Have data error after upgrade to 7.12.3

[Little Lyu]

My jira system is Centos 7.0, Mysql 5.6, 

In function Issues ->  Reported by me have an error!

The error log is too long, Here is only a part, How can fix this?

"DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.velocity.util.introspection.UberspectImpl$VelMethodImpl.doInvoke(UberspectImpl.java:385) at org.apache.velocity.util.introspection.UberspectImpl$VelMethodImpl.invoke(UberspectImpl.java:374) at com.atlassian.velocity.htmlsafe.introspection.AnnotationBoxingMethod.invoke(AnnotationBoxingMethod.java:26) at com.atlassian.velocity.htmlsafe.introspection.UnboxingMethod.invoke(UnboxingMethod.java:30) at org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:270) ... 371 more Caused by: com.atlassian.activeobjects.internal.ActiveObjectsInitException: bundle [com.atlassian.jira.plugins.jira-dvcs-connector-plugin] at com.atlassian.activeobjects.osgi.TenantAwareActiveObjects$1$1$1.call(TenantAwareActiveObjects.java:95) at com.atlassian.activeobjects.osgi.TenantAwareActiveObjects$1$1$1.call(TenantAwareActiveObjects.java:86) at com.atlassian.sal.core.executor.ThreadLocalDelegateCallable.call(ThreadLocalDelegateCallable.java:38) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ... 1 more Caused by: com.atlassian.activeobjects.internal.ActiveObjectsSqlException: There was a SQL exception thrown by the Active Objects library: Database: - name:MySQL - version:5.6.42-log - minor version:6 - major version:5 Driver: - name:MySQL Connector Java - version:mysql-connector-java-5.1.34 ( Revision: jess.balint@oracle.com-20141014163213-wqbwpf1ok2kvo1om ) com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Can't DROP 'fk_ao_e8b6cc_branch_repository_id'; check that column/key exists at com.atlassian.activeobjects.internal.EntityManagedActiveObjects.migrate(EntityManagedActiveObjects.java:53) at com.atlassian.jira.plugins.dvcs.activeobjects.v3.To_15_LinkUpdateAuthorisedInitialise.upgrade(To_15_LinkUpdateAuthorisedInitialise.java:24) at com.atlassian.activeobjects.internal.ActiveObjectUpgradeManagerImpl$1.doInTransaction(ActiveObjectUpgradeManagerImpl.java:68) at com.atlassian.activeobjects.internal.ActiveObjectUpgradeManagerImpl$1.doInTransaction(ActiveObjectUpgradeManagerImpl.java:64) at com.atlassian.sal.core.transaction.HostContextTransactionTemplate$1.doInTransaction(HostContextTransactionTemplate.java:21) at com.atlassian.jira.DefaultHostContextAccessor.doInTransaction(DefaultHostContextAccessor.java:36) at sun.reflect.GeneratedMethodAccessor166.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at com.atlassian.plugin.util.ContextClassLoaderSettingInvocationHandler.invoke(ContextClassLoaderSettingInvocationHandler.java:26) at com.sun.proxy.$Proxy133.doInTransaction(Unknown Source) at sun.reflect.GeneratedMethodAccessor166.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean$DynamicServiceInvocationHandler.invoke(HostComponentFactoryBean.java:136) at com.sun.proxy.$Proxy133.doInTransaction(Unknown Source) at com.atlassian.sal.core.transaction.HostContextTransactionTemplate.execute(HostContextTransactionTemplate.java:18) at sun.reflect.GeneratedMethodAccessor179.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302) at org.eclipse.gemini.blueprint.service.importer.support.internal.aop.ServiceInvoker.doInvoke(ServiceInvoker.java:56) at org.eclipse.gemini.blueprint.service.importer.support.internal.aop.ServiceInvoker.invoke(ServiceInvoker.java:60) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:133) at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.eclipse.gemini.blueprint.service.util.internal.aop.ServiceTCCLInterceptor.invokeUnprivileged(ServiceTCCLInterceptor.java:70) at org.eclipse.gemini.blueprint.service.util.internal.aop.ServiceTCCLInterceptor.invoke(ServiceTCCLInterceptor.java:53) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.eclipse.gemini.blueprint.service.importer.support.LocalBundleContextAdvice.invoke(LocalBundleContextAdvice.java:57) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.support.DelegatingIntroductionInterceptor.doProceed(DelegatingIntroductionInterceptor.java:133) at org.springframework.aop.support.DelegatingIntroductionInterceptor.invoke(DelegatingIntroductionInterceptor.java:121) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208) at com.sun.proxy.$Proxy1008.execute(Unknown Source) at com.atlassian.activeobjects.internal.SalTransactionManager.inTransaction(SalTransactionManager.java:42) at com.atlassian.activeobjects.internal.AbstractLoggingTransactionManager.doInTransaction(AbstractLoggingTransactionManager.java:16) at com.atlassian.activeobjects.internal.EntityManagedActiveObjects.executeInTransaction(EntityManagedActiveObjects.java:204) at com.atlassian.activeobjects.internal.ActiveObjectUpgradeManagerImpl.upgrade(ActiveObjectUpgradeManagerImpl.java:64) at com.atlassian.activeobjects.internal.ActiveObjectUpgradeManagerImpl.upgrade(ActiveObjectUpgradeManagerImpl.java:36) at com.atlassian.activeobjects.internal.AbstractActiveObjectsFactory.upgrade(AbstractActiveObjectsFactory.java:87) at com.atlassian.activeobjects.internal.AbstractActiveObjectsFactory.create(AbstractActiveObjectsFactory.java:67) at com.atlassian.activeobjects.internal.DelegatingActiveObjectsFactory.create(DelegatingActiveObjectsFactory.java:32) at com.atlassian.activeobjects.osgi.TenantAwareActiveObjects$1$1$1.call(TenantAwareActiveObjects.java:91) ... 6 more Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Can't DROP 'fk_ao_e8b6cc_branch_repository_id'; check that column/key exists at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at com.mysql.jdbc.Util.handleNewInstance(Util.java:377) at com.mysql.jdbc.Util.getInstance(Util.java:360) at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:978) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3887) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3823) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2435) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2582) at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2526) at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1618) at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1549) at org.apache.commons.dbcp2.DelegatingStatement.executeUpdate(DelegatingStatement.java:234) at org.apache.commons.dbcp2.DelegatingStatement.executeUpdate(DelegatingStatement.java:234) at net.java.ao.DatabaseProvider.executeUpdate(DatabaseProvider.java:2246) at net.java.ao.DatabaseProvider.executeUpdateForAction(DatabaseProvider.java:2302) at net.java.ao.DatabaseProvider.executeUpdatesForActions(DatabaseProvider.java:2274) at net.java.ao.schema.SchemaGenerator.migrate(SchemaGenerator.java:91) at net.java.ao.EntityManager.migrate(EntityManager.java:128) at com.atlassian.activeobjects.internal.EntityManagedActiveObjects.migrate(EntityManagedActiveObjects.java:51) ... 51 more" 

