Confluence upgrade from 6.11 to 7.0 fails

[ash91089]

Hi, forgive me if this is something obvious, I am running confluence and jira on the same ec2 instance backed off to mysql 5.6 in RDS. 

Jira is currently at version 8.5.4 and seems to be running ok, I have followed the upgrade steps for confluence to move from  6.11.2 to 7.0.5  (as i did not want to upgraded mysql just yet). 

However when i start confluence back up after the upgrade i get the following errors .. (see bold text)

catalina.out 

2020-05-19 11:41:27,898 INFO [main] [com.atlassian.confluence.lifecycle] contextInitialized Starting Confluence 7.0.5 [build 8202 based on commit hash 5410a0fcac15966c5635d34e4b8d5a6a5c11f266] - synchrony version 3.1.0-master-0f086db5
19-May-2020 11:41:42.060 SEVERE [main] org.apache.catalina.core.StandardContext.startInternal One or more Filters failed to start. Full details will be found in the appropriate container log file
19-May-2020 11:41:42.061 SEVERE [main] org.apache.catalina.core.StandardContext.startInternal Context [] startup failed due to previous errors
19-May-2020 11:41:42.110 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [ROOT] registered the JDBC driver [org.hsqldb.jdbc.JDBCDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
19-May-2020 11:41:42.111 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [ROOT] registered the JDBC driver [com.mysql.fabric.jdbc.FabricMySQLDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
19-May-2020 11:41:42.111 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [ROOT] registered the JDBC driver [org.postgresql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
19-May-2020 11:41:42.111 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [ROOT] registered the JDBC driver [net.sourceforge.jtds.jdbc.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
19-May-2020 11:41:42.111 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [ROOT] registered the JDBC driver [com.github.gquintana.metrics.sql.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
19-May-2020 11:41:42.112 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [ROOT] registered the JDBC driver [org.h2.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
19-May-2020 11:41:42.112 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [ROOT] registered the JDBC driver [com.microsoft.sqlserver.jdbc.SQLServerDriver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
19-May-2020 11:41:42.113 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesJdbc The web application [ROOT] registered the JDBC driver [com.mysql.jdbc.Driver] but failed to unregister it when the web application was stopped. To prevent a memory leak, the JDBC Driver has been forcibly unregistered.
19-May-2020 11:41:42.113 WARNING [main] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [mysql-cj-abandoned-connection-cleanup] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
java.lang.Object.wait(Native Method)
java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:144)
com.mysql.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:80)
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
java.lang.Thread.run(Thread.java:748)
19-May-2020 11:41:42.130 INFO [main] org.apache.catalina.startup.HostConfig.deployDescriptor Deploying deployment descriptor [/opt/confluence/installs/atlassian-confluence-7.0.5/conf/Standalone/localhost/synchrony-proxy.xml]
19-May-2020 11:41:42.137 WARNING [main] org.apache.catalina.startup.HostConfig.deployDescriptor The path attribute with value [/synchrony-proxy] in deployment descriptor [/opt/confluence/installs/atlassian-confluence-7.0.5/conf/Standalone/localhost/synchrony-proxy.xml] has been ignored
19-May-2020 11:41:42.142 WARNING [main] org.apache.catalina.startup.SetContextPropertiesRule.begin [SetContextPropertiesRule]{Context} Setting property 'debug' to '0' did not find a matching property.
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
19-May-2020 11:41:42.756 INFO [main] org.apache.catalina.core.ApplicationContext.log 1 Spring WebApplicationInitializers detected on classpath
19-May-2020 11:41:42.814 INFO [main] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
19-May-2020 11:41:42.900 INFO [main] org.apache.catalina.core.ApplicationContext.log Initializing Spring DispatcherServlet 'dispatcher'
19-May-2020 11:41:43.786 INFO [main] org.apache.catalina.startup.HostConfig.deployDescriptor Deployment of deployment descriptor [/opt/confluence/installs/atlassian-confluence-7.0.5/conf/Standalone/localhost/synchrony-proxy.xml] has finished in [1,656] ms
19-May-2020 11:41:43.790 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-9090"]
19-May-2020 11:41:43.807 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [17,724] milliseconds
19-May-2020 11:41:45.804 INFO [mysql-cj-abandoned-connection-cleanup] org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading Illegal access: this web application instance has been stopped already. Could not load []. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access.
java.lang.IllegalStateException: Illegal access: this web application instance has been stopped already. Could not load []. The following stack trace is thrown for debugging purposes as well as to attempt to terminate the thread which caused the illegal access.
at org.apache.catalina.loader.WebappClassLoaderBase.checkStateForResourceLoading(WebappClassLoaderBase.java:1385)
at org.apache.catalina.loader.WebappClassLoaderBase.getResource(WebappClassLoaderBase.java:1038)
at com.mysql.jdbc.AbandonedConnectionCleanupThread.checkThreadContextClassLoader(AbandonedConnectionCleanupThread.java:112)
at com.mysql.jdbc.AbandonedConnectionCleanupThread.run(AbandonedConnectionCleanupThread.java:79)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at java.lang.Thread.run(Thread.java:748)

