Upgrade from 7.13.7 to 7.19.9 is not working

[Fabian Wüst]

Hello community,

I'm trying to update Conflucene with my colleagues.

Currently we are trying to upgrade from 7.13.7 to 7.19.9.

We get the error message that the database connection to Mysql will be closed.

Below are the log files from atlassian-confluence.log:

---

at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1322)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.base/java.lang.Thread.run(Unknown Source)
2023-06-16 13:40:13,320 WARN [Catalina-utility-1] [confluence.impl.setup.DefaultBootstrapDatabaseAccessor] lambda$getBootstrapData$3 Unable to determine finalized build number from database [message: Unknown column 'FINALIZED' in 'where clause']. If you are upgrading from a Confluence version prior to 7.14, this is expected.
2023-06-16 13:40:13,410 INFO [Catalina-utility-1] [springframework.web.context.ContextLoader] initWebApplicationContext Root WebApplicationContext: initialization started
2023-06-16 13:40:16,767 INFO [Catalina-utility-1] [com.atlassian.confluence.lifecycle] <init> Loading EhCache cache manager
2023-06-16 13:40:33,424 INFO [Catalina-utility-1] [springframework.web.context.ContextLoader] initWebApplicationContext Root WebApplicationContext initialized in 20014 ms
2023-06-16 13:40:33,579 INFO [Catalina-utility-1] [atlassian.plugin.manager.DefaultPluginManager] lambda$earlyStartup$5 Plugin system earlyStartup begun
2023-06-16 13:40:34,169 WARN [Catalina-utility-1] [org.twdata.pkgscanner.ExportPackageListBuilder] logDuplicateWarning Package Scanner found duplicates for package 'org.cyberneko.html.xercesbridge' with different versions. Files: xerces-bridge-2-2-1.9.22-atlassian-2.jar and xerces-bridge-1.9.22-atlassian-2.jar
'/opt/confluence/standalone/confluence/WEB-INF/lib/xerces-bridge-2-2-1.9.22-atlassian-2.jar'
'/opt/confluence/standalone/confluence/WEB-INF/lib/xerces-bridge-1.9.22-atlassian-2.jar'
2023-06-16 13:40:34,171 WARN [Catalina-utility-1] [org.twdata.pkgscanner.ExportPackageListBuilder] logDuplicateWarning Package Scanner found duplicates for package 'org.cyberneko.html.xercesbridge' with different versions. Files: xerces-bridge-2-0-1.9.22-atlassian-2.jar and xerces-bridge-2-2-1.9.22-atlassian-2.jar
'/opt/confluence/standalone/confluence/WEB-INF/lib/xerces-bridge-2-0-1.9.22-atlassian-2.jar'
'/opt/confluence/standalone/confluence/WEB-INF/lib/xerces-bridge-2-2-1.9.22-atlassian-2.jar'
2023-06-16 13:40:34,171 WARN [Catalina-utility-1] [org.twdata.pkgscanner.ExportPackageListBuilder] logDuplicateWarning Package Scanner found duplicates for package 'org.cyberneko.html.xercesbridge' with different versions. Files: xerces-bridge-2-3-1.9.22-atlassian-2.jar and xerces-bridge-2-0-1.9.22-atlassian-2.jar
'/opt/confluence/standalone/confluence/WEB-INF/lib/xerces-bridge-2-3-1.9.22-atlassian-2.jar'
'/opt/confluence/standalone/confluence/WEB-INF/lib/xerces-bridge-2-0-1.9.22-atlassian-2.jar'
2023-06-16 13:40:36,414 WARN [FelixStartLevel] [extender.internal.support.ExtenderConfiguration] addDefaultDependencyFactories Gemini Blueprint extensions bundle not present, annotation processing disabled.
2023-06-16 13:40:56,990 WARN [ThreadPoolAsyncTaskExecutor::Thread 5] [scanner.runtime.impl.ComponentImportBeanFactoryPostProcessor] loadServiceClass Unable to load class 'com.atlassian.jira.user.UserKeyService' for component importation purposes. Skipping...
2023-06-16 13:40:56,991 WARN [ThreadPoolAsyncTaskExecutor::Thread 5] [scanner.runtime.impl.ComponentImportBeanFactoryPostProcessor] loadServiceClass Unable to load class 'com.atlassian.jira.util.I18nHelper' for component importation purposes. Skipping...
2023-06-16 13:41:07,905 INFO [Catalina-utility-1] [atlassian.plugin.manager.DefaultPluginManager] logTime Plugin system earlyStartup ended
2023-06-16 13:41:07,973 WARN [AtlassianEvent::CustomizableThreadFactory-6] [core.persistence.hibernate.HibernateVersionHistoryDao] getLatestBuildNumber Unable to determine build number from database. If you are upgrading from a Confluence version prior to 7.14.0, this is expected: Unknown column 'FINALIZED' in 'where clause'
