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Initialize PerconaXtraDB using Script

This tutorial will show you how to use KubeDB to initialize a PerconaXtraDB database with *.sql, *.sh and/or *.sql.gz script. In this tutorial we will use .sql script stored in GitHub repository kubedb/percona-xtradb-init-scripts.

Note: The yaml files that are used in this tutorial are stored in docs/examples folder in GitHub repository kubedb/docs.

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 kind.
Now, install KubeDB CLI on your workstation and KubeDB operator in your cluster following the steps here.
To keep things isolated, this tutorial uses a separate namespace called demo throughout this tutorial
```
$ kubectl create ns demo
namespace/demo created
```

Prepare Initialization Scripts

PerconaXtraDB supports initialization with .sh, .sql and .sql.gz files. In this tutorial, we will use init.sql script from percona-xtradb-init-scripts git repository to create a TABLE kubedb_table in the mysql database.

We will use a ConfigMap as script source. You can use any Kubernetes supported volume as script source.

At first, we will create a ConfigMap from init.sql file. Then, we will provide this ConfigMap as script source in .spec.init.scriptSource of PerconaXtraDB object spec.

Let’s create a ConfigMap with initialization script,

$ kubectl create configmap -n demo px-init-script \
--from-literal=init.sql="$(curl -fsSL https://github.com/kubedb/percona-xtradb-init-scripts/raw/master/init.sql)"
configmap/px-init-script created

Create a PerconaXtraDB database with Init-Script

Below is the PerconaXtraDB object created in this tutorial.

apiVersion: kubedb.com/v1alpha2
kind: PerconaXtraDB
metadata:
  name: px-init-script
  namespace: demo
spec:
  version: "5.7"
  replicas: 1
  storageType: Durable
  storage:
    storageClassName: "standard"
    accessModes:
    - ReadWriteOnce
    resources:
      requests:
        storage: 50Mi
  init:
    scriptSource:
      configMap:
        name: px-init-script
  terminationPolicy: DoNotTerminate

$ kubectl create -f https://github.com/kubedb/docs/raw/v2020.10.27-rc.1/docs/examples/percona-xtradb/px-init-script.yaml
perconaxtradb.kubedb.com/px-init-script created

Here,

.spec.init.scriptSource specifies a script source used to initialize the database before database server starts. The scripts will be executed alphabetically. In this tutorial, a sample .sql script from the git repository https://github.com/kubedb/percona-xtradb-init-scripts.git is used to create a test database. You can use other volume sources instead of ConfigMap. The *.sql, *sql.gz and/or *.sh scripts that are stored inside the directory /docker-entrypoint-initdb.d will be executed alphabetically. The scripts inside child folders will be skipped.

KubeDB operator watches for PerconaXtraDB objects using Kubernetes API. When a PerconaXtraDB object is created, KubeDB operator will create a new StatefulSet and a Service with the matching PerconaXtraDB object name. KubeDB operator will also create a governing service for StatefulSets with the name ``-gvr`, if one is not already present.

$ kubectl dba describe px -n demo px-init-script
Name:         px-init-script
Namespace:    demo
Labels:       <none>
Annotations:  kubectl.kubernetes.io/last-applied-configuration:
                {"apiVersion":"kubedb.com/v1alpha2","kind":"PerconaXtraDB","metadata":{"annotations":{},"name":"px-init-script","namespace":"demo"},"spec"...
API Version:  kubedb.com/v1alpha2
Kind:         PerconaXtraDB
Metadata:
  Creation Timestamp:  2020-01-09T13:45:43Z
  Finalizers:
    kubedb.com
  Generation:        2
  Resource Version:  64559
  Self Link:         /apis/kubedb.com/v1alpha2/namespaces/demo/perconaxtradbs/px-init-script
  UID:               d7ad081e-8b2d-41d1-aae3-6141a01a66f1
Spec:
  Database Secret:
    Secret Name:  px-init-script-auth
  Init:
    Script Source:
      Config Map:
        Name:  px-init-script
  Pod Template:
    Controller:
    Metadata:
    Spec:
      Readiness Probe:
        Exec:
          Command:
            bash
            -c
            export MYSQL_PWD="${MYSQL_ROOT_PASSWORD}"
ping_resp=$(mysqladmin -uroot ping)
if [[ "$ping_resp" != "mysqld is alive" ]]; then
    echo "[ERROR] server is not ready. PING_RESPONSE: $ping_resp"
    exit 1
fi

