Demo Setting up the MySQL Database

In this lesson we deploy a MySQL database for the Block Buster app using Flux (GitRepository source) and the Kustomize controller. Starting with application version 7.7.0, highscore.php persists the high score into MySQL — the app connects to the database at mysql.database.svc.cluster.local. Example snippet from highscore.php showing the connection details:

<?php
$servername = "mysql.database.svc.cluster.local";
$username = "root";
$password = "mysql-password-0123456789";
$dbname = "bricks";

$conn = new mysqli($servername, $username, $password, $dbname); // Create connection
if ($conn->connect_error) { // Check connection
    die("Connection failed: " . $conn->connect_error);
}

We deploy the database infrastructure first so the application can connect as soon as the database becomes available. Why use Flux + Kustomize for the database?

GitOps: manifests are tracked in Git and applied declaratively.
Selective deploy: point Kustomize to only ./database so only DB manifests are applied from the infra branch.
Reconciliation and drift detection are handled automatically by Flux.

Relevant docs and references

Flux GitRepository / Kustomization: https://fluxcd.io
Kustomize: https://kubectl.docs.kubernetes.io/references/kustomize/
Sealed Secrets (example encryption): https://github.com/bitnami-labs/sealed-secrets
Kubernetes concepts: https://kubernetes.io/docs/concepts/

Repository branches and infra layout

Application code: 7-demo branch.
Infrastructure manifests (cluster-level): infrastructure branch (Sealed Secrets, cert-manager, database, ingress-nginx, etc.)

Listing of the repository root on the infrastructure branch:

root ~/bb-app-source  infrastructure [?]
➜ ll
total 32
drwxr-xr-x  7 batman root 4096 Apr  6 18:08 ./
drwxr-xr-x 10 batman batman 4096 Apr  6 17:47 ../
drwxr-xr-x  8 batman root 4096 Apr  6 18:08 .git/
drwxr-xr-x  2 root root 4096 Apr  6 18:08 bitnami-sealed-secrets/
-rw-r--r--  1 root root 1569 Apr  6 17:56 block-buster-helm-app-7.7.1.tgz
drwxr-xr-x  2 root root 4096 Apr  6 18:08 cert-manager/
drwxr-xr-x  2 root root 4096 Apr  6 18:08 database/
drwxr-xr-x  2 root root 4096 Apr  6 18:08 ingress-nginx/

Database manifests overview Inside the database/ directory you should find manifests for:

Resource	Purpose
Namespace	Isolates database resources
ConfigMap (`mysql-initdb-config`)	Initial SQL or initialization scripts
Deployment (MySQL)	Runs the MySQL container
Service (ClusterIP)	Internal access at `mysql.database.svc.cluster.local:3306`
PersistentVolume / PersistentVolumeClaim	Durable storage for MySQL data
Secret	Root password and other credentials (should be sealed/encrypted)

Example plain-text Secret currently in the repo (for demonstration only):

apiVersion: v1
kind: Secret
metadata:
  name: secret-mysql
  namespace: database
stringData:
  password: mysql-password-0123456789

Secrets in plain text in a Git repository are a security risk. We will later encrypt these (for example, with Sealed Secrets — see Introduction to Sealed Secrets in Kubernetes) before storing them in Git.

Using Flux to deploy only the database manifests We create a Flux GitRepository source that points to the infrastructure branch and a Kustomization that references only the ./database path. This ensures only the database resources are applied, avoiding cluster-wide changes from other infra manifests. Example GitRepository manifest (save this as a Flux Source in the flux-system namespace):

apiVersion: source.toolkit.fluxcd.io/v1beta2
kind: GitRepository
metadata:
  name: infra-source-git
  namespace: flux-system
spec:
  interval: 1m0s
  ref:
    branch: infrastructure
  url: https://github.com/sidd-harth-2/bb-app-source

Create this source with the flux CLI. Example:

flux create source git infra-source-git \
  --url https://github.com/sidd-harth-2/bb-app-source \
  --branch infrastructure \
  --timeout 10s \
  --export > infra-source-git.yml

Kustomization that targets only the database subdirectory:

apiVersion: kustomize.toolkit.fluxcd.io/v1beta2
kind: Kustomization
metadata:
  name: infra-database-kustomize-git-mysql
  namespace: flux-system
spec:
  interval: 1m40s
  path: ./database
  prune: true
  sourceRef:
    kind: GitRepository
    name: infra-source-git

The path: ./database ensures Flux/Kustomize applies manifests only from the database directory of the infrastructure branch. Create, reconcile, and verify After placing infra-source-git.yml and infra-database-kustomize-git-mysql.yml in your Flux cluster manifests repo (for example, block-buster/flux-clusters/dev-cluster) commit and push them. You can then reconcile manually to apply immediately. Example terminal sequence (switching to the Flux cluster repo and exporting the Git source):

root ~/bb-app-source  infrastructure [?]
➤➤ cd ../block-buster/flux-clusters/dev-cluster/

root ~/block-buster/flux-clusters/dev-cluster  ● main
➤➤ flux create source git infra-source-git \
  --url https://github.com/sidd-harth-2/bb-app-source \
  --branch infrastructure \
  --timeout 10s \
  --export > infra-source-git.yml

