com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors

Atlassian JIRA | Ignat Alexeyenko | 5 months ago
  1. 0

    h3. JIRA 7.2 RC02 throwing Errors for MySQL   h3. Environment * JIRA 7.2-Server-RC02 * MySQL h3. Steps to Reproduce Do either of these options * Database Set up * XML Restore * ReIndex Process with our plugin and the error it triggers h3. Expected Results All operations finish successfully, without andy database-releated exceptions. h3. Actual Results * Exception on database setup ** java.lang.RuntimeException: Unable to obtain a connection from the underlying connection pool   *  Exception on Data Restore (XML Restore) The last packet successfully received from the server was 3 milliseconds ago. The last packet sent successfully to the server was 3 milliseconds ago.) java.lang.RuntimeException: com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Unable to establish a connection with the database. (Communications link failure   * Reindex causes the dropping index errors: at com.atlassian.sal.core.executor.ThreadLocalDelegateCallable.call(ThreadLocalDelegateCallable.java:42) at java.util.concurrent.FutureTask.run(Unknown Source) *During DB Set up* {noformat} 2016-07-21 22:47:31,961 http-nio-8080-exec-19 INFO anonymous 1366x19x1 10r3rrj 0:0:0:0:0:0:0:1 /secure/SetupDatabase.jspa [c.a.jira.plugin.JiraPluginManager] Plugin with key 'com.atlassian.jira.jira-issue-nav-components' and name 'jira-issue-nav-components' and version '8.1.21' is being added to the system. 2016-07-21 22:47:31,974 active-objects-init-JiraTenantImpl{id='system'}-0 ERROR anonymous 1366x19x1 10r3rrj 0:0:0:0:0:0:0:1 /secure/SetupDatabase.jspa [NoModule] There was an error getting a DBCP datasource. java.lang.RuntimeException: Unable to obtain a connection from the underlying connection pool at org.ofbiz.core.entity.jdbc.interceptors.connection.ConnectionTracker.trackConnection(ConnectionTracker.java:60) at org.ofbiz.core.entity.transaction.DBCPConnectionFactory.trackConnection(DBCPConnectionFactory.java:317) at org.ofbiz.core.entity.transaction.DBCPConnectionFactory.getConnection(DBCPConnectionFactory.java:81) at org.ofbiz.core.entity.ConnectionFactory.tryGenericConnectionSources(ConnectionFactory.java:69) at org.ofbiz.core.entity.transaction.JNDIFactory.getConnection(JNDIFactory.java:164) at org.ofbiz.core.entity.TransactionFactory.getConnection(TransactionFactory.java:136) at org.ofbiz.core.entity.ConnectionFactory.getConnection(ConnectionFactory.java:59) at com.atlassian.jira.ofbiz.DefaultOfBizConnectionFactory.getConnection(DefaultOfBizConnectionFactory.java:44) at com.atlassian.activeobjects.jira.JiraTenantAwareDataSourceProvider$OfBizDataSource.getConnection(JiraTenantAwareDataSourceProvider.java:103) at com.atlassian.activeobjects.internal.DataSourceProviderActiveObjectsFactory$ActiveObjectsDataSource.getConnection(DataSourceProviderActiveObjectsFactory.java:93) ... 2 filtered at java.lang.reflect.Method.invoke(Method.java:497) at net.java.ao.builder.DelegatingDisposableDataSourceHandler.delegate(DelegatingDisposableDataSourceHandler.java:37) at net.java.ao.builder.DelegatingDisposableDataSourceHandler.invoke(DelegatingDisposableDataSourceHandler.java:30) at com.sun.proxy.$Proxy2924.getConnection(Unknown Source) at net.java.ao.DatabaseProvider.getConnection(DatabaseProvider.java:855) at net.java.ao.DatabaseProvider.hasIndex(DatabaseProvider.java:1434) at net.java.ao.DatabaseProvider.renderDropIndex(DatabaseProvider.java:1419) at net.java.ao.DatabaseProvider.renderAction(DatabaseProvider.java:242) at net.java.ao.schema.SchemaGenerator$1.apply(SchemaGenerator.java:126) at net.java.ao.schema.SchemaGenerator$1.apply(SchemaGenerator.java:124) at com.google.common.collect.Iterators$8.transform(Iterators.java:799) at com.google.common.collect.TransformedIterator.next(TransformedIterator.java:48) at net.java.ao.schema.SchemaGenerator.migrate(SchemaGenerator.java:90) at net.java.ao.EntityManager.migrate(EntityManager.java:128) at com.atlassian.activeobjects.internal.EntityManagedActiveObjects.migrate(EntityManagedActiveObjects.java:45) at com.atlassian.activeobjects.internal.AbstractActiveObjectsFactory$1.doInTransaction(AbstractActiveObjectsFactory.java:77) at com.atlassian.activeobjects.internal.AbstractActiveObjectsFactory$1.doInTransaction(AbstractActiveObjectsFactory.java:72) at com.atlassian.sal.core.transaction.HostContextTransactionTemplate$1.doInTransaction(HostContextTransactionTemplate.java:25) at com.atlassian.jira.DefaultHostContextAccessor.doInTransaction(DefaultHostContextAccessor.java:34) ... 2 filtered at java.lang.reflect.Method.invoke(Method.java:497) at com.atlassian.plugin.util.ContextClassLoaderSettingInvocationHandler.invoke(ContextClassLoaderSettingInvocationHandler.java:26) at com.sun.proxy.