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Native Image Fails w/ Multiple DataSources #33656

Closed matthenry87 closed 1 year ago

matthenry87 commented 1 year ago

Trying to do all of the groundwork for our teams to start using native images. We use multiple data sources in over half of our applications.

Example project: https://github.com/matthenry87/native-image-multiple-datasource-testing

Spring Boot 3.0.1

GraalVM 22.3.0 Java 17 CE Java version info: '17.0.5+8-jvmci-22.3-b08' C compiler: gcc (linux, x86_64, 9.4.0) Garbage collector: Serial GC

Using GraalVM native-image directly via mvn native:compile -Pnative -DskipTests

Error:

  .   ____          _            __ _ _
 /\\ / ___'_ __ _ _(_)_ __  __ _ \ \ \ \
( ( )\___ | '_ | '_| | '_ \/ _` | \ \ \ \
 \\/  ___)| |_)| | | | | || (_| |  ) ) ) )
  '  |____| .__|_| |_|_| |_\__, | / / / /
 =========|_|==============|___/=/_/_/_/
 :: Spring Boot ::                (v3.0.1)

2022-12-29T19:13:40.616-07:00  INFO 30729 --- [           main] o.m.nativetesting.api.ApiApplication     : Starting AOT-processed ApiApplication using Java 17.0.5 with PID 30729 (/mnt/c/workspace/native-image-multimodule-testing/api/target/api started by matt in /mnt/c/workspace/native-image-multimodule-testing)
2022-12-29T19:13:40.617-07:00  INFO 30729 --- [           main] o.m.nativetesting.api.ApiApplication     : No active profile set, falling back to 1 default profile: "default"
2022-12-29T19:13:40.631-07:00  WARN 30729 --- [           main] o.s.c.support.GenericApplicationContext  : Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'db1Service': Unsatisfied dependency expressed through constructor parameter 0: Error creating bean with name 'fooEntityRepository': Unexpected exception during bean creation
2022-12-29T19:13:40.633-07:00 ERROR 30729 --- [           main] o.s.b.d.LoggingFailureAnalysisReporter   :

***************************
APPLICATION FAILED TO START
***************************

Description:

Parameter 0 of constructor in org.matthenry87.nativetesting.persistence.db1.Db1Service required a single bean, but 2 were found:
        - db1EntityManagerFactory: defined by method 'db1EntityManagerFactory' in null
        - db2EntityManagerFactory: defined by method 'db2EntityManagerFactory' in null

Action:

Consider marking one of the beans as @Primary, updating the consumer to accept multiple beans, or using @Qualifier to identify the bean that should be consumed

Funny thing, is that the Db1Service injects a single repository class, not an EntityManager.

clembo590 commented 1 year ago

Hello. I confirm that I also have issue with setting up a native spring boot applications with 2 databases.... I created a repo as usual to reproduce the issue.

git clone https://github.com/clembo590/issues.git --branch spring-native

my environement:

openjdk version "17.0.5" 2022-10-18
OpenJDK Runtime Environment GraalVM CE 22.3.0 (build 17.0.5+8-jvmci-22.3-b08)
OpenJDK 64-Bit Server VM GraalVM CE 22.3.0 (build 17.0.5+8-jvmci-22.3-b08, mixed mode, sharing)

Note: I have used the native-agent to create meta files.

mvn clean -P native native:compile success Then java -DspringAot=true -jar target/demo-0.0.1-SNAPSHOT.jar WORKS Then target/demo --> fails with following logs