Once pushed and reconciled, a new database namespace should be created by Flux:

root ~/block-buster/flux-clusters/dev-cluster  ● main
➤➤ kubectl get ns
NAME                  STATUS   AGE
1-demo                Active   16h
2-demo                Active   16h
3-demo                Active   16h
4-demo                Active   131m
5-demo                Active   104m
6-demo                Active   49m
database              Active   19s
default               Active   17h
flux-system           Active   17h
kube-node-lease       Active   17h
kube-public           Active   17h
kube-system           Active   17h
minio-dev             Active   139m

Confirm Flux source and Kustomization status:

root ~/block-buster/flux-clusters/dev-cluster  ● main
➤➤ flux get sources git infra-source-git

NAME                 REVISION                                   SUSPENDED READY MESSAGE
infra-source-git     infrastructure@sha1:c94a687d              False     True   stored artifact for revision 'infrastructure@sha1:c94a687d'

root ~/block-buster/flux-clusters/dev-cluster  ● main
➤➤ flux get kustomizations infra-database-kustomize-git-mysql

NAME                                   REVISION                                   SUSPENDED READY MESSAGE
infra-database-kustomize-git-mysql     infrastructure@sha1:c94a687d              False     True   Applied revision: infrastructure@sha1:c94a687d

Check the database namespace resources When first applied the MySQL pod may be Pending while PVs are provisioned. Example:

root ~/block-buster/flux-clusters/dev-cluster  main
➤➤ kubectl -n database get all
NAME                                    READY   STATUS    RESTARTS   AGE
pod/mysql-7d89476576-m7z12              0/1     Pending   0          58s

NAME                    TYPE        CLUSTER-IP      EXTERNAL-IP   PORT(S)     AGE
service/mysql            ClusterIP   10.96.154.12    <none>        3306/TCP    58s

NAME                                READY   UP-TO-DATE   AVAILABLE   AGE
deployment.apps/mysql                0/1     1            0           58s

NAME                                        DESIRED   CURRENT   READY   AGE
replicaset.apps/mysql-7d89476576             1         1         0       58s

After volumes are bound and the container starts up, resources become Running / Available:

root ~/block-buster/flux-clusters/dev-cluster  main
➤➤ kubectl -n database get all,cm,secrets
NAME                            READY   STATUS    RESTARTS   AGE
pod/mysql-7d89476576-m7z12      1/1     Running   0          72s

NAME               TYPE        CLUSTER-IP     EXTERNAL-IP   PORT(S)      AGE
service/mysql      ClusterIP   10.96.154.12   <none>        3306/TCP     72s

NAME                      READY   UP-TO-DATE   AVAILABLE   AGE
deployment.apps/mysql     1/1     1            1           72s

NAME                                  DESIRED   CURRENT   READY   AGE
replicaset.apps/mysql-7d89476576      1         1         1       72s

NAME                              DATA   AGE
configmap/kube-root-ca.crt         1      73s
configmap/mysql-initdb-config      1      73s

NAME                    TYPE     DATA   AGE
secret/secret-mysql     Opaque   1      72s

At this point you should verify:

Deployment/Pod status: kubectl -n database get pods,deploy
Service: kubectl -n database get svc mysql (ClusterIP, port 3306)
PVC / PV is Bound if using dynamic storage: kubectl -n database get pvc
ConfigMap initialization scripts applied and Secret exists (but remember it’s currently plain text)

Helpful checks and troubleshooting

View pod logs: kubectl -n database logs deploy/mysql
Check PVC status: kubectl -n database get pvc
Describe pod for events and volume errors: kubectl -n database describe pod <pod-name>

Tip: If the MySQL pod stays Pending, check your storage class and PV provisioning. Use kubectl describe pod and kubectl get pvc -o wide to inspect volume binding and related events.

Next steps

Seal or encrypt Secrets (e.g., Sealed Secrets) and store the sealed manifest in Git rather than plain text.
Add application Flux sources and Kustomizations that deploy the Block Buster app images (from your OCI registry) against this cluster namespace so the app can connect to mysql.database.svc.cluster.local.
Monitor Flux reconciliation and application health:
- flux get kustomizations
- kubectl -n <app-namespace> get pods,svc

Quick checklist before deploying the app

Database namespace exists and is Active.
MySQL pod is Running and Deployment is Available.
Service mysql is a ClusterIP on port 3306.
PVC is Bound and data directory is writable.
Secrets are sealed/encrypted before committing to Git.

References

Flux: https://fluxcd.io
Kustomize: https://kubectl.docs.kubernetes.io/references/kustomize/
Sealed Secrets: https://github.com/bitnami-labs/sealed-secrets
Kubernetes docs: https://kubernetes.io/docs/
MySQL Docker image: https://hub.docker.com/_/mysql

GitOps Overview

Flux Overview

Source and Kustomize Controller

Helm Controller and OCI Registry

Image Automation Controller

Secret Management & Sign Verification

Notification Controller

Monitoring & User Interface

Demo Setting up the MySQL Database

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