2023-06-16 13:41:08,125 INFO [Catalina-utility-1] [confluence.upgrade.impl.DefaultUpgradeManager] beforeUpgrade Generating pre-upgrade recovery file...
2023-06-16 13:41:08,152 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] begin Starting
2023-06-16 13:41:08,157 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] logTask Starting DATABASE_INFORMATION
2023-06-16 13:41:08,162 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] logTask Finishing DATABASE_INFORMATION
2023-06-16 13:41:08,162 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] logTask Starting TABLE_DEFINITION
2023-06-16 13:41:08,721 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] logTask Finishing TABLE_DEFINITION
2023-06-16 13:41:08,722 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] totalNumberOfTables Total number of tables: 224
2023-06-16 13:41:08,722 INFO [Catalina-utility-1] [confluence.upgrade.recovery.ConfluenceProgressMonitor] logTask Starting TABLES_DATA
2023-06-16 13:42:38,960 WARN [Catalina-utility-1] [confluence.impl.hibernate.ConfluenceHibernateTransactionManager] doRollback Performing rollback. Transactions:
->[null]: PROPAGATION_REQUIRES_NEW,ISOLATION_DEFAULT (Session #462935388)
2023-06-16 13:42:38,963 WARN [Catalina-utility-1] [v2.c3p0.impl.NewPooledConnection] log [c3p0] A PooledConnection that has already signalled a Connection error is still in use!
2023-06-16 13:42:38,964 WARN [Catalina-utility-1] [v2.c3p0.impl.NewPooledConnection] log [c3p0] Another error has occurred [ com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed. ] which will not be reported to listeners!
com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed.
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.base/java.lang.reflect.Constructor.newInstance(Unknown Source)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
at com.mysql.jdbc.Util.getInstance(Util.java:408)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:919)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:898)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:887)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:861)
at com.mysql.jdbc.ConnectionImpl.throwConnectionClosedException(ConnectionImpl.java:1192)
at com.mysql.jdbc.ConnectionImpl.checkClosed(ConnectionImpl.java:1187)
at com.mysql.jdbc.ConnectionImpl.rollback(ConnectionImpl.java:4534)
at com.mchange.v2.c3p0.impl.NewProxyConnection.rollback(NewProxyConnection.java:1033)
at org.hibernate.resource.jdbc.internal.AbstractLogicalConnectionImplementor.rollback(AbstractLogicalConnectionImplementor.java:116)
at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcResourceLocalTransactionCoordinatorImpl$TransactionDriverControlImpl.rollback(JdbcResourceLocalTransactionCoordinatorImpl.java:251)
at org.hibernate.engine.transaction.internal.TransactionImpl.rollback(TransactionImpl.java:100)
at com.atlassian.hibernate.adapter.adapters.TransactionV2Adapter.rollback(TransactionV2Adapter.java:44)
at org.springframework.orm.hibernate.HibernateTransactionManager.doRollback(HibernateTransactionManager.java:532)
at com.atlassian.confluence.impl.hibernate.ConfluenceHibernateTransactionManager.doRollback(ConfluenceHibernateTransactionManager.java:81)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.processRollback(AbstractPlatformTransactionManager.java:835)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.rollback(AbstractPlatformTransactionManager.java:809)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
at com.sun.proxy.$Proxy79.rollback(Unknown Source)
at org.springframework.transaction.support.TransactionTemplate.rollbackOnException(TransactionTemplate.java:168)
at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:144)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.generate(DefaultRecoveryFileGenerator.java:61)
at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.beforeUpgrade(DefaultUpgradeManager.java:173)
at com.atlassian.confluence.upgrade.AbstractUpgradeManager.upgrade(AbstractUpgradeManager.java:134)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.launchUpgrades(PluginFrameworkContextListener.java:122)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.contextInitialized(PluginFrameworkContextListener.java:82)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4491)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4939)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1332)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1322)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.lang.OutOfMemoryError: Java heap space