org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'application': Unsatisfied dependency expressed through field 'productRepository': Error creating bean with name 'productRepository': Not a managed type: class com.baeldung.multipledb.model.product.Product
        at org.springframework.beans.factory.aot.AutowiredFieldValueResolver.resolveValue(AutowiredFieldValueResolver.java:195) ~[na:na]
        at org.springframework.beans.factory.aot.AutowiredFieldValueResolver.resolveAndSet(AutowiredFieldValueResolver.java:167) ~[na:na]
        at com.baeldung.Application__Autowiring.apply(Application__Autowiring.java:14) ~[na:na]
        at org.springframework.beans.factory.support.InstanceSupplier$1.get(InstanceSupplier.java:82) ~[na:na]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.obtainInstanceFromSupplier(AbstractAutowireCapableBeanFactory.java:1225) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.obtainFromSupplier(AbstractAutowireCapableBeanFactory.java:1210) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1157) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:561) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:521) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:326) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:324) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:961) ~[demo:6.0.3]
        at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:915) ~[demo:6.0.3]
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:584) ~[demo:6.0.3]
        at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:146) ~[demo:3.0.1]
        at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:730) ~[demo:3.0.1]
        at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:432) ~[demo:3.0.1]
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:308) ~[demo:3.0.1]
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1302) ~[demo:3.0.1]
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1291) ~[demo:3.0.1]
        at com.baeldung.Application.main(Application.java:24) ~[demo:na]
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'productRepository': Not a managed type: class com.baeldung.multipledb.model.product.Product
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1751) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:599) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:521) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:326) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:324) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200) ~[demo:6.0.3]
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:254) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1405) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1325) ~[demo:6.0.3]
        at org.springframework.beans.factory.aot.AutowiredFieldValueResolver.resolveValue(AutowiredFieldValueResolver.java:189) ~[na:na]
        ... 22 common frames omitted
Caused by: java.lang.IllegalArgumentException: Not a managed type: class com.baeldung.multipledb.model.product.Product
        at org.hibernate.metamodel.model.domain.internal.JpaMetamodelImpl.managedType(JpaMetamodelImpl.java:181) ~[na:na]
        at org.hibernate.metamodel.model.domain.internal.MappingMetamodelImpl.managedType(MappingMetamodelImpl.java:496) ~[na:na]
        at org.hibernate.metamodel.model.domain.internal.MappingMetamodelImpl.managedType(MappingMetamodelImpl.java:99) ~[na:na]
        at org.springframework.data.jpa.repository.support.JpaMetamodelEntityInformation.<init>(JpaMetamodelEntityInformation.java:77) ~[demo:na]
        at org.springframework.data.jpa.repository.support.JpaEntityInformationSupport.getEntityInformation(JpaEntityInformationSupport.java:69) ~[demo:na]
        at org.springframework.data.jpa.repository.support.JpaRepositoryFactory.getEntityInformation(JpaRepositoryFactory.java:246) ~[demo:na]
        at org.springframework.data.jpa.repository.support.JpaRepositoryFactory.getTargetRepository(JpaRepositoryFactory.java:211) ~[demo:na]
        at org.springframework.data.jpa.repository.support.JpaRepositoryFactory.getTargetRepository(JpaRepositoryFactory.java:194) ~[demo:na]
        at org.springframework.data.jpa.repository.support.JpaRepositoryFactory.getTargetRepository(JpaRepositoryFactory.java:81) ~[demo:na]
        at org.springframework.data.repository.core.support.RepositoryFactorySupport.getRepository(RepositoryFactorySupport.java:317) ~[demo:3.0.0]
        at org.springframework.data.repository.core.support.RepositoryFactoryBeanSupport.lambda$afterPropertiesSet$5(RepositoryFactoryBeanSupport.java:279) ~[demo:3.0.0]
        at org.springframework.data.util.Lazy.getNullable(Lazy.java:229) ~[demo:3.0.0]
        at org.springframework.data.util.Lazy.get(Lazy.java:113) ~[demo:3.0.0]
        at org.springframework.data.repository.core.support.RepositoryFactoryBeanSupport.afterPropertiesSet(RepositoryFactoryBeanSupport.java:285) ~[demo:3.0.0]
        at org.springframework.data.jpa.repository.support.JpaRepositoryFactoryBean.afterPropertiesSet(JpaRepositoryFactoryBean.java:132) ~[demo:na]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1797) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1747) ~[demo:6.0.3]
        ... 32 common frames omitted

@matthenry87 I tested and if you add @Primary like this and multiple times in the file it will work "one step further" but will still fail later with a Caused by: java.lang.NoSuchMethodException: com.zaxxer.hikari.HikariDataSource.<init>() (I went down this path already and that is when I decided to use the agent, then it solved that issue... but not the one that I posted above)

matthenry87 commented 1 year ago

Hello. I confirm that I also have issue with setting up a native spring boot applications with 2 databases.... I created a repo as usual to reproduce the issue.

