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[Treebase-devel] A problem running local treebase
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From: Vladimir G. <vga...@ne...> - 2010-09-09 20:41:30
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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 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
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