Re: [Treebase-devel] Deploying under Tomcat

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Youjun - I don't know whether by TreeBASE installation you mean the  
database or the web-application or both. I think it's pretty critical  
that every developer can bring up a local version of the web- 
application. They may all be accessing the same database, but if  
everyone is updating and redeploying on the same application server  
for every change or debugging run then chaos of the unproductive kind  
will ensue quickly.

	-hilmar

On Dec 15, 2009, at 11:17 PM, youjun guo wrote:

> Vladimir,
>
> Why do you want to deploy a new TreeBASE installation? If you just  
> want to add a java encrypt implementation like MD5 to TreeBASE code,  
> I my be able to help with it. Then you can focus on some other task.
>
> Youjun
>
> On Tue, Dec 15, 2009 at 5:50 PM, Vladimir Gapeyev <vga...@ne... 
> > wrote:
>
> On Dec 15, 2009, at 4:41 PM, youjun guo wrote:
>
> Vladimir,
>
> jdbc.properties should be add to main/resource of treebase-core  
> before bilud, and it will be built into treebase-core jar file.
>
>
> Thanks, this has moved me forward.  The deployment still fails,  
> apparently due to mesquite again. See the excerpt from logs/ 
> catalina.out below.
>
> I do see numerous Eclipse complaints about failing 'import  
> mesquite.lib.*'., which I did not see earlier in the day!  I did  
> update from SVN, as well as all Maven-related update commands I  
> could see in the UI.
>
> --Vladimir
>
>
>
> [main] ERROR org.springframework.web.context.ContextLoader - Context  
> initialization failed
> org.springframework.beans.factory.BeanCreationException: Error  
> creating bean with name 'sessionFactory' defined in URL [jar:file:/ 
> Users/vgapeyev/Work/TreeBase/devel/applications/apache-tomcat-5.5.28/ 
> webapps/treebase-web/WEB-INF/lib/treebase-core-1.0-SNAPSHOT.jar!/ 
> applicationContext-dao.xml]: Invocation of init method failed;  
> nested exception is org.hibernate.InstantiationException: could not  
> instantiate test objectorg.cipres.treebase.domain.taxon.TaxonLabelSet
> Caused by:
> org.hibernate.InstantiationException: could not instantiate test  
> objectorg.cipres.treebase.domain.taxon.TaxonLabelSet
>        at  
> org 
> .hibernate 
> .engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:25)
>        at  
> org 
> .hibernate 
> .engine 
> .UnsavedValueFactory 
> .getUnsavedIdentifierValue(UnsavedValueFactory.java:44)
>        at  
> org 
> .hibernate 
> .tuple.PropertyFactory.buildIdentifierProperty(PropertyFactory.java: 
> 44)
>        at  
> org 
> .hibernate.tuple.entity.EntityMetamodel.<init>(EntityMetamodel.java: 
> 124)
>        at  
> org 
> .hibernate 
> .persister 
> .entity.AbstractEntityPersister.<init>(AbstractEntityPersister.java: 
> 434)
>        at  
> org 
> .hibernate 
> .persister 
> .entity 
> .SingleTableEntityPersister.<init>(SingleTableEntityPersister.java: 
> 109)
>        at  
> org 
> .hibernate 
> .persister 
> .PersisterFactory.createClassPersister(PersisterFactory.java:55)
>        at  
> org.hibernate.impl.SessionFactoryImpl.<init>(SessionFactoryImpl.java: 
> 226)
>        at  
> org 
> .hibernate.cfg.Configuration.buildSessionFactory(Configuration.java: 
> 1300)
>        at  
> org 
> .hibernate 
> .cfg 
> .AnnotationConfiguration 
> .buildSessionFactory(AnnotationConfiguration.java:859)
>        at  
> org 
> .springframework 
> .orm 
> .hibernate3 
> .LocalSessionFactoryBean 
> .newSessionFactory(LocalSessionFactoryBean.java:805)
>        at  
> org 
> .springframework 
> .orm 
> .hibernate3 
> .LocalSessionFactoryBean 
> .buildSessionFactory(LocalSessionFactoryBean.java:745)
>        at  
> org 
> .springframework 
> .orm 
> .hibernate3 
> .AbstractSessionFactoryBean 
> .afterPropertiesSet(AbstractSessionFactoryBean.java:134)
>        at  
> org 
> .springframework 
> .beans 
> .factory 
> .support 
> .AbstractAutowireCapableBeanFactory 
> .invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1198)
>        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:285)
>        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.deployWAR(HostConfig.java:831)
>        at  
> org.apache.catalina.startup.HostConfig.deployWARs(HostConfig.java:720)
>        at  
> org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:490)
>        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)
> Caused by: java.lang.reflect.InvocationTargetException
>        at  
> sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
>        at  
> sun 
> .reflect 
> .NativeConstructorAccessorImpl 
> .newInstance(NativeConstructorAccessorImpl.java:39)
>        at  
> sun 
> .reflect 
> .DelegatingConstructorAccessorImpl 
> .newInstance(DelegatingConstructorAccessorImpl.java:27)
>        at java.lang.reflect.Constructor.newInstance(Constructor.java: 
> 501)
>        at  
> org 
> .hibernate 
> .engine.UnsavedValueFactory.instantiate(UnsavedValueFactory.java:22)
>        ... 49 more
> Caused by: java.lang.Error: Unresolved compilation problems:
>        The import mesquite.lib cannot be resolved
>        StringUtil cannot be resolved
>        StringUtil cannot be resolved
>        StringUtil cannot be resolved
>        StringUtil cannot be resolved
>
>        at  
> org 
> .cipres 
> .treebase.domain.taxon.TaxonLabelSet.<init>(TaxonLabelSet.java:18)
>        ... 54 more
>
>
>
>
>
>
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-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================