Issue with DB initialization with Spring Batch and Flyway in Spring Boot 2.5.3

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After upgrading from Spring Boot 2.5.2 to 2.5.3 we get following error:

org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'flywayInitializer' defined in class path resource [org/springframework/boot/autoconfigure/flyway/FlywayAutoConfiguration$FlywayConfiguration.class]: Invocation of init method failed; nested exception is org.flywaydb.core.api.FlywayException: Found non-empty schema(s) "PUBLIC" but no schema history table. Use baseline() or set baselineOnMigrate to true to initialize the schema history table.
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1786) ~[spring-beans-5.3.9.jar:5.3.9]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:602) ~[spring-beans-5.3.9.jar:5.3.9]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:524) ~[spring-beans-5.3.9.jar:5.3.9]
    at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) ~[spring-beans-5.3.9.jar:5.3.9]
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[spring-beans-5.3.9.jar:5.3.9]
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) ~[spring-beans-5.3.9.jar:5.3.9]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) ~[spring-beans-5.3.9.jar:5.3.9]
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:322) ~[spring-beans-5.3.9.jar:5.3.9]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) ~[spring-beans-5.3.9.jar:5.3.9]
    at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1154) ~[spring-context-5.3.9.jar:5.3.9]
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:908) ~[spring-context-5.3.9.jar:5.3.9]
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:583) ~[spring-context-5.3.9.jar:5.3.9]
    at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:145) ~[spring-boot-2.5.3.jar:2.5.3]
    at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:754) ~[spring-boot-2.5.3.jar:2.5.3]
    at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:434) ~[spring-boot-2.5.3.jar:2.5.3]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:338) ~[spring-boot-2.5.3.jar:2.5.3]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1343) ~[spring-boot-2.5.3.jar:2.5.3]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1332) ~[spring-boot-2.5.3.jar:2.5.3]
    at com.example.demo.DemoApplication.main(DemoApplication.java:10) ~[classes/:na]
Caused by: org.flywaydb.core.api.FlywayException: Found non-empty schema(s) "PUBLIC" but no schema history table. Use baseline() or set baselineOnMigrate to true to initialize the schema history table.
    at org.flywaydb.core.Flyway$1.execute(Flyway.java:196) ~[flyway-core-7.7.3.jar:na]
    at org.flywaydb.core.Flyway$1.execute(Flyway.java:165) ~[flyway-core-7.7.3.jar:na]
    at org.flywaydb.core.Flyway.execute(Flyway.java:572) ~[flyway-core-7.7.3.jar:na]
    at org.flywaydb.core.Flyway.migrate(Flyway.java:165) ~[flyway-core-7.7.3.jar:na]
    at org.springframework.boot.autoconfigure.flyway.FlywayMigrationInitializer.afterPropertiesSet(FlywayMigrationInitializer.java:66) ~[spring-boot-autoconfigure-2.5.3.jar:2.5.3]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1845) ~[spring-beans-5.3.9.jar:5.3.9]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1782) ~[spring-beans-5.3.9.jar:5.3.9]
    ... 18 common frames omitted

We tried to reproduce with a fresh project from https://start.spring.io. We have the following two classes (Main Class and configuration class for Spring Batch) and a db initialization script in the resource folder (db/migration) DemoApplication.java

@SpringBootApplication
public class DemoApplication {

    public static void main(String[] args) {
        SpringApplication.run(DemoApplication.class, args);
    }

}

BatchConfig.java

@Configuration
@EnableBatchProcessing
public class BatchConfig {
}

pom.xml

<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 https://maven.apache.org/xsd/maven-4.0.0.xsd">
    <modelVersion>4.0.0</modelVersion>
    <parent>
        <groupId>org.springframework.boot</groupId>
        <artifactId>spring-boot-starter-parent</artifactId>
        <version>2.5.3</version>
        <relativePath/> <!-- lookup parent from repository -->
    </parent>
    <groupId>com.example</groupId>
    <artifactId>demo</artifactId>
    <version>0.0.1-SNAPSHOT</version>
    <name>demo</name>
    <description>Demo project for Spring Boot</description>
    <properties>
        <java.version>11</java.version>
    </properties>
    <dependencies>
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-batch</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-data-jdbc</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-data-jpa</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-security</artifactId>
        </dependency>
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-web</artifactId>
        </dependency>
        <dependency>
            <groupId>org.flywaydb</groupId>
            <artifactId>flyway-core</artifactId>
        </dependency>
        <dependency>
            <groupId>com.h2database</groupId>
            <artifactId>h2</artifactId>
            <scope>runtime</scope>
        </dependency>
        <dependency>
            <groupId>org.springframework.boot</groupId>
            <artifactId>spring-boot-starter-test</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.springframework.batch</groupId>
            <artifactId>spring-batch-test</artifactId>
            <scope>test</scope>
        </dependency>
        <dependency>
            <groupId>org.springframework.security</groupId>
            <artifactId>spring-security-test</artifactId>
            <scope>test</scope>
        </dependency>
    </dependencies>
    <build>
        <plugins>
            <plugin>
                <groupId>org.springframework.boot</groupId>
                <artifactId>spring-boot-maven-plugin</artifactId>
            </plugin>
        </plugins>
    </build>
</project>

V1_100_test.sql in resources/db/migration

create table test;

With this setup, we face the described flyway exception.

When we downgrade to 2.5.2 or set the property spring.batch.jdbc.initialize-schema=never, we get rid of the error message.

Are we missing something to use Spring Batch DB initialization or is there a version mismatch in Spring Boot ?

spring-batch flyway spring-boot
1 Answers

For exactly this sort of reason, splitting the initialization of your database between Flyway and Spring Batch's scripts is not recommended:

If you are using a Higher-level Database Migration Tool, like Flyway or Liquibase, you should use them alone to create and initialize the schema.

There has never been a guarantee that Flyway will run first. In the case of your application it was running first by chance and something has changed in Spring Boot 2.5.3 that means that's no longer the case.

Rather than using multiple different database initializers, I would recommend setting spring.batch.jdbc.initialize-schema=never and adding a Flyway migration script to initialize Spring Batch's schema instead.

Alternatively, you can set spring.flyway.baseline-on-migrate=true. This will cause Flyway to call baseline() automatically when it detects the non-empty schema.

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