Backup and Restore MongoDB database using KubeStash

KubeStash v0.1.0+ supports backup and restoration of MongoDB databases. This guide will show you how you can backup and restore your MongoDB database with KubeStash.

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 KubeStash Enterprise in your cluster following the steps here.
Install KubeStash kubectl plugin following the steps here.
If you are not familiar with how KubeStash 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

This section will demonstrate how to backup MongoDB database. Here, we are going to deploy a MongoDB database using KubeDB. Then, we are going to backup this database into a S3 bucket. Finally, we are going to restore the backed up data into another MongoDB database.

Deploy Sample MongoDB Database

Let’s deploy a sample MongoDB 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-mongodb
  namespace: demo
spec:
  version: "4.2.24"
  storageType: Durable
  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/v2024.8.21/docs/guides/mongodb/backup/kubestash/logical/standalone/examples/mongodb.yaml
mongodb.kubedb.com/sample-mongodb 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-mongodb
NAME             VERSION       STATUS    AGE
sample-mongodb   4.2.24         Ready     2m9s

The database is Ready. 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-mongodb
NAME                  TYPE     DATA   AGE
sample-mongodb-auth   Opaque   2      2m28s

$ kubectl get service -n demo -l=app.kubernetes.io/instance=sample-mongodb
NAME                 TYPE        CLUSTER-IP      EXTERNAL-IP   PORT(S)     AGE
sample-mongodb       ClusterIP   10.107.58.222   <none>        27017/TCP   2m48s
sample-mongodb-gvr   ClusterIP   None            <none>        27017/TCP   2m48s

Here, we have to use service sample-mongodb and secret sample-mongodb-auth to connect with the database.

Insert Sample Data:

Note: You can insert data into this MongoDB database using our KubeDB CLI.

For simplicity, 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-mongodb"
NAME               READY   STATUS    RESTARTS   AGE
sample-mongodb-0   1/1     Running   0          12m

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

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

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

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

> show dbs
admin          0.000GB
config         0.000GB
kubedb-system  0.000GB
local          0.000GB

> show users
{
	"_id" : "admin.root",
	"userId" : UUID("b82f8a34-1fc4-4ffe-b616-c6ffa278ecc8"),
	"user" : "root",
	"db" : "admin",
	"roles" : [
		{
			"role" : "root",
			"db" : "admin"
		}
	],
	"mechanisms" : [
		"SCRAM-SHA-1",
		"SCRAM-SHA-256"
	]
}

> use newdb
switched to db newdb

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

> db.movie.find().pretty()
{ "_id" : ObjectId("5d19d1cdc93d828f44e37735"), "name" : "batman" }

> exit
bye

Now, we are ready to backup this sample database.

Prepare Backend

We are going to store our backed up data into a S3 bucket. At first, we need to create a secret with S3 credentials then we need to create a BackupStorage 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 s3-secret with access credentials to our desired S3 bucket,

$ echo -n '<your-aws-access-key-id-here>' > AWS_ACCESS_KEY_ID
$ echo -n '<your-aws-secret-access-key-here>' > AWS_SECRET_ACCESS_KEY
$ kubectl create secret generic -n demo s3-secret \
    --from-file=./AWS_ACCESS_KEY_ID \
    --from-file=./AWS_SECRET_ACCESS_KEY
secret/s3-secret created

Create BackupStorage:

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

apiVersion: storage.kubestash.com/v1alpha1
kind: BackupStorage
metadata:
  name: s3-storage
  namespace: demo
spec:
  storage:
    provider: s3
    s3:
      endpoint: us-east-1.linodeobjects.com
      bucket: kubestash-testing
      region: us-east-1
      prefix: demo
      secretName: s3-secret
  usagePolicy:
    allowedNamespaces:
      from: All
  deletionPolicy: WipeOut

Let’s create the BackupStorage we have shown above,

$ kubectl apply -f https://github.com/kubedb/docs/raw/v2024.8.21/docs/guides/mongodb/backup/kubestash/logical/standalone/examples/backupstorage.yaml
storage.kubestash.com/s3-storage created

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

Backup

We have to create a BackupConfiguration targeting respective MongoDB crd of our desired database. Then KubeStash will create a CronJob to periodically backup the database. Before that we need to create an secret for encrypt data and retention policy.

