Backup and Restore standalone Percona XtraDB database using Stash

Stash 0.9.0+ supports backup and restoration of Percona XtraDB databases. This guide will show you how you can backup and restore your Percona XtraDB database 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 Enterprise in your cluster following the steps here.
If you are not familiar with how Stash takes backup and restores Percona XtraDB databases, please check the following guide here.

You have to be familiar with the 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 Percona XtraDB

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

Deploy Sample Percona XtraDB Database

Let’s deploy a sample Percona XtraDB database and insert some data into it.

Create Percona XtraDB CRD

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

apiVersion: kubedb.com/v1alpha2
kind: PerconaXtraDB
metadata:
  name: sample-xtradb
  namespace: demo
spec:
  version: "5.7"
  replicas: 1
  storageType: Durable
  storage:
    storageClassName: "standard"
    accessModes:
    - ReadWriteOnce
    resources:
      requests:
        storage: 1Gi
  terminationPolicy: WipeOut

Create the above PerconaXtraDB CRD,

$ kubectl apply -f https://github.com/kubedb/docs/raw/v2021.03.17/docs/guides/percona-xtradb/backup/standalone/examples/sample-xtradb.yaml
perconaxtradb.kubedb.com/sample-xtradb created

KubeDB will deploy a Percona XtraDB 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 px -n demo sample-xtradb
NAME            VERSION   STATUS  AGE
sample-xtradb   5.7       Ready   54s

The database is Provisioning. 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-xtradb
NAME                 TYPE     DATA   AGE
sample-xtradb-auth   Opaque   2      85s

$ kubectl get service -n demo -l=app.kubernetes.io/instance=sample-xtradb
NAME                TYPE        CLUSTER-IP      EXTERNAL-IP   PORT(S)    AGE
sample-xtradb       ClusterIP   10.108.43.167   <none>        3306/TCP   111s
sample-xtradb-gvr   ClusterIP   None            <none>        3306/TCP   111s

Here, we have to use service sample-xtradb and secret sample-xtradb-auth to connect with the database. 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            TYPE                       VERSION   AGE
sample-xtradb   kubedb.com/perconaxtradb   5.7       89s

Let’s check the YAML of the above AppBinding,

$ kubectl get appbindings -n demo sample-xtradb -o yaml

Output is as follows,

apiVersion: appcatalog.appscode.com/v1alpha1
kind: AppBinding
metadata:
  creationTimestamp: "2020-01-26T06:57:35Z"
  generation: 1
  labels:
    app.kubernetes.io/component: database
    app.kubernetes.io/instance: sample-xtradb
    app.kubernetes.io/managed-by: kubedb.com
    app.kubernetes.io/name: perconaxtradbs.kubedb.com
  name: sample-xtradb
  namespace: demo
  ownerReferences:
  - apiVersion: kubedb.com/v1alpha2
    blockOwnerDeletion: true
    controller: true
    kind: PerconaXtraDB
    name: sample-xtradb
    uid: 279e90e5-7596-4cd2-b971-99e9a3dff839
  resourceVersion: "16218"
  selfLink: /apis/appcatalog.appscode.com/v1alpha1/namespaces/demo/appbindings/sample-xtradb
  uid: 5aff9236-e886-4a0d-b767-85d639cfe7c4
spec:
  clientConfig:
    service:
      name: sample-xtradb
      path: /
      port: 3306
      scheme: mysql
    url: tcp(sample-xtradb:3306)/
  secret:
    name: sample-xtradb-auth
  parameters:
    apiVersion: config.kubedb.com/v1alpha2
    kind: GaleraArbitratorConfiguration
    stash:
      addon:
        backupTask:
          name: perconaxtradb-backup-5.7.0
        restoreTask:
          name: perconaxtradb-restore-5.7.0
  type: kubedb.com/perconaxtradb
  version: "5.7"

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

.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 the necessary credentials to access the database.
spec.parameters.stash contains the addon information that will be used for backup and restore this database.
.spec.type specifies the type of the app that this AppBinding is pointing to. The format KubeDB generated AppBinding follows to set the value of .spec.type is <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 pods using the following command,

$ kubectl get pods -n demo --selector="app.kubernetes.io/instance=sample-xtradb"
NAME              READY   STATUS    RESTARTS   AGE
sample-xtradb-0   1/1     Running   0          6m56s

And copy the username and password of the root user to access into mysql shell.