git clone https://github.com/clembo590/issues.git --branch spring-native

my environement:

openjdk version "17.0.5" 2022-10-18
OpenJDK Runtime Environment GraalVM CE 22.3.0 (build 17.0.5+8-jvmci-22.3-b08)
OpenJDK 64-Bit Server VM GraalVM CE 22.3.0 (build 17.0.5+8-jvmci-22.3-b08, mixed mode, sharing)

Note: I have used the native-agent to create meta files.

mvn clean -P native native:compile success Then java -DspringAot=true -jar target/demo-0.0.1-SNAPSHOT.jar WORKS Then target/demo --> fails with following logs

org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'application': Unsatisfied dependency expressed through field 'productRepository': Error creating bean with name 'productRepository': Not a managed type: class com.baeldung.multipledb.model.product.Product
        at org.springframework.beans.factory.aot.AutowiredFieldValueResolver.resolveValue(AutowiredFieldValueResolver.java:195) ~[na:na]
        at org.springframework.beans.factory.aot.AutowiredFieldValueResolver.resolveAndSet(AutowiredFieldValueResolver.java:167) ~[na:na]
        at com.baeldung.Application__Autowiring.apply(Application__Autowiring.java:14) ~[na:na]
        at org.springframework.beans.factory.support.InstanceSupplier$1.get(InstanceSupplier.java:82) ~[na:na]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.obtainInstanceFromSupplier(AbstractAutowireCapableBeanFactory.java:1225) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.obtainFromSupplier(AbstractAutowireCapableBeanFactory.java:1210) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1157) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:561) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:521) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:326) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:324) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:961) ~[demo:6.0.3]
        at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:915) ~[demo:6.0.3]
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:584) ~[demo:6.0.3]
        at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:146) ~[demo:3.0.1]
        at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:730) ~[demo:3.0.1]
        at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:432) ~[demo:3.0.1]
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:308) ~[demo:3.0.1]
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1302) ~[demo:3.0.1]
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1291) ~[demo:3.0.1]
        at com.baeldung.Application.main(Application.java:24) ~[demo:na]
Caused by: org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'productRepository': Not a managed type: class com.baeldung.multipledb.model.product.Product
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1751) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:599) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:521) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:326) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:324) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200) ~[demo:6.0.3]
        at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:254) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1405) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1325) ~[demo:6.0.3]
        at org.springframework.beans.factory.aot.AutowiredFieldValueResolver.resolveValue(AutowiredFieldValueResolver.java:189) ~[na:na]
        ... 22 common frames omitted
Caused by: java.lang.IllegalArgumentException: Not a managed type: class com.baeldung.multipledb.model.product.Product
        at org.hibernate.metamodel.model.domain.internal.JpaMetamodelImpl.managedType(JpaMetamodelImpl.java:181) ~[na:na]
        at org.hibernate.metamodel.model.domain.internal.MappingMetamodelImpl.managedType(MappingMetamodelImpl.java:496) ~[na:na]
        at org.hibernate.metamodel.model.domain.internal.MappingMetamodelImpl.managedType(MappingMetamodelImpl.java:99) ~[na:na]
        at org.springframework.data.jpa.repository.support.JpaMetamodelEntityInformation.<init>(JpaMetamodelEntityInformation.java:77) ~[demo:na]
        at org.springframework.data.jpa.repository.support.JpaEntityInformationSupport.getEntityInformation(JpaEntityInformationSupport.java:69) ~[demo:na]
        at org.springframework.data.jpa.repository.support.JpaRepositoryFactory.getEntityInformation(JpaRepositoryFactory.java:246) ~[demo:na]
        at org.springframework.data.jpa.repository.support.JpaRepositoryFactory.getTargetRepository(JpaRepositoryFactory.java:211) ~[demo:na]
        at org.springframework.data.jpa.repository.support.JpaRepositoryFactory.getTargetRepository(JpaRepositoryFactory.java:194) ~[demo:na]
        at org.springframework.data.jpa.repository.support.JpaRepositoryFactory.getTargetRepository(JpaRepositoryFactory.java:81) ~[demo:na]
        at org.springframework.data.repository.core.support.RepositoryFactorySupport.getRepository(RepositoryFactorySupport.java:317) ~[demo:3.0.0]
        at org.springframework.data.repository.core.support.RepositoryFactoryBeanSupport.lambda$afterPropertiesSet$5(RepositoryFactoryBeanSupport.java:279) ~[demo:3.0.0]
        at org.springframework.data.util.Lazy.getNullable(Lazy.java:229) ~[demo:3.0.0]
        at org.springframework.data.util.Lazy.get(Lazy.java:113) ~[demo:3.0.0]
        at org.springframework.data.repository.core.support.RepositoryFactoryBeanSupport.afterPropertiesSet(RepositoryFactoryBeanSupport.java:285) ~[demo:3.0.0]
        at org.springframework.data.jpa.repository.support.JpaRepositoryFactoryBean.afterPropertiesSet(JpaRepositoryFactoryBean.java:132) ~[demo:na]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1797) ~[demo:6.0.3]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1747) ~[demo:6.0.3]
        ... 32 common frames omitted

