NPE in Sql.dbRead
Description
Activity
Stephen Marquard March 29, 2008 at 2:51 AM
Reported as mysql bug:
http://bugs.mysql.com/bug.php?id=35666
As the default and recommended configuration for Sakai deployments is useServerPrepStmts=false (to enable query caching), this does not really affect us.
Stephen Marquard March 29, 2008 at 1:45 AM
This seems to be a bug in the mysql connector related to logging profile info (slow queries) when useServerPrepStmts=true, e.g. these connection properties:
url@javax.sql.BaseDataSource=jdbc:mysql://localhost:3306/sakai?useUnicode=true&characterEncoding=UTF-8&useServerPrepStmts=true&slowQueryThresholdMillis=1&logSlowQueries=true&maxQuerySizeToLog=128000
will trigger many exceptions like this:
java.sql.SQLException: java.lang.NullPointerException
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1055)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:956)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:926)
at com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:864)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1885)
at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatement.java:93)
at org.sakaiproject.db.impl.BasicSqlService.dbRead(BasicSqlService.java:549)
at org.sakaiproject.db.impl.BasicSqlService.dbRead(BasicSqlService.java:468)
at org.sakaiproject.authz.impl.DbAuthzGroupService$DbStorage.isAllowed(DbAuthzGroupService.java:1505)
at org.sakaiproject.authz.impl.BaseAuthzGroupService.isAllowed(BaseAuthzGroupService.java:832)
at org.sakaiproject.authz.impl.SakaiSecurity.checkAuthzGroups(SakaiSecurity.java:289)
at org.sakaiproject.authz.impl.SakaiSecurity.unlock(SakaiSecurity.java:256)
at org.sakaiproject.authz.impl.SakaiSecurity.unlock(SakaiSecurity.java:223)
at org.sakaiproject.authz.impl.SakaiSecurity.unlock(SakaiSecurity.java:215)
at org.sakaiproject.authz.impl.SakaiSecurity.unlock(SakaiSecurity.java:201)
at org.sakaiproject.site.impl.BaseSiteService.unlockCheck(BaseSiteService.java:165)
at org.sakaiproject.site.impl.BaseSiteService.unlock(BaseSiteService.java:185)
at org.sakaiproject.site.impl.BaseSiteService.getSiteVisit(BaseSiteService.java:701)
at org.sakaiproject.site.cover.SiteService.getSiteVisit(SiteService.java:130)
at org.sakaiproject.portal.util.PortalSiteHelper.getSiteVisit(PortalSiteHelper.java:559)
at org.sakaiproject.portal.charon.handlers.SiteHandler.doSite(SiteHandler.java:189)
at org.sakaiproject.portal.charon.handlers.SiteHandler.doGet(SiteHandler.java:114)
at org.sakaiproject.portal.charon.SkinnableCharonPortal.doGet(SkinnableCharonPortal.java:891)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:690)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.sakaiproject.util.RequestFilter.doFilter(RequestFilter.java:592)
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:210)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:174)
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:151)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:870)
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:685)
at java.lang.Thread.run(Thread.java:595)
Caused by: java.lang.NullPointerException
at com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1396)
at com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:838)
... 38 more
2-5-x r43808, mysql-connector-java-5.1.6-bin.jar, mysqld 5.0.26, connector string:
url@javax.sql.BaseDataSource=jdbc:mysql://localhost:3306/vula25uct?useUnicode=true&characterEncoding=UTF-8&useServerPrepStmts=true&slowQueryThresholdMillis=750&logSlowQueries=true&maxQuerySizeToLog=128000
This may be some very specific error to do with mysql connector versions & parameters, or may be some issue in recent 2-5-x. Can't reproduce in trunk however. Still investigating.
