Migrating to MySQL fails with migrateDBProgressAjax error message

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Symptoms

Migrating from HSQL to MySQL using the administration panel fails, and the following appears in the atlassian-fisheye.log:

2013-12-18 08:01:10,220 ERROR [qtp876256661-111906 ] fisheye TotalityFilter-logExceptionDetails - Exception "Hibernate has been shutdown" (org.hibernate.HibernateException) while processing "/setup/migrateDBProgressAjax" (Referer:"https://crucible.mycompany.com/admin/database.do")
org.hibernate.HibernateException: Hibernate has been shutdown
	at com.cenqua.crucible.hibernate.HibernateUtil.currentState(HibernateUtil.java:196)
	at com.cenqua.crucible.hibernate.HibernateUtil.currentSession(HibernateUtil.java:187)
	at com.cenqua.crucible.hibernate.HibernateUtilCurrentSessionProvider.currentSession(HibernateUtilCurrentSessionProvider.java:10)
	at com.atlassian.fecru.user.UserDAOImpl.session(UserDAOImpl.java:38)
	at com.atlassian.fecru.user.UserDAOImpl.getByUsername(UserDAOImpl.java:127)
	at com.cenqua.fisheye.user.DefaultUserManager.isUserInBuiltinGroup(DefaultUserManager.java:1087)
	at com.cenqua.fisheye.user.DefaultUserManager.isUserInGroup(DefaultUserManager.java:1105)
	at com.cenqua.fisheye.user.AdminUserConfig.isInAnAdminGroup(AdminUserConfig.java:112)
	at com.cenqua.fisheye.user.DefaultUserManager.hasSysAdminPrivileges(DefaultUserManager.java:1740)
	at com.cenqua.fisheye.user.DefaultUserManager.hasSysAdminPrivileges(DefaultUserManager.java:1747)
	at sun.reflect.GeneratedMethodAccessor281.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:309)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:196)
	at $Proxy44.hasSysAdminPrivileges(Unknown Source)
	at com.cenqua.fisheye.web.admin.interceptors.LoginInterceptor.isAdminUser(LoginInterceptor.java:44)
	at com.atlassian.sal.fisheye.user.DefaultUserManager.isAdminRequest(DefaultUserManager.java:90)
	at com.atlassian.sal.fisheye.user.DefaultUserManager.fakeAdminUsername(DefaultUserManager.java:178)
	at com.atlassian.sal.fisheye.user.DefaultUserManager.getRemoteUsername(DefaultUserManager.java:54)
	at com.atlassian.sal.fisheye.user.DefaultUserManager.getRemoteUsername(DefaultUserManager.java:143)
	at com.atlassian.sal.fisheye.auth.FisheyeAuthenticationController.shouldAttemptAuthentication(FisheyeAuthenticationController.java:34)
	at sun.reflect.GeneratedMethodAccessor267.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:307)
	at org.springframework.osgi.service.importer.support.internal.aop.ServiceInvoker.doInvoke(ServiceInvoker.java:58)
	at org.springframework.osgi.service.importer.support.internal.aop.ServiceInvoker.invoke(ServiceInvoker.java:62)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:131)
	at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:119)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.osgi.service.util.internal.aop.ServiceTCCLInterceptor.invokeUnprivileged(ServiceTCCLInterceptor.java:56)
	at org.springframework.osgi.service.util.internal.aop.ServiceTCCLInterceptor.invoke(ServiceTCCLInterceptor.java:39)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.osgi.service.importer.support.LocalBundleContextAdvice.invoke(LocalBundleContextAdvice.java:59)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:131)
	at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:119)
	at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:171)
	at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:204)
	at $Proxy478.shouldAttemptAuthentication(Unknown Source)
	at com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.mayProceed(OAuthFilter.java:86)
	at com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:55)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:455)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:575)
	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1075)
	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:384)
	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1009)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
	at org.eclipse.jetty.server.Dispatcher.forward(Dispatcher.java:276)
	at org.eclipse.jetty.server.Dispatcher.forward(Dispatcher.java:103)
	at com.cenqua.fisheye.web.setup.MigrateDBProgressServlet.service(MigrateDBProgressServlet.java:53)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:848)
	at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:669)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1526)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	at com.atlassian.applinks.core.rest.context.ContextFilter.doFilter(ContextFilter.java:25)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	at com.atlassian.prettyurls.filter.PrettyUrlsSiteMeshFixupFilter.doFilter(PrettyUrlsSiteMeshFixupFilter.java:36)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	at com.atlassian.prettyurls.filter.PrettyUrlsDispatcherFilter.doFilter(PrettyUrlsDispatcherFilter.java:60)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	at com.atlassian.prettyurls.filter.PrettyUrlsSiteMeshFilter.doFilter(PrettyUrlsSiteMeshFilter.java:92)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	at com.atlassian.prettyurls.filter.PrettyUrlsMatcherFilter.doFilter(PrettyUrlsMatcherFilter.java:56)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:83)
	at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:76)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at com.atlassian.crucible.filters.CrucibleFilter.doFilter(CrucibleFilter.java:146)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at com.cenqua.fisheye.web.filters.TotalityFilter.doFilter(TotalityFilter.java:228)
	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at com.atlassian.security.auth.trustedapps.filter.TrustedApplicationsFilter.doFilter(TrustedApplicationsFilter.java:100)
	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	at com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:61)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at org.eclipse.jetty.servlets.UserAgentFilter.doFilter(UserAgentFilter.java:82)
	at org.eclipse.jetty.servlets.GzipFilter.doFilter(GzipFilter.java:256)
	at com.cenqua.fisheye.web.filters.CustomIncludableGzipFilter.doFilter(CustomIncludableGzipFilter.java:27)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at com.cenqua.fisheye.web.filters.ProductInfoFilter.doFilter(ProductInfoFilter.java:44)
	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	at com.atlassian.prettyurls.filter.PrettyUrlsCombinedMatchDispatcherFilter.doFilter(PrettyUrlsCombinedMatchDispatcherFilter.java:61)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:77)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:63)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at com.cenqua.fisheye.web.filters.UpfrontFilter.doFilter(UpfrontFilter.java:59)
	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at com.atlassian.fecru.profiling.ProfilingServletFilter.doFilter(ProfilingServletFilter.java:74)
	at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)
	at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)
	at org.eclipse.jetty.servlet.ServletHandler$Chain.doFilter(ServletHandler.java:1502)
	at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:455)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:137)
	at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:557)
	at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:231)
	at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1075)
	at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:384)
	at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:193)
	at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1009)
	at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:135)
	at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:255)
	at org.eclipse.jetty.server.handler.HandlerCollection.handle(HandlerCollection.java:154)
	at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:116)
	at org.eclipse.jetty.server.Server.handle(Server.java:368)
	at org.eclipse.jetty.server.AbstractHttpConnection.handleRequest(AbstractHttpConnection.java:489)
	at org.eclipse.jetty.server.AbstractHttpConnection.headerComplete(AbstractHttpConnection.java:942)
	at org.eclipse.jetty.server.AbstractHttpConnection$RequestHandler.headerComplete(AbstractHttpConnection.java:1004)
	at org.eclipse.jetty.http.HttpParser.parseNext(HttpParser.java:640)
	at org.eclipse.jetty.http.HttpParser.parseAvailable(HttpParser.java:235)
	at org.eclipse.jetty.server.AsyncHttpConnection.handle(AsyncHttpConnection.java:82)
	at org.eclipse.jetty.io.nio.SelectChannelEndPoint.handle(SelectChannelEndPoint.java:628)
	at org.eclipse.jetty.io.nio.SelectChannelEndPoint$1.run(SelectChannelEndPoint.java:52)
	at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:608)
	at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:543)
	at java.lang.Thread.run(Thread.java:619)