atlassian-confluence.log

2020-05-19 11:41:40,007 ERROR [main] [springframework.web.context.ContextLoader] initWebApplicationContext Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'cacheStatisticsManager' defined in class path resource [services/cacheServiceContext.xml]: Invocation of init method failed; nested exception is org.
springframework.beans.factory.BeanCreationException: Error creating bean with name 'ehCacheStatisticsManager' defined in URL [jar:file:/opt/confluence/installs/atlassian-confluence-7.0.5/confluence/WEB-INF/lib/confluence-cache-ehcache-7.
0.5.jar!/cacheProviderContext.xml]: Cannot resolve reference to bean 'userI18NBeanFactory' while setting constructor argument; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'us
erI18NBeanFactory' defined in class path resource [i18NContext.xml]: Cannot resolve reference to bean 'localeManager' while setting bean property 'localeManager'; nested exception is org.springframework.beans.factory.BeanCreationExceptio
n: Error creating bean with name 'localeManager' defined in class path resource [i18NContext.xml]: Cannot resolve reference to bean 'languageManager' while setting bean property 'languageManager'; nested exception is org.springframework.
beans.factory.BeanCreationException: Error creating bean with name 'languageManager' defined in class path resource [applicationContext.xml]: Cannot resolve reference to bean 'settingsManager' while setting bean property 'settingsManager
'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'settingsManager' defined in class path resource [applicationContext.xml]: Cannot resolve reference to bean 'upgradeManager' wh
ile setting bean property 'upgradeManager'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'upgradeManager' defined in class path resource [upgradeSubsystemContext.xml]: Cannot
resolve reference to bean 'attachmentToCeoConversionUpgradeTask' while setting bean property 'schemaUpgradeTasks' with key [4]; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean wit
h name 'attachmentToCeoConversionUpgradeTask' defined in class path resource [upgradeSubsystemContext.xml]: Unsatisfied dependency expressed through constructor parameter 2: Could not convert argument value of type [java.lang.String] to
required type [int]: Failed to convert value of type 'java.lang.String' to required type 'int'; nested exception is java.lang.NumberFormatException: For input string: ""
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1778)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:593)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:515)
at org.springframework.beans.factory.support.AbstractBeanFactory.lambda$doGetBean$0(AbstractBeanFactory.java:320)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:318)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:199)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:826)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:877)
at org.springframework.context.support.AbstractApplicationContext.refresh(AbstractApplicationContext.java:549)
at org.springframework.web.context.ContextLoader.configureAndRefreshWebApplicationContext(ContextLoader.java:400)
at org.springframework.web.context.ContextLoader.initWebApplicationContext(ContextLoader.java:291)
at org.springframework.web.context.ContextLoaderListener.contextInitialized(ContextLoaderListener.java:103)
at com.atlassian.spring.container.ContainerContextLoaderListener.contextInitialized(ContainerContextLoaderListener.java:32)
at com.atlassian.confluence.setup.ConfluenceBootstrappedContextLoaderListener.contextInitialized(ConfluenceBootstrappedContextLoaderListener.java:38)
at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4685)
at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5146)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1384)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1374)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:909)
at org.apache.catalina.core.StandardHost.startInternal(StandardHost.java:841)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1384)
at org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1374)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at org.apache.tomcat.util.threads.InlineExecutorService.execute(InlineExecutorService.java:75)
at java.util.concurrent.AbstractExecutorService.submit(AbstractExecutorService.java:134)
at org.apache.catalina.core.ContainerBase.startInternal(ContainerBase.java:909)
at org.apache.catalina.core.StandardEngine.startInternal(StandardEngine.java:262)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.StandardService.startInternal(StandardService.java:421)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.core.StandardServer.startInternal(StandardServer.java:930)
at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:183)
at org.apache.catalina.startup.Catalina.start(Catalina.java:633)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.catalina.startup.Bootstrap.start(Bootstrap.java:344)
at org.apache.catalina.startup.Bootstrap.main(Bootstrap.java:475)