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treebase-devel
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From: Vladimir G. <vga...@ne...> - 2009-12-15 20:27:28
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I am now trying to deploy treebase-web.war under Tomcat. Question: where should I place jdbc.properties so that Tomcat finds it when it starts treebase-web? I deploy by placing the war into my CATALINA-HOME/webapps, but it does not start correctly -- see below the relevant log fragment from logs/ catalina.out A looking-ahead question: should also install any dependency JARS in CATALINA/common/lib or something like that, or treebase-web.war comes with all dependencies included? --Vladimir [main] ERROR org.springframework.web.context.ContextLoader - Context initialization failed org.springframework.beans.factory.BeanInitializationException: Could not load properties; nested exception is java.io.FileNotFoundException: class path resource [jdbc.properties] cannot be opened because it does not exist Caused by: java.io.FileNotFoundException: class path resource [jdbc.properties] cannot be opened because it does not exist at org .springframework .core.io.ClassPathResource.getInputStream(ClassPathResource.java:135) at org .springframework .core .io .support .PropertiesLoaderSupport.loadProperties(PropertiesLoaderSupport.java: 179) at org .springframework .core .io .support .PropertiesLoaderSupport.mergeProperties(PropertiesLoaderSupport.java: 158) at org .springframework .beans .factory .config .PropertyResourceConfigurer .postProcessBeanFactory(PropertyResourceConfigurer.java:68) at org .springframework .context .support .AbstractApplicationContext .invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:467) at org .springframework .context .support .AbstractApplicationContext.refresh(AbstractApplicationContext.java:334) 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) [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.BeanInitializationException: Could not load properties; nested exception is java.io.FileNotFoundException: class path resource [jdbc.properties] cannot be opened because it does not exist Caused by: java.io.FileNotFoundException: class path resource [jdbc.properties] cannot be opened because it does not exist at org .springframework .core.io.ClassPathResource.getInputStream(ClassPathResource.java:135) at org .springframework .core .io .support .PropertiesLoaderSupport.loadProperties(PropertiesLoaderSupport.java: 179) at org .springframework .core .io .support .PropertiesLoaderSupport.mergeProperties(PropertiesLoaderSupport.java: 158) at org .springframework .beans .factory .config .PropertyResourceConfigurer .postProcessBeanFactory(PropertyResourceConfigurer.java:68) at org .springframework .context .support .AbstractApplicationContext .invokeBeanFactoryPostProcessors(AbstractApplicationContext.java:467) at org .springframework .context .support .AbstractApplicationContext.refresh(AbstractApplicationContext.java:334) 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) Dec 15, 2009 2:31:16 PM org.apache.catalina.core.StandardContext start SEVERE: Error listenerStart Dec 15, 2009 2:31:16 PM org.apache.catalina.core.StandardContext start SEVERE: Context [/treebase-web] startup failed due to previous errors |
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From: Vladimir G. <vga...@ne...> - 2009-12-15 22:50:26
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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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From: youjun g. <you...@ya...> - 2009-12-15 23:10:13
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uncomment the mesquite dependency in treebase-core/pom.xml see if it works. 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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From: youjun g. <you...@ya...> - 2009-12-15 23:23:46
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Vladimir, Do you know why I cannot access the treebase-web @ treebase-dev.nescent.org:6666? I saw the home page flash and gone. Youjun |
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From: youjun g. <you...@ya...> - 2009-12-16 04:17:58
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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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From: Hilmar L. <hl...@ne...> - 2009-12-16 04:23:32
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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 > > > > > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
|
From: Rutger V. <rut...@gm...> - 2009-12-16 10:07:59
|
I agree that it's useful to have a local web application inside a local tomcat, and it shouldn't be too hard to get that up and running beyond the point where you are now. I am aware of the mesquite.lib.* issues and have just sent out an email discussing this on the "Mesquite troubles" thread. On Wed, Dec 16, 2009 at 4:23 AM, Hilmar Lapp <hl...@ne...> wrote: > 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 >> >> >> >> >> > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: youjun g. <you...@ya...> - 2009-12-16 14:02:49
|
Never mind, I was confused about what Vladimir want to do. Accurately eclipse offer so many ways to integrity a testing purpose Tomcat. As long as one can build the war file, the deployment and testing is just one button away. Youjun On Wed, Dec 16, 2009 at 5:07 AM, Rutger Vos <rut...@gm...> wrote: > I agree that it's useful to have a local web application inside a > local tomcat, and it shouldn't be too hard to get that up and running > beyond the point where you are now. I am aware of the mesquite.lib.* > issues and have just sent out an email discussing this on the > "Mesquite troubles" thread. > > On Wed, Dec 16, 2009 at 4:23 AM, Hilmar Lapp <hl...@ne...> wrote: > > 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 > >> > >> > >> > >> > >> > > > > > ------------------------------------------------------------------------------ > > This SF.Net email is sponsored by the Verizon Developer Community > > Take advantage of Verizon's best-in-class app development support > > A streamlined, 14 day to market process makes app distribution fast and > easy > > Join now and get one step closer to millions of Verizon customers > > http://p.sf.net/sfu/verizon-dev2dev > > _______________________________________________ > > Treebase-devel mailing list > > Tre...@li... > > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > > -- > > =========================================================== > > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > > =========================================================== > > > > > > > > > ------------------------------------------------------------------------------ > > This SF.Net email is sponsored by the Verizon Developer Community > > Take advantage of Verizon's best-in-class app development support > > A streamlined, 14 day to market process makes app distribution fast and > easy > > Join now and get one step closer to millions of Verizon customers > > http://p.sf.net/sfu/verizon-dev2dev > > _______________________________________________ > > Treebase-devel mailing list > > Tre...@li... > > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > > > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > |
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From: Vladimir G. <vga...@ne...> - 2009-12-16 15:02:23
|
On Dec 15, 2009, at 6:23 PM, youjun guo wrote: > Vladimir, > > Do you know why I cannot access the treebase-web @ treebase- > dev.nescent.org:6666? I saw the home page flash and gone. > > Youjun The server itself is up: http://treebase-dev.nescent.org/. My first guess that 6666 is down due to Rutger's ongoing experimentation with Mesquite. (The same reasons I could not set up my deployment yesterday?) I'll try to find and check the logs. I'll also drop a message to Jon, but he is mostly out of reach since yesterday. --Vladimir |
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From: Vladimir G. <vga...@ne...> - 2009-12-16 15:20:16
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On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: > > On Dec 15, 2009, at 6:23 PM, youjun guo wrote: > >> Vladimir, >> >> Do you know why I cannot access the treebase-web @ treebase- >> dev.nescent.org:6666? I saw the home page flash and gone. >> >> Youjun > > The server itself is up: http://treebase-dev.nescent.org/. My first > guess that 6666 is down due to Rutger's ongoing experimentation with > Mesquite. (The same reasons I could not set up my deployment > yesterday?) > > I'll try to find and check the logs. Il'' take the last one back: according to the notes Jon gave me, 6666 starts from Rutger's homedir, to which only he has access. --Vladimir |
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From: youjun g. <you...@ya...> - 2009-12-16 15:40:26
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Do you know which Tomcat server is assigned for all the TreeBASE developers? Youjun On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne...>wrote: > > On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: > > > On Dec 15, 2009, at 6:23 PM, youjun guo wrote: > > Vladimir, > > Do you know why I cannot access the treebase-web @ > treebase-dev.nescent.org:6666? I saw the home page flash and gone. > > Youjun > > > The server itself is up: http://treebase-dev.nescent.org/. My first guess > that 6666 is down due to Rutger's ongoing experimentation with Mesquite. > (The same reasons I could not set up my deployment yesterday?) > > I'll try to find and check the logs. > > > Il'' take the last one back: according to the notes Jon gave me, 6666 > starts from Rutger's homedir, to which only he has access. > > --Vladimir > |
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From: Vladimir G. <vga...@ne...> - 2009-12-16 15:48:05
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http://treebase-dev.nescent.org:6666/treebase-web is the only common TreeBase instance I am aware of. I presumed everyone had their own local tomcats for development purposes -- that's what I have been trying to set up for myself for the past two days... --Vladimir On Dec 16, 2009, at 10:40 AM, youjun guo wrote: > Do you know which Tomcat server is assigned for all the TreeBASE > developers? > > Youjun > > On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne... > > wrote: > > On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: > >> >> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >> >>> Vladimir, >>> >>> Do you know why I cannot access the treebase-web @ treebase- >>> dev.nescent.org:6666? I saw the home page flash and gone. >>> >>> Youjun >> >> The server itself is up: http://treebase-dev.nescent.org/. My >> first guess that 6666 is down due to Rutger's ongoing >> experimentation with Mesquite. (The same reasons I could not set >> up my deployment yesterday?) >> >> I'll try to find and check the logs. > > Il'' take the last one back: according to the notes Jon gave me, > 6666 starts from Rutger's homedir, to which only he has access. > > --Vladimir > |
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From: youjun g. <you...@ya...> - 2009-12-16 16:01:40
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Now I kind of understand, once other developers finish a task and pass the testing on their own environment, just submit the code to sourceforg, Rutger will be the person who redeploy the new code. Thanks Youjun On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne...>wrote: > > http://treebase-dev.nescent.org:6666/treebase-web is the only common > TreeBase instance I am aware of. I presumed everyone had their own local > tomcats for development purposes -- that's what I have been trying to set up > for myself for the past two days... > --Vladimir > > > On Dec 16, 2009, at 10:40 AM, youjun guo wrote: > > Do you know which Tomcat server is assigned for all the TreeBASE > developers? > > Youjun > > On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne...>wrote: > >> >> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >> >> >> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >> >> Vladimir, >> >> Do you know why I cannot access the treebase-web @ >> treebase-dev.nescent.org:6666? I saw the home page flash and gone. >> >> Youjun >> >> >> The server itself is up: http://treebase-dev.nescent.org/. My first >> guess that 6666 is down due to Rutger's ongoing experimentation with >> Mesquite. (The same reasons I could not set up my deployment yesterday?) >> >> I'll try to find and check the logs. >> >> >> Il'' take the last one back: according to the notes Jon gave me, 6666 >> starts from Rutger's homedir, to which only he has access. >> >> --Vladimir >> > > > |
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From: Hilmar L. <hl...@ne...> - 2009-12-16 16:16:57
