Docker + Spring Boot Error : could not create Vfs.

Question

I've been getting this error when running a Spring Boot app in a Docker container. I'm not sure how to fix it. I've tried creating the directory /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/ext/ but that did not seem to help. I also tried mounting a volume with that directory. This appears to be a Docker issue because I am able to run the app as a .jar. This also prevents the system from communicating at all.

org.reflections.ReflectionsException: could not create Vfs.Dir from url, no matching UrlType was found [file:/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/ext/libatk-wrapper.so]
either use fromURL(final URL url, final List<UrlType> urlTypes) or use the static setDefaultURLTypes(final List<UrlType> urlTypes) or addDefaultURLTypes(UrlType urlType) with your specialized UrlType.
    at org.reflections.vfs.Vfs.fromURL(Vfs.java:109) ~[reflections-0.9.10.jar!/:na]
    at org.reflections.vfs.Vfs.fromURL(Vfs.java:91) ~[reflections-0.9.10.jar!/:na]
    at org.reflections.Reflections.scan(Reflections.java:237) [reflections-0.9.10.jar!/:na]
    at org.reflections.Reflections.scan(Reflections.java:204) [reflections-0.9.10.jar!/:na]
    at org.reflections.Reflections.<init>(Reflections.java:129) [reflections-0.9.10.jar!/:na]
    at org.reflections.Reflections.<init>(Reflections.java:170) [reflections-0.9.10.jar!/:na]
    at org.reflections.Reflections.<init>(Reflections.java:143) [reflections-0.9.10.jar!/:na]
    at io.katharsis.resource.registry.DefaultResourceLookup.<init>(DefaultResourceLookup.java:27) [katharsis-core-2.4.2.jar!/:na]
    at io.katharsis.resource.registry.ResourceRegistryBuilder.build(ResourceRegistryBuilder.java:38) [katharsis-core-2.4.2.jar!/:na]
    at io.katharsis.spring.boot.KatharsisRegistryConfiguration.resourceRegistry(KatharsisRegistryConfiguration.java:36) [katharsis-spring-2.4.2.jar!/:na]
    at io.katharsis.spring.boot.KatharsisRegistryConfiguration$$EnhancerBySpringCGLIB$$e5b864ad.CGLIB$resourceRegistry$0(<generated>) [katharsis-spring-2.4.2.jar!/:na]
    at io.katharsis.spring.boot.KatharsisRegistryConfiguration$$EnhancerBySpringCGLIB$$e5b864ad$$FastClassBySpringCGLIB$$2c6d529a.invoke(<generated>) [katharsis-spring-2.4.2.jar!/:na]
    at org.springframework.cglib.proxy.MethodProxy.invokeSuper(MethodProxy.java:228) [spring-core-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.context.annotation.ConfigurationClassEnhancer$BeanMethodInterceptor.intercept(ConfigurationClassEnhancer.java:356) [spring-context-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at io.katharsis.spring.boot.KatharsisRegistryConfiguration$$EnhancerBySpringCGLIB$$e5b864ad.resourceRegistry(<generated>) [katharsis-spring-2.4.2.jar!/:na]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_102]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_102]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_102]
    at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_102]
    at org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:162) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:588) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1123) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1018) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:510) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.config.DependencyDescriptor.resolveCandidate(DependencyDescriptor.java:207) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.findAutowireCandidates(DefaultListableBeanFactory.java:1214) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.doResolveDependency(DefaultListableBeanFactory.java:1054) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.DefaultListableBeanFactory.resolveDependency(DefaultListableBeanFactory.java:1019) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor$AutowiredFieldElement.inject(AutowiredAnnotationBeanPostProcessor.java:566) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.annotation.InjectionMetadata.inject(InjectionMetadata.java:88) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.annotation.AutowiredAnnotationBeanPostProcessor.postProcessPropertyValues(AutowiredAnnotationBeanPostProcessor.java:349) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:1214) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:543) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.ConstructorResolver.instantiateUsingFactoryMethod(ConstructorResolver.java:372) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.instantiateUsingFactoryMethod(AbstractAutowireCapableBeanFactory.java:1123) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:1018) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:510) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:202) [spring-beans-4.3.2.RELEASE.jar!/:4.3.2.RELEASE]
    at org.springframework.boot.web.servlet.ServletContextInitializerBeans.getOrderedBeansOfType(ServletContextInitializerBeans.java:233) [spring-boot-1.4.0.RELEASE.jar!/:1.4.0.RELEASE]
    at org.springframework.boot.web.servlet.ServletContextInitializerBeans.getOrderedBeansOfType(ServletContextInitializerBeans.java:214) [spring-boot-1.4.0.RELEASE.jar!/:1.4.0.RELEASE]
    at org.springframework.boot.web.servlet.ServletContextInitializerBeans.addServletContextInitializerBeans(ServletContextInitializerBeans.java:90) [spring-boot-1.4.0.RELEASE.jar!/:1.4.0.RELEASE]
    at org.springframework.boot.web.servlet.ServletContextInitializerBeans.<init>(ServletContextInitializerBeans.java:78) [spring-boot-1.4.0.RELEASE.jar!/:1.4.0.RELEASE]
    at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.getServletContextInitializerBeans(EmbeddedWebApplicationContext.java:241) [spring-boot-1.4.0.RELEASE.jar!/:1.4.0.RELEASE]
    at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.selfInitialize(EmbeddedWebApplicationContext.java:228) [spring-boot-1.4.0.RELEASE.jar!/:1.4.0.RELEASE]
    at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext.access$000(EmbeddedWebApplicationContext.java:89) [spring-boot-1.4.0.RELEASE.jar!/:1.4.0.RELEASE]
    at org.springframework.boot.context.embedded.EmbeddedWebApplicationContext$1.onStartup(EmbeddedWebApplicationContext.java:213) [spring-boot-1.4.0.RELEASE.jar!/:1.4.0.RELEASE]
    at org.springframework.boot.context.embedded.tomcat.TomcatStarter.onStartup(TomcatStarter.java:55) [spring-boot-1.4.0.RELEASE.jar!/:1.4.0.RELEASE]
    at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5167) [tomcat-embed-core-8.5.4.jar!/:8.5.4]
    at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:152) [tomcat-embed-core-8.5.4.jar!/:8.5.4]
    at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1403) [tomcat-embed-core-8.5.4.jar!/:8.5.4]
    at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1393) [tomcat-embed-core-8.5.4.jar!/:8.5.4]
    at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_102]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_102]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_102]
    at java.lang.Thread.run(Thread.java:745) [na:1.8.0_102]

UPDATE:

I logged into docker container and the libatk-wrapper.so file exists.

Answer 1

If you are not tightly into OpenJdk then try using OracleJdk. I had the same problem and changing to Oracle based docker fixed it.

Answer 2

We got the same issue in our company. In our case this issue shows up when we instanitiate new org.reflections.Reflections Object with a package which is not part of the classpath. We have some application parts which we add as external jar libs, because they are optional. When we create a reflection with a package which is only part of this external jar, and this jar is not part of the classpath then this error message shows up. We could reproduce this issue within a docker container as well as with a self configured tomcat server. Hope this will help solving this issue, because it costs us much time.