$ kubectl get secret -n demo  sample-xtradb-auth -o jsonpath='{.data.username}'| base64 -d
root⏎

$ kubectl get secret -n demo  sample-xtradb-auth -o jsonpath='{.data.password}'| base64 -d
5qtWP192NLD-nwgd⏎

Now, let’s exec into the Pod to enter into mysql shell and create a database and a table,

$ kubectl exec -it -n demo sample-xtradb-0 -- mysql --user=root --password=5qtWP192NLD-nwgd
mysql: [Warning] Using a password on the command line interface can be insecure.
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 48
Server version: 5.7.26-29 Percona Server (GPL), Release 29, Revision 11ad961

Copyright (c) 2009-2019 Percona LLC and/or its affiliates
Copyright (c) 2000, 2019, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> CREATE DATABASE playground;
Query OK, 1 row affected (0.00 sec)

mysql> SHOW DATABASES;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| mysql              |
| performance_schema |
| playground         |
| sys                |
+--------------------+
5 rows in set (0.00 sec)

mysql> CREATE TABLE playground.equipment ( id INT NOT NULL AUTO_INCREMENT, type VARCHAR(50), quant INT, color VARCHAR(25), PRIMARY KEY(id));
Query OK, 0 rows affected (0.06 sec)

mysql> INSERT INTO playground.equipment (type, quant, color) VALUES ("slide", 2, "blue");
Query OK, 1 row affected (0.01 sec)

mysql> SELECT * FROM playground.equipment;
+----+-------+-------+-------+
| id | type  | quant | color |
+----+-------+-------+-------+
|  1 | slide |     2 | blue  |
+----+-------+-------+-------+
1 row in set (0.00 sec)

mysql> exit
Bye

Now, we are ready to back up the 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-json.key > 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-sample-xtradb
  namespace: demo
spec:
  backend:
    gcs:
      bucket: appscode-qa
      prefix: /demo/xtradb/sample-xtradb
    storageSecretName: gcs-secret

Let’s create the Repository we have shown above,

$ kubectl create -f https://github.com/kubedb/docs/raw/v2021.03.17/docs/guides/percona-xtradb/backup/standalone/examples/repository.yaml
repository.stash.appscode.com/gcs-repo-sample-xtradb created

Now, we are ready to back up our database to our desired backend.

Backup

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-xtradb database we have deployed earlier,

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

Here,

.spec.schedule specifies that we want to back up the database at 5 minutes interval.
.spec.target.ref refers to the AppBinding CRD that was created for the sample-xtradb database.

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

$ kubectl create -f https://github.com/kubedb/docs/raw/v2021.03.17/docs/guides/percona-xtradb/backup/standalone/examples/backupconfiguration.yaml
backupconfiguration.stash.appscode.com/sample-xtradb-backup created

Verify CronJob

If everything goes well, 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
stash-backup-sample-xtradb-backup   */5 * * * *   False     0        <none>          38s

Wait for BackupSession

The sample-xtradb-backup CronJob will trigger a backup on each scheduled slot by creating a BackupSession CRD.