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Except that that person can't remain Rutger. -hilmar On Dec 16, 2009, at 11:01 AM, youjun guo wrote: > Now I kind of understand, once other developers finish a task and > pass the testing on their own environment, just submit the code to > sourceforg, Rutger will be the person who redeploy the new code. > > Thanks > > Youjun > > On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne... > > wrote: > > http://treebase-dev.nescent.org:6666/treebase-web is the only > common TreeBase instance I am aware of. I presumed everyone had > their own local tomcats for development purposes -- that's what I > have been trying to set up for myself for the past two days... > --Vladimir > > > On Dec 16, 2009, at 10:40 AM, youjun guo wrote: > >> Do you know which Tomcat server is assigned for all the TreeBASE >> developers? >> >> Youjun >> >> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne... >> > wrote: >> >> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >> >>> >>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>> >>>> Vladimir, >>>> >>>> Do you know why I cannot access the treebase-web @ treebase- >>>> dev.nescent.org:6666? I saw the home page flash and gone. >>>> >>>> Youjun >>> >>> The server itself is up: http://treebase-dev.nescent.org/. My >>> first guess that 6666 is down due to Rutger's ongoing >>> experimentation with Mesquite. (The same reasons I could not set >>> up my deployment yesterday?) >>> >>> I'll try to find and check the logs. >> >> Il'' take the last one back: according to the notes Jon gave me, >> 6666 starts from Rutger's homedir, to which only he has access. >> >> --Vladimir >> > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2009-12-16 16:22:21
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Didn't we talk about this already, that we wanted to create a shared developer account or group so that we're all talking about the same environment with the same configuration? I'm not sure what the best way would be to set this up. On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> wrote: > Except that that person can't remain Rutger. -hilmar > On Dec 16, 2009, at 11:01 AM, youjun guo wrote: > > Now I kind of understand, once other developers finish a task and pass the > testing on their own environment, just submit the code to sourceforg, Rutger > will be the person who redeploy the new code. > > Thanks > > Youjun > > On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne...> > wrote: >> >> http://treebase-dev.nescent.org:6666/treebase-web is the only common >> TreeBase instance I am aware of. I presumed everyone had their own local >> tomcats for development purposes -- that's what I have been trying to set up >> for myself for the past two days... >> --Vladimir >> >> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >> >> Do you know which Tomcat server is assigned for all the TreeBASE >> developers? >> >> Youjun >> >> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne...> >> wrote: >>> >>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>> >>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>> >>> Vladimir, >>> >>> Do you know why I cannot access the treebase-web @ >>> treebase-dev.nescent.org:6666? I saw the home page flash and gone. >>> >>> Youjun >>> >>> The server itself is up: http://treebase-dev.nescent.org/. My first >>> guess that 6666 is down due to Rutger's ongoing experimentation with >>> Mesquite. (The same reasons I could not set up my deployment yesterday?) >>> I'll try to find and check the logs. >>> >>> Il'' take the last one back: according to the notes Jon gave me, 6666 >>> starts from Rutger's homedir, to which only he has access. >>> --Vladimir >> > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Hilmar L. <hl...@ne...> - 2009-12-16 16:23:44
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We did - does anyone know where that currently stands? -hilmar On Dec 16, 2009, at 11:22 AM, Rutger Vos wrote: > Didn't we talk about this already, that we wanted to create a shared > developer account or group so that we're all talking about the same > environment with the same configuration? I'm not sure what the best > way would be to set this up. > > On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> > wrote: >> Except that that person can't remain Rutger. -hilmar >> On Dec 16, 2009, at 11:01 AM, youjun guo wrote: >> >> Now I kind of understand, once other developers finish a task and >> pass the >> testing on their own environment, just submit the code to >> sourceforg, Rutger >> will be the person who redeploy the new code. >> >> Thanks >> >> Youjun >> >> On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne... >> > >> wrote: >>> >>> http://treebase-dev.nescent.org:6666/treebase-web is the only >>> common >>> TreeBase instance I am aware of. I presumed everyone had their >>> own local >>> tomcats for development purposes -- that's what I have been trying >>> to set up >>> for myself for the past two days... >>> --Vladimir >>> >>> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >>> >>> Do you know which Tomcat server is assigned for all the TreeBASE >>> developers? >>> >>> Youjun >>> >>> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne... >>> > >>> wrote: >>>> >>>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>>> >>>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>>> >>>> Vladimir, >>>> >>>> Do you know why I cannot access the treebase-web @ >>>> treebase-dev.nescent.org:6666? I saw the home page flash and gone. >>>> >>>> Youjun >>>> >>>> The server itself is up: http://treebase-dev.nescent.org/. My >>>> first >>>> guess that 6666 is down due to Rutger's ongoing experimentation >>>> with >>>> Mesquite. (The same reasons I could not set up my deployment >>>> yesterday?) >>>> I'll try to find and check the logs. >>>> >>>> Il'' take the last one back: according to the notes Jon gave me, >>>> 6666 >>>> starts from Rutger's homedir, to which only he has access. >>>> --Vladimir >>> >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast >> and easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast >> and easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2009-12-16 17:07:46
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Rutger - it looks like at this point we do not have a second deployment-capable installation on treebase-dev, and I get the sense that no one has one local to their lap/desktop either. Since Jon is on parental leave, can you reconfigure your account so that it can function as the shared developer account for now until Jon gets a minute to create that? Also, given that we want to do development work on the web-application in parallel, I'd consider it high priority that we work out local deployments of the web-application on the developers' own machines. Vladimir seems to be almost there - what is missing right now? -hilmar On Dec 16, 2009, at 11:22 AM, Rutger Vos wrote: > Didn't we talk about this already, that we wanted to create a shared > developer account or group so that we're all talking about the same > environment with the same configuration? I'm not sure what the best > way would be to set this up. > > On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> > wrote: >> Except that that person can't remain Rutger. -hilmar >> On Dec 16, 2009, at 11:01 AM, youjun guo wrote: >> >> Now I kind of understand, once other developers finish a task and >> pass the >> testing on their own environment, just submit the code to >> sourceforg, Rutger >> will be the person who redeploy the new code. >> >> Thanks >> >> Youjun >> >> On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne... >> > >> wrote: >>> >>> http://treebase-dev.nescent.org:6666/treebase-web is the only >>> common >>> TreeBase instance I am aware of. I presumed everyone had their >>> own local >>> tomcats for development purposes -- that's what I have been trying >>> to set up >>> for myself for the past two days... >>> --Vladimir >>> >>> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >>> >>> Do you know which Tomcat server is assigned for all the TreeBASE >>> developers? >>> >>> Youjun >>> >>> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev <vga...