$Proxy43.doInTransaction(Unknown Source) ... 2 filtered at java.lang.reflect.Method.invoke(Method.java:497) at com.atlassian.plugin.osgi.bridge.external.HostComponentFactoryBean$DynamicServiceInvocationHandler.invoke(HostComponentFactoryBean.java:136) at com.sun.proxy.$Proxy43.doInTransaction(Unknown Source) at com.atlassian.sal.core.transaction.HostContextTransactionTemplate.execute(HostContextTransactionTemplate.java:21) ... 2 filtered at java.lang.reflect.Method.invoke(Method.java:497) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:317) 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:207) at com.sun.proxy.$Proxy994.execute(Unknown Source) at com.atlassian.activeobjects.internal.AbstractActiveObjectsFactory.create(AbstractActiveObjectsFactory.java:72) at com.atlassian.activeobjects.internal.DelegatingActiveObjectsFactory.create(DelegatingActiveObjectsFactory.java:32) at com.atlassian.activeobjects.osgi.TenantAwareActiveObjects$1$1$1.call(TenantAwareActiveObjects.java:91) at com.atlassian.activeobjects.osgi.TenantAwareActiveObjects$1$1$1.call(TenantAwareActiveObjects.java:86) at com.atlassian.sal.core.executor.ThreadLocalDelegateCallable.call(ThreadLocalDelegateCallable.java:42) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure The last packet successfully received from the server was 1 milliseconds ago. The last packet sent successfully to the server was 1 milliseconds ago. at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at com.mysql.jdbc.Util.handleNewInstance(Util.java:409) at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1127) at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3715) at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3604) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4155) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:926) at com.mysql.jdbc.MysqlIO.proceedHandshakeWithPluggableAuthentication(MysqlIO.java:1748) at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1288) at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2506) at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2539) at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2321) at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:832) at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46) ... 3 filtered at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at com.mysql.jdbc.Util.handleNewInstance(Util.java:409) at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:417) at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:344) at org.apache.commons.dbcp2.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:39) at org.apache.commons.dbcp2.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:256) at org.apache.commons.pool2.impl.GenericObjectPool.create(GenericObjectPool.java:861) at org.apache.commons.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:435) at org.apache.commons.pool2.impl.GenericObjectPool.borrowObject(GenericObjectPool.java:363) at org.apache.commons.dbcp2.PoolingDataSource.getConnection(PoolingDataSource.java:134) at org.apache.commons.dbcp2.BasicDataSource.getConnection(BasicDataSource.java:1533) at org.ofbiz.core.entity.transaction.DBCPConnectionFactory$1.call(DBCPConnectionFactory.java:321) at org.ofbiz.core.entity.transaction.DBCPConnectionFactory$1.call(DBCPConnectionFactory.java:318) at org.ofbiz.core.entity.jdbc.interceptors.connection.ConnectionTracker.trackConnection(ConnectionTracker.java:54) ... 70 more Caused by: java.io.EOFException: Can not read response from server. Expected to read 4 bytes, read 0 bytes before connection was unexpectedly lost. at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:3161) at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3615) {noformat} *During Data Restore* {noformat} 2016-07-21 23:04:49,877 JiraImportTaskExecutionThread-1 WARN admin 1383x701x1 10r3rrj 0:0:0:0:0:0:0:1 /secure/admin/XmlRestore.jspa [c.a.jira.index.AccumulatingResultBuilder] com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Unable to establish a connection with the database. (Communications link failure The last packet successfully received from the server was 3 milliseconds ago. The last packet sent successfully to the server was 3 milliseconds ago.) java.lang.RuntimeException: com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Unable to establish a connection with the database. (Communications link failure The last packet successfully received from the server was 3 milliseconds ago. The last packet sent successfully to the server was 3 milliseconds ago.) at com.atlassian.jira.index.DefaultIndex$Failure.