Re: [Treebase-devel] A problem running local treebase

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Hi, Vladimir,

Looks like you got jar version conflict on xercesImpl-X.X.X.jar . See if
this link help and make sure the installation use the newer version:
http://www.mail-archive.com/cxf...@in.../msg03916.html

Youjun

On Thu, Sep 9, 2010 at 4:26 PM, Vladimir Gapeyev <vga...@ne...>wrote:

> Hi, Youjun,
>
> I cannot start a local TB instance in Tomcat, for any of the recent
> versions: the application breaks on startup. The catalina.out error
> log for the tomcat startup sequence is appended below.
>
> I tracked the problem down to SVN#731 that you committed on 7/13:
> versions up to 730 start up and run just fine, while 731 and the later
> ones, up to the head (#748) break at startup with the same error.
> Inexplicably, rebuild on treebase-dev works just fine.
>
> Looking at the error log below and the SVN log for 731 that I am
> resending separately, do you have any idea what has changed in #731
> that made things go wrong?
>
> Thanks,
>
> --Vladimir
>
>
>
> -----------------------------------------------------------------------------------------------
>  Thursday, September 9, 2010 4:20:30 PM US/Eastern
> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.AprLifecycleListener
> lifecycleEvent
> INFO: The Apache Tomcat Native library which allows optimal
> performance in production environments was not found on the
> java.library.path: .:/Library/Java/Extensions:/System/Library/Java/
> Extensions:/usr/lib/java
> Sep 9, 2010 4:20:33 PM org.apache.coyote.http11.Http11BaseProtocol init
> INFO: Initializing Coyote HTTP/1.1 on http-8080
> Sep 9, 2010 4:20:33 PM org.apache.catalina.startup.Catalina load
> INFO: Initialization processed in 479 ms
> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardService start
> INFO: Starting service Catalina
> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardEngine start
> INFO: Starting Servlet Engine: Apache Tomcat/5.5.28
> Sep 9, 2010 4:20:33 PM org.apache.catalina.core.StandardHost start
> INFO: XML validation disabled
> Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader
> validateJarFile
> INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache-
> tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/geronimo-
> servlet_2.5_spec-1.2.jar) - jar not loaded. See Servlet Spec 2.3,
> section 9.7.2. Offending class: javax/servlet/Servlet.class
> Sep 9, 2010 4:20:34 PM org.apache.catalina.loader.WebappClassLoader
> validateJarFile
> INFO: validateJarFile(/Users/vgapeyev/Work/TreeBase/mytomcat/apache-
> tomcat-5.5.28/webapps/treebase-web/WEB-INF/lib/servlet-api-2.4.jar) -
> jar not loaded. See Servlet Spec 2.3, section 9.7.2. Offending class:
> javax/servlet/Servlet.class
> [main] DEBUG org.cipres.treebase.web.listeners.StartupListener -
> contextInitialized(ServletContextEvent) -
> FORMAT_DELIMITER_MSG= :FORMAT_RETURN_VALUE_NAME=return valuestart
> [main] WARN org.hibernate.cache.CacheFactory - read-only cache
> configured for mutable class: staticCache
> [main] WARN org.hibernate.cache.EhCacheProvider - Could not find
> configuration [org.hibernate.cache.UpdateTimestampsCache]; using
> defaults.
> [main] WARN org.hibernate.cache.EhCacheProvider - Could not find
> configuration [org.hibernate.cache.StandardQueryCache]; using defaults.
> [main] INFO org.cipres.treebase.service.nexus.NexusServiceMesquite -
> Setting mesquite folder location from JNDI: /Users/vgapeyev/Work/
> TreeBase/mytomcat/mesquite-2.01.tb
> Sep 9, 2010 4:20:40 PM
> org.apache.cxf.service.factory.ReflectionServiceFactoryBean
> buildServiceFromClass
> INFO: Creating Service {http://
> webservices.web.treebase.cipres.org/}StudiesContainingKeyword<http://webservices.web.treebase.cipres.org/%7DStudiesContainingKeyword>from
> class org.cipres.treebase.web.webservices.StudyServiceByKeyword
> [main] ERROR org.springframework.web.context.ContextLoader - Context
> initialization failed
> org.springframework.beans.factory.BeanCreationException: Error
> creating bean with name 'searchStudiesByKeyword': Invocation of init
> method failed; nested exception is java.lang.AbstractMethodError:
> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
> Caused by:
> java.lang.AbstractMethodError:
> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun
> .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
>        at
> sun
> .reflect
> .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
> 25)
>        at java.lang.reflect.Method.invoke(Method.java:592)
>        at
> org
> .apache.ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java:
> 602)
>        at
> org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java:84)
>        at
> org
> .apache
> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
> 424)
>        at
> org
> .apache
> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
> 418)
>        at
> org
> .apache
> .cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java:142)
>        at
> org
> .apache
> .cxf
> .databinding
> .AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93)
>        at
> org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java:345)
>        at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean
> .buildServiceFromClass(ReflectionServiceFactoryBean.java:345)
>        at
> org
> .apache
> .cxf
> .jaxws
> .support
> .JaxWsServiceFactoryBean
> .buildServiceFromClass(JaxWsServiceFactoryBean.java:513)
>        at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean
> .initializeServiceModel(ReflectionServiceFactoryBean.java:396)
>        at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean.create(ReflectionServiceFactoryBean.java:
> 181)
>        at
> org
> .apache
> .cxf
> .jaxws
> .support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java:
> 163)
>        at
> org
> .apache