Create Encryption Secret:

EncryptionSecret refers to the Secret containing the encryption key which will be used to encode/decode the backed up data. Let’s create a secret called encry-secret

$ kubectl create secret generic encry-secret -n demo \
    --from-literal=RESTIC_PASSWORD='123' -n demo
secret/encry-secret created

Create Retention Policy:

RetentionPolicy specifies how the old Snapshots should be cleaned up. This is a namespaced CRD.However, we can refer it from other namespaces as long as it is permitted via .spec.usagePolicy. Below is the YAML of the RetentionPolicy called backup-rp

apiVersion: storage.kubestash.com/v1alpha1
kind: RetentionPolicy
metadata:
  name: backup-rp
  namespace: demo
spec:
  maxRetentionPeriod: 2mo
  successfulSnapshots:
    last: 10
  usagePolicy:
    allowedNamespaces:
      from: All

Let’s create the RetentionPolicy we have shown above,

$ kubectl apply -f https://github.com/kubedb/docs/raw/v2024.8.21/docs/guides/mongodb/backup/kubestash/logical/standalone/examples/retentionpolicy.yaml
retentionpolicy.storage.kubestash.com/backup-rp created

Create BackupConfiguration:

As we just create our encryption secret and retention policy, we are now ready to apply BackupConfiguration crd to take backup out database.

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

apiVersion: core.kubestash.com/v1alpha1
kind: BackupConfiguration
metadata:
  name: mg
  namespace: demo
spec:
  target:
    apiGroup: kubedb.com
    kind: MongoDB
    namespace: demo
    name: sample-mongodb
  backends:
    - name: s3-backend
      storageRef:
        namespace: demo
        name: s3-storage
      retentionPolicy:
        name: backup-rp
        namespace: demo
  sessions:
    - name: frequent
      scheduler:
        jobTemplate:
          backoffLimit: 1
        schedule: "*/3 * * * *"
      repositories:
        - name: s3-repo
          backend: s3-backend
          directory: /mongodb
          encryptionSecret:
            name: encry-secret
            namespace: demo
      addon:
        name: mongodb-addon
        tasks:
          - name: LogicalBackup

Here,

spec.target specifies our targeted MongoDB database.
spec.backends specifies BackupStorage information for storing data.
spec.sessions specifies common session configurations for this backup
spec.sessions.schedule specifies that we want to backup the database at 5 minutes interval.
spec.sessions.addon refers to the Addon crd for backup task

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

$ kubectl apply -f https://github.com/kubedb/docs/raw/v2024.8.21/docs/guides/mongodb/backup/kubestash/logical/standalone/examples/backupconfiguration.yaml
backupconfiguration.core.kubestash.com/mg 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   PHASE   PAUSED   AGE
mg     Ready            85s

Verify CronJob:

KubeStash will create a CronJob with the schedule specified in spec.sessions.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
trigger-mg-frequent   */3 * * * *   False     0        <none>          101s

Wait for BackupSession:

The trigger-mg-frequent CronJob will trigger a backup on each schedule by creating a BackpSession crd.

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

$ kubectl get backupsession -n demo
NAME                     INVOKER-TYPE          INVOKER-NAME   PHASE       DURATION   AGE
mg-frequent-1701923402   BackupConfiguration   mg             Succeeded              3m4s
mg-frequent-1701923582   BackupConfiguration   mg             Running                4s

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, KubeStash will update the respective Snapshot crd to reflect the backup. It will be created when a backup is triggered. Check that the Snapshot Phase to verify backup.

$ kubectl get snapshot -n demo
NAME                             REPOSITORY   SESSION    SNAPSHOT-TIME          DELETION-POLICY   PHASE       VERIFICATION-STATUS   AGE
s3-repo-mg-frequent-1701923402   s3-repo      frequent   2023-12-07T04:30:10Z   Delete            Succeeded                         3m25s
s3-repo-mg-frequent-1701923582   s3-repo      frequent   2023-12-07T04:33:06Z   Delete            Succeeded                         25s

KubeStash will also update the respective Repository crd to reflect the backup. Check that the repository s3-repo has been updated by the following command,

$ kubectl get repository -n demo s3-repo
NAME      INTEGRITY   SNAPSHOT-COUNT   SIZE        PHASE   LAST-SUCCESSFUL-BACKUP   AGE
s3-repo   true        2                2.613 KiB   Ready   2m42s                    8m38s

Now, if we navigate to the S3 bucket, we are going to see backed up data has been stored in demo/mongodb/ directory as specified by spec.sessions.repositories.directory field of BackupConfiguration crd.

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

Restore MongoDB

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.

