Can not start BioMart v0.9 with java 11

[Olivier Arnaiz]

Hello,

I am trying to install BioMart 0.9 on debian 11. The compilation seems OK with a small patch of PortalServiceImpl.java but I have this error when I start the biomart-server.sh.

I think the problem comes from my version 11 of java ...

Has anyone managed to install it? 

Thanks

Olivier

2021-12-20T12:05:15+0100 INFO  [main:Log.java:165]: Adding to classpath: /data/parameciumdb/BioMart/dist/plugins/sequence/lib/sequence-processor.jar
déc. 20, 2021 12:05:15 PM com.google.inject.MessageProcessor visit
INFOS: An exception was caught and reported. Message: java.lang.ClassCastException: class jdk.internal.loader.ClassLoaders$AppClassLoader cannot be cast to class java.net.URLClassLoader (jdk.internal.loader.ClassLoaders$AppClassLoader and java.net.URLClassLoader are in module java.base of loader 'bootstrap')
java.lang.ClassCastException: class jdk.internal.loader.ClassLoaders$AppClassLoader cannot be cast to class java.net.URLClassLoader (jdk.internal.loader.ClassLoaders$AppClassLoader and java.net.URLClassLoader are in module java.base of loader 'bootstrap')
        at org.biomart.common.utils.ClassPathUtils.addToClassPath(ClassPathUtils.java:26)
        at org.biomart.processors.ProcessorRegistry.install(ProcessorRegistry.java:88)
        at org.biomart.processors.ProcessorModule.configure(ProcessorModule.java:12)
        at com.google.inject.AbstractModule.configure(AbstractModule.java:59)
        at com.google.inject.spi.Elements$RecordingBinder.install(Elements.java:223)
        at com.google.inject.AbstractModule.install(AbstractModule.java:118)
        at org.biomart.web.WebServiceModule.configureServlets(WebServiceModule.java:24)
        at com.google.inject.servlet.ServletModule.configure(ServletModule.java:45)
        at com.google.inject.AbstractModule.configure(AbstractModule.java:59)
        at com.google.inject.spi.Elements$RecordingBinder.install(Elements.java:223)
        at com.google.inject.spi.Elements.getElements(Elements.java:101)
        at com.google.inject.InjectorShell$Builder.build(InjectorShell.java:135)
        at com.google.inject.InjectorBuilder.build(InjectorBuilder.java:102)
        at com.google.inject.Guice.createInjector(Guice.java:92)
        at com.google.inject.Guice.createInjector(Guice.java:80)
        at org.biomart.web.GuiceServletConfig.getInjector(GuiceServletConfig.java:173)
        at com.google.inject.servlet.GuiceServletContextListener.contextInitialized(GuiceServletContextListener.java:43)
        at org.biomart.web.GuiceServletConfig.contextInitialized(GuiceServletConfig.java:64)
        at org.mortbay.jetty.handler.ContextHandler.startContext(ContextHandler.java:548)
        at org.mortbay.jetty.servlet.Context.startContext(Context.java:136)
        at org.mortbay.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1250)
        at org.mortbay.jetty.handler.ContextHandler.doStart(ContextHandler.java:517)
        at org.mortbay.jetty.webapp.WebAppContext.doStart(WebAppContext.java:467)
        at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
        at org.mortbay.jetty.handler.HandlerCollection.doStart(HandlerCollection.java:152)
        at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
        at org.mortbay.jetty.handler.HandlerWrapper.doStart(HandlerWrapper.java:130)
        at org.mortbay.jetty.Server.doStart(Server.java:224)
        at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
        at org.biomart.start.Main.start(Main.java:177)
        at org.biomart.start.Main.main(Main.java:224)

Error on server startup: Guice creation errors:

1) An exception was caught and reported. Message: class jdk.internal.loader.ClassLoaders$AppClassLoader cannot be cast to class java.net.URLClassLoader (jdk.internal.loader.ClassLoaders$AppClassLoader and java.net.URLClassLoader are in module java.base of loader 'bootstrap')
  at org.biomart.web.WebServiceModule.configureServlets(WebServiceModule.java:24)