<init>(DefaultIndex.java:101) at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:400) at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:369) at com.atlassian.jira.issue.index.DefaultIssueIndexer.lambda$null$202(DefaultIssueIndexer.java:308) at com.atlassian.jira.issue.index.DefaultIssueIndexer$$Lambda$1193/524039629.get(Unknown Source) at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:7) at com.atlassian.jira.index.SimpleIndexingStrategy.get(SimpleIndexingStrategy.java:5) at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:33) at com.atlassian.jira.index.MultiThreadedIndexingStrategy$1.call(MultiThreadedIndexingStrategy.java:31) at com.atlassian.jira.util.concurrent.BoundedExecutor$2.call(BoundedExecutor.java:68) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) Caused by: com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Unable to establish a connection with the database. (Communications link failure The last packet successfully received from the server was 3 milliseconds ago. The last packet sent successfully to the server was 3 milliseconds ago.) at com.atlassian.jira.ofbiz.DefaultOfBizDelegator.findByAnd(DefaultOfBizDelegator.java:94) at com.atlassian.jira.ofbiz.WrappingOfBizDelegator.findByAnd(WrappingOfBizDelegator.java:73) at com.atlassian.jira.issue.changehistory.DefaultChangeHistoryManager.getAllChangeItems(DefaultChangeHistoryManager.java:187) at com.atlassian.jira.issue.index.DefaultChangeHistoryRetriever.apply(DefaultChangeHistoryRetriever.java:24) at com.atlassian.jira.issue.index.DefaultIssueIndexer$DefaultDocumentCreationStrategy$1.apply(DefaultIssueIndexer.java:564) at com.atlassian.jira.issue.index.DefaultIssueIndexer$DefaultDocumentCreationStrategy$1.apply(DefaultIssueIndexer.java:561) at com.atlassian.jira.issue.index.DefaultIssueIndexer$DefaultDocumentCreationStrategy.get(DefaultIssueIndexer.java:554) at com.atlassian.jira.issue.index.DefaultIssueIndexer$IndexIssuesOperation.perform(DefaultIssueIndexer.java:380) ... 12 more Caused by: org.ofbiz.core.entity.GenericDataSourceException: Unable to establish a connection with the database. (Communications link failure The last packet successfully received from the server was 3 milliseconds ago. The last packet sent successfully to the server was 3 milliseconds ago.) at org.ofbiz.core.entity.jdbc.SQLProcessor.getConnection(SQLProcessor.java:399) at org.ofbiz.core.entity.jdbc.SQLProcessor.prepareStatement(SQLProcessor.java:543) at org.ofbiz.core.entity.GenericDAO.createEntityListIterator(GenericDAO.java:960) at org.ofbiz.core.entity.GenericDAO.selectByAnd(GenericDAO.java:730) at org.ofbiz.core.entity.GenericHelperDAO.findByAnd(GenericHelperDAO.java:150) at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:903) at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:881) at com.atlassian.jira.ofbiz.DefaultOfBizDelegator.findByAnd(DefaultOfBizDelegator.java:92) ... 20 more Caused by: com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure The last packet successfully received from the server was 3 milliseconds ago. The last packet sent successfully to the server was 3 milliseconds ago. at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at com.mysql.jdbc.Util.handleNewInstance(Util.java:409) at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:1127) at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3715) at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3604) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4155) at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:926) at com.mysql.jdbc.MysqlIO.proceedHandshakeWithPluggableAuthentication(MysqlIO.java:1748) at com.mysql.jdbc.MysqlIO.doHandshake(MysqlIO.java:1288) at com.mysql.jdbc.ConnectionImpl.coreConnect(ConnectionImpl.java:2506) at com.mysql.jdbc.ConnectionImpl.connectOneTryOnly(ConnectionImpl.java:2539) at com.mysql.jdbc.ConnectionImpl.createNewIO(ConnectionImpl.java:2321) at com.mysql.jdbc.ConnectionImpl.<init>(ConnectionImpl.java:832) at com.mysql.jdbc.JDBC4Connection.<init>(JDBC4Connection.java:46) ... 2 filtered at java.lang.reflect.Constructor.newInstance(Constructor.java:422) at com.mysql.jdbc.Util.handleNewInstance(Util.java:409) at com.mysql.jdbc.ConnectionImpl.getInstance(ConnectionImpl.java:417) at com.mysql.jdbc.NonRegisteringDriver.connect(NonRegisteringDriver.java:344) at java.sql.DriverManager.getConnection(DriverManager.java:664) at java.sql.DriverManager.getConnection(DriverManager.java:247) at org.ofbiz.core.entity.ConnectionFactory.tryGenericConnectionSources(ConnectionFactory.java:87) at org.ofbiz.core.entity.transaction.JNDIFactory.getConnection(JNDIFactory.java:164) at org.ofbiz.core.entity.TransactionFactory.getConnection(TransactionFactory.java:136) at org.ofbiz.core.entity.ConnectionFactory.getConnection(ConnectionFactory.java:59) at org.ofbiz.core.entity.jdbc.SQLProcessor.getConnection(SQLProcessor.java:394) ... 