Problem with HibernateJpaConfiguration after migrating from com.sun.xml.bind:jaxb-impl to org.glassfish.jaxb:jaxb-runtime

[rcsilva83]

What version of OpenRewrite are you using?

I am using

• Maven plugin v5.42.2
• rewrite-spring v5.21.0

How are you running OpenRewrite?

I am using the Maven plugin, and my project is a single module project.

<plugin>
        <groupId>org.openrewrite.maven</groupId>
        <artifactId>rewrite-maven-plugin</artifactId>
        <version>5.42.2</version>
        <configuration>
          <activeRecipes>
            <recipe>org.openrewrite.java.spring.boot3.UpgradeSpringBoot_3_3</recipe>
          </activeRecipes>
        </configuration>
        <dependencies>
          <dependency>
            <groupId>org.openrewrite.recipe</groupId>
            <artifactId>rewrite-spring</artifactId>
            <version>5.21.0</version>
          </dependency>
        </dependencies>
      </plugin>

What is the smallest, simplest way to reproduce the problem?

    <dependency>
      <groupId>com.sun.xml.bind</groupId>
      <artifactId>jaxb-impl</artifactId>
      <version>2.3.1</version>
    </dependency>

What did you expect to see?

No change.

What did you see instead?

    <dependency>
      <groupId>org.glassfish.jaxb</groupId>
      <artifactId>jaxb-runtime</artifactId>
    </dependency>

What is the full stack trace of any errors you encountered?

org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [org/springframework/boot/autoconfigure/orm/jpa/HibernateJpaConfiguration.class]: javax/xml/bind/annotation/XmlElement
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1806)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:600)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:522)
	at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:337)
	at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234)
	at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:335)
	at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:205)
	at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:954)
	at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:625)
	at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:146)
	at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:754)
	at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:456)
	at org.springframework.boot.SpringApplication.run(SpringApplication.java:335)
	at org.springframework.boot.SpringApplication.run(SpringApplication.java:1363)
	at org.springframework.boot.SpringApplication.run(SpringApplication.java:1352)
	at my.company.app.App.main(App.java:14)
Caused by: java.lang.NoClassDefFoundError: javax/xml/bind/annotation/XmlElement
	at com.fasterxml.jackson.module.jaxb.JaxbAnnotationIntrospector.<init>(JaxbAnnotationIntrospector.java:137)
	at com.fasterxml.jackson.module.jaxb.JaxbAnnotationIntrospector.<init>(JaxbAnnotationIntrospector.java:124)
	at com.fasterxml.jackson.module.jaxb.JaxbAnnotationModule.setupModule(JaxbAnnotationModule.java:98)
	at com.fasterxml.jackson.databind.ObjectMapper.registerModule(ObjectMapper.java:908)
	at com.fasterxml.jackson.databind.ObjectMapper.registerModules(ObjectMapper.java:1110)
	at com.fasterxml.jackson.databind.ObjectMapper.findAndRegisterModules(ObjectMapper.java:1194)
	at org.hibernate.type.format.jackson.JacksonJsonFormatMapper.<init>(JacksonJsonFormatMapper.java:27)
	at org.hibernate.type.format.jackson.JacksonIntegration.<clinit>(JacksonIntegration.java:18)
	at org.hibernate.boot.internal.SessionFactoryOptionsBuilder.lambda$determineJsonFormatMapper$7(SessionFactoryOptionsBuilder.java:833)
	at org.hibernate.boot.registry.selector.internal.StrategySelectorImpl.resolveStrategy(StrategySelectorImpl.java:220)
	at org.hibernate.boot.registry.selector.internal.StrategySelectorImpl.resolveDefaultableStrategy(StrategySelectorImpl.java:180)
	at org.hibernate.boot.internal.SessionFactoryOptionsBuilder.determineJsonFormatMapper(SessionFactoryOptionsBuilder.java:829)
	at org.hibernate.boot.internal.SessionFactoryOptionsBuilder.<init>(SessionFactoryOptionsBuilder.java:313)
	at org.hibernate.boot.internal.SessionFactoryBuilderImpl.<init>(SessionFactoryBuilderImpl.java:50)
	at org.hibernate.boot.internal.DefaultSessionFactoryBuilderService.createSessionFactoryBuilder(DefaultSessionFactoryBuilderService.java:26)
	at org.hibernate.boot.internal.MetadataImpl.getSessionFactoryBuilder(MetadataImpl.java:169)
	at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:1502)
	at org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider.createContainerEntityManagerFactory(SpringHibernateJpaPersistenceProvider.java:75)
	at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:390)
	at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:409)
	at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:396)
	at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.afterPropertiesSet(LocalContainerEntityManagerFactoryBean.java:366)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1853)
	at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1802)
	... 15 common frames omitted
Caused by: java.lang.ClassNotFoundException: javax.xml.bind.annotation.XmlElement
	at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641)
	at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
	at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:525)
	... 39 common frames omitted

Are you interested in contributing a fix to OpenRewrite?