@ne... >>> > >>> wrote: >>>> >>>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>>> >>>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>>> >>>> Vladimir, >>>> >>>> Do you know why I cannot access the treebase-web @ >>>> treebase-dev.nescent.org:6666? I saw the home page flash and gone. >>>> >>>> Youjun >>>> >>>> The server itself is up: http://treebase-dev.nescent.org/. My >>>> first >>>> guess that 6666 is down due to Rutger's ongoing experimentation >>>> with >>>> Mesquite. (The same reasons I could not set up my deployment >>>> yesterday?) >>>> I'll try to find and check the logs. >>>> >>>> Il'' take the last one back: according to the notes Jon gave me, >>>> 6666 >>>> starts from Rutger's homedir, to which only he has access. >>>> --Vladimir >>> >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast >> and easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast >> and easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel >> >> > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2009-12-16 17:18:25
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http://treebasedb-dev.nescent.org:6666/treebase-web is up and running again, though the mesquite runtime issue is still not resolved. I fixed the compile time issue by putting the dependency on treebase-2.01.tb.jar back in the pom.xml (and committed this). I just got an email from Wayne suggesting a programmatic way to tell mesquite its location at runtime, I still have to try this. I am quite happy to "reconfigure" my account by sharing my login credentials with Youjun and Vladimir off-list (or is there a better way to do this)? I thought Youjun was capable locally of building and deploying the war (while talking to the remote db). I certainly can so I don't *have* to use the rv...@tr... account to get any work done. Vladimir, if you do an update on your end, will the source now build on your system? The complaints about mesquite.lib.* missing should go away. Rutger On Wed, Dec 16, 2009 at 5:07 PM, Hilmar Lapp <hl...@ne...> wrote: > Rutger - > > it looks like at this point we do not have a second deployment-capable > installation on treebase-dev, and I get the sense that no one has one local > to their lap/desktop either. > > Since Jon is on parental leave, can you reconfigure your account so that it > can function as the shared developer account for now until Jon gets a minute > to create that? > > Also, given that we want to do development work on the web-application in > parallel, I'd consider it high priority that we work out local deployments > of the web-application on the developers' own machines. Vladimir seems to be > almost there - what is missing right now? > > -hilmar > > On Dec 16, 2009, at 11:22 AM, Rutger Vos wrote: > >> Didn't we talk about this already, that we wanted to create a shared >> developer account or group so that we're all talking about the same >> environment with the same configuration? I'm not sure what the best >> way would be to set this up. >> >> On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> wrote: >>> >>> Except that that person can't remain Rutger. -hilmar >>> On Dec 16, 2009, at 11:01 AM, youjun guo wrote: >>> >>> Now I kind of understand, once other developers finish a task and pass >>> the >>> testing on their own environment, just submit the code to sourceforg, >>> Rutger >>> will be the person who redeploy the new code. >>> >>> Thanks >>> >>> Youjun >>> >>> On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne...> >>> wrote: >>>> >>>> http://treebase-dev.nescent.org:6666/treebase-web is the only common >>>> TreeBase instance I am aware of. I presumed everyone had their own >>>> local >>>> tomcats for development purposes -- that's what I have been trying to >>>> set up >>>> for myself for the past two days... >>>> --Vladimir >>>> >>>> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >>>> >>>> Do you know which Tomcat server is assigned for all the TreeBASE >>>> developers? >>>> >>>> Youjun >>>> >>>> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev >>>> <vga...@ne...> >>>> wrote: >>>>> >>>>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>>>> >>>>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>>>> >>>>> Vladimir, >>>>> >>>>> Do you know why I cannot access the treebase-web @ >>>>> treebase-dev.nescent.org:6666? I saw the home page flash and gone. >>>>> >>>>> Youjun >>>>> >>>>> The server itself is up: http://treebase-dev.nescent.org/. My first >>>>> guess that 6666 is down due to Rutger's ongoing experimentation with >>>>> Mesquite. (The same reasons I could not set up my deployment >>>>> yesterday?) >>>>> I'll try to find and check the logs. >>>>> >>>>> Il'' take the last one back: according to the notes Jon gave me, 6666 >>>>> starts from Rutger's homedir, to which only he has access. >>>>> --Vladimir >>>> >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.Net email is sponsored by the Verizon Developer Community >>> Take advantage of Verizon's best-in-class app development support >>> A streamlined, 14 day to market process makes app distribution fast and >>> easy >>> Join now and get one step closer to millions of Verizon customers >>> http://p.sf.net/sfu/verizon-dev2dev >>> _______________________________________________ >>> Treebase-devel mailing list >>> Tre...@li... >>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>> >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>> =========================================================== >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> This SF.Net email is sponsored by the Verizon Developer Community >>> Take advantage of Verizon's best-in-class app development support >>> A streamlined, 14 day to market process makes app distribution fast and >>> easy >>> Join now and get one step closer to millions of Verizon customers >>> http://p.sf.net/sfu/verizon-dev2dev >>> _______________________________________________ >>> Treebase-devel mailing list >>> Tre...@li... >>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>> >>> >> >> >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2009-12-16 17:36:04