> .cxf
> .frontend
> .AbstractWSDLBasedEndpointFactory
> .createEndpoint(AbstractWSDLBasedEndpointFactory.java:79)
>        at
> org
> .apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java:
> 114)
>        at
> org
> .apache
> .cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java:
> 164)
>        at
> org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java:334)
>        at
> org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java:251)
>        at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201)
>        at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392)
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun
> .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
>        at
> sun
> .reflect
> .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
> 25)
>        at java.lang.reflect.Method.invoke(Method.java:592)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .createBean(AbstractAutowireCapableBeanFactory.java:427)
>        at org.springframework.beans.factory.support.AbstractBeanFactory
> $1.getObject(AbstractBeanFactory.java:249)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .DefaultSingletonBeanRegistry
> .getSingleton(DefaultSingletonBeanRegistry.java:155)
>        at
> org
> .springframework
> .beans
> .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
> 246)
>        at
> org
> .springframework
> .beans
> .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
> 160)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .DefaultListableBeanFactory
> .preInstantiateSingletons(DefaultListableBeanFactory.java:291)
>        at
> org
> .springframework
> .context
> .support
> .AbstractApplicationContext.refresh(AbstractApplicationContext.java:352)
>        at
> org.springframework.web.context.ContextLoader.createWebApplicationContext
> (ContextLoader.java:245)
>        at
> org.springframework.web.context.ContextLoader.initWebApplicationContext
> (ContextLoader.java:188)
>        at
> org.springframework.web.context.ContextLoaderListener.contextInitialized
> (ContextLoaderListener.java:49)
>        at
> org
> .cipres
> .treebase
> .web.listeners.StartupListener.contextInitialized(StartupListener.java:
> 45)
>        at
> org
> .apache
> .catalina.core.StandardContext.listenerStart(StandardContext.java:3795)
>        at
> org.apache.catalina.core.StandardContext.start(StandardContext.java:
> 4252)
>        at
> org
> .apache
> .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
>        at
> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:
> 740)
>        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:
> 544)
>        at
> org
> .apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:
> 626)
>        at
> org
> .apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:
> 553)
>        at
> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:
> 488)
>        at
> org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150)
>        at
> org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:
> 311)
>        at
> org
> .apache
> .catalina
> .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
>        at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
> 1022)
>        at
> org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
>        at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
> 1014)
>        at
> org.apache.catalina.core.StandardEngine.start(StandardEngine.java:
> 443)
>        at
> org.apache.catalina.core.StandardService.start(StandardService.java:448)
>        at
> org.apache.catalina.core.StandardServer.start(StandardServer.java:
> 700)
>        at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun
> .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
>        at
> sun
> .reflect
> .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
> 25)
>        at java.lang.reflect.Method.invoke(Method.java:592)
>        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
>        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
> [main] ERROR org.apache.catalina.core.ContainerBase.[Catalina].
> [localhost].[/treebase-web] - Exception sending context initialized
> event to listener instance of class
> org.cipres.treebase.web.listeners.StartupListener
> org.springframework.beans.factory.BeanCreationException: Error
> creating bean with name 'searchStudiesByKeyword': Invocation of init
> method failed; nested exception is java.lang.AbstractMethodError:
> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
> Caused by:
> java.lang.AbstractMethodError:
> org.apache.xerces.dom.DocumentImpl.getInputEncoding()Ljava/lang/String;
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun
> .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
>        at
> sun
> .reflect
> .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
> 25)
>        at java.lang.reflect.Method.invoke(Method.java:592)
>        at
> org
> .apache.ws.commons.schema.utils.DOMUtil.getInputEncoding(DOMUtil.java:
> 602)
>        at
> org.apache.ws.commons.schema.SchemaBuilder.build(SchemaBuilder.java:84)
>        at
> org
> .apache
> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
> 424)
>        at
> org
> .apache
> .ws.commons.schema.XmlSchemaCollection.read(XmlSchemaCollection.java:
> 418)
>        at
> org
> .apache
> .cxf.common.xmlschema.SchemaCollection.read(SchemaCollection.java:142)
>        at
> org
> .apache
> .cxf
> .databinding
> .AbstractDataBinding.addSchemaDocument(AbstractDataBinding.java:93)
>        at
> org.apache.cxf.jaxb.JAXBDataBinding.initialize(JAXBDataBinding.java:345)
>        at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean
> .buildServiceFromClass(ReflectionServiceFactoryBean.java:345)
>        at
> org
> .apache
> .cxf
> .jaxws
> .support
> .JaxWsServiceFactoryBean
> .buildServiceFromClass(JaxWsServiceFactoryBean.java:513)