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3515)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3462)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3905)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:871)
at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1999)
at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:3413)
at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:471)
at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:3115)
at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:2344)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2739)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2491)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2449)
at com.mysql.jdbc.StatementImpl.executeQuery(StatementImpl.java:1381)
at com.mchange.v2.c3p0.impl.NewProxyStatement.executeQuery(NewProxyStatement.java:327)
at com.atlassian.dbexporter.exporter.DataExporter.executeQueryWithFetchSize100(DataExporter.java:335)
at com.atlassian.dbexporter.exporter.DataExporter.exportTable(DataExporter.java:78)
at com.atlassian.dbexporter.exporter.DataExporter.lambda$null$0(DataExporter.java:51)
at com.atlassian.dbexporter.exporter.DataExporter$$Lambda$1942/0x00000008020ea840.call(Unknown Source)
at com.atlassian.dbexporter.jdbc.JdbcUtils.withNoAutoCommit(JdbcUtils.java:52)
at com.atlassian.dbexporter.exporter.DataExporter.lambda$export$1(DataExporter.java:50)
at com.atlassian.dbexporter.exporter.DataExporter$$Lambda$1940/0x00000008020ea040.call(Unknown Source)
at com.atlassian.dbexporter.jdbc.JdbcUtils.withConnection(JdbcUtils.java:29)
at com.atlassian.dbexporter.exporter.DataExporter.export(DataExporter.java:48)
at com.atlassian.dbexporter.DbExporter.exportData(DbExporter.java:65)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.lambda$generate$0(DefaultRecoveryFileGenerator.java:80)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator$$Lambda$1924/0x00000008020d7440.doInTransaction(Unknown Source)
at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:140)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.generate(DefaultRecoveryFileGenerator.java:61)
at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.beforeUpgrade(DefaultUpgradeManager.java:173)
at com.atlassian.confluence.upgrade.AbstractUpgradeManager.upgrade(AbstractUpgradeManager.java:134)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.launchUpgrades(PluginFrameworkContextListener.java:122)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.contextInitialized(PluginFrameworkContextListener.java:82)
2023-06-16 13:42:39,006 ERROR [Catalina-utility-1] [springframework.transaction.support.TransactionTemplate] rollbackOnException Application exception overridden by rollback exception
com.atlassian.confluence.upgrade.recovery.DbDumpException: Failed to generate recovery file
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.lambda$generate$0(DefaultRecoveryFileGenerator.java:86)
at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:140)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.generate(DefaultRecoveryFileGenerator.java:61)
at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.beforeUpgrade(DefaultUpgradeManager.java:173)
at com.atlassian.confluence.upgrade.AbstractUpgradeManager.upgrade(AbstractUpgradeManager.java:134)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.launchUpgrades(PluginFrameworkContextListener.java:122)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.contextInitialized(PluginFrameworkContextListener.java:82)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4491)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4939)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1332)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1322)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: com.atlassian.confluence.upgrade.recovery.DbDumpException: Problem with table "null":