WARN: Sql.dbRead: sql: select COUNT(RESOURCE_ID) from CONTENT_RESOURCE where FILE_SIZE is NULL (2008
-03-28 20:16:14,458 main_org.sakaiproject.db.impl.BasicSqlService)
java.sql.SQLException: java.lang.NullPointerException
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1055)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:956)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:926)
at com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:864)
at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1885)
at org.apache.commons.dbcp.DelegatingPreparedStatement.executeQuery(DelegatingPreparedStatem
ent.java:93)
at org.sakaiproject.db.impl.BasicSqlService.dbRead(BasicSqlService.java:550)
at org.sakaiproject.db.impl.BasicSqlService.dbRead(BasicSqlService.java:469)
at org.sakaiproject.db.impl.BasicSqlService.dbRead(BasicSqlService.java:447)
at org.sakaiproject.content.impl.DbContentService.countNullFilesizeValues(DbContentService.j
ava:593)
at org.sakaiproject.content.impl.DbContentService.readyToUseFilesizeColumn(DbContentService.
java:574)
at org.sakaiproject.content.impl.DbContentService.init(DbContentService.java:367)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeCustom
InitMethod(AbstractAutowireCapableBeanFactory.java:1240)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMe
thods(AbstractAutowireCapableBeanFactory.java:1205)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBe
an(AbstractAutowireCapableBeanFactory.java:1171)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(A
bstractAutowireCapableBeanFactory.java:425)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFac
tory.java:251)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(Defau
ltSingletonBeanRegistry.java:156)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory
.java:248)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory
.java:160)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(Be
anDefinitionValueResolver.java:261)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNeces
sary(BeanDefinitionValueResolver.java:109)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropert
yValues(AbstractAutowireCapableBeanFactory.java:1099)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean
(AbstractAutowireCapableBeanFactory.java:861)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:421)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:251)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:156)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:248)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:160)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:261)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:109)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1099)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:861)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:421)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:251)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:156)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:248)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:160)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveReference(BeanDefinitionValueResolver.java:261)
at org.springframework.beans.factory.support.BeanDefinitionValueResolver.resolveValueIfNecessary(BeanDefinitionValueResolver.java:109)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyPropertyValues(AbstractAutowireCapableBeanFactory.java:1099)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.populateBean(AbstractAutowireCapableBeanFactory.java:861)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:421)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:251)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:156)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:248)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:160)
at org.springframework.context.support.AbstractApplicationContext.getBean(AbstractApplicationContext.java:733)
at org.sakaiproject.entitybroker.impl.entityprovider.EntityProviderAutoRegistrar.setApplicationContext(EntityProviderAutoRegistrar.java:41)
at org.springframework.context.support.ApplicationContextAwareProcessor.postProcessBeforeInitialization(ApplicationContextAwareProcessor.java:72)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:301)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1167)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:425)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:251)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:156)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:248)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:160)
at org.sakaiproject.util.NoisierDefaultListableBeanFactory.preInstantiateSingletons(NoisierDefaultListableBeanFactory.java:63)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:352)
at org.sakaiproject.component.impl.SpringCompMgr.init(SpringCompMgr.java:254)
at org.sakaiproject.component.cover.ComponentManager.getInstance(ComponentManager.java:62)
at org.sakaiproject.component.cover.ComponentManager.get(ComponentManager.java:71)
at org.sakaiproject.component.cover.ServerConfigurationService.getInstance(ServerConfigurationService.java:53)
at org.sakaiproject.component.cover.ServerConfigurationService.getStrings(ServerConfigurationService.java:206)
at org.sakaiproject.dav.DavServlet.init(DavServlet.java:521)
at javax.servlet.GenericServlet.init(GenericServlet.java:212)
at org.apache.catalina.core.StandardWrapper.loadServlet(StandardWrapper.java:1139)
at org.apache.catalina.core.StandardWrapper.load(StandardWrapper.java:966)
at org.apache.catalina.core.StandardContext.loadOnStartup(StandardContext.java:3956)
at org.apache.catalina.core.StandardContext.start(StandardContext.java:4230)
at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:760)
at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:740)
at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:544)
at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:626)
at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:553)
at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:488)
at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1138)
at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:311)
at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:120)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1022)
at org.apache.catalina.core.StandardHost.start(StandardHost.java:736)
at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1014)
at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:443)
at org.apache.catalina.core.StandardService.start(StandardService.java:448)
at org.apache.catalina.core.StandardServer.start(StandardServer.java:700)
at org.apache.catalina.startup.Catalina.start(Catalina.java:552)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:585)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:295)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:433)
Caused by: java.lang.NullPointerException
at com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1396)
at com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:838)
... 92 more