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From: Jon A. <jon...@ne...> - 2010-03-21 19:38:25
|
I've restarted the server. I've also added a robots.txt file to block *all* robots. Google started indexing the entire site which ended up creating *thousands* of temp files in the postgresql temp folder, resulting in over a dozen GBs of chewed up space. Eventually the disk volume throws itself into 'read-only' mode. The only fix that I know is to then reboot the server. Since I've disabled the search engines, I think we'll be OK. Someone may want to think about writing a finer tuned robots.txt to only allow indexing of certain parts of the site. -Jon On Mar 21, 2010, at 3:02 PM, William Piel wrote: > 3:02 PM EST: When I try to do a simple query, I get a "could not execute query" exception. > > bp > > > > Uncaught Exception Encountered > org.hibernate.exception.SQLGrammarException: could not execute query at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:67) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.loader.Loader.doList(Loader.java:2216) at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104) at org.hibernate.loader.Loader.list(Loader.java:2099) at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:94) at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1569) at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:283) at org.hibernate.impl.CriteriaImpl$Subcriteria.list(CriteriaImpl.java:458) at org.cipres.treebase.dao.study.StudyDAO.findByAuthor(StudyDAO.java:224) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy63.findByAuthor(Unknown Source) at org.cipres.treebase.service.study.StudyServiceImpl.findByAuthor(StudyServiceImpl.java:423) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy80.findByAuthor(Unknown Source) at org.cipres.treebase.web.controllers.StudySearchController.doSearch(StudySearchController.java:277) at org.cipres.treebase.web.controllers.StudySearchController.onSubmit(StudySearchController.java:132) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) Caused by: org.postgresql.util.PSQLException: ERROR: could not seek to end of segment 0 of relation base/73916/74290: Read-only file system at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1592) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1327) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:192) at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:451) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:350) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:254) at org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:93) at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:186) at org.hibernate.loader.Loader.getResultSet(Loader.java:1787) at org.hibernate.loader.Loader.doQuery(Loader.java:674) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236) at org.hibernate.loader.Loader.doList(Loader.java:2213) ... 84 more Cookies: JSESSIONID=[5B4317D7894DB80066B13D0ED75F6270] __utma=[216002130.839762607.1263756393.1264687215.1264739521.8] __utmz=[216002130.1263756393.1.1.utmccn] > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > 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... ------------------------------------------------------ |
|
From: William P. <wil...@ya...> - 2010-03-21 19:02:38
|
3:02 PM EST: When I try to do a simple query, I get a "could not execute query" exception. bp Uncaught Exception Encountered org.hibernate.exception.SQLGrammarException: could not execute query at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:67) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.loader.Loader.doList(Loader.java:2216) at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2104) at org.hibernate.loader.Loader.list(Loader.java:2099) at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:94) at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1569) at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:283) at org.hibernate.impl.CriteriaImpl$Subcriteria.list(CriteriaImpl.java:458) at org.cipres.treebase.dao.study.StudyDAO.findByAuthor(StudyDAO.java:224) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy63.findByAuthor(Unknown Source) at org.cipres.treebase.service.study.StudyServiceImpl.findByAuthor(StudyServiceImpl.java:423) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:616) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:304) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:182) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:149) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:106) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy80.findByAuthor(Unknown Source) at org.cipres.treebase.web.controllers.StudySearchController.doSearch(StudySearchController.java:277) at org.cipres.treebase.web.controllers.StudySearchController.onSubmit(StudySearchController.java:132) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) Caused by: org.postgresql.util.PSQLException: ERROR: could not seek to end of segment 0 of relation base/73916/74290: Read-only file system at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:1592) at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:1327) at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:192) at org.postgresql.jdbc2.AbstractJdbc2Statement.execute(AbstractJdbc2Statement.java:451) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeWithFlags(AbstractJdbc2Statement.java:350) at org.postgresql.jdbc2.AbstractJdbc2Statement.executeQuery(AbstractJdbc2Statement.java:254) at org.apache.tomcat.dbcp.