@matthenry87 I tested and if you add @Primary like this and multiple times in the file it will work "one step further" but will still fail later with a Caused by: java.lang.NoSuchMethodException: com.zaxxer.hikari.HikariDataSource.<init>() (I went down this path already and that is when I decided to use the agent, then it solved that issue... but not the one that I posted above)

Right, but you wouldn't want it to inject the same entityManager for all repositories. The reflection hints for the constructor should be easy to overcome but I don't think using @Primary is the answer.

wilkinsona commented 1 year ago

It looks to me like the references configured on @EnableJpaRepositories aren't being applied correctly. I suspect that this is a Spring Data JPA bug but it could also be a Spring Framework problem. @matthenry87 please open a Spring Data JPA issue and we can take things from there.

wilkinsona commented 1 year ago

Re-opening so that we can look at improving the failure analysis's error message. It's currently glossing over the intermediate repository which is where the dependency on the entity manager actually resides.

wilkinsona commented 1 year ago

I don't think we can improve the failure analysis as there's only a single exception with no cause thrown:

org.springframework.beans.factory.NoUniqueBeanDefinitionException: No qualifying bean of type 'jakarta.persistence.EntityManagerFactory' available: expected single matching bean but found 2: db1EntityManagerFactory,db2EntityManagerFactory
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveNamedBean(DefaultListableBeanFactory.java:1287) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveBean(DefaultListableBeanFactory.java:483) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBean(DefaultListableBeanFactory.java:338) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBean(DefaultListableBeanFactory.java:331) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.orm.jpa.EntityManagerFactoryUtils.findEntityManagerFactory(EntityManagerFactoryUtils.java:120) ~[spring-orm-6.0.3.jar!/:6.0.3]
    at org.springframework.data.jpa.repository.support.JpaRepositoryFactoryBean__PersistenceInjection.getEntityManager(JpaRepositoryFactoryBean__PersistenceInjection.java:18) ~[classes!/:1.0.0]
    at org.springframework.data.jpa.repository.support.JpaRepositoryFactoryBean__PersistenceInjection.apply(JpaRepositoryFactoryBean__PersistenceInjection.java:27) ~[classes!/:1.0.0]
    at org.springframework.beans.factory.support.InstanceSupplier$1.get(InstanceSupplier.java:82) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.InstanceSupplier$1.get(InstanceSupplier.java:82) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.obtainInstanceFromSupplier(AbstractAutowireCapableBeanFactory.java:1225) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.obtainFromSupplier(AbstractAutowireCapableBeanFactory.java:1210) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1157) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:561) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:521) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:326) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:324) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:254) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1405) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1325) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.aot.BeanInstanceSupplier.resolveArgument(BeanInstanceSupplier.java:334) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.aot.BeanInstanceSupplier.resolveArguments(BeanInstanceSupplier.java:271) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.aot.BeanInstanceSupplier.get(BeanInstanceSupplier.java:206) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.obtainInstanceFromSupplier(AbstractAutowireCapableBeanFactory.java:1225) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.obtainFromSupplier(AbstractAutowireCapableBeanFactory.java:1210) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1157) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:561) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:521) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:326) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:324) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:961) ~[spring-beans-6.0.3.jar!/:6.0.3]
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:915) ~[spring-context-6.0.3.jar!/:6.0.3]
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:584) ~[spring-context-6.0.3.jar!/:6.0.3]
    at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:730) ~[spring-boot-3.0.1.jar!/:3.0.1]
    at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:432) ~[spring-boot-3.0.1.jar!/:3.0.1]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:308) ~[spring-boot-3.0.1.jar!/:3.0.1]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1302) ~[spring-boot-3.0.1.jar!/:3.0.1]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1291) ~[spring-boot-3.0.1.jar!/:3.0.1]
    at org.matthenry87.nativetesting.api.ApiApplication.main(ApiApplication.java:17) ~[classes!/:1.0.0]
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na]
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) ~[na:na]
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
    at java.base/java.lang.reflect.Method.invoke(Method.java:568) ~[na:na]
    at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49) ~[api-1.0.0.jar:1.0.0]
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:95) ~[api-1.0.0.jar:1.0.0]
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:58) ~[api-1.0.0.jar:1.0.0]
    at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:65) ~[api-1.0.0.jar:1.0.0]