[AhmadDanial · Accepted solution]

Hi, Lyu.

The error that we are seeing could potentially mean that the repository_id column in the fk_ao_e8b6cc_branch table (related to JIRA DVCS Connector Plugin) was somehow corrupted during the upgrade process:

6 more Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Can't DROP 'fk_ao_e8b6cc_branch_repository_id'; check that column/key exists at

sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at 

In this case, let us try to delete the plugin tables by referring to the steps below:

1. VERY IMPORTANT: Please note that the next steps will require manual manipulations on the database. We strongly recommend you to keep a backup, so we can rollback in case of any problems by referring to the Backing up data documentation.
2. Once done, navigate to Plugin Data Storage that is located in JIRA Administration >> System. Alternatively, you can also use keyboard shortcuts by typing g+g and search for Plugin Data Storage
3. Make a list of the tables associated with the JIRA DVCS Connector Plugin. For example, here are some of them:
   
   AO_E8B6CC_ISSUE_TO_CHANGESET
   AO_E8B6CC_REPOSITORY_MAPPING
   AO_E8B6CC_CHANGESET_MAPPING
   
   
4. Shutdown JIRA
5. Uninstall the JIRA DVCS Connector Plugin by navigating to $JIRA_HOME/plugins/installed-plugins and moving the DVCS plugin to another file location (such as desktop). The DVCS plugin name would be something like jira-dvcs-connector-plugin-4.3.1.jar
6. Drop the tables from step #2 by running the DROP command in the database.
7. Restart JIRA.
8. Re-install DVCS plugin, if needed.

Let me know how that goes on your end. Thanks.

[Little Lyu]

It works for me! Thank you!

[AhmadDanial]

Hello, Lyu.

You are most welcome. Any time!