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:93) at org.hibernate.jdbc.AbstractBatcher.getResultSet(AbstractBatcher.java:186) at org.hibernate.loader.Loader.getResultSet(Loader.java:1787) at org.hibernate.loader.Loader.doQuery(Loader.java:674) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:236) at org.hibernate.loader.Loader.doList(Loader.java:2213) ... 84 more Cookies: JSESSIONID=[5B4317D7894DB80066B13D0ED75F6270] __utma=[216002130.839762607.1263756393.1264687215.1264739521.8] __utmz=[216002130.1263756393.1.1.utmccn] |
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From: William P. <wil...@ya...> - 2010-03-21 17:48:46
|
Sorry!! This was a false warning. I think Yale's wireless went down right in the middle of transfer -- and that was the cause of the "Bad Gateway." I jumped to the gun prematurely. I uploaded the file again -- worked fine. bp On Mar 21, 2010, at 1:41 PM, William Piel wrote: > > On Mar 21, 2010, at 10:37 AM, Jon Auman wrote: > >> The database disk volume was thrown offline. This is not good. I had this happen before and I'm fairly certain that the application query issues is throwing the database into a deadlock. I've submitted a bug for this that has been deemed not critical, but I think that decision should be reconsidered. >> >> Meanwhile, I will look to see if postgresql has options to limit the time a query will run. Alternately, I will need to right a cron job that will kill the processes of hung queries. >> >> -Jon > > > I tried uploading a fairly modest file (43 taxa x 1727 characters) but after some time I got the (below) time-out. A few days earlier I had uploaded the exact same file to stage, and it worked fine. In this case I didn't time how long it took to generate the "Bad Gateway" response, but it didn't feel very long (2 min?) -- so for a starter perhaps the server's time-out parameter should be increased. > > bp > > Bad Gateway > > The proxy server received an invalid response from an upstream server. > Apache/2.2.3 (CentOS) Server at www.treebase.org Port 80 > > |
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From: William P. <wil...@ya...> - 2010-03-21 17:42:58
|
On Mar 21, 2010, at 10:37 AM, Jon Auman wrote: > The database disk volume was thrown offline. This is not good. I had this happen before and I'm fairly certain that the application query issues is throwing the database into a deadlock. I've submitted a bug for this that has been deemed not critical, but I think that decision should be reconsidered. > > Meanwhile, I will look to see if postgresql has options to limit the time a query will run. Alternately, I will need to right a cron job that will kill the processes of hung queries. > > -Jon I tried uploading a fairly modest file (43 taxa x 1727 characters) but after some time I got the (below) time-out. A few days earlier I had uploaded the exact same file to stage, and it worked fine. In this case I didn't time how long it took to generate the "Bad Gateway" response, but it didn't feel very long (2 min?) -- so for a starter perhaps the server's time-out parameter should be increased. bp Bad Gateway The proxy server received an invalid response from an upstream server. Apache/2.2.3 (CentOS) Server at www.treebase.org Port 80 |
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From: William P. <wil...@ya...> - 2010-03-21 16:04:24
|
Thanks for investigating this so quickly. I'm going to hazard a guess that the long time-out queries may be the result of robots clicking on anything clickable. If we don't have a robots.txt file in place, can we add a few in relevant places? bp On Mar 21, 2010, at 10:37 AM, Jon Auman wrote: > The database disk volume was thrown offline. This is not good. I had this happen before and I'm fairly certain that the application query issues is throwing the database into a deadlock. I've submitted a bug for this that has been deemed not critical, but I think that decision should be reconsidered. > > Meanwhile, I will look to see if postgresql has options to limit the time a query will run. Alternately, I will need to right a cron job that will kill the processes of hung queries. > > -Jon |
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From: Jon A. <jon...@ne...> - 2010-03-21 14:37:49
|