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On Dec 16, 2009, at 12:18 PM, Rutger Vos wrote: > I just got an email from Wayne suggesting a programmatic way to tell > mesquite its location at runtime, I still have to try this. Has Jin Ruan responded? I'd imagine that he might be very useful, seeing as he modified Mesquite in the first place. If you think it would help, Val or I can write to him separately. On Dec 16, 2009, at 12:07 PM, Hilmar Lapp wrote: > I get the sense that no one has one local to their lap/desktop either. Youjun has one at the Peabody: http://130.132.27.212:8080/treebase-web/home.html (the code runs on his machine but it pulls data from postgresql at NESCent) ... but he's having some problems getting it to update with the latest code. He's working on that.. bp |
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From: Rutger V. <rut...@gm...> - 2009-12-16 17:42:51
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>> I just got an email from Wayne suggesting a programmatic way to tell >> mesquite its location at runtime, I still have to try this. > > Has Jin Ruan responded? I'd imagine that he might be very useful, seeing as he modified Mesquite in the first place. If you think it would help, Val or I can write to him separately. Jin has not yet responded. If he has a good memory he's most likely to be the most useful person so if you or Val could write him that would be excellent. -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Jon A. <jon...@du...> - 2009-12-16 18:22:24
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I suggest that treebase-dev be configured to run from the treebase account on the server. I think all the developers have the login info for that user. I further suggest CATALINA_HOME : /home/treebase/tomcat Tomcat can run from this location with default ports (8080, for web, for example) as long as the 6666 instance is not running (which uses some of the non-web interface default ports) The environment for this user should be setup from scratch instead of copied over from an existing user's home dir. I need to be able to programatically recreate this environment on the staging and production server, so I'll need instructions on how to set everything up. I think those instructions currently exist except for some mesquite issues. Once that is setup, I'll create an initd script that starts tomcat on startup of the server. All developers will be able to start and stop that instance of tomcat as well. Before I left fro parental leave, I created both a staging and a production environment like this for Vladimir. BTW, I tired to start Rutger's instance of tomcat with sudo this morning and was not able to because it needed some environment variables to start. Will this be necessary on production? I would prefer not. I usually put those variables in tomcat5.conf or in the catalina.sh script. Ok, I'll probably check email again tonight or tomorrow. -Jon On Dec 16, 2009, at 12:18 PM, Rutger Vos wrote: > http://treebasedb-dev.nescent.org:6666/treebase-web is up and running > again, though the mesquite runtime issue is still not resolved. I > fixed the compile time issue by putting the dependency on > treebase-2.01.tb.jar back in the pom.xml (and committed this). > > I just got an email from Wayne suggesting a programmatic way to tell > mesquite its location at runtime, I still have to try this. > > I am quite happy to "reconfigure" my account by sharing my login > credentials with Youjun and Vladimir off-list (or is there a better > way to do this)? > > I thought Youjun was capable locally of building and deploying the war > (while talking to the remote db). I certainly can so I don't *have* to > use the rv...@tr... account to get any work done. > Vladimir, if you do an update on your end, will the source now build > on your system? The complaints about mesquite.lib.* missing should go > away. > > Rutger > > On Wed, Dec 16, 2009 at 5:07 PM, Hilmar Lapp <hl...@ne...> > wrote: >> Rutger - >> >> it looks like at this point we do not have a second deployment- >> capable >> installation on treebase-dev, and I get the sense that no one has >> one local >> to their lap/desktop either. >> >> Since Jon is on parental leave, can you reconfigure your account so >> that it >> can function as the shared developer account for now until Jon gets >> a minute >> to create that? >> >> Also, given that we want to do development work on the web- >> application in >> parallel, I'd consider it high priority that we work out local >> deployments >> of the web-application on the developers' own machines. Vladimir >> seems to be >> almost there - what is missing right now? >> >> -hilmar >> >> On Dec 16, 2009, at 11:22 AM, Rutger Vos wrote: >> >>> Didn't we talk about this already, that we wanted to create a shared >>> developer account or group so that we're all talking about the same >>> environment with the same configuration? I'm not sure what the best >>> way would be to set this up. >>> >>> On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> >>> wrote: >>>> >>>> Except that that person can't remain Rutger. -hilmar >>>> On Dec 16, 2009, at 11:01 AM, youjun guo wrote: >>>> >>>> Now I kind of understand, once other developers finish a task and >>>> pass >>>> the >>>> testing on their own environment, just submit the code to >>>> sourceforg, >>>> Rutger >>>> will be the person who redeploy the new code. >>>> >>>> Thanks >>>> >>>> Youjun >>>> >>>> On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne... >>>> > >>>> wrote: >>>>> >>>>> http://treebase-dev.nescent.org:6666/treebase-web is the only >>>>> common >>>>> TreeBase instance I am aware of. I presumed everyone had their >>>>> own >>>>> local >>>>> tomcats for development purposes -- that's what I have been >>>>> trying to >>>>> set up >>>>> for myself for the past two days... >>>>> --Vladimir >>>>> >>>>> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >>>>> >>>>> Do you know which Tomcat server is assigned for all the TreeBASE >>>>> developers? >>>>> >>>>> Youjun >>>>> >>>>> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev >>>>> <vga...@ne...