        Initial Delay Seconds:  30
        Period Seconds:         10
      Resources:
  Replicas:  1
  Service Template:
    Metadata:
    Spec:
  Storage:
    Access Modes:
      ReadWriteOnce
    Resources:
      Requests:
        Storage:         50Mi
    Storage Class Name:  standard
  Storage Type:          Durable
  Termination Policy:    DoNotTerminate
  Update Strategy:
    Type:   RollingUpdate
  Version:  5.7
Status:
  Observed Generation:  2
  Phase:                Running
Events:
  Type    Reason      Age    From                    Message
  ----    ------      ----   ----                    -------
  Normal  Successful  4m50s  PerconaXtraDB operator  Successfully created Service
  Normal  Successful  4m16s  PerconaXtraDB operator  Successfully created StatefulSet demo/px-init-script
  Normal  Successful  4m16s  PerconaXtraDB operator  Successfully created PerconaXtraDB
  Normal  Successful  4m16s  PerconaXtraDB operator  Successfully created appbinding
  Normal  Successful  4m16s  PerconaXtraDB operator  Successfully patched StatefulSet demo/px-init-script
  Normal  Successful  4m16s  PerconaXtraDB operator  Successfully patched PerconaXtraDB

$ kubectl get statefulset -n demo
NAME             READY   AGE
px-init-script   1/1     5m28s

$ kubectl get pvc -n demo
NAME                    STATUS   VOLUME                                     CAPACITY   ACCESS MODES   STORAGECLASS   AGE
data-px-init-script-0   Bound    pvc-5188bbf9-6a71-4f00-a27c-d9590d7c71f4   50Mi       RWO            standard       19m

$ kubectl get pv -n demo
NAME                                       CAPACITY   ACCESS MODES   RECLAIM POLICY   STATUS   CLAIM                              STORAGECLASS   REASON   AGE
pvc-5188bbf9-6a71-4f00-a27c-d9590d7c71f4   50Mi       RWO            Delete           Bound    demo/data-px-init-script-0         standard                19m

$ kubectl get service -n demo
NAME                 TYPE        CLUSTER-IP      EXTERNAL-IP   PORT(S)    AGE
px-init-script       ClusterIP   10.97.113.212   <none>        3306/TCP   6m47s
px-init-script-gvr   ClusterIP   None            <none>        3306/TCP   6m47s

KubeDB operator sets the .status.phase to Running once the database is successfully created. Run the following command to see the modified PerconaXtraDB object:

$ kubectl get px -n demo px-init-script -o yaml

Output:

apiVersion: kubedb.com/v1alpha2
kind: PerconaXtraDB
metadata:
  annotations:
    kubectl.kubernetes.io/last-applied-configuration: |
      {"apiVersion":"kubedb.com/v1alpha2","kind":"PerconaXtraDB","metadata":{"annotations":{},"name":"px-init-script","namespace":"demo"},"spec":{"init":{"scriptSource":{"configMap":{"name":"px-init-script"}}},"replicas":1,"storage":{"accessModes":["ReadWriteOnce"],"resources":{"requests":{"storage":"50Mi"}},"storageClassName":"standard"},"storageType":"Durable","terminationPolicy":"DoNotTerminate","updateStrategy":{"type":"RollingUpdate"},"version":"5.7"}}      
  creationTimestamp: "2020-01-09T13:45:43Z"
  finalizers:
  - kubedb.com
  generation: 2
  name: px-init-script
  namespace: demo
  resourceVersion: "64559"
  selfLink: /apis/kubedb.com/v1alpha2/namespaces/demo/perconaxtradbs/px-init-script
  uid: d7ad081e-8b2d-41d1-aae3-6141a01a66f1
spec:
  authSecret:
    name: px-init-script-auth
  init:
    scriptSource:
      configMap:
        name: px-init-script
  podTemplate:
    controller: {}
    metadata: {}
    spec:
      readinessProbe:
        exec:
          command:
          - bash
          - -c
          - |
            export MYSQL_PWD="${MYSQL_ROOT_PASSWORD}"
            ping_resp=$(mysqladmin -uroot ping)
            if [[ "$ping_resp" != "mysqld is alive" ]]; then
                echo "[ERROR] server is not ready. PING_RESPONSE: $ping_resp"
                exit 1
            fi            
        initialDelaySeconds: 30
        periodSeconds: 10
      resources: {}
  replicas: 1
  serviceTemplate:
    metadata: {}
    spec: {}
  storage:
    accessModes:
    - ReadWriteOnce
    resources:
      requests:
        storage: 50Mi
    storageClassName: standard
  storageType: Durable
  terminationPolicy: DoNotTerminate
  version: "5.7"
status:
  observedGeneration: 2
  phase: Running

