.000GB
config  0.000GB
local   0.000GB

rs0:PRIMARY> exit
bye

Create RestoreSession:

Now, we need to create a RestoreSession crd pointing to the AppBinding of sample-mgo-rs database. Below is the YAML for the RestoreSession crd that we are going to create to restore the backed up data,

apiVersion: stash.appscode.com/v1beta1
kind: RestoreSession
metadata:
  name: sample-mgo-rs-restore
  namespace: demo
spec:
  repository:
    name: gcs-repo-replicaset
  target:
    ref:
      apiVersion: appcatalog.appscode.com/v1alpha1
      kind: AppBinding
      name: sample-mgo-rs
  rules:
  - snapshots: [latest]

Here,

spec.repository.name specifies the Repository crd that holds the backend information where our backed up data has been stored.
spec.target.ref refers to the AppBinding crd for the restored-mgo-rs database.
spec.rules specifies that we are restoring from the latest backup snapshot of the database.

Let’s create the RestoreSession crd we have shown above,

$ kubectl apply -f https://github.com/kubedb/docs/raw/v2024.1.26-rc.0/docs/guides/mongodb/backup/logical/replicaset/examples/estoresession-replicaset.yaml
restoresession.stash.appscode.com/sample-mgo-rs-restore created

Once, you have created the RestoreSession crd, Stash will create a job to restore. We can watch the RestoreSession phase to check if the restore process is succeeded or not.

Run the following command to watch RestoreSession phase,

$ kubectl get restoresession -n demo sample-mgo-rs-restore -w
NAME                    REPOSITORY-NAME        PHASE       AGE
sample-mgo-rs-restore   gcs-repo-replicaset    Running     5s
sample-mgo-rs-restore   gcs-repo-replicaset    Succeeded   43s

So, we can see from the output of the above command that the restore process succeeded.

Verify Restored Data:

In this section, we are going to verify that the desired data has been restored successfully. We are going to connect to mongos and check whether the table we had created in the original database is restored or not.

Lets, exec into the database pod and list available tables,

$ kubectl exec -it -n demo sample-mgo-rs-0 -- mongo admin -u $USER -p $PASSWORD

rs0:PRIMARY> rs.isMaster().primary
restored-mgo-rs-0.restored-mgo-rs-gvr.demo.svc.cluster.local:27017

rs0:PRIMARY> show dbs
admin   0.000GB
config  0.000GB
local   0.000GB
newdb   0.000GB

rs0:PRIMARY> show users
{
	"_id" : "admin.root",
	"userId" : UUID("00f521b5-2b43-4712-ba80-efaa6b382813"),
	"user" : "root",
	"db" : "admin",
	"roles" : [
		{
			"role" : "root",
			"db" : "admin"
		}
	]
}

rs0:PRIMARY> use newdb
switched to db newdb

rs0:PRIMARY> db.movie.find().pretty()
{ "_id" : ObjectId("5d31b9d44db670db130d7a5c"), "name" : "batman" }

rs0:PRIMARY> exit
bye

So, from the above output, we can see the database newdb that we had created earlier is restored.

Backup MongoDB ReplicaSet Cluster and Restore into a Standalone database

It is possible to take backup of a MongoDB ReplicaSet Cluster and restore it into a standalone database, but user need to create the appbinding for this process.

Backup a replicaset cluster

Keep all the fields of appbinding that is explained earlier in this guide, except spec.parameter. Do not set spec.parameter.configServer and spec.parameter.replicaSet. By doing this, the job will use spec.clientConfig.service.name as host, which is replicaset DSN. So, the backup will treat this cluster as a standalone and will skip the idiomatic way of taking backups of a replicaset cluster. Then follow the rest of the procedure as described above.

apiVersion: appcatalog.appscode.com/v1alpha1
kind: AppBinding
metadata:
  name: sample-mgo-rs-custom
  namespace: demo
spec:
  clientConfig:
    service:
      name: sample-mgo-rs
      port: 27017
      scheme: mongodb
  secret:
    name: sample-mgo-rs-auth
  type: kubedb.com/mongodb

---
apiVersion: stash.appscode.com/v1alpha1
kind: Repository
metadata:
  name: gcs-repo-custom
  namespace: demo
spec:
  backend:
    gcs:
      bucket: appscode-qa
      prefix: demo/mongodb/sample-mgo-rs/standalone
    storageSecretName: gcs-secret

---
apiVersion: stash.appscode.com/v1beta1
kind: BackupConfiguration
metadata:
  name: sample-mgo-rs-backup2
  namespace: demo
spec:
  schedule: "*/5 * * * *"
  task:
    name: mongodb-backup-4.4.6
  repository:
    name: gcs-repo-custom
  target:
    ref:
      apiVersion: appcatalog.appscode.com/v1alpha1
      kind: AppBinding
      name: sample-mgo-rs-custom
  retentionPolicy:
    name: keep-last-5
    keepLast: 5
    prune: true

This time, we have to provide the Stash Addon information in spec.task section of BackupConfiguration object as it does not present in the AppBinding object that we are creating manually.