> >>>>> wrote: >>>>>> >>>>>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>>>>> >>>>>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>>>>> >>>>>> Vladimir, >>>>>> >>>>>> Do you know why I cannot access the treebase-web @ >>>>>> treebase-dev.nescent.org:6666? I saw the home page flash and >>>>>> gone. >>>>>> >>>>>> Youjun >>>>>> >>>>>> The server itself is up: http://treebase-dev.nescent.org/. My >>>>>> first >>>>>> guess that 6666 is down due to Rutger's ongoing experimentation >>>>>> with >>>>>> Mesquite. (The same reasons I could not set up my deployment >>>>>> yesterday?) >>>>>> I'll try to find and check the logs. >>>>>> >>>>>> Il'' take the last one back: according to the notes Jon gave >>>>>> me, 6666 >>>>>> starts from Rutger's homedir, to which only he has access. >>>>>> --Vladimir >>>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> This SF.Net email is sponsored by the Verizon Developer Community >>>> Take advantage of Verizon's best-in-class app development support >>>> A streamlined, 14 day to market process makes app distribution >>>> fast and >>>> easy >>>> Join now and get one step closer to millions of Verizon customers >>>> http://p.sf.net/sfu/verizon-dev2dev >>>> _______________________________________________ >>>> Treebase-devel mailing list >>>> Tre...@li... >>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>> >>>> -- >>>> =========================================================== >>>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>>> =========================================================== >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> This SF.Net email is sponsored by the Verizon Developer Community >>>> Take advantage of Verizon's best-in-class app development support >>>> A streamlined, 14 day to market process makes app distribution >>>> fast and >>>> easy >>>> Join now and get one step closer to millions of Verizon customers >>>> http://p.sf.net/sfu/verizon-dev2dev >>>> _______________________________________________ >>>> Treebase-devel mailing list >>>> Tre...@li... >>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>> >>>> >>> >>> >>> >>> -- >>> Dr. Rutger A. Vos >>> School of Biological Sciences >>> Philip Lyle Building, Level 4 >>> University of Reading >>> Reading >>> RG6 6BX >>> United Kingdom >>> Tel: +44 (0) 118 378 7535 >>> http://www.nexml.org >>> http://rutgervos.blogspot.com >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> >> > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: Rutger V. <rut...@gm...> - 2009-12-17 09:37:02
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> The environment for this user should be setup from scratch instead of copied > over from an existing user's home dir. I need to be able to programatically > recreate this environment on the staging and production server, so I'll need > instructions on how to set everything up. I think those instructions > currently exist except for some mesquite issues. That's right, on the wiki I describe my user environment on treebase-dev.nescent.org. A fairly important part in this is played by a number of environment variables (https://sourceforge.net/apps/mediawiki/treebase/index.php?title=HostEnvironment), as you've noticed. If you prefer it's not done this way we may have to split these into variables to do with building and maintenance and variables to do with deployment (which would go into catalina.sh or tomcat5.conf). > On Dec 16, 2009, at 12:18 PM, Rutger Vos wrote: > >> http://treebasedb-dev.nescent.org:6666/treebase-web is up and running >> again, though the mesquite runtime issue is still not resolved. I >> fixed the compile time issue by putting the dependency on >> treebase-2.01.tb.jar back in the pom.xml (and committed this). >> >> I just got an email from Wayne suggesting a programmatic way to tell >> mesquite its location at runtime, I still have to try this. >> >> I am quite happy to "reconfigure" my account by sharing my login >> credentials with Youjun and Vladimir off-list (or is there a better >> way to do this)? >> >> I thought Youjun was capable locally of building and deploying the war >> (while talking to the remote db). I certainly can so I don't *have* to >> use the rv...@tr... account to get any work done. >> Vladimir, if you do an update on your end, will the source now build >> on your system? The complaints about mesquite.lib.* missing should go >> away. >> >> Rutger >> >> On Wed, Dec 16, 2009 at 5:07 PM, Hilmar Lapp <hl...@ne...> wrote: >>> >>> Rutger - >>> >>> it looks like at this point we do not have a second deployment-capable >>> installation on treebase-dev, and I get the sense that no one has one >>> local >>> to their lap/desktop either. >>> >>> Since Jon is on parental leave, can you reconfigure your account so that >>> it >>> can function as the shared developer account for now until Jon gets a >>> minute >>> to create that? >>> >>> Also, given that we want to do development work on the web-application in >>> parallel, I'd consider it high priority that we work out local >>> deployments >>> of the web-application on the developers' own machines. Vladimir seems to >>> be >>> almost there - what is missing right now? >>> >>> -hilmar >>> >>> On Dec 16, 2009, at 11:22 AM, Rutger Vos wrote: >>> >>>> Didn't we talk about this already, that we wanted to create a shared >>>> developer account or group so that we're all talking about the same >>>> environment with the same configuration? I'm not sure what the best >>>> way would be to set this up. >>>> >>>> On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> wrote: >>>>> >>>>> Except that that person can't remain Rutger. -hilmar >>>>> On Dec 16, 2009, at 11:01 AM, youjun guo wrote: >>>>> >>>>> Now I kind of understand, once other developers finish a task and pass >>>>> the >>>>> testing on their own environment, just submit the code to sourceforg, >>>>> Rutger >>>>> will be the person who redeploy the new code. >>>>> >>>>> Thanks >>>>> >>>>> Youjun >>>>> >>>>> On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev >>>>> <vga...@ne...> >>>>> wrote: >>>>>> >>>>>> http://treebase-dev.nescent.org:6666/treebase-web is the only common >>>>>> TreeBase instance I am aware of. I presumed everyone had their own >>>>>> local >>>>>> tomcats for development purposes -- that's what I have been trying to >>>>>> set up >>>>>> for myself for the past two days... >>>>>> --Vladimir >>>>>> >>>>>> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >>>>>> >>>>>> Do you know which Tomcat server is assigned for all the TreeBASE >>>>>> developers? >>>>>> >>>>>> Youjun >>>>>> >>>>>> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev >>>>>> <vga...@ne...