>        at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean
> .initializeServiceModel(ReflectionServiceFactoryBean.java:396)
>        at
> org
> .apache
> .cxf
> .service
> .factory
> .ReflectionServiceFactoryBean.create(ReflectionServiceFactoryBean.java:
> 181)
>        at
> org
> .apache
> .cxf
> .jaxws
> .support.JaxWsServiceFactoryBean.create(JaxWsServiceFactoryBean.java:
> 163)
>        at
> org
> .apache
> .cxf
> .frontend
> .AbstractWSDLBasedEndpointFactory
> .createEndpoint(AbstractWSDLBasedEndpointFactory.java:79)
>        at
> org
> .apache.cxf.frontend.ServerFactoryBean.create(ServerFactoryBean.java:
> 114)
>        at
> org
> .apache
> .cxf.jaxws.JaxWsServerFactoryBean.create(JaxWsServerFactoryBean.java:
> 164)
>        at
> org.apache.cxf.jaxws.EndpointImpl.getServer(EndpointImpl.java:334)
>        at
> org.apache.cxf.jaxws.EndpointImpl.doPublish(EndpointImpl.java:251)
>        at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:201)
>        at org.apache.cxf.jaxws.EndpointImpl.publish(EndpointImpl.java:392)
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun
> .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
>        at
> sun
> .reflect
> .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
> 25)
>        at java.lang.reflect.Method.invoke(Method.java:592)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1237)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1203)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .AbstractAutowireCapableBeanFactory
> .createBean(AbstractAutowireCapableBeanFactory.java:427)
>        at org.springframework.beans.factory.support.AbstractBeanFactory
> $1.getObject(AbstractBeanFactory.java:249)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .DefaultSingletonBeanRegistry
> .getSingleton(DefaultSingletonBeanRegistry.java:155)
>        at
> org
> .springframework
> .beans
> .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
> 246)
>        at
> org
> .springframework
> .beans
> .factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:
> 160)
>        at
> org
> .springframework
> .beans
> .factory
> .support
> .DefaultListableBeanFactory
> .preInstantiateSingletons(DefaultListableBeanFactory.java:291)
>        at
> org
> .springframework
> .context
> .support
> .AbstractApplicationContext.refresh(AbstractApplicationContext.java:352)
>        at
> org.springframework.web.context.ContextLoader.createWebApplicationContext
> (ContextLoader.java:245)
>        at
> org.springframework.web.context.ContextLoader.initWebApplicationContext
> (ContextLoader.java:188)
>        at
> org.springframework.web.context.ContextLoaderListener.contextInitialized
> (ContextLoaderListener.java:49)
>        at
> org
> .cipres
> .treebase
> .web.listeners.StartupListener.contextInitialized(StartupListener.java:
> 45)
>        at
> org
> .apache
> .catalina.core.StandardContext.listenerStart(StandardContext.java:3795)
>        at
> org.apache.catalina.core.StandardContext.start(StandardContext.java:
> 4252)
>        at
> org
> .apache
> .catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
>        at
> org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:
> 740)
>        at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:
> 544)
>        at
> org
> .apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:
> 626)
>        at
> org
> .apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:
> 553)
>        at
> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:
> 488)
>        at
> org.apache.catalina.startup.HostConfig.start(HostConfig.java:1150)
>        at
> org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:
> 311)
>        at
> org
> .apache
> .catalina
> .util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
>        at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
> 1022)
>        at
> org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
>        at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:
> 1014)
>        at
> org.apache.catalina.core.StandardEngine.start(StandardEngine.java:
> 443)
>        at
> org.apache.catalina.core.StandardService.start(StandardService.java:448)
>        at
> org.apache.catalina.core.StandardServer.start(StandardServer.java:
> 700)
>        at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
>        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>        at
> sun
> .reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:
> 39)
>        at
> sun
> .reflect
> .DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:
> 25)
>        at java.lang.reflect.Method.invoke(Method.java:592)
>        at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
>        at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
> SEVERE: Error listenerStart
> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
> SEVERE: Context [/treebase-web] startup failed due to previous errors
> WARN: The method class
> org.apache.commons.logging.impl.SLF4JLogFactory#release() was invoked.
> WARN: Please see http://www.slf4j.org/codes.html for an explanation.
> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
> SEVERE: Error filterStart
> Sep 9, 2010 4:20:41 PM org.apache.catalina.core.StandardContext start
> SEVERE: Context [/balancer] startup failed due to previous errors
> Sep 9, 2010 4:20:41 PM org.apache.coyote.http11.Http11BaseProtocol start
> INFO: Starting Coyote HTTP/1.1 on http-8080
> Sep 9, 2010 4:20:41 PM org.apache.jk.common.ChannelSocket init
> INFO: JK: ajp13 listening on /0.0.0.0:8009
> Sep 9, 2010 4:20:41 PM org.apache.jk.server.JkMain start
> INFO: Jk running ID=0 time=0/16  config=null
> Sep 9, 2010 4:20:41 PM org.apache.catalina.storeconfig.StoreLoader load
> INFO: Find registry server-registry.xml at classpath resource
> Sep 9, 2010 4:20:42 PM org.apache.catalina.startup.Catalina start
> INFO: Server startup in 8433 ms
>
>
>