The database disk volume was thrown offline. This is not good. I had this happen before and I'm fairly certain that the application query issues is throwing the database into a deadlock. I've submitted a bug for this that has been deemed not critical, but I think that decision should be reconsidered. Meanwhile, I will look to see if postgresql has options to limit the time a query will run. Alternately, I will need to right a cron job that will kill the processes of hung queries. -Jon On Mar 21, 2010, at 9:26 AM, William Piel wrote: > Already?! > > bp > Could not open Hibernate Session for transaction; nested exception is org.hibernate.exception.JDBCConnectionException: Cannot open connection > > org.springframework.transaction.CannotCreateTransactionException: Could not open Hibernate Session for transaction; nested exception is org.hibernate.exception.JDBCConnectionException: Cannot open connection Caused by: org.hibernate.exception.JDBCConnectionException: Cannot open connection at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:74) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:29) at org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:426) at org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:144) at org.hibernate.jdbc.JDBCContext.connection(JDBCContext.java:119) at org.hibernate.transaction.JDBCTransaction.begin(JDBCTransaction.java:57) at org.hibernate.impl.SessionImpl.beginTransaction(SessionImpl.java:1326) at org.springframework.orm.hibernate3.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:510) at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:350) at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:262) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:101) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy84.getStudyService(Unknown Source) at org.cipres.treebase.web.controllers.StudySearchController.doSearch(StudySearchController.java:247) at org.cipres.treebase.web.controllers.StudySearchController.onSubmit(StudySearchController.java:132) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) Caused by: org.postgresql.util.PSQLException: Connection refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections. at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:123) at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66) at org.postgresql.jdbc2.AbstractJdbc2Connection.(AbstractJdbc2Connection.java:124) at org.postgresql.jdbc3.AbstractJdbc3Connection.(AbstractJdbc3Connection.java:30) at org.postgresql.jdbc3.Jdbc3Connection.(Jdbc3Connection.java:24) at org.postgresql.Driver.makeConnection(Driver.java:386) at org.postgresql.Driver.connect(Driver.java:260) at org.apache.tomcat.dbcp.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38) at org.apache.tomcat.dbcp.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:294) at org.apache.tomcat.dbcp.pool.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:1147) at org.apache.tomcat.dbcp.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:96) at org.apache.tomcat.dbcp.dbcp.BasicDataSource.getConnection(BasicDataSource.java:880) at org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider.getConnection(LocalDataSourceConnectionProvider.java:81) at org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:423) ... 65 more Caused by: java.net.ConnectException: Connection refused at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:310) at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:176) at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:163) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:381) at java.net.Socket.connect(Socket.java:537) at java.net.Socket.connect(Socket.java:487) at java.net.Socket.(Socket.java:384) at java.net.Socket.(Socket.java:198) at org.postgresql.core.PGStream.(PGStream.java:62) at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:77) ... 78 more « Back > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > 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: Jon A. <jon...@ne...> - 2010-03-21 14:17:48
|
Looking into it. -Jon On Mar 21, 2010, at 9:26 AM, William Piel wrote: > Already?! > > bp > Could not open Hibernate Session for transaction; nested exception is org.hibernate.exception.JDBCConnectionException: Cannot open connection > > org.springframework.transaction.CannotCreateTransactionException: Could not open Hibernate Session for transaction; nested exception is org.hibernate.exception.JDBCConnectionException: Cannot open connection Caused by: org.hibernate.exception.JDBCConnectionException: Cannot open connection at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:74) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:29) at org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:426) at org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:144) at org.hibernate.jdbc.JDBCContext.connection(JDBCContext.java:119) at org.hibernate.transaction.JDBCTransaction.begin(JDBCTransaction.java:57) at org.hibernate.impl.SessionImpl.beginTransaction(SessionImpl.java:1326) at org.springframework.orm.hibernate3.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:510) at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:350) at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:262) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:101) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy84.getStudyService(Unknown Source) at org.cipres.treebase.web.controllers.StudySearchController.doSearch(StudySearchController.java:247) at org.cipres.treebase.web.controllers.StudySearchController.onSubmit(StudySearchController.java:132) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) Caused by: org.postgresql.util.PSQLException: Connection refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections. at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:123) at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66) at org.postgresql.jdbc2.AbstractJdbc2Connection.