1 error
com.google.inject.CreationException: Guice creation errors:

1) An exception was caught and reported. Message: class jdk.internal.loader.ClassLoaders$AppClassLoader cannot be cast to class java.net.URLClassLoader (jdk.internal.loader.ClassLoaders$AppClassLoader and java.net.URLClassLoader are in module java.base of loader 'bootstrap')
  at org.biomart.web.WebServiceModule.configureServlets(WebServiceModule.java:24)

1 error
        at com.google.inject.internal.Errors.throwCreationExceptionIfErrorsExist(Errors.java:354)
        at com.google.inject.InjectorBuilder.initializeStatically(InjectorBuilder.java:152)
        at com.google.inject.InjectorBuilder.build(InjectorBuilder.java:105)
        at com.google.inject.Guice.createInjector(Guice.java:92)
        at com.google.inject.Guice.createInjector(Guice.java:80)
        at org.biomart.web.GuiceServletConfig.getInjector(GuiceServletConfig.java:173)
        at com.google.inject.servlet.GuiceServletContextListener.contextInitialized(GuiceServletContextListener.java:43)
        at org.biomart.web.GuiceServletConfig.contextInitialized(GuiceServletConfig.java:64)
        at org.mortbay.jetty.handler.ContextHandler.startContext(ContextHandler.java:548)
        at org.mortbay.jetty.servlet.Context.startContext(Context.java:136)
        at org.mortbay.jetty.webapp.WebAppContext.startContext(WebAppContext.java:1250)
        at org.mortbay.jetty.handler.ContextHandler.doStart(ContextHandler.java:517)
        at org.mortbay.jetty.webapp.WebAppContext.doStart(WebAppContext.java:467)
        at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
        at org.mortbay.jetty.handler.HandlerCollection.doStart(HandlerCollection.java:152)
        at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
        at org.mortbay.jetty.handler.HandlerWrapper.doStart(HandlerWrapper.java:130)
        at org.mortbay.jetty.Server.doStart(Server.java:224)
        at org.mortbay.component.AbstractLifeCycle.start(AbstractLifeCycle.java:50)
        at org.biomart.start.Main.start(Main.java:177)
        at org.biomart.start.Main.main(Main.java:224)
Caused by: java.lang.ClassCastException: class jdk.internal.loader.ClassLoaders$AppClassLoader cannot be cast to class java.net.URLClassLoader (jdk.internal.loader.ClassLoaders$AppClassLoader and java.net.URLClassLoader are in module java.base of loader 'bootstrap')
        at org.biomart.common.utils.ClassPathUtils.addToClassPath(ClassPathUtils.java:26)
        at org.biomart.processors.ProcessorRegistry.install(ProcessorRegistry.java:88)
        at org.biomart.processors.ProcessorModule.configure(ProcessorModule.java:12)
        at com.google.inject.AbstractModule.configure(AbstractModule.java:59)
        at com.google.inject.spi.Elements$RecordingBinder.install(Elements.java:223)
        at com.google.inject.AbstractModule.install(AbstractModule.java:118)
        at org.biomart.web.WebServiceModule.configureServlets(WebServiceModule.java:24)
        at com.google.inject.servlet.ServletModule.configure(ServletModule.java:45)
        at com.google.inject.AbstractModule.configure(AbstractModule.java:59)
        at com.google.inject.spi.Elements$RecordingBinder.install(Elements.java:223)
        at com.google.inject.spi.Elements.getElements(Elements.java:101)
        at com.google.inject.InjectorShell$Builder.build(InjectorShell.java:135)
        at com.google.inject.InjectorBuilder.build(InjectorBuilder.java:102)
        ... 18 more
Stopping server
déc. 20, 2021 12:05:16 PM com.sun.xml.ws.transport.http.servlet.WSServletContextListener contextDestroyed