> >>>>>> wrote: >>>>>>> >>>>>>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>>>>>> >>>>>>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>>>>>> >>>>>>> Vladimir, >>>>>>> >>>>>>> Do you know why I cannot access the treebase-web @ >>>>>>> treebase-dev.nescent.org:6666? I saw the home page flash and gone. >>>>>>> >>>>>>> Youjun >>>>>>> >>>>>>> The server itself is up: http://treebase-dev.nescent.org/. My first >>>>>>> guess that 6666 is down due to Rutger's ongoing experimentation with >>>>>>> Mesquite. (The same reasons I could not set up my deployment >>>>>>> yesterday?) >>>>>>> I'll try to find and check the logs. >>>>>>> >>>>>>> Il'' take the last one back: according to the notes Jon gave me, 6666 >>>>>>> starts from Rutger's homedir, to which only he has access. >>>>>>> --Vladimir >>>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> This SF.Net email is sponsored by the Verizon Developer Community >>>>> Take advantage of Verizon's best-in-class app development support >>>>> A streamlined, 14 day to market process makes app distribution fast and >>>>> easy >>>>> Join now and get one step closer to millions of Verizon customers >>>>> http://p.sf.net/sfu/verizon-dev2dev >>>>> _______________________________________________ >>>>> Treebase-devel mailing list >>>>> Tre...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>>> >>>>> -- >>>>> =========================================================== >>>>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>>>> =========================================================== >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> This SF.Net email is sponsored by the Verizon Developer Community >>>>> Take advantage of Verizon's best-in-class app development support >>>>> A streamlined, 14 day to market process makes app distribution fast and >>>>> easy >>>>> Join now and get one step closer to millions of Verizon customers >>>>> http://p.sf.net/sfu/verizon-dev2dev >>>>> _______________________________________________ >>>>> Treebase-devel mailing list >>>>> Tre...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>>> >>>>> >>>> >>>> >>>> >>>> -- >>>> Dr. Rutger A. Vos >>>> School of Biological Sciences >>>> Philip Lyle Building, Level 4 >>>> University of Reading >>>> Reading >>>> RG6 6BX >>>> United Kingdom >>>> Tel: +44 (0) 118 378 7535 >>>> http://www.nexml.org >>>> http://rutgervos.blogspot.com >>> >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>> =========================================================== >>> >>> >>> >>> >> >> >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com >> >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast and >> easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Vladimir G. <vla...@du...> - 2009-12-16 18:39:35
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I hope we can agree that what Jon suggests is worthwhile doing. I also hope we can do one more thing alongside this: move whatever settings are currently specified in treebase-core/src/main/resources/ jdbc.properties out of the WAR file and into tomcat configuration. This should enable deploying the same WAR in multiple installations and make everyone's life much easier. --VG On Dec 16, 2009, at 1:22 PM, Jon Auman wrote: > I suggest that treebase-dev be configured to run from the treebase > account on the server. I think all the developers have the login info > for that user. I further suggest > > CATALINA_HOME : /home/treebase/tomcat > Tomcat can run from this location with default ports (8080, for web, > for example) as long as the 6666 instance is not running (which uses > some of the non-web interface default ports) > > The environment for this user should be setup from scratch instead of > copied over from an existing user's home dir. I need to be able to > programatically recreate this environment on the staging and > production server, so I'll need instructions on how to set everything > up. I think those instructions currently exist except for some > mesquite issues. > > Once that is setup, I'll create an initd script that starts tomcat on > startup of the server. All developers will be able to start and stop > that instance of tomcat as well. > > Before I left fro parental leave, I created both a staging and a > production environment like this for Vladimir. > > BTW, I tired to start Rutger's instance of tomcat with sudo this > morning and was not able to because it needed some environment > variables to start. Will this be necessary on production? I would > prefer not. I usually put those variables in tomcat5.conf or in the > catalina.sh script. > > Ok, I'll probably check email again tonight or tomorrow. > > -Jon > > > > On Dec 16, 2009, at 12:18 PM, Rutger Vos wrote: > >> http://treebasedb-dev.nescent.org:6666/treebase-web is up and running >> again, though the mesquite runtime issue is still not resolved. I >> fixed the compile time issue by putting the dependency on >> treebase-2.01.tb.jar back in the pom.xml (and committed this). >> >> I just got an email from Wayne suggesting a programmatic way to tell >> mesquite its location at runtime, I still have to try this. >> >> I am quite happy to "reconfigure" my account by sharing my login >> credentials with Youjun and Vladimir off-list (or is there a better >> way to do this)? >> >> I thought Youjun was capable locally of building and deploying the >> war >> (while talking to the remote db). I certainly can so I don't *have* >> to >> use the rv...@tr... account to get any work done. >> Vladimir, if you do an update on your end, will the source now build >> on your system? The complaints about mesquite.lib.* missing should go >> away. >> >> Rutger >> >> On Wed, Dec 16, 2009 at 5:07 PM, Hilmar Lapp <hl...@ne...> >> wrote: >>> Rutger - >>> >>> it looks like at this point we do not have a second deployment- >>> capable >>> installation on treebase-dev, and I get the sense that no one has >>> one local >>> to their lap/desktop either. >>> >>> Since Jon is on parental leave, can you reconfigure your account so >>> that it >>> can function as the shared developer account for now until Jon gets >>> a minute >>> to create that? >>> >>> Also, given that we want to do development work on the web- >>> application in >>> parallel, I'd consider it high priority that we work out local >>> deployments >>> of the web-application on the developers' own machines. Vladimir >>> seems to be >>> almost there - what is missing right now? >>> >>> -hilmar >>> >>> On Dec 16, 2009, at 11:22 AM, Rutger Vos wrote: >>> >>>> Didn't we talk about this already, that we wanted to create a >>>> shared >>>> developer account or group so that we're all talking about the same >>>> environment with the same configuration? I'm not sure what the best >>>> way would be to set this up. >>>> >>>> On Wed, Dec 16, 2009 at 4:16 PM, Hilmar Lapp <hl...@ne...> >>>> wrote: >>>>> >>>>> Except that that person can't remain Rutger. -hilmar >>>>> On Dec 16, 2009, at 11:01 AM, youjun guo wrote: >>>>> >>>>> Now I kind of understand, once other developers finish a task and >>>>> pass >>>>> the >>>>> testing on their own environment, just submit the code to >>>>> sourceforg, >>>>> Rutger >>>>> will be the person who redeploy the new code. >>>>> >>>>> Thanks >>>>> >>>>> Youjun >>>>> >>>>> On Wed, Dec 16, 2009 at 10:47 AM, Vladimir Gapeyev <vga...