28 more Caused by: java.io.EOFException: Can not read response from server. Expected to read 4 bytes, read 0 bytes before connection was unexpectedly lost. at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:3161) at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3615) ... 51 more 2016-07-21 23:04:49,884 JiraImportTaskExecutionThread-1 ERROR admin 1383x701x1 10r3rrj 0:0:0:0:0:0:0:1 /secure/admin/XmlRestore.jspa [c.a.j.bc.dataimport.DefaultDataImportService] Error importing data: com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors at com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await(AccumulatingResultBuilder.java:150) at com.atlassian.jira.issue.index.DefaultIndexManager.doIndexIssuesInBatchMode(DefaultIndexManager.java:986) at com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:961) at com.atlassian.jira.issue.index.DefaultIndexManager.lambda$reIndexAll$787(DefaultIndexManager.java:326) at com.atlassian.jira.issue.index.DefaultIndexManager$$Lambda$543/1593758938.run(Unknown Source) at com.atlassian.jira.issue.index.DefaultIndexManager.withReindexLock(DefaultIndexManager.java:359) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:326) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:241) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:234) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:230) at com.atlassian.jira.issue.index.DefaultIndexManager.activate(DefaultIndexManager.java:203) ... 3 filtered at java.lang.reflect.Method.invoke(Method.java:497) at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:22) at com.sun.proxy.$Proxy163.activate(Unknown Source) at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.activate(CompositeIndexLifecycleManager.java:134) at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.activate(CompositeIndexLifecycleManager.java:128) at com.atlassian.jira.bc.dataimport.DefaultDataImportService.reindex(DefaultDataImportService.java:972) at com.atlassian.jira.bc.dataimport.DefaultDataImportService.performImport(DefaultDataImportService.java:766) at com.atlassian.jira.bc.dataimport.DefaultDataImportService.doImport(DefaultDataImportService.java:324) at com.atlassian.jira.web.action.setup.DataImportAsyncCommand.call(DataImportAsyncCommand.java:60) at com.atlassian.jira.web.action.setup.DataImportAsyncCommand.call(DataImportAsyncCommand.java:28) at com.atlassian.jira.task.ImportTaskManagerImpl$TaskCallableDecorator.call(ImportTaskManagerImpl.java:157) at com.atlassian.jira.task.ImportTaskManagerImpl$TaskCallableDecorator.call(ImportTaskManagerImpl.java:133) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745) {noformat} Apart from this we are also seeing Dropping Index errors during the reIndex process. See Below error {noformat} 2016-07-21 14:02:15,734 http-nio-8302-exec-10 ERROR admin 842x1499x1 gav866 0:0:0:0:0:0:0:1 /rest/zephyr/latest/execution/indexAll [c.a.p.r.c.error.jersey.ThrowableExceptionMapper] Uncaught exception thrown by REST service: bundle [com.thed.zephyr.je] com.atlassian.activeobjects.internal.ActiveObjectsInitException: bundle [com.thed.zephyr.je] at com.atlassian.activeobjects.osgi.TenantAwareActiveObjects$1$1$1.call(TenantAwareActiveObjects.java:95) at com.atlassian.activeobjects.osgi.TenantAwareActiveObjects$1$1$1.call(TenantAwareActiveObjects.java:86) at com.atlassian.sal.core.executor.ThreadLocalDelegateCallable.call(ThreadLocalDelegateCallable.java:42) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) at java.lang.Thread.run(Unknown Source) Caused by: com.atlassian.activeobjects.internal.ActiveObjectsSqlException: There was a SQL exception thrown by the Active Objects library: Database: - name:MySQL - version:5.6.29 - minor version:6 - major version:5 - name:MySQL Connector Java - version:mysql-connector-java-5.1.38 ( Revision: fe541c166cec739c74cc727c5da96c1028b4834a ) java.sql.SQLException: Cannot drop index 'index_ao_7deabf_ste1617810863': needed in a foreign key constraint at com.atlassian.activeobjects.internal.EntityManagedActiveObjects.migrate(EntityManagedActiveObjects.java:47) at com.atlassian.activeobjects.internal.AbstractActiveObjectsFactory$1.doInTransaction(AbstractActiveObjectsFactory.java:77) at com.atlassian.activeobjects.internal.AbstractActiveObjectsFactory$1.doInTransaction(AbstractActiveObjectsFactory.java:72) at com.atlassian.sal.core.transaction.HostContextTransactionTemplate$1.doInTransaction(HostContextTransactionTemplate.java:25) at com.atlassian.jira.DefaultHostContextAccessor.doInTransaction(DefaultHostContextAccessor.java:34) ... 2 filtered at java.lang.reflect.Method.invoke(Unknown Source) at com.atlassian.plugin.util.ContextClassLoaderSettingInvocationHandler.invoke(ContextClassLoaderSettingInvocationHandler.java:26) at com.sun.proxy.$Proxy136.doInTransaction(Unknown Source) {noformat}   {color:#292929}Notes{color} It seems working fine with JIRA 7.2 RC01. h3.  