Stop Taking Backup of the Old Database:

It’s important to stop taking any further backup of the old database so that no backup is stored in our repository during restore process. KubeStash operator will automatically pause the BackupConfiguration when a RestoreSession is running. However if we want to pause the BackupConfiguration manually, we can do that by patching or using KubeStash CLI.

Let’s pause the mg BackupConfiguration by patching,

$ kubectl patch backupconfiguration -n demo mg --type="merge" --patch='{"spec": {"paused": true}}'
backupconfiguration.core.kubestash.com/mg patched

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

$ kubectl get backupconfiguration -n demo mg
NAME   PHASE   PAUSED   AGE
mg     Ready   true     26m

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

Deploy New MongoDB Database For Restoring:

We are going to deploy a new mongodb standalone database for restoring backed up data.

Below is the YAML of a sample MongoDB crd that we are going to create

apiVersion: kubedb.com/v1alpha2
kind: MongoDB
metadata:
  name: restore-mongodb
  namespace: demo
spec:
  version: "4.2.24"
  storageType: Durable
  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/v2024.8.21/docs/guides/mongodb/backup/kubestash/logical/standalone/examples/mongodb-restore.yaml
mongodb.kubedb.com/restore-mongodb created

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

$ kubectl get mg -n demo restore-mongodb
NAME              VERSION   STATUS   AGE
restore-mongodb   4.2.24     Ready    3m30s

Let’s verify all the databases of this restore-mongodb by exec into its pod

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

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

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

> show dbs
admin          0.000GB
config         0.000GB
kubedb-system  0.000GB
local          0.000GB

> show users
{
	"_id" : "admin.root",
	"userId" : UUID("a4decc6b-959a-434d-9e4b-19cb9bfa783b"),
	"user" : "root",
	"db" : "admin",
	"roles" : [
		{
			"role" : "root",
			"db" : "admin"
		}
	],
	"mechanisms" : [
		"SCRAM-SHA-1",
		"SCRAM-SHA-256"
	]
}

> exit
bye

As we can see no database named newdb exist in this new restore-mongodb database.

Create RestoreSession:

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

apiVersion: core.kubestash.com/v1alpha1
kind: RestoreSession
metadata:
  name: mg-restore
  namespace: demo
spec:
  target:
    name: restore-mongodb
    namespace: demo
    apiGroup: kubedb.com
    kind: MongoDB
  dataSource:
    snapshot: latest
    repository: s3-repo
    encryptionSecret:
      name: encry-secret 
      namespace: demo
  addon:
    name: mongodb-addon
    tasks:
      - name: LogicalBackupRestore

Here,

spec.dataSource.repository specifies the Repository crd that holds the backend information where our backed up data has been stored.
spec.target refers to the MongoDB crd for the restore-mongodb database.
spec.dataSource.snapshot specifies that we are restoring from the latest backup snapshot of the spec.dataSource.repository.

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

$ kubectl apply -f https://github.com/kubedb/docs/raw/v2024.8.21/docs/guides/mongodb/backup/kubestash/logical/standalone/examples/restoresession.yaml
restoresession.core.kubestash.com/mg-restore created

Once, you have created the RestoreSession crd, KubeStash 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-mongodb-restore -w
NAME         REPOSITORY   FAILURE-POLICY   PHASE       DURATION   AGE
mg-restore   s3-repo                       Succeeded   8s         49s

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 the restore-mongodb database and check whether the table we had created earlier is restored or not.

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

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

> show dbs
admin          0.000GB
config         0.000GB
kubedb-system  0.000GB
local          0.000GB
newdb          0.000GB

> show users
{
	"_id" : "admin.root",
	"userId" : UUID("a4decc6b-959a-434d-9e4b-19cb9bfa783b"),
	"user" : "root",
	"db" : "admin",
	"roles" : [
		{
			"role" : "root",
			"db" : "admin"
		}
	],
	"mechanisms" : [
		"SCRAM-SHA-1",
		"SCRAM-SHA-256"
	]
}

> use newdb
switched to db newdb

> db.movie.find().pretty()
{ "_id" : ObjectId("5d19d1cdc93d828f44e37735"), "name" : "batman" }

> exit
bye

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

Cleanup

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

kubectl delete -n demo restoresession mg-restore
kubectl delete -n demo backupconfiguration mg
kubectl delete -n demo mg sample-mongodb
kubectl delete -n demo mg restore-mongodb
kubectl delete -n demo backupstorage s3-storage

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