Running spring boot build: Error creating bean with name 'entityManagerFactory' defined in class path

Question

I have built a Spring Boot app and I am now ready to deploy it. However, I try to build a "fat jar" which will contain everything but it seems that I have done something wrong but it is unclear what.

application.properties (true credentials removed)

#Template engine conf
spring.thymeleaf.check-template-location=true

#Database stuff
spring.jpa.hibernate.ddl-auto=update
spring.datasource.url= jdbc:mysql://localhost:3306/db
spring.datasource.username=username
spring.datasource.password=pw

Gradle build script (some names changed):

buildscript {
    ext {
        springBootVersion = '2.0.2.RELEASE'
    }
    repositories {
        mavenCentral()
    }
    dependencies {
        classpath("org.springframework.boot:spring-boot-gradle-plugin:${springBootVersion}")
    }
}

apply plugin: 'java'
apply plugin: 'eclipse'
apply plugin: 'org.springframework.boot'
apply plugin: 'io.spring.dependency-management'

group = 'se.myapp'
version = '0.0.1-SNAPSHOT'
sourceCompatibility = 1.8

repositories {
    mavenCentral()
}

bootJar {
    classifier = 'boot'
    mainClassName = 'se.myapp.myapp.SnartledigApplication'
    launchScript()
    baseName = 'myapp'
    version =  '0.1.0'
}

dependencies {
    compile('org.springframework.boot:spring-boot-starter-actuator')
    compile('org.springframework.boot:spring-boot-starter-data-jpa')
    compile('org.springframework.boot:spring-boot-starter-thymeleaf')
    compile('org.springframework.boot:spring-boot-starter-web')
    compile('nz.net.ultraq.thymeleaf:thymeleaf-layout-dialect')
    runtime('mysql:mysql-connector-java')
    testCompile('org.springframework.boot:spring-boot-starter-test')
}

Then I am running gradle clean build and try to execute the jar java -jar build/libs/my-jar-yada-yada.jar only to get the following exception:

org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'entityManagerFactory' defined in class path resource [org/springframework/boot/autoconfigure/orm/jpa/HibernateJpaConfiguration.class]: Invocation of init method failed; nested exception is java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1706) ~[spring-beans-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:579) ~[spring-beans-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:501) ~[spring-beans-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:317) ~[spring-beans-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:228) ~[spring-beans-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:315) ~[spring-beans-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199) ~[spring-beans-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1089) ~[spring-context-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:859) ~[spring-context-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:550) ~[spring-context-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:140) ~[spring-boot-2.0.2.RELEASE.jar!/:2.0.2.RELEASE]
        at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:759) [spring-boot-2.0.2.RELEASE.jar!/:2.0.2.RELEASE]
        at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:395) [spring-boot-2.0.2.RELEASE.jar!/:2.0.2.RELEASE]
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:327) [spring-boot-2.0.2.RELEASE.jar!/:2.0.2.RELEASE]
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1255) [spring-boot-2.0.2.RELEASE.jar!/:2.0.2.RELEASE]
        at org.springframework.boot.SpringApplication.run(SpringApplication.java:1243) [spring-boot-2.0.2.RELEASE.jar!/:2.0.2.RELEASE]
        at se.snartledig.snartledig.SnartledigApplication.main(SnartledigApplication.java:13) [classes!/:na]
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:na]
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) ~[na:na]
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) ~[na:na]
        at java.base/java.lang.reflect.Method.invoke(Unknown Source) ~[na:na]
        at org.springframework.boot.loader.MainMethodRunner.run(MainMethodRunner.java:48) [snartledig-0.1.0-boot.jar:na]
        at org.springframework.boot.loader.Launcher.launch(Launcher.java:87) [snartledig-0.1.0-boot.jar:na]
        at org.springframework.boot.loader.Launcher.launch(Launcher.java:50) [snartledig-0.1.0-boot.jar:na]
        at org.springframework.boot.loader.JarLauncher.main(JarLauncher.java:51) [snartledig-0.1.0-boot.jar:na]
Caused by: java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
        at org.hibernate.boot.spi.XmlMappingBinderAccess.<init>(XmlMappingBinderAccess.java:43) ~[hibernate-core-5.2.17.Final.jar!/:5.2.17.Final]
        at org.hibernate.boot.MetadataSources.<init>(MetadataSources.java:87) ~[hibernate-core-5.2.17.Final.jar!/:5.2.17.Final]
        at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.<init>(EntityManagerFactoryBuilderImpl.java:209) ~[hibernate-core-5.2.17.Final.jar!/:5.2.17.Final]
        at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.<init>(EntityManagerFactoryBuilderImpl.java:164) ~[hibernate-core-5.2.17.Final.jar!/:5.2.17.Final]
        at org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider.createContainerEntityManagerFactory(SpringHibernateJpaPersistenceProvider.java:51) ~[spring-orm-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:365) ~[spring-orm-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:390) ~[spring-orm-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:377) ~[spring-orm-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.afterPropertiesSet(LocalContainerEntityManagerFactoryBean.java:341) ~[spring-orm-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1765) ~[spring-beans-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1702) ~[spring-beans-5.0.6.RELEASE.jar!/:5.0.6.RELEASE]
        ... 24 common frames omitted
Caused by: java.lang.ClassNotFoundException: javax.xml.bind.JAXBException
        at java.base/java.net.URLClassLoader.findClass(Unknown Source) ~[na:na]
        at java.base/java.lang.ClassLoader.loadClass(Unknown Source) ~[na:na]
        at org.springframework.boot.loader.LaunchedURLClassLoader.loadClass(LaunchedURLClassLoader.java:93) ~[snartledig-0.1.0-boot.jar:na]
        at java.base/java.lang.ClassLoader.loadClass(Unknown Source) ~[na:na]
        ... 35 common frames omitted

What am I doing wrong? I am using windows.

EDIT, java version

java 10.0.1 2018-04-17
Java(TM) SE Runtime Environment 18.3 (build 10.0.1+10)
Java HotSpot(TM) 64-Bit Server VM 18.3 (build 10.0.1+10, mixed mode)

Answer 1

When upgrading you may face the following: java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException Hibernate typically requires JAXB that's no longer provided by default. You either need to add a dependency to your project:

 <dependency>
     <groupId>javax.xml.bind</groupId>
     <artifactId>jaxb-api</artifactId>
 </dependency>

Or you could add the java.xml.bind module to restore this functionality with Java9.

from github