    Atlassian JIRA | 5 months ago | Ignat Alexeyenko
    com.atlassian.jira.index.IndexingFailureException: Indexing completed with 1 errors
  2. 0

    [JRA-36857] Reindex all fails with an com.atlassian.jira.index.IndexingFailureException using Java 7 - Atlassian JIRA

    atlassian.com | 1 year ago
    com.atlassian.jira.index.IndexingFailureException: Indexing completed with 3 errors
  3. 0

    Somehow we got into a situation, when Jira insists on reindexing (with exclusive locking only), but is unable to finish the job. While the reindexing is running, the following message is spamming the log: {{2014-02-27 23:11:35,485 JiraTaskExectionThread-15 WARN mteterinXXX 1388x24224x1 8zq2ol 10.187.234.6,127.0.0.1 /secure/admin/jira/IndexReIndex.jspa \[atlassian.jira.index.Accumulati gResultBuilder] java.util.concurrent.ExecutionException: java.lang.NullPointerException: Cannot invoke method getValidators() on null object}} It ends with the following: {quote} Indexing completed with 12256 errors Task completed in 3 minutes, 7 seconds with unexpected error. Started Today 11:08 PM EST. Finished Today 11:11 PM EST. com.atlassian.jira.index.IndexingFailureException: Indexing completed with 12256 errors at com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await(AccumulatingResultBuilder.java:147) at com.atlassian.jira.issue.index.DefaultIndexManager.doIndexIssuesInBatchMode(DefaultIndexManager.java:877) at com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:844) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:307) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:272) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:267) 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:601) at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83) at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28) at $Proxy152.reIndexAll(Unknown Source) at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:56) at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.doReindex(ReIndexAsyncIndexerCommand.java:28) at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:54) at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.call(ReIndexAsyncIndexerCommand.java:16) at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:23) at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:374) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334) at java.util.concurrent.FutureTask.run(FutureTask.java:166) at com.atlassian.jira.task.ForkedThreadExecutor$ForkedRunnableDecorator.run(ForkedThreadExecutor.java:250) at java.lang.Thread.run(Thread.java:722) {quote} While we await a fix, any hint as to the work-around would be appreciated.

