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plantbreeding / brapi-Java-TestServer

BrAPI Java Spring-Boot Test Server
https://brapi.org
MIT License
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Exception when running TestServer: Error creating bean with name 'entityManagerFactory' #37

Closed chaneylc closed 4 years ago

chaneylc commented 4 years ago

Hey Peter and brapi-staff,

I ran into a small issue when trying to run the v2 test server on Eclipse using the installation instructions.

My properties file:

server.port = 8080
server.servlet.context-path=/brapi/v2

spring.datasource.url=jdbc:postgresql://localhost:5432/brapi
spring.datasource.username=postgres
spring.datasource.password=test

spring.datasource.driver-class-name=org.postgresql.Driver

spring.jpa.hibernate.ddl-auto=create-drop
spring.jpa.show-sql=false
spring.jpa.properties.hibernate.hbm2ddl.import_files=sql/crops.sql, sql/lists.sql, sql/locations.sql, sql/people.sql, sql/programs.sql, sql/trials.sql, sql/seasons.sql, sql/studies.sql, sql/breeding_methods.sql, sql/germplasm.sql, sql/attribute_defs.sql, sql/attribute_values.sql, sql/seed_lots.sql, sql/observation_units.sql, sql/crosses.sql, sql/pedigree.sql, sql/events.sql, sql/images.sql, sql/observation_variables.sql, sql/observations.sql, sql/samples.sql, sql/allele_calls.sql, sql/genome_maps.sql, sql/references.sql, sql/vendor.sql    

spring.mvc.dispatch-options-request=true

After building the project with maven, creating the database, and updating the postgres user password to 'test', I ran into this exception when running the TestServer:

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:1704) ~[spring-beans-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:583) ~[spring-beans-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:502) ~[spring-beans-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:312) ~[spring-beans-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:228) ~[spring-beans-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:310) ~[spring-beans-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:200) ~[spring-beans-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:1083) ~[spring-context-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:858) ~[spring-context-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:549) ~[spring-context-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.boot.web.servlet.context.ServletWebServerApplicationContext.refresh(ServletWebServerApplicationContext.java:122) ~[spring-boot-2.0.0.M5.jar:2.0.0.M5]
    at org.springframework.boot.SpringApplication.refresh(SpringApplication.java:750) ~[spring-boot-2.0.0.M5.jar:2.0.0.M5]
    at org.springframework.boot.SpringApplication.refreshContext(SpringApplication.java:386) ~[spring-boot-2.0.0.M5.jar:2.0.0.M5]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:327) ~[spring-boot-2.0.0.M5.jar:2.0.0.M5]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1245) ~[spring-boot-2.0.0.M5.jar:2.0.0.M5]
    at org.springframework.boot.SpringApplication.run(SpringApplication.java:1233) ~[spring-boot-2.0.0.M5.jar:2.0.0.M5]
    at org.brapi.test.BrAPITestServer.BrapiTestServer.main(BrapiTestServer.java:17) ~[classes/:na]
Caused by: java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
    at org.hibernate.boot.spi.XmlMappingBinderAccess.<init>(XmlMappingBinderAccess.java:43) ~[hibernate-core-5.2.11.Final.jar:5.2.11.Final]
    at org.hibernate.boot.MetadataSources.<init>(MetadataSources.java:87) ~[hibernate-core-5.2.11.Final.jar:5.2.11.Final]
    at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.<init>(EntityManagerFactoryBuilderImpl.java:208) ~[hibernate-core-5.2.11.Final.jar:5.2.11.Final]
    at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.<init>(EntityManagerFactoryBuilderImpl.java:163) ~[hibernate-core-5.2.11.Final.jar:5.2.11.Final]
    at org.springframework.orm.jpa.vendor.SpringHibernateJpaPersistenceProvider.createContainerEntityManagerFactory(SpringHibernateJpaPersistenceProvider.java:51) ~[spring-orm-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean.createNativeEntityManagerFactory(LocalContainerEntityManagerFactoryBean.java:358) ~[spring-orm-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.buildNativeEntityManagerFactory(AbstractEntityManagerFactoryBean.java:384) ~[spring-orm-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.orm.jpa.AbstractEntityManagerFactoryBean.afterPropertiesSet(AbstractEntityManagerFactoryBean.java:373) ~[spring-orm-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1763) ~[spring-beans-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1700) ~[spring-beans-5.0.0.RELEASE.jar:5.0.0.RELEASE]
    ... 16 common frames omitted
Caused by: java.lang.ClassNotFoundException: javax.xml.bind.JAXBException
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:581) ~[na:na]
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:178) ~[na:na]
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:522) ~[na:na]
    ... 26 common frames omitted

I'm fairly new to using Eclipse as an IDE so apologies if this was a simple configuration error on my end.

I added this dependency to the pom.xml and rebuilt the project, and it works.

<dependency>
            <groupId>javax.xml.bind</groupId>
            <artifactId>jaxb-api</artifactId>
            <version>2.3.1</version>
</dependency>

Thanks again for this great project :)

BrapiCoordinatorSelby commented 4 years ago

hey @chaneylc I think this is a Java version problem. I built the BrAPI Test Server using Java 8, and this was mostly due to plain old laziness hahaha.

If you are using Java 9+, then you have done exactly the right solution. Java 8 used to include the JAXB libraries, but they were deprecated in Java 9, and removed entirely in Java 11.

The BrAPI Test Server doesn't actually use any JAXB functionality (as far as I know), but it does use the Spring framework which requires JAXB as a dependency. It is probably possible to cut down the Spring libraries and remove the need for JAXB all together, but for now adding the jaxb-api dependency directly will work.

Feel free to make a pull request adding the jaxb-api dependency to the POM. I'm sure others will appreciate it.

chaneylc commented 4 years ago

Thanks for the quick response, I went ahead and made a pull request here: https://github.com/plantbreeding/brapi-Java-TestServer/pull/38