Which of Flyway or JPA should be responsible of generating your db structure?

Which of Flyway or JPA should be responsible of generating your db structure?

Posted by Xavier Bouclet on October 13, 2021 · 4 mins read

Which of Flyway or JPA should be responsible of generating your db structure?

1. What is Flyway ?

Flyway is an open-source database migration tool. It helps to keep track of all the changes done on the DB. It’s done with the help of the table "flyway_schema_history".

Flyway Schema History

In a Java project, Flyway applies SQL file or Java Migration code to the database (through command-line, Maven plugin,…​).

2. How Flyway is intended to be used with Spring Boot ?

In Spring Boot everything being configured by default, the Spring Boot developers have chosen to execute Flyway and then trigger the Entity Manager. But some people have decided to delegate that to JPA and most of them visited at some point that StackOverflow page.

Most of this post comes from the content on that page and the few hours I needed to make it work on our project.

3. What happens if people wants to let JPA create the tables structure instead of Flyway ?

Prior 2.5.X

As someone on the stackoverflow page wrote, we could prior to 2.3 trigger Flyway after JPA by adding this property to our application.properties file.


That property prevent Flyway to be autoconfigured by Spring Boot.

And to use Flyway anyway and trigger it after JPA you need to add this following @Configuration file.

public class MigrationConfiguration {

     * Override default flyway initializer to do nothing
    FlywayMigrationInitializer flywayInitializer(Flyway flyway) {
        return new FlywayMigrationInitializer(flyway, (f) ->{} );

     * Create a second flyway initializer to run after jpa has created the schema
    FlywayMigrationInitializer delayedFlywayInitializer(Flyway flyway) {
        return new FlywayMigrationInitializer(flyway);

The @DependsOn annotation is what trigger the Flyway migration after the "EntityManagerFactory" has been created by Spring Boot.

Unfortunately for us that way doesn’t work anymore with Spring boot 2.5.X

After 2.5.X

We need to remove the Flyway autoconfigure with another way than the one we used prior. It’s done with a "BeanFactoryPostProcessor". We need to exclude the DependsOn from 2 classes :

  • DataSourceScriptDatabaseInitializer

  • EntityManagerFactory

Let’s call our bean "FlywayDeferrerPostProcessor".

public class FlywayDeferrerPostProcessor implements BeanFactoryPostProcessor {

    public void postProcessBeanFactory(ConfigurableListableBeanFactory beanFactory) throws BeansException {
        excludeDependsOnFlywayFromBean(beanFactory, DataSourceScriptDatabaseInitializer.class);
        excludeDependsOnFlywayFromBean(beanFactory, EntityManagerFactory.class);

    private void excludeDependsOnFlywayFromBean(ConfigurableListableBeanFactory beanFactory, Class<?> beanClass) {
            .filter(it -> it.getDependsOn() != null && it.getDependsOn().length > 0)
            .forEach(it -> it.setDependsOn(Stream.of(it.getDependsOn()).filter(name -> !name.equals("flyway")).toArray(String[]::new)));

4. Conclusion

When we migrated from Spring Boot 2.3.X to 2.5.X, It took me a few hours to make Flyway work properly after JPA. It worked with 2.3 but Spring Boot changed something and it broke. And that’s normal because that’s not the way Spring Boot is supposed to work. So we shouldn’t fight against the Spring Boot way of using Flyway. Now that our migration works we are gonna move away from JPA building the db structure and go back to use plain old Flyway. And you should to.