Yes

[timtebeek]

Hi @rcsilva83 , welcome back! The change made here might be spread across multiple repositories: https://github.com/openrewrite/rewrite-hibernate https://github.com/openrewrite/rewrite-migrate-java https://github.com/openrewrite/rewrite-spring

We'd need to figure out if there's a missing parallel change to be made in rewrite-hibernate, or whether there's more to the one to one replacement that's done currently. Any help appreciated as I lack a bit of detail on which version of Hibernate you're using, as the HibernateJpaConfiguration class for v3.3.x itself does not refer to javax/xml/bind/annotation/XmlElement, but does refer to javax.sql.DataSource also referenced in

• https://github.com/spring-projects/spring-boot/issues/42178

[rcsilva83]

Hi, @timtebeek !

I tracked this problem and it isn't related to HibernateJpaConfiguration but to Jackson. We use some Jackson annotations on some @Entity classes, so the error occurred on 'entityManagerFactory' bean initialization. We use jackson-module-jaxb-annotations package that depends on javax.xml.bind classes... So we had the javax.xml.bind:jaxb-api dependency declared, as we are using Java 11/17.

The problem is that, after running the UpgradeSpringBoot_3_3 recipe, javax.xml.bind:jaxb-api as replaced by jakarta.xml.bind:jakarta.xml.bind-api which is managed para Spring Boot to version 4.0.2. This version doesn't provide javax.xml.bind classes.

I found some recipes that do this change:

• org.openrewrite.java.migrate.javax.AddJaxbDependencies which is called by org.openrewrite.java.migrate.Java8toJava11 called by org.openrewrite.java.migrate.UpgradeToJava17 called by org.openrewrite.java.spring.boot3.UpgradeSpringBoot_3_0
• org.openrewrite.java.migrate.jakarta.JavaxXmlBindMigrationToJakartaXmlBind which is called by org.openrewrite.java.migrate.jakarta.JavaxMigrationToJakarta called by org.openrewrite.java.spring.boot3.UpgradeSpringBoot_3_0

Given that, is there any way to tell OpenRewrite not to run that recipes or to ignore that dependency and leave it as it is?

[timtebeek]

Thanks for diving in! The most convenient way to customizing an existing composite recipe is through the recipe builder at https://app.moderne.io/. We're working on getting that integrated into docs.openrewrite.org now that it's using Docusaurus, but that might take a while longer.

That said; looking at the changes I wonder if instead of removing recipes we should be adding a migration step instead:

• https://github.com/FasterXML/jackson-module-jaxb-annotations
• https://github.com/FasterXML/jackson-modules-base/tree/2.19/jakarta-xmlbind

With a change dependency to go from jackson-module-jaxb-annotations to jackson-module-jakarta-xmlbind-annotations and a change type to go from JaxbAnnotationModule to JakartaXmlBindAnnotationModule. What are your thoughts on adding those?

[rcsilva83]

Actually, these dependencies are being pulled by external packages we depend on and they aren't update yet, unfortunately... I think, for my use case, it is better to make a new recipe using UpgradeSpringBoot_3_3 and then add javax.xml.bind:jaxb-api dependency. This way, we wouldn't need to maintain a custom UpgradeSpringBoot_3_3 recipe and having to manually update it, which seams a lot of work...

On the long term, don't you think this kind of change is a bit intrusive to make? I think situations like this, where the developer don't have full control on the migration to jakarta packages, may be quite common. What do you think?

In this case, I see 2 solutions:

1. modify org.openrewrite.java.migrate.javax.AddJaxbDependencies and org.openrewrite.java.migrate.jakarta.JavaxXmlBindMigrationToJakartaXmlBind to, instead of changing the dependencies, just add jakarta.xml.bind:jakarta.xml.bind-api;
2. Create a way to bypass certain changes on OpenRewrite, with 2 options:
   1. define a <inactiveRecipes> tag
   2. adding an comment like <!-- OpenRewrite OFF --> around the dependency we don't want OpenRewrite change;