This is seen in the web browser:

Cause

The cause is unknown.

Resolution

  1. Create a backup using the admin interface;
  2. Create the MySQL database;
  3. Shutdown Fisheye;

  4. Using a command line client, go to FISHEYE_HOME/bin and restore only the database from the backup using the database command line options:
    Example (Linux / Mac):

    ./fisheyectl.sh restore --sql --file /path/to/fecru/backup_2013-20-12_0915.zip --dbtype mysql --jdbcurl jdbc:mysql://hostname:3306/fisheye --username dbuser --password dbuserpwd

    Example (Windows):

    ./fisheyectl.bat restore --sql --file /path/to/fecru/backup_2013-20-12_0915.zip --dbtype mysql --jdbcurl jdbc:mysql://hostname:3306/fisheye --username dbuser --password dbuserpwd
  5. When the restore process is finished, backup the config.xml and edit the original one this way:

    1. Search for the <check-for-updates/> element. Right after this element, insert this:

      <database type="mysql">
   <connection dialect="org.hibernate.dialect.MySQL5InnoDBDialect" 
      driver="com.mysql.jdbc.Driver"
      jdbcurl="jdbc:mysql://host_name_here:3306/fisheye_database_name_here" 
      username="db_username_here" 
      password="db_user_password_here" 
      maxPoolSize="20" 
      minPoolSize="5" 
      driverSource="bundled"/>
   <parameters>useUnicode=true
characterEncoding=UTF8
connectionCollation=UTF8_bin
   </parameters>
</database>

      Please remember to edit jdbcurl, username and password parameters accordingly.

    2. Save and close the file;
  6. Start Fisheye.
Last modified on Jul 31, 2018

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