Connect with PerconaXtraDB database

KubeDB operator has created a new Secret called px-init-script-auth (format: {percona-xtradb-object-name}-auth) for storing the password for mysql superuser. This secret contains a username key which contains the “username” for mysql superuser and a password key which contains the “password” for the superuser.

If you want to use an existing secret please specify that when creating the PerconaXtraDB object using .spec.authSecret.name. While creating this secret manually, make sure the secret contains these two keys (username and password) in .data section and also make sure of using root as value of username key. For more details see here.

Now, you can connect to this database using the database pod IP and and root user password.

$ kubectl get pods px-init-script-0 -n demo -o yaml | grep podIP
  podIP: 10.244.2.52

$ kubectl get secrets -n demo px-init-script-auth -o jsonpath='{.data.username}' | base64 -d
root

$ kubectl get secrets -n demo px-init-script-auth -o jsonpath='{.data.password}' | base64 -d
B0BMhl1ECz1C0uIN

To connect you just need to specify the host name for the database we created (either PodIP or the fully-qualified-domain-name for that Pod using the governing service named -gvr or the fully-qualified-domain-name for the database Service with matching name of PerconaXtraDB object) by –host flag.

Do not worry about the warning messages in the following output. Those are coming for providing a password on the command line

# connect to the server
$ kubectl exec -it -n demo px-init-script-0 -- mysql -u root --password=B0BMhl1ECz1C0uIN --host=px-init-script.demo.svc -e "select 1;"
mysql: [Warning] Using a password on the command line interface can be insecure.
+---+
| 1 |
+---+
| 1 |
+---+

# read
$ kubectl exec -it -n demo px-init-script-0 -- mysql -u root --password=B0BMhl1ECz1C0uIN --host=px-init-script.demo.svc -e "SHOW databases;"
mysql: [Warning] Using a password on the command line interface can be insecure.
+--------------------+
| Database           |
+--------------------+
| information_schema |
| mysql              |
| performance_schema |
| sys                |
+--------------------+

$ kubectl exec -it -n demo px-init-script-0 -- mysql -u root --password=B0BMhl1ECz1C0uIN --host=px-init-script.demo.svc -e "SHOW tables IN mysql;"
mysql: [Warning] Using a password on the command line interface can be insecure.
+---------------------------+
| Tables_in_mysql           |
+---------------------------+
| ...                       |
| kubedb_table              |
| ...                       |
+---------------------------+

$ kubectl exec -it -n demo px-init-script-0 -- mysql -u root --password=B0BMhl1ECz1C0uIN --host=px-init-script.demo.svc -e "SELECT * FROM mysql.kubedb_table;"
mysql: [Warning] Using a password on the command line interface can be insecure.
+----+-------+
| id | name  |
+----+-------+
|  1 | name1 |
|  2 | name2 |
|  3 | name3 |
+----+-------+

As you can see here, the initial script has successfully created a table named kubedb_table in mysql database and inserted three rows of data into that table successfully.

Cleaning up

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

kubectl patch -n demo px/px-init-script -p '{"spec":{"terminationPolicy":"WipeOut"}}' --type="merge"
kubectl delete -n demo px/px-init-script

kubectl delete ns demo

Next Steps

Monitor your PerconaXtraDB database with KubeDB using out-of-the-box Prometheus operator.
Monitor your PerconaXtraDB database with KubeDB using out-of-the-box builtin-Prometheus.
Use private Docker registry to deploy PerconaXtraDB with KubeDB.
How to use custom configuration.
How to use custom rbac resource for PerconaXtraDB.
Use Stash to Backup PerconaXtraDB.
Detail concepts of PerconaXtraDB object.
Detail concepts of PerconaXtraDBVersion object.
Want to hack on KubeDB? Check our contribution guidelines.

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