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2018-03-28 01:04:06,171 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]

Database configuration OK

___ Database Configuration _________________

Loading entityengine.xml from : file:/opt/atlassian/jira/atlassian-jira/WEB-INF/classes/entityengine.xml
Entity model field type name : mysql
Entity model schema name :
Database Version : MySQL - 5.6.38
Database Driver : MySQL Connector Java - mysql-connector-java-5.1.44 ( Revision: b3cda4f864902ffdde495b9df93937c3e20009be )
Database URL : jdbc:mysql://46.101.149.157:3306/ea_jira?useUnicode=true&characterEncoding=UTF8&sessionVariables=default_storage_engine=InnoDB
Database JDBC config : mysql jdbc:mysql://46.101.149.157:3306/ea_jira?useUnicode=true&characterEncoding=UTF8&sessionVariables=default_storage_engine=InnoDB

2018-03-28 01:04:06,180 JIRA-Bootstrap ERROR [c.a.jira.upgrade.PluginSystemLauncher] A fatal error occured during initialisation. JIRA has been locked.
com.atlassian.plugin.osgi.container.OsgiContainerException: Unable to clean the cache directory: /var/atlassian/application-data/jira/plugins/.osgi-plugins/felix
at com.atlassian.plugin.osgi.container.impl.DefaultOsgiPersistentCache.validate(DefaultOsgiPersistentCache.java:81)
at com.atlassian.plugin.osgi.container.impl.DefaultOsgiPersistentCache.<init>(DefaultOsgiPersistentCache.java:38)
at com.atlassian.jira.plugin.PluginPath$JiraHomeAdapter.<init>(PluginPath.java:135)
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
... 1 filtered
at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
at org.picocontainer.injectors.AbstractInjector.newInstance(AbstractInjector.java:145)
at org.picocontainer.injectors.ConstructorInjector$1.run(ConstructorInjector.java:342)
at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:270)
at org.picocontainer.injectors.ConstructorInjector.getComponentInstance(ConstructorInjector.java:364)
at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64)
at org.picocontainer.behaviors.Stored.getComponentInstance(Stored.java:91)
at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64)
at org.picocontainer.behaviors.Locked.getComponentInstance(Locked.java:40)
at org.picocontainer.DefaultPicoContainer.getInstance(DefaultPicoContainer.java:698)
at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:646)
at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:631)
at org.picocontainer.parameters.BasicComponentParameter$1.resolveInstance(BasicComponentParameter.java:118)
at org.picocontainer.parameters.ComponentParameter$1.resolveInstance(ComponentParameter.java:136)
at org.picocontainer.injectors.SingleMemberInjector.getParameter(SingleMemberInjector.java:78)
at org.picocontainer.injectors.ConstructorInjector$CtorAndAdapters.getParameterArguments(ConstructorInjector.java:309)
at org.picocontainer.injectors.ConstructorInjector$1.run(ConstructorInjector.java:335)
at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:270)
at org.picocontainer.injectors.ConstructorInjector.getComponentInstance(ConstructorInjector.java:364)
at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64)
at org.picocontainer.behaviors.Stored.getComponentInstance(Stored.java:91)
at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64)
at org.picocontainer.behaviors.Locked.getComponentInstance(Locked.java:40)
at org.picocontainer.DefaultPicoContainer.getInstance(DefaultPicoContainer.java:698)
at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:646)
at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:631)
at org.picocontainer.parameters.BasicComponentParameter$1.resolveInstance(BasicComponentParameter.java:118)
at org.picocontainer.parameters.ComponentParameter$1.resolveInstance(ComponentParameter.java:136)
at org.picocontainer.injectors.SingleMemberInjector.getParameter(SingleMemberInjector.java:78)
at org.picocontainer.injectors.ConstructorInjector$CtorAndAdapters.getParameterArguments(ConstructorInjector.java:309)
at org.picocontainer.injectors.ConstructorInjector$1.run(ConstructorInjector.java:335)
at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:270)
at org.picocontainer.injectors.ConstructorInjector.getComponentInstance(ConstructorInjector.java:364)
at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64)
at org.picocontainer.behaviors.Stored.getComponentInstance(Stored.java:91)
at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64)
at org.picocontainer.behaviors.Locked.getComponentInstance(Locked.java:40)
at org.picocontainer.DefaultPicoContainer.getInstance(DefaultPicoContainer.java:698)
at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:646)
