Spring ApplicationContext is closed before shutdown hook finishes its job

Question

I am using a shutdown hook to do some database operation before application is closed.

Runtime.getRuntime().addShutdownHook(shutdownDaemonHook);

I am adding my shutdown hook to RunTime like this. Application Context should be closed after this thread finishes its job but in the middle of this job, application context is closed and giving JPA is closed exception.

2022-10-12 16:51:54.217  INFO 25468 --- [tomcat-shutdown] o.s.b.w.e.tomcat.GracefulShutdown        : Graceful shutdown complete
2022-10-12 16:51:54.240  WARN 25468 --- [extShutdownHook] o.s.b.f.support.DisposableBeanAdapter    : Destroy method 'close' on bean with name 'mappedBusReader' threw an exception: java.io.IOException: Unable to close the file
2022-10-12 16:51:54.244  INFO 25468 --- [extShutdownHook] j.LocalContainerEntityManagerFactoryBean : Closing JPA EntityManagerFactory for persistence unit 'default'
2022-10-12 16:51:54.247  INFO 25468 --- [extShutdownHook] o.s.s.c.ThreadPoolTaskScheduler          : Shutting down ExecutorService 'taskScheduler'
2022-10-12 16:51:54.247  INFO 25468 --- [extShutdownHook] o.s.s.concurrent.ThreadPoolTaskExecutor  : Shutting down ExecutorService 'applicationTaskExecutor'

as in the logs, you can see JPA is closed.

@EnableJpaRepositories declared on JpaRepositoriesRegistrar.EnableJpaRepositoriesConfiguration: Cannot create inner bean '(inner bean) of type [org.springframework.orm.jpa.SharedEntityManagerCreator] while setting bean property 'entityManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name '(inner bean)#3d7314b3': Cannot resolve reference to bean 'entityManagerFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'org.springframework.boot.autoconfigure.orm.jpa.HibernateJpaConfiguration': Unsatisfied dependency expressed through constructor parameter 0; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'hikari' defined in class path resource: Initialization of bean failed; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'org.springframework.boot.autoconfigure.jdbc.DataSourceInitializerInvoker': Unsatisfied dependency expressed through constructor parameter 1; nested exception is org.springframework.boot.context.properties.ConfigurationPropertiesBindException: Error creating bean with name 'spring.datasource-org.springframework.boot.autoconfigure.jdbc.DataSourceProperties': Could not bind properties to 'DataSourceProperties' : prefix=spring.datasource, ignoreInvalidFields=false, ignoreUnknownFields=true; nested exception is java.lang.IllegalStateException: org.springframework.boot.web.servlet.context.AnnotationConfigServletWebServerApplicationContext has been closed already 

is there any way to prevent this ? , Applicatin Context or JPA should not be closed until shutdown hook finishes it job.