Wait for a schedule to appear. Run the following command to watch BackupSession CRD,

$ kubectl get backupsession -n demo -l=stash.appscode.com/invoker-name=sample-xtradb-backup --watch
NAME                              INVOKER-TYPE          INVOKER-NAME           PHASE       AGE
sample-xtradb-backup-1580023322   BackupConfiguration   sample-xtradb-backup               0s
sample-xtradb-backup-1580023322   BackupConfiguration   sample-xtradb-backup               0s
sample-xtradb-backup-1580023322   BackupConfiguration   sample-xtradb-backup   Running     0s
sample-xtradb-backup-1580023322   BackupConfiguration   sample-xtradb-backup   Running     36s
sample-xtradb-backup-1580023322   BackupConfiguration   sample-xtradb-backup   Succeeded   36s

Here, the phase Succeeded means that the backupsession has been succeeded.

Note: Backup CronJob creates BackupSession CRD the label stash.appscode.com/invoker-name=<BackupConfiguration_crd_name>. We can use this label to watch only the BackupSession of our desired BackupConfiguration.

Verify Backup

Now, we are going to verify whether the backed up data is in the backend. Once a backup is completed, Stash will update the respective Repository CRD to reflect the backup completion. Check that the repository gcs-repo-sample-xtradb has been updated by the following command,

$ kubectl get repository -n demo gcs-repo-sample-xtradb
NAME                     INTEGRITY   SIZE   SNAPSHOT-COUNT   LAST-SUCCESSFUL-BACKUP   AGE
gcs-repo-sample-xtradb   true               3                82s                      17m

Now, if we navigate to the GCS bucket, we will see the backed up data has been stored in demo/xtradb/sample-xtradb 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 Percona XtraDB

In this section, we are going to restore the database from the backup we have taken in the previous section. We are going to deploy a new database and initialize it from the backup.

Stop Taking Backup of the Old Database

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

Let’s pause the sample-xtradb-backup BackupConfiguration,

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

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

$ kkubectl get backupconfiguration -n demo sample-xtradb-backup
NAME                   TASK                         SCHEDULE      PAUSED   AGE
sample-xtradb-backup   perconaxtradb-backup-5.7.0   */5 * * * *   true     13m

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

Deploy Restored Database

Now, we have to deploy the restored database similarly as we have deployed the original sample-xtradb database. However, this time there will be the following differences:

We have to use the same secret that was used in the original database. We are going to specify it using .spec.databaseSecret field.
We are going to specify .spec.init.waitForInitialRestore field to tell KubeDB that it should wait for the first restore to complete before marking this database as ready to use.

Below is the YAML for PerconaXtraDB CRD we are going deploy to initialize from backup,

apiVersion: kubedb.com/v1alpha2
kind: PerconaXtraDB
metadata:
  name: restored-xtradb
  namespace: demo
spec:
  version: "5.7"
  replicas: 1
  authSecret:
    name: sample-xtradb-auth
  storageType: Durable
  storage:
    storageClassName: "standard"
    accessModes:
    - ReadWriteOnce
    resources:
      requests:
        storage: 1Gi
  init:
    waitForInitialRestore: true
  terminationPolicy: WipeOut

Let’s create the above database,

$ kubectl apply -f https://github.com/kubedb/docs/raw/v2021.03.17/docs/guides/percona-xtradb/backup/standalone/examples/restored-xtradb.yaml
perconaxtradb.kubedb.com/restored-xtradb created

If you check the database status, you will see it is stuck in Provisioning state.

$ kubectl get px -n demo restored-xtradb --watch
NAME              VERSION   STATUS         AGE
restored-xtradb   5.7       Provisioning   74s

Create RestoreSession

Now, we need to create a RestoreSession CRD pointing to the newly created restored database.

Using the following command, check that another AppBinding object has been created for the restored-xtradb object,

$ kubectl get appbindings -n demo restored-xtradb
NAME              TYPE                       VERSION   AGE
restored-xtradb   kubedb.com/perconaxtradb   5.7       4m6s

If you are not using KubeDB to deploy database, create the AppBinding manually.