at com.atlassian.confluence.upgrade.recovery.RecoveryErrorService.newImportExportSqlException(RecoveryErrorService.java:21)
at com.atlassian.dbexporter.jdbc.JdbcUtils.withNoAutoCommit(JdbcUtils.java:57)
at com.atlassian.dbexporter.exporter.DataExporter.lambda$export$1(DataExporter.java:50)
at com.atlassian.dbexporter.jdbc.JdbcUtils.withConnection(JdbcUtils.java:29)
at com.atlassian.dbexporter.exporter.DataExporter.export(DataExporter.java:48)
at com.atlassian.dbexporter.DbExporter.exportData(DbExporter.java:65)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.lambda$generate$0(DefaultRecoveryFileGenerator.java:80)
... 17 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed.
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.base/java.lang.reflect.Constructor.newInstance(Unknown Source)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
at com.mysql.jdbc.Util.getInstance(Util.java:408)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:919)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:898)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:887)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:861)
at com.mysql.jdbc.ConnectionImpl.throwConnectionClosedException(ConnectionImpl.java:1192)
at com.mysql.jdbc.ConnectionImpl.checkClosed(ConnectionImpl.java:1187)
at com.mysql.jdbc.ConnectionImpl.setAutoCommit(ConnectionImpl.java:4766)
at com.mchange.v2.c3p0.impl.NewProxyConnection.setAutoCommit(NewProxyConnection.java:1059)
at com.atlassian.config.db.DelegatingConnection.setAutoCommit(DelegatingConnection.java:53)
at jdk.internal.reflect.GeneratedMethodAccessor295.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at com.atlassian.activeobjects.spi.ConnectionHandler.delegate(ConnectionHandler.java:39)
at com.atlassian.activeobjects.spi.ConnectionHandler.invoke(ConnectionHandler.java:34)
at com.sun.proxy.$Proxy2448.setAutoCommit(Unknown Source)
at com.atlassian.dbexporter.jdbc.JdbcUtils.withNoAutoCommit(JdbcUtils.java:54)
... 22 more
Caused by: java.lang.OutOfMemoryError: Java heap space
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3515)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3462)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3905)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:871)
at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1999)
at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:3413)
at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:471)
at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:3115)
at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:2344)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2739)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2491)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2449)
at com.mysql.jdbc.StatementImpl.executeQuery(StatementImpl.java:1381)
at com.mchange.v2.c3p0.impl.NewProxyStatement.executeQuery(NewProxyStatement.java:327)
at com.atlassian.dbexporter.exporter.DataExporter.executeQueryWithFetchSize100(DataExporter.java:335)
at com.atlassian.dbexporter.exporter.DataExporter.exportTable(DataExporter.java:78)
at com.atlassian.dbexporter.exporter.DataExporter.lambda$null$0(DataExporter.java:51)
at com.atlassian.dbexporter.exporter.DataExporter$$Lambda$1942/0x00000008020ea840.call(Unknown Source)
at com.atlassian.dbexporter.jdbc.JdbcUtils.withNoAutoCommit(JdbcUtils.java:52)
at com.atlassian.dbexporter.exporter.DataExporter.lambda$export$1(DataExporter.java:50)
at com.atlassian.dbexporter.exporter.DataExporter$$Lambda$1940/0x00000008020ea040.call(Unknown Source)
at com.atlassian.dbexporter.jdbc.JdbcUtils.withConnection(JdbcUtils.java:29)
at com.atlassian.dbexporter.exporter.DataExporter.export(DataExporter.java:48)
at com.atlassian.dbexporter.DbExporter.exportData(DbExporter.java:65)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.lambda$generate$0(DefaultRecoveryFileGenerator.java:80)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator$$Lambda$1924/0x00000008020d7440.doInTransaction(Unknown Source)
at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:140)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.generate(DefaultRecoveryFileGenerator.java:61)
