treebase-devel

[Treebase-devel] journals page and search

[Hilmar L. <hl...@ne...>]

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 :
===========================================================

Re: [Treebase-devel] journals page and search

[youjun g. <you...@ya...>]

>
> 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

Re: [Treebase-devel] journals page and search

[Rutger V. <rut...@gm...>]

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

[Treebase-devel] TreeBASE is down!!

[William P. <wil...@ya...>]

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

Re: [Treebase-devel] TreeBASE is down!!

[youjun g. <you...@ya...>]

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>
>
>
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Re: [Treebase-devel] TreeBASE is down!!

[Jon A. <jon...@ne...>]

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...
------------------------------------------------------

Re: [Treebase-devel] TreeBASE is down!!

[Jon A. <jon...@ne...>]

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...
------------------------------------------------------

Re: [Treebase-devel] TreeBASE is down!!

[William P. <wil...@ya...>]

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

Re: [Treebase-devel] TreeBASE is down!!

[William P. <wil...@ya...>]

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

Re: [Treebase-devel] TreeBASE is down!!

[William P. <wil...@ya...>]

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
> 
> 

[Treebase-devel] Down again

[William P. <wil...@ya...>]

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]

Re: [Treebase-devel] Down again

[Jon A. <jon...@ne...>]

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...
------------------------------------------------------

Re: [Treebase-devel] Down again

[William P. <wil...@ya...>]

On Mar 21, 2010, at 3:38 PM, Jon Auman wrote:

> I've restarted the server.   I've also added a robots.txt file to block *all* robots. 

It was up for some time, but now when I do a search I get an 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]

Re: [Treebase-devel] Down again

[Vladimir G. <vla...@du...>]

On Mar 21, 2010, at 4:29 PM, William Piel wrote:

> Caused by: org.postgresql.util.PSQLException: ERROR: could not seek  
> to end of segment 0 of relation base/73916/74290: Read-only file  
> system


Jon,
The above looks like the core exception in both of Bill's recent  
reports.  Could it be that, besides being read-only, the file system  
runs out of space or the relation is corrupted?  These are only  
guesses, though.
--VG

Re: [Treebase-devel] Down again

[Jon A. <jon...@ne...>]

Yes, the file system is running out of space. And google wasn't honoring the robots.txt. Since the last reboot, it seems that no spiders are searching the site, so let's see how that goes.

It wasn't just google, but msn, snap.com, baidu.com, ro...@ga...  (WTF?), etc. It was like hey boys, I found a 100GB database, let's index it!

Anywho, I'll be keeping an eye on it. No temp files for the last 1/2 hour.

-Jon


On Mar 21, 2010, at 5:18 PM, Vladimir Gapeyev wrote:

> 
> On Mar 21, 2010, at 4:29 PM, William Piel wrote:
> 
>> Caused by: org.postgresql.util.PSQLException: ERROR: could not seek  
>> to end of segment 0 of relation base/73916/74290: Read-only file  
>> system
> 
> 
> Jon,
> The above looks like the core exception in both of Bill's recent  
> reports.  Could it be that, besides being read-only, the file system  
> runs out of space or the relation is corrupted?  These are only  
> guesses, though.
> --VG
> 
> ------------------------------------------------------------------------------
> 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...
------------------------------------------------------

Re: [Treebase-devel] Down again

[William P. <wil...@ya...>]

On Mar 21, 2010, at 5:30 PM, Jon Auman wrote:

> Yes, the file system is running out of space. And google wasn't honoring the robots.txt. Since the last reboot, it seems that no spiders are searching the site, so let's see how that goes.
> 
> It wasn't just google, but msn, snap.com, baidu.com, ro...@ga...  (WTF?), etc. It was like hey boys, I found a 100GB database, let's index it!
> 
> Anywho, I'll be keeping an eye on it. No temp files for the last 1/2 hour.
> 
> -Jon

Wow.  Thanks Jon. Indeed, in TreebASE1, I found plenty of robots did not respect robots.txt -- when they hit, it would slow me down and I'd listen to a lot of disk activity noise all day...

But I can't help but think -- if we can't keep TreeBASE up for more than a few hours at a time, might it make more sense to pause on the press release until have a lasting solution? I'm concerned that when we make an announcement and all sorts of people head to the site to check it out, I don't want their first experience to be one of an exception barf. 

bp

Re: [Treebase-devel] Down again

[Jon A. <jon...@ne...>]

I think they are respecting robots.txt now.  The database volume has not grown for hours and the apache logs no longer show google searching the database.

-Jon

On Mar 21, 2010, at 9:05 PM, William Piel wrote:

> 
> On Mar 21, 2010, at 5:30 PM, Jon Auman wrote:
> 
>> Yes, the file system is running out of space. And google wasn't honoring the robots.txt. Since the last reboot, it seems that no spiders are searching the site, so let's see how that goes.
>> 
>> It wasn't just google, but msn, snap.com, baidu.com, ro...@ga...  (WTF?), etc. It was like hey boys, I found a 100GB database, let's index it!
>> 
>> Anywho, I'll be keeping an eye on it. No temp files for the last 1/2 hour.
>> 
>> -Jon
> 
> Wow.  Thanks Jon. Indeed, in TreebASE1, I found plenty of robots did not respect robots.txt -- when they hit, it would slow me down and I'd listen to a lot of disk activity noise all day...
> 
> But I can't help but think -- if we can't keep TreeBASE up for more than a few hours at a time, might it make more sense to pause on the press release until have a lasting solution? I'm concerned that when we make an announcement and all sorts of people head to the site to check it out, I don't want their first experience to be one of an exception barf. 
> 
> bp
> 
> 
> ------------------------------------------------------------------------------
> 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.
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-------------------------------------------------------
Jon Auman
Systems Administrator
National Evolutionary Synthesis Center
Duke University
http:www.nescent.org
jon...@ne...
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[Treebase-devel] Deleting junk

[William P. <wil...@ya...>]

We had our first attempt to submit data. A Dutchman, Ben Wielstra, has been uploading NEXUS files -- some a bit malformed (as is common).  However, because issue 2960886 has not been fixed, we can't get rid of the junk data. Plus, even if we could delete a matrix (or tree), taxon labels that are exclusively linked to that matrix will not be deleted with them. 

So, as we resolve 2960886 I think it's important to also simultaneously delete any taxon labels linked to the deleted object but not found in any other tree or matrix. As bad data gets in, the taxon label table gets crowded with a lot of garbage.  

Attached, you can see that his "Taxon Labels Information" page is loaded with weird things like numbers and semi-colons -- things that crept in via poorly NEXUS in which Mesquite did a botched job of parsing.  (also it's got the repeated names, per issue 2973661). 

bp

ps - Frankly, I was hoping that the whole idea of using Mesquite was that it would be a gatekeeper for preventing trash from getting in -- apparently not. 

Re: [Treebase-devel] Deleting junk

[Rutger V. <rut...@gm...>]

> ps - Frankly, I was hoping that the whole idea of using Mesquite was that it
> would be a gatekeeper for preventing trash from getting in -- apparently
> not.

Yeah, this is unfortunate - but not even Mesquite can actually
"validate" nexus files, it just gives it its best shot. Which is why
NeXML is so great, of course.