    Atlassian JIRA | 3 years ago | Mikhail T
    com.atlassian.jira.index.IndexingFailureException: Indexing completed with 12256 errors
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  5. 0

    h3. Summary Attempting to reindex JIRA fails with the below exception. This does not fail for *all* issues, only a couple. It also causes JIRA Agile's upgrade tasks to fail, as tracked in GHS-10348. h3. Environment * Java 7 h3. Steps to Reproduce # Restore an instance with problematic data. # Install JIRA Agile and upgrade. h3. Expected Results The reindex completes without error. h3. Actual Results The below exception is thrown: {noformat} 2014-02-04 11:31:28,768 JiraTaskExectionThread-2 ERROR admin 685x278x1 o72kxu 127.0.0.1 /secure/admin/jira/IndexReIndex.jspa [jira.util.index.CompositeIndexLifecycleManager] Reindex All FAILED. Indexer: DefaultIndexManager: paths: [/Users/dcurrie/deployments/jira617/jira-home/caches/indexes/comments, /Users/dcurrie/deployments/jira617/jira-home/caches/indexes/issues, /Users/dcurrie/deployments/jira617/jira-home/caches/indexes/changes] com.atlassian.jira.index.IndexingFailureException: Indexing completed with 3 errors at com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await(AccumulatingResultBuilder.java:147) at com.atlassian.jira.issue.index.DefaultIndexManager.doIndexIssuesInBatchMode(DefaultIndexManager.java:877) at com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:844) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:307) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:272) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:267) <+3> (NativeMethodAccessorImpl.java:57) (DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83) at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28) at com.sun.proxy.$Proxy140.reIndexAll(Unknown Source) at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:56) at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.doReindex(ReIndexAsyncIndexerCommand.java:28) at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:54) at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.call(ReIndexAsyncIndexerCommand.java:16) at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:23) at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:374) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at com.atlassian.jira.task.ForkedThreadExecutor$ForkedRunnableDecorator.run(ForkedThreadExecutor.java:250) at java.lang.Thread.run(Thread.java:744) {noformat} Tracking back into the logs reveals that exceptions were thrown during the indexing (the timestamp on this log is different however it's the same problem): {noformat} 2014-03-08 21:07:32,716 JiraTaskExectionThread-1 WARN captain.planet 1267x112x1 h86sjy 74.57.203.161,127.0.0.1 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Comparison method violates its general contract! {noformat} h3. Notes It is important to note that indexing _mostly_ finishes. It seems to fail for one or more issues that throws that exception. h3. Workaround Switching to Java 6 will allow the issues to be indexed. Please note that Java 6 is not supported in later versions of JIRA as per [Supported Platforms|http://confluence.atlassian.com/display/JIRA/Supported+Platforms].

    Atlassian JIRA | 3 years ago | Bryan Karsh
    com.atlassian.jira.index.IndexingFailureException: Indexing completed with 3 errors
  6. 0