at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.beforeUpgrade(DefaultUpgradeManager.java:173)
at com.atlassian.confluence.upgrade.AbstractUpgradeManager.upgrade(AbstractUpgradeManager.java:134)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.launchUpgrades(PluginFrameworkContextListener.java:122)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.contextInitialized(PluginFrameworkContextListener.java:82)
2023-06-16 13:42:39,008 ERROR [Catalina-utility-1] [atlassian.confluence.plugin.PluginFrameworkContextListener] contextInitialized Error initialising plugin manager: Could not roll back Hibernate transaction; nested exception is net.sf.hibernate.TransactionException: Unable to rollback against JDBC Connection
org.springframework.transaction.TransactionSystemException: Could not roll back Hibernate transaction; nested exception is net.sf.hibernate.TransactionException: Unable to rollback against JDBC Connection
at org.springframework.orm.hibernate.HibernateTransactionManager.doRollback(HibernateTransactionManager.java:535)
at com.atlassian.confluence.impl.hibernate.ConfluenceHibernateTransactionManager.doRollback(ConfluenceHibernateTransactionManager.java:81)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.processRollback(AbstractPlatformTransactionManager.java:835)
at org.springframework.transaction.support.AbstractPlatformTransactionManager.rollback(AbstractPlatformTransactionManager.java:809)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
at java.base/java.lang.reflect.Method.invoke(Unknown Source)
at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:344)
at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208)
at com.sun.proxy.$Proxy79.rollback(Unknown Source)
at org.springframework.transaction.support.TransactionTemplate.rollbackOnException(TransactionTemplate.java:168)
at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:144)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.generate(DefaultRecoveryFileGenerator.java:61)
at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.beforeUpgrade(DefaultUpgradeManager.java:173)
at com.atlassian.confluence.upgrade.AbstractUpgradeManager.upgrade(AbstractUpgradeManager.java:134)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.launchUpgrades(PluginFrameworkContextListener.java:122)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.contextInitialized(PluginFrameworkContextListener.java:82)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4491)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:4939)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1332)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1322)
at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: net.sf.hibernate.TransactionException: Unable to rollback against JDBC Connection
at org.hibernate.resource.jdbc.internal.AbstractLogicalConnectionImplementor.rollback(AbstractLogicalConnectionImplementor.java:122)
at org.hibernate.resource.transaction.backend.jdbc.internal.JdbcResourceLocalTransactionCoordinatorImpl$TransactionDriverControlImpl.rollback(JdbcResourceLocalTransactionCoordinatorImpl.java:251)
at org.hibernate.engine.transaction.internal.TransactionImpl.rollback(TransactionImpl.java:100)
at com.atlassian.hibernate.adapter.adapters.TransactionV2Adapter.rollback(TransactionV2Adapter.java:44)
at org.springframework.orm.hibernate.HibernateTransactionManager.doRollback(HibernateTransactionManager.java:532)
... 28 more
Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException: No operations allowed after connection closed.
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
at java.base/java.lang.reflect.Constructor.newInstance(Unknown Source)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:425)
at com.mysql.jdbc.Util.getInstance(Util.java:408)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:919)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:898)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:887)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:861)
at com.mysql.jdbc.ConnectionImpl.throwConnectionClosedException(ConnectionImpl.java:1192)
at com.mysql.jdbc.ConnectionImpl.checkClosed(ConnectionImpl.java:1187)