Below is the contents of YAML file of the RestoreSession CRD that we are going to create to restore the backed up data into the newly created database provisioned by PerconaXtrDB CRD named restored-xtradb.

apiVersion: stash.appscode.com/v1beta1
kind: RestoreSession
metadata:
  name: restored-xtradb-restore
  namespace: demo
spec:
  repository:
    name: gcs-repo-sample-xtradb
  target:
    ref:
      apiVersion: appcatalog.appscode.com/v1alpha1
      kind: AppBinding
      name: restored-xtradb
  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 object for the restored-xtradb PerconaXtraDB object.
.spec.rules specifies that we are restoring data from the latest backup snapshot of the database.

Let’s create the RestoreSession CRD object we have shown above,

$ kubectl apply -f https://github.com/kubedb/docs/raw/v2021.03.17/docs/guides/percona-xtradb/backup/standalone/examples/restoresession.yaml
restoresession.stash.appscode.com/restored-xtradb-restore created

Once you have created the RestoreSession object, Stash will create a restore Job. We can watch the phase of the RestoreSession object to check whether the restore process has succeeded or not.

Run the following command to watch the phase of the RestoreSession object,

$ kubectl get restoresession -n demo restored-xtradb-restore --watch
NAME                      REPOSITORY               PHASE       AGE
restored-xtradb-restore   gcs-repo-sample-xtradb   Running     35s
restored-xtradb-restore   gcs-repo-sample-xtradb   Succeeded   44s

Here, 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 whether the desired data has restored successfully. We are going to connect to the database server and check whether the database and the table we created earlier in the original database have restored.

At first, check if the database has gone into Running state,

$ kubectl get px -n demo restored-xtradb --watch
NAME              VERSION   STATUS         AGE
restored-xtradb   5.7       Provisioning   10m
restored-xtradb   5.7       Running        13m

Now, find out the database Pod,

$ kubectl get pods -n demo --selector="app.kubernetes.io/instance=restored-xtradb" --watch
NAME                READY   STATUS    RESTARTS   AGE
restored-xtradb-0   1/1     Running   0          15m

And then copy the user name and password of the root user to access into mysql shell.

Notice: We used the same Secret for the restored-xtradb object. So, we will use the same commands as before.

$ kubectl get secret -n demo  sample-xtradb-auth -o jsonpath='{.data.username}'| base64 -d
root⏎

$ kubectl get secret -n demo  sample-xtradb-auth -o jsonpath='{.data.password}'| base64 -d
5qtWP192NLD-nwgd⏎

Now, let’s exec into the Pod to enter into mysql shell and check the database and the table we created before,

$ kubectl exec -it -n demo restored-xtradb-0 -- mysql --user=root --password=5qtWP192NLD-nwgd
mysql: [Warning] Using a password on the command line interface can be insecure.
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 103
Server version: 5.7.26-29 Percona Server (GPL), Release 29, Revision 11ad961

Copyright (c) 2009-2019 Percona LLC and/or its affiliates
Copyright (c) 2000, 2019, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> SHOW DATABASES;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| mysql              |
| performance_schema |
| playground         |
| sys                |
+--------------------+
5 rows in set (0.00 sec)

mysql> SHOW TABLES IN playground;
+----------------------+
| Tables_in_playground |
+----------------------+
| equipment            |
+----------------------+
1 row in set (0.00 sec)

mysql> SELECT * FROM playground.equipment;
+----+-------+-------+-------+
| id | type  | quant | color |
+----+-------+-------+-------+
|  1 | slide |     2 | blue  |
+----+-------+-------+-------+
1 row in set (0.00 sec)

mysql> exit
Bye

So, from the above output, we can see that the playground database and the equipment table we created before in the original database are restored successfully.

Cleanup

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

kubectl delete restoresession -n demo restored-xtradb-restore
kubectl delete px -n demo restored-xtradb
kubectl delete repository -n demo gcs-repo-sample-xtradb
kubectl delete backupconfiguration -n demo sample-xtradb-backup
kubectl delete px -n demo sample-xtradb

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