at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:631)
at org.picocontainer.parameters.BasicComponentParameter$1.resolveInstance(BasicComponentParameter.java:118)
at org.picocontainer.parameters.ComponentParameter$1.resolveInstance(ComponentParameter.java:136)
at org.picocontainer.injectors.SingleMemberInjector.getParameter(SingleMemberInjector.java:78)
at org.picocontainer.injectors.ConstructorInjector$CtorAndAdapters.getParameterArguments(ConstructorInjector.java:309)
at org.picocontainer.injectors.ConstructorInjector$1.run(ConstructorInjector.java:335)
at org.picocontainer.injectors.AbstractInjector$ThreadLocalCyclicDependencyGuard.observe(AbstractInjector.java:270)
at org.picocontainer.injectors.ConstructorInjector.getComponentInstance(ConstructorInjector.java:364)
at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64)
at org.picocontainer.behaviors.Stored.getComponentInstance(Stored.java:91)
at org.picocontainer.behaviors.AbstractBehavior.getComponentInstance(AbstractBehavior.java:64)
at org.picocontainer.behaviors.Locked.getComponentInstance(Locked.java:40)
at org.picocontainer.DefaultPicoContainer.getInstance(DefaultPicoContainer.java:698)
at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:646)
at org.picocontainer.DefaultPicoContainer.getComponent(DefaultPicoContainer.java:677)
at com.atlassian.jira.component.CachingMutablePicoContainer.getComponent(CachingMutablePicoContainer.java:137)
at com.atlassian.jira.ComponentManager.getComponent(ComponentManager.java:546)
at com.atlassian.jira.ComponentManager.quickStart(ComponentManager.java:194)
at com.atlassian.jira.ComponentManager.start(ComponentManager.java:165)
at com.atlassian.jira.upgrade.PluginSystemLauncher.start(PluginSystemLauncher.java:47)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$postDbLaunch$2(DefaultJiraLauncher.java:154)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrEnqueue(DatabaseConfigurationManagerImpl.java:304)
at com.atlassian.jira.config.database.DatabaseConfigurationManagerImpl.doNowOrWhenDatabaseActivated(DatabaseConfigurationManagerImpl.java:199)
at com.atlassian.jira.startup.DefaultJiraLauncher.postDbLaunch(DefaultJiraLauncher.java:146)
at com.atlassian.jira.startup.DefaultJiraLauncher.lambda$start$0(DefaultJiraLauncher.java:105)
at com.atlassian.jira.util.devspeed.JiraDevSpeedTimer.run(JiraDevSpeedTimer.java:31)
at com.atlassian.jira.startup.DefaultJiraLauncher.start(DefaultJiraLauncher.java:103)
at com.atlassian.jira.startup.LauncherContextListener.initSlowStuff(LauncherContextListener.java:157)
at java.lang.Thread.run(Thread.java:745)
Caused by: java.io.IOException: Failed to list contents of /var/atlassian/application-data/jira/plugins/.osgi-plugins/felix/felix-cache
at org.apache.commons.io.FileUtils.cleanDirectory(FileUtils.java:1393)
at org.apache.commons.io.FileUtils.deleteDirectory(FileUtils.java:1331)
at org.apache.commons.io.FileUtils.forceDelete(FileUtils.java:1910)
at org.apache.commons.io.FileUtils.cleanDirectory(FileUtils.java:1399)
at com.atlassian.plugin.osgi.container.impl.DefaultOsgiPersistentCache.validate(DefaultOsgiPersistentCache.java:79)
2018-03-28 01:04:07,122 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] Could not execute health check, DatabaseConfigurationManager not available.
2018-03-28 01:04:07,122 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] Could not execute health check, DatabaseConfigurationManager not available.
2018-03-28 01:04:07,122 JIRA-Bootstrap ERROR [c.a.jira.startup.DefaultJiraLauncher] JIRA has failed to start because of the following errors: [(Event: Level = (EventLevel: fatal) , Key = (EventType: startup-unexpected) , Desc = We couldn't start JIRA , Exception = An error occurred while trying to start JIRA. We can't give you any more detail right now, we suggest checking the logs for more detail and contacting our support team.<br/>See our documentation for more information on contacting our support team and creating a support zip.), (Event: Level = (EventLevel: fatal) , Key = (EventType: database) , Desc = Could not execute health check, DatabaseConfigurationManager not available. , Exception = ]

1 answer

1 accepted

1 vote
Answer accepted
Nic Brough Community Leader Mar 27, 2018

It's not a bug, you have misconfigured the file system.

The user running the Jira service does not have the right access to the installation and/or home directories.  Stop Jira, make sure both directories are owned by the user that Jira will run as, and that it has full access to them (and all sub-directories) and restart it.

How can I do that?

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