at com.mysql.jdbc.ConnectionImpl.rollback(ConnectionImpl.java:4534)
at com.mchange.v2.c3p0.impl.NewProxyConnection.rollback(NewProxyConnection.java:1033)
at org.hibernate.resource.jdbc.internal.AbstractLogicalConnectionImplementor.rollback(AbstractLogicalConnectionImplementor.java:116)
... 32 more
Caused by: java.lang.OutOfMemoryError: Java heap space
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3515)
at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:3462)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3905)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:871)
at com.mysql.jdbc.MysqlIO.nextRow(MysqlIO.java:1999)
at com.mysql.jdbc.MysqlIO.readSingleRowSet(MysqlIO.java:3413)
at com.mysql.jdbc.MysqlIO.getResultSet(MysqlIO.java:471)
at com.mysql.jdbc.MysqlIO.readResultsForQueryOrUpdate(MysqlIO.java:3115)
at com.mysql.jdbc.MysqlIO.readAllResults(MysqlIO.java:2344)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2739)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2491)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2449)
at com.mysql.jdbc.StatementImpl.executeQuery(StatementImpl.java:1381)
at com.mchange.v2.c3p0.impl.NewProxyStatement.executeQuery(NewProxyStatement.java:327)
at com.atlassian.dbexporter.exporter.DataExporter.executeQueryWithFetchSize100(DataExporter.java:335)
at com.atlassian.dbexporter.exporter.DataExporter.exportTable(DataExporter.java:78)
at com.atlassian.dbexporter.exporter.DataExporter.lambda$null$0(DataExporter.java:51)
at com.atlassian.dbexporter.exporter.DataExporter$$Lambda$1942/0x00000008020ea840.call(Unknown Source)
at com.atlassian.dbexporter.jdbc.JdbcUtils.withNoAutoCommit(JdbcUtils.java:52)
at com.atlassian.dbexporter.exporter.DataExporter.lambda$export$1(DataExporter.java:50)
at com.atlassian.dbexporter.exporter.DataExporter$$Lambda$1940/0x00000008020ea040.call(Unknown Source)
at com.atlassian.dbexporter.jdbc.JdbcUtils.withConnection(JdbcUtils.java:29)
at com.atlassian.dbexporter.exporter.DataExporter.export(DataExporter.java:48)
at com.atlassian.dbexporter.DbExporter.exportData(DbExporter.java:65)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.lambda$generate$0(DefaultRecoveryFileGenerator.java:80)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator$$Lambda$1924/0x00000008020d7440.doInTransaction(Unknown Source)
at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:140)
at com.atlassian.confluence.upgrade.recovery.DefaultRecoveryFileGenerator.generate(DefaultRecoveryFileGenerator.java:61)
at com.atlassian.confluence.upgrade.impl.DefaultUpgradeManager.beforeUpgrade(DefaultUpgradeManager.java:173)
at com.atlassian.confluence.upgrade.AbstractUpgradeManager.upgrade(AbstractUpgradeManager.java:134)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.launchUpgrades(PluginFrameworkContextListener.java:122)
at com.atlassian.confluence.plugin.PluginFrameworkContextListener.contextInitialized(PluginFrameworkContextListener.java:82)
2023-06-16 13:42:39,079 INFO [Catalina-utility-1] [confluence.upgrade.impl.DefaultUpgradeGate] waitForBooleanValue Waiting to find if plugin dependent upgrades are required. Maximum wait time will be 90 seconds.
2023-06-16 13:42:39,080 INFO [Catalina-utility-1] [confluence.upgrade.impl.DefaultUpgradeGate] waitForBooleanValue plugin dependent upgrades are required : true.
2023-06-16 13:42:39,085 INFO [Catalina-utility-1] [confluence.upgrade.impl.DefaultUpgradeGate] waitForBooleanValue Waiting to find if plugin dependent upgrades are complete. Maximum wait time will be 1800 seconds.
2023-06-16 13:47:09,087 INFO [Catalina-utility-1] [confluence.upgrade.impl.DefaultUpgradeGate] waitForBooleanValue Still waiting to find if plugin dependent upgrades are complete. Remaining wait time is 1500 seconds.
2023-06-16 13:52:09,090 INFO [Catalina-utility-1] [confluence.upgrade.impl.DefaultUpgradeGate] waitForBooleanValue Still waiting to find if plugin dependent upgrades are complete. Remaining wait time is 1200 seconds.
^C

[Julian Governale]

@Fabian Wüst were you able to figure this one out? 

[Craig Nodwell]

Hi @Fabian Wüst welcome to the community.  I would recommend logging a support ticket for this.