(AbstractJdbc2Connection.java:124) at org.postgresql.jdbc3.AbstractJdbc3Connection.(AbstractJdbc3Connection.java:30) at org.postgresql.jdbc3.Jdbc3Connection.(Jdbc3Connection.java:24) at org.postgresql.Driver.makeConnection(Driver.java:386) at org.postgresql.Driver.connect(Driver.java:260) at org.apache.tomcat.dbcp.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38) at org.apache.tomcat.dbcp.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:294) at org.apache.tomcat.dbcp.pool.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:1147) at org.apache.tomcat.dbcp.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:96) at org.apache.tomcat.dbcp.dbcp.BasicDataSource.getConnection(BasicDataSource.java:880) at org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider.getConnection(LocalDataSourceConnectionProvider.java:81) at org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:423) ... 65 more Caused by: java.net.ConnectException: Connection refused at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:310) at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:176) at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:163) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:381) at java.net.Socket.connect(Socket.java:537) at java.net.Socket.connect(Socket.java:487) at java.net.Socket.(Socket.java:384) at java.net.Socket.(Socket.java:198) at org.postgresql.core.PGStream.(PGStream.java:62) at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:77) ... 78 more « Back > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > 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... ------------------------------------------------------ |
|
From: youjun g. <you...@ya...> - 2010-03-21 13:41:20
|
most likely the database is down or the file $CATALINA_HOME/conf/Catalina/localhost/treebase-web.xml is crashed. Youjun On Sun, Mar 21, 2010 at 9:26 AM, William Piel <wil...@ya...> wrote: > Already?! > > bp > > Could not open Hibernate Session for transaction; nested exception is > org.hibernate.exception.JDBCConnectionException: Cannot open connection > org.springframework.transaction.CannotCreateTransactionException: Could not > open Hibernate Session for transaction; nested exception is > org.hibernate.exception.JDBCConnectionException: Cannot open connection > Caused by: org.hibernate.exception.JDBCConnectionException: Cannot open > connection at > org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:74) > at > org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) > at > org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:29) > at > org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:426) > at > org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:144) > at org.hibernate.jdbc.JDBCContext.connection(JDBCContext.java:119) at > org.hibernate.transaction.JDBCTransaction.begin(JDBCTransaction.java:57) at > org.hibernate.impl.SessionImpl.beginTransaction(SessionImpl.java:1326) at > org.springframework.orm.hibernate3.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:510) > at > org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:350) > at > org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:262) > at > org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:101) > at > org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) > at > org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) > at $Proxy84.getStudyService(Unknown Source) at > org.cipres.treebase.web.controllers.StudySearchController.doSearch(StudySearchController.java:247) > at > org.cipres.treebase.web.controllers.StudySearchController.onSubmit(StudySearchController.java:132) > at > org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) > at > org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) > at > org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) > at > org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) > at > org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) > at > org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) > at > org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) > at > org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) > at > org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) > at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at > javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) > at > org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) > at > com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) > at > org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) > at > org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) > at > org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) > at > org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) > at > org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) > at > org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) > at > org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) > at > org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) > at > org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) > at > org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) > at > org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) > at > org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) > at > org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) > at > org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) > at > org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) > at > org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) > at > org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) > at > org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) > at > org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) > at > org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) > at > org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) > at > org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) > at > org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) > at > org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) > at > org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) > at > org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) > at java.lang.Thread.run(Thread.java:636) Caused by: > org.postgresql.util.PSQLException: Connection refused. Check that the > hostname and port are correct and that the postmaster is accepting TCP/IP > connections. at > org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:123) > at > org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66) > at > org.postgresql.jdbc2.AbstractJdbc2Connection.(AbstractJdbc2Connection.java:124) > at > org.postgresql.jdbc3.AbstractJdbc3Connection.(AbstractJdbc3Connection.java:30) > at org.postgresql.jdbc3.Jdbc3Connection.(Jdbc3Connection.java:24) at > org.postgresql.Driver.makeConnection(Driver.java:386) at > org.postgresql.Driver.connect(Driver.java:260) at > org.apache.tomcat.dbcp.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38) > at > org.apache.tomcat.dbcp.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:294) > at > org.apache.tomcat.dbcp.pool.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:1147) > at > org.apache.tomcat.dbcp.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:96) > at > org.apache.tomcat.dbcp.dbcp.BasicDataSource.getConnection(BasicDataSource.java:880) > at > org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider.getConnection(LocalDataSourceConnectionProvider.java:81) > at > org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:423) > ... 65 more Caused by: java.net.ConnectException: Connection refused at > java.net.PlainSocketImpl.socketConnect(Native Method) at > java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:310) > at > java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:176) > at > java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:163) > at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:381) at > java.net.Socket.connect(Socket.java:537) at > java.net.Socket.connect(Socket.java:487) at > java.net.Socket.(Socket.java:384) at java.net.Socket.(Socket.java:198) at > org.postgresql.core.PGStream.(PGStream.java:62) at > org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:77) > ... 78 more « Back <http://treebase.nescent.org/user/submissionList.html> > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > |
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From: William P. <wil...@ya...> - 2010-03-21 13:26:46
|
Already?! bp Could not open Hibernate Session for transaction; nested exception is org.hibernate.exception.JDBCConnectionException: Cannot open connection org.springframework.transaction.CannotCreateTransactionException: Could not open Hibernate Session for transaction; nested exception is org.hibernate.exception.JDBCConnectionException: Cannot open connection Caused by: org.hibernate.exception.JDBCConnectionException: Cannot open connection at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:74) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43) at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:29) at org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:426) at org.hibernate.jdbc.ConnectionManager.getConnection(ConnectionManager.java:144) at org.hibernate.jdbc.JDBCContext.connection(JDBCContext.java:119) at org.hibernate.transaction.JDBCTransaction.begin(JDBCTransaction.java:57) at org.hibernate.impl.SessionImpl.beginTransaction(SessionImpl.java:1326) at org.springframework.orm.hibernate3.HibernateTransactionManager.doBegin(HibernateTransactionManager.java:510) at org.springframework.transaction.support.AbstractPlatformTransactionManager.getTransaction(AbstractPlatformTransactionManager.java:350) at org.springframework.transaction.interceptor.TransactionAspectSupport.createTransactionIfNecessary(TransactionAspectSupport.java:262) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:101) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204) at $Proxy84.getStudyService(Unknown Source) at org.cipres.treebase.web.controllers.StudySearchController.doSearch(StudySearchController.java:247) at org.cipres.treebase.web.controllers.StudySearchController.onSubmit(StudySearchController.java:132) at org.springframework.web.servlet.mvc.SimpleFormController.processFormSubmission(SimpleFormController.java:267) at org.springframework.web.servlet.mvc.CancellableFormController.processFormSubmission(CancellableFormController.java:140) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:265) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441) at javax.servlet.http.HttpServlet.service(HttpServlet.java:647) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:873) at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665) at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528) at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81) at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689) at java.lang.Thread.run(Thread.java:636) Caused by: org.postgresql.util.PSQLException: Connection refused. Check that the hostname and port are correct and that the postmaster is accepting TCP/IP connections. at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:123) at org.postgresql.core.ConnectionFactory.openConnection(ConnectionFactory.java:66) at org.postgresql.jdbc2.AbstractJdbc2Connection.