Re: [threadfix] [ThreadFix 2.1M2] HibernateJdbcException: JDBC exception on Hibernate data access

[Dan Cornell]

Couple of questions:

-Is the login successful? (ie after you see the error screen can you navigate ThreadFix normally?)

-Did you notice if you were having a similar issue with the default HSQL installation?

[Dan Cornell]

For some reason I can't find the original post. It is below.

Also this is being tracked in this GitHub issue:

https://github.com/denimgroup/threadfix/issues/188

---------------------------------

ThreadFix 2.1M2
Freshly installed Ubuntu 14.04.1 x64 server w/ Oracle Java 7
Using external MySQL 5.5.38 database

This happens every login and loading of the dashboard. It appears a transaction is set to readonly.

Here is the stack:

org.springframework.orm.hibernate3.HibernateJdbcException: JDBC exception on Hibernate data access: SQLException for SQL [update DefaultConfiguration set activeDirectoryBase=?, activeDirectoryCredentials=?, activeDirectoryURL=?, activeDirectoryUsername=?, defaultRoleId=?, globalGroupEnabled=?, hasCachedData=?, lastScannerMappingsUpdate=?, proxyHost=?, proxyPasswordEncrypted=?, proxyPort=?, proxyUsernameEncrypted=?, shouldProxyBugzilla=?, shouldProxyHPQC=?, shouldProxyJira=?, shouldProxyQualys=?, shouldProxyTFS=?, shouldProxyVeracode=?, shouldProxyVersionOne=?, shouldProxyWhiteHat=?, shouldUseProxyCredentials=? where id=?]; SQL state [S1009]; error code [0]; Could not execute JDBC batch update; nested exception is org.hibernate.exception.GenericJDBCException: Could not execute JDBC batch update
at org.springframework.orm.hibernate3.SessionFactoryUtils.convertHibernateAccessException(SessionFactoryUtils.java:651)
at org.springframework.orm.hibernate3.HibernateExceptionTranslator.convertHibernateAccessException(HibernateExceptionTranslator.java:89)
at org.springframework.orm.hibernate3.HibernateExceptionTranslator.translateExceptionIfPossible(HibernateExceptionTranslator.java:68)
at org.springframework.dao.support.ChainedPersistenceExceptionTranslator.translateExceptionIfPossible(ChainedPersistenceExceptionTranslator.java:58)
at org.springframework.dao.support.DataAccessUtils.translateIfNecessary(DataAccessUtils.java:213)
at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:163)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
at com.sun.proxy.$Proxy100.retrieveAll(Unknown Source)
at com.denimgroup.threadfix.service.DefaultConfigServiceImpl.loadCurrentConfiguration(DefaultConfigServiceImpl.java:51)
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:606)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:96)
at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:260)
at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:94)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
at com.sun.proxy.$Proxy101.loadCurrentConfiguration(Unknown Source)
at com.denimgroup.threadfix.webapp.controller.DashboardController.index(DashboardController.java:85)
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:606)
at org.springframework.web.method.support.InvocableHandlerMethod.invoke(InvocableHandlerMethod.java:215)
at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:132)
at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:104)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandleMethod(RequestMappingHandlerAdapter.java:745)
at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:685)
at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:80)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:919)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:851)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:953)
at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:844)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:829)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:690)
at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:477)
at org.apache.catalina.core.ApplicationDispatcher.doForward(ApplicationDispatcher.java:402)
at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:329)
at org.tuckey.web.filters.urlrewrite.NormalRewrittenUrl.doRewrite(NormalRewrittenUrl.java:195)
at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:159)
at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141)
at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90)
at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:417)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:232)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:106)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at com.denimgroup.threadfix.webapp.filter.CsrfPreventionFilter.doFilter(CsrfPreventionFilter.java:241)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at com.denimgroup.threadfix.webapp.filter.ClickjackHeaderFilter.doFilter(ClickjackHeaderFilter.java:42)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at com.opensymphony.sitemesh.webapp.SiteMeshFilter.obtainContent(SiteMeshFilter.java:129)
at com.opensymphony.sitemesh.webapp.SiteMeshFilter.doFilter(SiteMeshFilter.java:77)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:88)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:106)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:118)
at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:54)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:150)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:183)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:105)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87)
at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342)
at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192)
at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160)
at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:343)
at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:260)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at com.denimgroup.threadfix.webapp.filter.EnterpriseFilter.doFilter(EnterpriseFilter.java:71)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:225)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:581)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:168)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:927)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1001)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:585)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:312)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.hibernate.exception.GenericJDBCException: Could not execute JDBC batch update
at org.hibernate.exception.SQLStateConverter.handledNonSpecificException(SQLStateConverter.java:140)
at org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:128)
at org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:275)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:262)
at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:179)
at org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)
at org.hibernate.event.def.DefaultAutoFlushEventListener.onAutoFlush(DefaultAutoFlushEventListener.java:64)
at org.hibernate.impl.SessionImpl.autoFlushIfRequired(SessionImpl.java:1175)
at org.hibernate.impl.SessionImpl.list(SessionImpl.java:1699)
at org.hibernate.impl.CriteriaImpl.list(CriteriaImpl.java:347)
at com.denimgroup.threadfix.data.dao.AbstractObjectDao.retrieveAll(AbstractObjectDao.java:75)
at sun.reflect.GeneratedMethodAccessor106.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317)
at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
at org.springframework.dao.support.PersistenceExceptionTranslationInterceptor.invoke(PersistenceExceptionTranslationInterceptor.java:155)
... 111 more
Caused by: java.sql.SQLException: Connection is read-only. Queries leading to data modification are not allowed
at com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:1431)
at org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:70)
at org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:268)
... 126 more

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