@ne... >>>>>> >>>>> wrote: >>>>>> >>>>>> http://treebase-dev.nescent.org:6666/treebase-web is the only >>>>>> common >>>>>> TreeBase instance I am aware of. I presumed everyone had their >>>>>> own >>>>>> local >>>>>> tomcats for development purposes -- that's what I have been >>>>>> trying to >>>>>> set up >>>>>> for myself for the past two days... >>>>>> --Vladimir >>>>>> >>>>>> On Dec 16, 2009, at 10:40 AM, youjun guo wrote: >>>>>> >>>>>> Do you know which Tomcat server is assigned for all the TreeBASE >>>>>> developers? >>>>>> >>>>>> Youjun >>>>>> >>>>>> On Wed, Dec 16, 2009 at 10:20 AM, Vladimir Gapeyev >>>>>> <vga...@ne...> >>>>>> wrote: >>>>>>> >>>>>>> On Dec 16, 2009, at 10:02 AM, Vladimir Gapeyev wrote: >>>>>>> >>>>>>> On Dec 15, 2009, at 6:23 PM, youjun guo wrote: >>>>>>> >>>>>>> Vladimir, >>>>>>> >>>>>>> Do you know why I cannot access the treebase-web @ >>>>>>> treebase-dev.nescent.org:6666? I saw the home page flash and >>>>>>> gone. >>>>>>> >>>>>>> Youjun >>>>>>> >>>>>>> The server itself is up: http://treebase-dev.nescent.org/. My >>>>>>> first >>>>>>> guess that 6666 is down due to Rutger's ongoing experimentation >>>>>>> with >>>>>>> Mesquite. (The same reasons I could not set up my deployment >>>>>>> yesterday?) >>>>>>> I'll try to find and check the logs. >>>>>>> >>>>>>> Il'' take the last one back: according to the notes Jon gave >>>>>>> me, 6666 >>>>>>> starts from Rutger's homedir, to which only he has access. >>>>>>> --Vladimir >>>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> This SF.Net email is sponsored by the Verizon Developer Community >>>>> Take advantage of Verizon's best-in-class app development support >>>>> A streamlined, 14 day to market process makes app distribution >>>>> fast and >>>>> easy >>>>> Join now and get one step closer to millions of Verizon customers >>>>> http://p.sf.net/sfu/verizon-dev2dev >>>>> _______________________________________________ >>>>> Treebase-devel mailing list >>>>> Tre...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>>> >>>>> -- >>>>> =========================================================== >>>>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>>>> =========================================================== >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> This SF.Net email is sponsored by the Verizon Developer Community >>>>> Take advantage of Verizon's best-in-class app development support >>>>> A streamlined, 14 day to market process makes app distribution >>>>> fast and >>>>> easy >>>>> Join now and get one step closer to millions of Verizon customers >>>>> http://p.sf.net/sfu/verizon-dev2dev >>>>> _______________________________________________ >>>>> Treebase-devel mailing list >>>>> Tre...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/treebase-devel >>>>> >>>>> >>>> >>>> >>>> >>>> -- >>>> Dr. Rutger A. Vos >>>> School of Biological Sciences >>>> Philip Lyle Building, Level 4 >>>> University of Reading >>>> Reading >>>> RG6 6BX >>>> United Kingdom >>>> Tel: +44 (0) 118 378 7535 >>>> http://www.nexml.org >>>> http://rutgervos.blogspot.com >>> >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >>> =========================================================== >>> >>> >>> >>> >> >> >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com >> >> ------------------------------------------------------------------------------ >> This SF.Net email is sponsored by the Verizon Developer Community >> Take advantage of Verizon's best-in-class app development support >> A streamlined, 14 day to market process makes app distribution fast >> and easy >> Join now and get one step closer to millions of Verizon customers >> http://p.sf.net/sfu/verizon-dev2dev >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast > and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: Vladimir G. <vla...@du...> - 2009-12-16 19:33:02
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On Dec 16, 2009, at 12:18 PM, Rutger Vos wrote: > Vladimir, if you do an update on your end, will the source now build > on your system? The complaints about mesquite.lib.* missing should go > away. Uff, the easy step is done: I was able to build treebase-web.war that runs on localhost (revision 398). I attach below the cumulative instructions on how I did it. Now I need to figure out what are the most comfortable currently known setups for (1) development and (2) server. The one I figured out so far is not good for either, while the instructions on the wiki did not work for me. Also, I am sure, there are many more details I need to know about the project and now am in a position to start to understand. Who would be the best person to spend a few hours talking to me sometime soon? Rutger, since Wednesday is probably over for you, would you be able to start with me on this Thu morning, around 9am my (US Eastern) time? --Vladimir ==Development environment in Eclipse== * Install Subclipse and Maven Integration plugins * Register Treebase SVN repository in Eclipse ** Open SVN Repositories view: menu Window > Show View > Other ... > SVN / SVN Repositories ** Right-click > New > Repository Location ** Enter https://treebase.svn.sourceforge.net/svnroot/treebase * Connect to the Maven project in SVN ** In Project Explorer, Right-click > New > Project > Maven / Checkout Maven Projects from SCM ** SCM url: SVN as type, browse for the repository registered above, and select the 'trunk' folder. ** Next ** Location: specify as desired (to an empty directory) ** Finish (Takes awhile, not much action visible) * Place <tt>jdbc.properties</tt> file, containing appropriate credentials, into <tt>treebase-core/src/main/resources</tt>. * Build the Maven project, skipping the tests. ** On the 'treebase' project: Run As > m2 6 Maven build ... > *** Goals: package *** Skip tests: checkmark *** Resolve Workspace artifacts: uncheck *** Run ** When successful, this creates treebase/treebase-web/target/treebase- web.war * Deploy treebase-web.war under Tomcat ** Place treebase-web.war into $CATALINA_HOME/webapps ** Start Tomcat via $CATALINA_HOME/bin/startup.sh ** The app should be available at http://localhost:8080/treebase-web/ ** In case of trouble, check logs in $CATALINA_HOME/logs, especially the <tt>catalina.out</tt> log. |
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From: Rutger V. <rut...@gm...> - 2009-12-17 09:31:08
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> Who would be the best person to spend a few hours talking to me sometime > soon? Rutger, since Wednesday is probably over for you, would you be able > to start with me on this Thu morning, around 9am my (US Eastern) time? Sure, I always have gmail chat open (user rutgeraldo) so that's the best way to reach me - or do you really prefer some other means? -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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