(AbstractJdbc2Connection.java:124) at org.postgresql.jdbc3.AbstractJdbc3Connection.(AbstractJdbc3Connection.java:30) at org.postgresql.jdbc3.Jdbc3Connection.(Jdbc3Connection.java:24) at org.postgresql.Driver.makeConnection(Driver.java:386) at org.postgresql.Driver.connect(Driver.java:260) at org.apache.tomcat.dbcp.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38) at org.apache.tomcat.dbcp.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:294) at org.apache.tomcat.dbcp.pool.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:1147) at org.apache.tomcat.dbcp.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:96) at org.apache.tomcat.dbcp.dbcp.BasicDataSource.getConnection(BasicDataSource.java:880) at org.springframework.orm.hibernate3.LocalDataSourceConnectionProvider.getConnection(LocalDataSourceConnectionProvider.java:81) at org.hibernate.jdbc.ConnectionManager.openConnection(ConnectionManager.java:423) ... 65 more Caused by: java.net.ConnectException: Connection refused at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:310) at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:176) at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:163) at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:381) at java.net.Socket.connect(Socket.java:537) at java.net.Socket.connect(Socket.java:487) at java.net.Socket.(Socket.java:384) at java.net.Socket.(Socket.java:198) at org.postgresql.core.PGStream.(PGStream.java:62) at org.postgresql.core.v3.ConnectionFactoryImpl.openConnectionImpl(ConnectionFactoryImpl.java:77) ... 78 more « Back |
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From: Rutger V. <rut...@gm...> - 2010-03-21 12:13:21
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Hi all, I cleaned up the html in the recently added static pages. > I'm a little surprised actually that the '=' character in the query > strong doesn't need to be URL-encoded - not sure to what extent that's > by chance or demanded by the HTTP spec. To be on the safe side, I > encoded them all as %3D. I think everything between the first = and the & is considered a single value regardless how many subsequent = there are. Certainly our application does, so I don't think we have to encode them (though I've left them as is, for now). > I also made them == so that it's an exact search. It turns out that > regardless the search is a substring search. I suppose that's a bug > and will submit to the tracker. It means that right now a search for > journal Evolution won't work - it's in too many journal names. Yeah, I know, that needs some work. Rutger |
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From: Hilmar L. <hl...@ne...> - 2010-03-21 02:25:04
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That's a browser cache issue. Reset your cache and it will work. -hilmar Sent from away On Mar 20, 2010, at 7:35 PM, Ryan Scherle <rsc...@ne...> wrote: > BUT http://treebase.org redirects to http://treebase.org/treebase/index.html > which produces a 404. |
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From: youjun g. <you...@ya...> - 2010-03-21 01:58:26
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> > Apparently the copy&paste resulted in a bit of a mess > Since the time issue, I remove the style attributes from the page to avoid overwriting of the treebase style sheet, and leave the html elements untouched. I can clean the code later. thanks Youjun |
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From: Jon A. <jon...@ne...> - 2010-03-21 01:09:52
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It may be a temporary DNS resolution issue. It works fine for me. -Jon On Mar 20, 2010, at 8:35 PM, Ryan Scherle wrote: > http://www.treebase.org looks correct. > > BUT http://treebase.org redirects to http://treebase.org/treebase/index.html which produces a 404. > > -- Ryan > > On Mar 20, 2010, at 8:15 PM, Jon Auman wrote: > >> I fixed the redirect. It should all be treebase.org from here on. >> -Jon >> >> >> On Mar 20, 2010, at 5:56 PM, William Piel wrote: >> >>> >>> On Mar 20, 2010, at 5:01 PM, Jon Auman wrote: >>> >>>> Scripts have been run to update database, latest war file deployed, treeebase.nescent.org points towards production database, and treebase.org now points to treebase.nescent.org >>>> >>>> treebase.org should start resolving soon! >>> >>> Great! Thanks Jon. >>> >>> By the way, I gather you have a redirect so that http://treebase.nescent.org or http://www.treebase.org