As a result, there isn't sufficient information for us to know that there's an intermediate step involved. This would have to be addressed in Spring Framework so that the part played by JpaRepositoryFactoryBean is clear from the exceptions and their messages. FWIW, this problem isn't specific to Spring Framework 6 as I can reproduce a somewhat similar problem by updating the sample to use Spring Boot 2.7 and running it on the JVM without the entityManagerFactoryRef attributes on the @EnableJpaRepositories annotations:

org.springframework.beans.factory.NoSuchBeanDefinitionException: No bean named 'entityManagerFactory' available
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.getBeanDefinition(DefaultListableBeanFactory.java:874) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getMergedLocalBeanDefinition(AbstractBeanFactory.java:1358) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:309) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:330) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:113) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.ConstructorResolver.resolveConstructorArguments(ConstructorResolver.java:693) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:510) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1352) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1195) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:582) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveInnerBean(BeanDefinitionValueResolver.java:374) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:134) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1707) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1452) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:619) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:276) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1391) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1311) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.ConstructorResolver.resolveAutowiredArgument(ConstructorResolver.java:887) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.ConstructorResolver.createArgumentArray(ConstructorResolver.java:791) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:229) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1372) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1222) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:582) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:542) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:335) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:234) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:333) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:208) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:955) ~[spring-beans-5.3.24.jar!/:5.3.24]
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:918) ~[spring-context-5.3.24.jar!/:5.3.24]
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:583) ~[spring-context-5.3.24.jar!/:5.3.24]
    at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:731) ~[spring-boot-2.7.7.jar!/:2.7.7]
    at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:408) ~[spring-boot-2.7.7.jar!/:2.7.7]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:307) ~[spring-boot-2.7.7.jar!/:2.7.7]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1303) ~[spring-boot-2.7.7.jar!/:2.7.7]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1292) ~[spring-boot-2.7.7.jar!/:2.7.7]
    at org.matthenry87.nativetesting.api.ApiApplication.main(ApiApplication.java:17) ~[classes!/:1.0.0]
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na]
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) ~[na:na]
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:na]
    at java.base/java.lang.reflect.Method.invoke(Method.java:568) ~[na:na]
    at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:49) ~[api-1.0.0.jar:1.0.0]
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:108) ~[api-1.0.0.jar:1.0.0]
    at org.springframework.boot.loader.Launcher.launch(Launcher.java:58) ~[api-1.0.0.jar:1.0.0]
    at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:65) ~[api-1.0.0.jar:1.0.0]

The involvement of the repository bean is unclear here as well.

@matthenry87 If you'd like to pursue this aspect of the problem, please open a Spring Framework issue.