$ kubectl create -f https://github.com/kubedb/docs/raw/v2024.1.26-rc.0/docs/guides/mongodb/backup/logical/replicaset/examples/standalone-backup.yaml
appbinding.appcatalog.appscode.com/sample-mgo-rs-custom created
repository.stash.appscode.com/gcs-repo-custom created
backupconfiguration.stash.appscode.com/sample-mgo-rs-backup2 created


$ kubectl get backupsession -n demo
NAME                               BACKUPCONFIGURATION    PHASE       AGE
sample-mgo-rs-backup2-1563541509   sample-mgo-rs-backup   Succeeded   35s


$ kubectl get repository -n demo gcs-repo-custom
NAME              INTEGRITY   SIZE        SNAPSHOT-COUNT   LAST-SUCCESSFUL-BACKUP   AGE
gcs-repo-custom   true        1.640 KiB   1                1m                       5m

Restore to a standalone database

No additional configuration is needed to restore the replicaset cluster to a standalone database. Follow the normal procedure of restoring a MongoDB Database.

Standalone MongoDB,

apiVersion: kubedb.com/v1alpha2
kind: MongoDB
metadata:
  name: restored-mongodb
  namespace: demo
spec:
  version: "4.4.26"
  storageType: Durable
  storage:
    storageClassName: "standard"
    accessModes:
      - ReadWriteOnce
    resources:
      requests:
        storage: 1Gi
  init:
    waitForInitialRestore: true
  terminationPolicy: WipeOut

You have to provide the respective Stash restore Task info in spec.task section of RestoreSession object,

apiVersion: stash.appscode.com/v1beta1
kind: RestoreSession
metadata:
  name: sample-mongodb-restore
  namespace: demo
spec:
  task:
    name: mongodb-restore-4.4.6
  repository:
    name: gcs-repo-custom
  target:
    ref:
      apiVersion: appcatalog.appscode.com/v1alpha1
      kind: AppBinding
      name: restored-mongodb
  rules:
  - snapshots: [latest]

$ kubectl create -f https://github.com/kubedb/docs/raw/v2024.1.26-rc.0/docs/guides/mongodb/backup/logical/replicaset/rexamples/estored-standalone.yaml
mongodb.kubedb.com/restored-mongodb created

$ kubectl get mg -n demo restored-mongodb
NAME               VERSION        STATUS         AGE
restored-mongodb   4.4.26         Provisioning   56s

$ kubectl create -f https://github.com/kubedb/docs/raw/v2024.1.26-rc.0/docs/guides/mongodb/backup/logical/replicaset/rexamples/estoresession-standalone.yaml
restoresession.stash.appscode.com/sample-mongodb-restore created

$ kubectl get mg -n demo restored-mongodb
NAME               VERSION       STATUS    AGE
restored-mongodb   4.4.26         Ready   2m

Now, exec into the database pod and list available tables,

$ export USER=$(kubectl get secrets -n demo restored-mongodb-auth -o jsonpath='{.data.\username}' | base64 -d)

$ export PASSWORD=$(kubectl get secrets -n demo restored-mongodb-auth -o jsonpath='{.data.\password}' | base64 -d)

$ kubectl exec -it -n demo restored-mongodb-0 -- mongo admin -u $USER -p $PASSWORD

mongodb@restored-mongodb-0:/$ mongo admin -u root -p CRz6EuxvKdFjopfP

> show dbs
admin   0.000GB
config  0.000GB
local   0.000GB
newdb   0.000GB

> show users
{
	"_id" : "admin.root",
	"userId" : UUID("11e00a38-7b08-4864-b452-ae356350e50f"),
	"user" : "root",
	"db" : "admin",
	"roles" : [
		{
			"role" : "root",
			"db" : "admin"
		}
	]
}

> use newdb
switched to db newdb

> db.movie.find().pretty()
{ "_id" : ObjectId("5d31b9d44db670db130d7a5c"), "name" : "batman" }

> exit
bye

So, from the above output, we can see the database newdb that we had created in the original database sample-mgo-rs is restored in the restored database restored-mongodb.

Cleanup

To cleanup the Kubernetes resources created by this tutorial, run:

kubectl delete -n demo restoresession sample-mgo-rs-restore sample-mongodb-restore
kubectl delete -n demo backupconfiguration sample-mgo-rs-backup sample-mgo-rs-backup2
kubectl delete -n demo mg sample-mgo-rs restored-mongodb
kubectl delete -n demo repository gcs-repo-replicaset gcs-repo-custom
kubectl delete -n demo appbinding sample-mgo-rs-custom

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