    h3. Summary Attempting to reindex JIRA fails with the below exception. This does not fail for *all* issues, only a couple. It also causes JIRA Agile's upgrade tasks to fail, as tracked in GHS-10348. h3. Environment * Java 7 h3. Steps to Reproduce # Restore an instance with problematic data. # Install JIRA Agile and upgrade. h3. Expected Results The reindex completes without error. h3. Actual Results The below exception is thrown: {noformat} 2014-02-04 11:31:28,768 JiraTaskExectionThread-2 ERROR admin 685x278x1 o72kxu 127.0.0.1 /secure/admin/jira/IndexReIndex.jspa [jira.util.index.CompositeIndexLifecycleManager] Reindex All FAILED. Indexer: DefaultIndexManager: paths: [/Users/dcurrie/deployments/jira617/jira-home/caches/indexes/comments, /Users/dcurrie/deployments/jira617/jira-home/caches/indexes/issues, /Users/dcurrie/deployments/jira617/jira-home/caches/indexes/changes] com.atlassian.jira.index.IndexingFailureException: Indexing completed with 3 errors at com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await(AccumulatingResultBuilder.java:147) at com.atlassian.jira.issue.index.DefaultIndexManager.doIndexIssuesInBatchMode(DefaultIndexManager.java:877) at com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:844) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:307) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:272) at com.atlassian.jira.issue.index.DefaultIndexManager.reIndexAll(DefaultIndexManager.java:267) <+3> (NativeMethodAccessorImpl.java:57) (DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at com.atlassian.util.profiling.object.ObjectProfiler.profiledInvoke(ObjectProfiler.java:83) at com.atlassian.jira.config.component.SwitchingInvocationHandler.invoke(SwitchingInvocationHandler.java:28) at com.sun.proxy.$Proxy140.reIndexAll(Unknown Source) at com.atlassian.jira.util.index.CompositeIndexLifecycleManager.reIndexAll(CompositeIndexLifecycleManager.java:56) at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.doReindex(ReIndexAsyncIndexerCommand.java:28) at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:54) at com.atlassian.jira.web.action.admin.index.ReIndexAsyncIndexerCommand.call(ReIndexAsyncIndexerCommand.java:16) at com.atlassian.jira.web.action.admin.index.AbstractAsyncIndexerCommand.call(AbstractAsyncIndexerCommand.java:23) at com.atlassian.jira.task.TaskManagerImpl$TaskCallableDecorator.call(TaskManagerImpl.java:374) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask.run(FutureTask.java:262) at com.atlassian.jira.task.ForkedThreadExecutor$ForkedRunnableDecorator.run(ForkedThreadExecutor.java:250) at java.lang.Thread.run(Thread.java:744) {noformat} Tracking back into the logs reveals that exceptions were thrown during the indexing (the timestamp on this log is different however it's the same problem): {noformat} 2014-03-08 21:07:32,716 JiraTaskExectionThread-1 WARN captain.planet 1267x112x1 h86sjy 74.57.203.161,127.0.0.1 /secure/admin/IndexReIndex.jspa [atlassian.jira.index.AccumulatingResultBuilder] java.util.concurrent.ExecutionException: java.lang.IllegalArgumentException: Comparison method violates its general contract! {noformat} h3. Notes It is important to note that indexing _mostly_ finishes. It seems to fail for one or more issues that throws that exception. h3.Solution Upgrade JIRA to 6.2.3+ using the instructions at [Upgrading JIRA|https://confluence.atlassian.com/display/JIRA/Upgrading+JIRA]. h3. Workaround # Some customers have reported that reindexing has worked after upgrading to Java 1.7_u51. To check if this works for you, download the new Java and declare your JAVA_HOME variable in {{bin/setenv.bat}} (Windows) or {{bin/setenv.sh}} before you restart JIRA. Downtime is required to restart JIRA and re-index. # Downgrade Java to 1.6, perform the index, then switch JIRA back to 1.7. We recommend to do this only do this if there is no other option. Switching to Java 6 will allow the issues to be indexed. Please note that Java 6 is not supported in later versions of JIRA as per [Supported Platforms|http://confluence.atlassian.com/display/JIRA/Supported+Platforms]. Downtime is required for two JIRA restarts and an indexing.

    Atlassian JIRA | 3 years ago | David Currie [Atlassian]
    com.atlassian.jira.index.IndexingFailureException: Indexing completed with 3 errors

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    Root Cause Analysis

    1. com.atlassian.jira.index.IndexingFailureException

      Indexing completed with 1 errors

      at com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await()
    2. com.atlassian.jira
      DefaultIndexManager.lambda$reIndexAll$787
      1. com.atlassian.jira.index.AccumulatingResultBuilder$CompositeResult.await(AccumulatingResultBuilder.java:150)
      2. com.atlassian.jira.issue.index.DefaultIndexManager.doIndexIssuesInBatchMode(DefaultIndexManager.java:986)
      3. com.atlassian.jira.issue.index.DefaultIndexManager.doStopTheWorldReindex(DefaultIndexManager.java:961)
      4. com.atlassian.jira.issue.index.DefaultIndexManager.lambda$reIndexAll$787(DefaultIndexManager.java:326)
      4 frames