resolves to http://treebase.nescent.org/treebase-web/home.html. Can you change this so that instead it redirects to http://www.treebase.org/treebase-web/home.html ? (otherwise people will start bookmarking the nescent.org domain, which will be confusing if we ever change it) >>> >>> thanks, >>> >>> Bill >>> >>> >>> ------------------------------------------------------------------------------ >>> Download Intel® Parallel Studio Eval >>> Try the new software tools for yourself. Speed compiling, find bugs >>> proactively, and fine-tune applications for parallel performance. >>> See why Intel Parallel Studio got high marks during beta. >>> http://p.sf.net/sfu/intel-sw-dev_______________________________________________ >>> 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... >> ------------------------------------------------------ >> >> >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev_______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > 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: Ryan S. <rsc...@ne...> - 2010-03-21 00:35:55
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http://www.treebase.org looks correct. BUT http://treebase.org redirects to http://treebase.org/treebase/index.html which produces a 404. -- Ryan On Mar 20, 2010, at 8:15 PM, Jon Auman wrote: > I fixed the redirect. It should all be treebase.org from here on. > -Jon > > > On Mar 20, 2010, at 5:56 PM, William Piel wrote: > >> >> On Mar 20, 2010, at 5:01 PM, Jon Auman wrote: >> >>> Scripts have been run to update database, latest war file deployed, treeebase.nescent.org points towards production database, and treebase.org now points to treebase.nescent.org >>> >>> treebase.org should start resolving soon! >> >> Great! Thanks Jon. >> >> By the way, I gather you have a redirect so that http://treebase.nescent.org or http://www.treebase.org resolves to http://treebase.nescent.org/treebase-web/home.html. Can you change this so that instead it redirects to http://www.treebase.org/treebase-web/home.html ? (otherwise people will start bookmarking the nescent.org domain, which will be confusing if we ever change it) >> >> thanks, >> >> Bill >> >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev_______________________________________________ >> 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... > ------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: Jon A. <jon...@ne...> - 2010-03-21 00:15:21
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I fixed the redirect. It should all be treebase.org from here on. -Jon On Mar 20, 2010, at 5:56 PM, William Piel wrote: > > On Mar 20, 2010, at 5:01 PM, Jon Auman wrote: > >> Scripts have been run to update database, latest war file deployed, treeebase.nescent.org points towards production database, and treebase.org now points to treebase.nescent.org >> >> treebase.org should start resolving soon! > > Great! Thanks Jon. > > By the way, I gather you have a redirect so that http://treebase.nescent.org or http://www.treebase.org resolves to http://treebase.nescent.org/treebase-web/home.html. Can you change this so that instead it redirects to http://www.treebase.org/treebase-web/home.html ? (otherwise people will start bookmarking the nescent.org domain, which will be confusing if we ever change it) > > thanks, > > Bill > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > 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: Val T. <va...@ci...> - 2010-03-20 22:44:09
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Congratulations to all! BTW, am at a conference in Lausanne and will meet Bernard Moret early next week. I am sure he will be delighted! Val |
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From: Hilmar L. <hl...@ne...> - 2010-03-20 22:32:02
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I understand that this will be proxied so the nescent.org domain will not show. -hilmar On Mar 20, 2010, at 4:56 PM, William Piel wrote: > > On Mar 20, 2010, at 5:01 PM, Jon Auman wrote: > >> Scripts have been run to update database, latest war file deployed, >> treeebase.nescent.org points towards production database, and >> treebase.org now points to treebase.nescent.org >> >> treebase.org should start resolving soon! > > Great! Thanks Jon. > > By the way, I gather you have a redirect so that http://treebase.nescent.org > or http://www.treebase.org resolves to http://treebase.nescent.org/treebase-web/home.html > . Can you change this so that instead it redirects to http://www.treebase.org/treebase-web/home.html > ? (otherwise people will start bookmarking the nescent.org domain, > which will be confusing if we ever change it) > > thanks, > > Bill > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev_______________________________________________ > 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: William P. <wil...@ya...> - 2010-03-20 21:56:22
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On Mar 20, 2010, at 5:01 PM, Jon Auman wrote: > Scripts have been run to update database, latest war file deployed, treeebase.nescent.org points towards production database, and treebase.org now points to treebase.nescent.org > > treebase.org should start resolving soon! Great! Thanks Jon. By the way, I gather you have a redirect so that http://treebase.nescent.org or http://www.treebase.org resolves to http://treebase.nescent.org/treebase-web/home.html. Can you change this so that instead it redirects to http://www.treebase.org/treebase-web/home.html ? (otherwise people will start bookmarking the nescent.org domain, which will be confusing if we ever change it) thanks, Bill |
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From: Jon A. <jon...@ne...> - 2010-03-20 21:01:59
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Scripts have been run to update database, latest war file deployed, treeebase.nescent.org points towards production database, and treebase.org now points to treebase.nescent.org treebase.org should start resolving soon! -Jon On Mar 20, 2010, at 3:33 PM, Vladimir Gapeyev wrote: > Jon, > > It sounds like we are ready to go for a final check. Please > > - Fix the production database by running the script treebase-core/db/ > cleaning/pre-release_hotfixes/fix_taxonlabelset.sql > Save the output into SVN, just for reference. > > - Deploy the most recent WAR (#16) to nescent.treebase.org. Just > for consistency, deploy it to treebase-dev as well. > > - Point nescent.treebase.org to the production DB. > > Let treebase-dev mailing list know when this happens. > > There will be a later call from Hilmar or Bill to switch DNS or to > repeat the above cycle. > > Thanks, > > --Vladimir > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > 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: Vladimir G. <vga...@ne...> - 2010-03-20 19:33:12
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Jon,
It sounds like we are ready to go for a final check. Please
- Fix the production database by running the script treebase-core/db/
cleaning/pre-release_hotfixes/fix_taxonlabelset.sql
Save the output into SVN, just for reference.
- Deploy the most recent WAR (#16) to nescent.treebase.org. Just
for consistency, deploy it to treebase-dev as well.
- Point nescent.treebase.org to the production DB.
Let treebase-dev mailing list know when this happens.
There will be a later call from Hilmar or Bill to switch DNS or to
repeat the above cycle.
Thanks,
--Vladimir
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From: William P. <met...@gm...> - 2010-03-20 19:07:46
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I'm still away from my computer - i defer to your judgements. Feel free to go ahead. Bill On 3/20/10, Hilmar Lapp <hl...@ne...> wrote: > It looks to me like we are ready to flip the switch. Jon - this is > your signal, unless Bill overrides it before 3.30pm. Let me know when > you switch so I can adjust the PURL. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > |
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From: Hilmar L. <hl...@ne...> - 2010-03-20 18:54:12
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It looks to me like we are ready to flip the switch. Jon - this is your signal, unless Bill overrides it before 3.30pm. Let me know when you switch so I can adjust the PURL. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2010-03-20 18:51:01
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I fixed up the links and titles for the Journals page. Apparently the copy&paste resulted in a bit of a mess, useless title="" tags, and MS Office artifacts like class=MsoNormal. I'm a little surprised actually that the '=' character in the query strong doesn't need to be URL-encoded - not sure to what extent that's by chance or demanded by the HTTP spec. To be on the safe side, I encoded them all as %3D. I also made them == so that it's an exact search. It turns out that regardless the search is a substring search. I suppose that's a bug and will submit to the tracker. It means that right now a search for journal Evolution won't work - it's in too many journal names. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: youjun g. <you...@gm...> - 2010-03-20 16:13:32
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Dear All, The page text updating has been done. Thanks Youjun |
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From: William P. <wil...@ya...> - 2010-03-20 12:57:38
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Last night I added a bug report about taxon labels that get duplicated, triplicated, etc: http://sourceforge.net/tracker/?func=detail&aid=2973661&group_id=248804&atid=1126676 I gave it an "8" so as not to slow us down. But I just wanted to mention that this is a new thing that did not happen even as recently as the build before last. For example, the bug does not exist if you go here: http://treebasedb-dev.nescent.org:6666/treebase-web/ But it does exist on production and port 80 dev. In the attached example, you can see that each taxon label is repeated four times. And then looking at the very same data through 6666, each taxon label is shown once (as it should be). So while this is not a show-stopper, I wanted to mention it because maybe this is an easy, quick fix -- perhaps someone can recall a very recent change he made to the code that might affect the taxon labels page? Or perhaps some configuration file changed? bp |
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