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JIRA access problem

Rick Lupori_i2x4qu

Hello, I'm having trouble launching Jira on my local machine, http://localhost:8081. I get the following errors below but they appear to :be only warnings and not the root cause of the problem. I would be happy to submit my logs.

An unexpected error has occured during startup.: We couldn't start JIRA

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.
See our documentation for more information on contacting our support team and creating a support zip.

Thank you,

Rick

Accepted answers

Fazila Ashraf

Hi @Rick Lupori

Please share the logs

Nic Brough -Adaptavist-

Ok, that looks like you are having SQL errors, which suggest you may have a damaged database. This is not unexpected for the internal database (there's good reasons for the warning about the database type not being suitable for production)

The next thing I would try is restoring from the last backup you took - if this has the same errors, we know it's data or config, if it works, we know the database is corrupt. If you didn't do one manually, check <jira home>/export for the newest file.

All comments

Fazila Ashraf

Hi @Rick Lupori

Please share the logs

Rick Lupori_i2x4qu

Hi thanks for your response. I read there is a way to do this once you log into Jira but I cannot log into Jira. Where should I upload the logs?

Thanks,

Rick

Nic Brough -Adaptavist-

Here really - we're not looking for the whole log, just the bit where your login fails.

Rick Lupori_i2x4qu

ok got it thank you. These are error logs from the jirasoftware230418180204-stderr.2018-12-12.log and jirasoftware230418180204-stdout.2018-12-12.log log files. Please let me know if I'm missing a log event?

--------------------------------------------------
-- FROM LOG
--jirasoftware230418180204-stderr.2018-12-12.log
--------------------------------------------------
12-Dec-2018 06:20:14.347 INFO [Thread-32] org.apache.coyote.AbstractProtocol.pause Pausing ProtocolHandler ["http-nio-8081"]
12-Dec-2018 06:20:14.427 INFO [Thread-32] org.apache.catalina.core.StandardService.stopInternal Stopping service Catalina
12-Dec-2018 06:20:26.004 WARNING [localhost-startStop-2] 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.
12-Dec-2018 06:20:26.004 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [JonasBatch] 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.Object.wait(Object.java:502)
org.objectweb.jonas_timer.TimerManager.batch(TimerManager.java:193)
org.objectweb.jonas_timer.Batch.run(TimerManager.java:65)
12-Dec-2018 06:20:26.004 WARNING [localhost-startStop-2] org.apache.catalina.loader.WebappClassLoaderBase.clearReferencesThreads The web application [ROOT] appears to have started a thread named [JonasClock] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:
java.lang.Thread.sleep(Native Method)
org.objectweb.jonas_timer.TimerManager.clock(TimerManager.java:142)
org.objectweb.jonas_timer.Clock.run(TimerManager.java:46)
12-Dec-2018 06:20:26.020 INFO [Thread-32] org.apache.coyote.AbstractProtocol.stop Stopping ProtocolHandler ["http-nio-8081"]
12-Dec-2018 06:20:26.020 INFO [Thread-33] org.apache.catalina.util.LifecycleBase.stop The stop() method was called on component [StandardServer[8006]] after stop() had already been called. The second call will be ignored.

--------------------------------------------------
-- FROM LOG
-- jirasoftware230418180204-stdout.2018-12-12.log
--------------------------------------------------
**************************************************************************************
h2 is an in-memory database, and susceptible to corruption when abnormally terminated.
DO NOT USE IN PRODUCTION, please switch to a regular database.
**************************************************************************************

2018-12-12 07:56:22,312 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseLauncher] Database transactions enabled: true
2018-12-12 07:56:22,315 JIRA-Bootstrap INFO [c.a.jira.startup.DatabaseLauncher] Using JIRA's default for database transaction isolation level: 2
2018-12-12 07:56:22,320 JIRA-Bootstrap INFO [c.a.jira.startup.JiraStartupLogger]

Database configuration OK

___ Database Configuration ________________

Loading entityengine.xml from : file:/C:/Program%20Files/Atlassian/JIRA/atlassian-jira/WEB-INF/classes/entityengine.xml
Entity model field type name : h2
Entity model schema name : PUBLIC
Database Version : H2 - 1.4.185 (2015-01-16)
Database Driver : H2 JDBC Driver - 1.4.185 (2015-01-16)
Database URL : jdbc:h2:file:C:\Program Files\Atlassian\Application Data\JIRA/database/h2db
Database JDBC config : h2 jdbc:h2:file:C:\Program Files\Atlassian\Application Data\JIRA/database/h2db

2018-12-12 07:57:25,520 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (5): [com.atlassian.jira.plugins.jira-development-integration-plugin, com.radiantminds.roadmaps-jira, com.atlassian.jpo, com.atlassian.gadgets.directory, com.pyxis.greenhopper.jira], 286 seconds remaining
2018-12-12 07:57:26,264 ThreadPoolAsyncTaskExecutor::Thread 3 ERROR [c.a.p.osgi.factory.OsgiPlugin] Unable to start the plugin container for plugin 'com.atlassian.jira.plugins.jira-development-integration-plugin'
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'devSummaryUpdateJob': Invocation of init method failed; nested exception is com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Generic Entity Exception occurred in deleteByAnd (SQL Exception while executing the following:DELETE FROM PUBLIC.clusteredjob WHERE JOB_ID=? (General error: "java.lang.IllegalArgumentException"; SQL statement:
DELETE FROM PUBLIC.clusteredjob WHERE JOB_ID=? [50000-185]))
at org.springframework.beans.factory.annotation.InitDestroyAnnotationBeanPostProcessor.postProcessBeforeInitialization(InitDestroyAnnotationBeanPostProcessor.java:136)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.applyBeanPostProcessorsBeforeInitialization(AbstractAutowireCapableBeanFactory.java:408)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1570)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:545)
at org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:482)
at org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:306)
at org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:230)
at org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:302)
at org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:197)
at org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:772)
at org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:839)
at org.eclipse.gemini.blueprint.context.support.AbstractDelegatedExecutionApplicationContext.access$1600(AbstractDelegatedExecutionApplicationContext.java:60)
at org.eclipse.gemini.blueprint.context.support.AbstractDelegatedExecutionApplicationContext$4.run(AbstractDelegatedExecutionApplicationContext.java:325)
at org.eclipse.gemini.blueprint.util.internal.PrivilegedUtils.executeWithCustomTCCL(PrivilegedUtils.java:85)
at org.eclipse.gemini.blueprint.context.support.AbstractDelegatedExecutionApplicationContext.completeRefresh(AbstractDelegatedExecutionApplicationContext.java:290)
at org.eclipse.gemini.blueprint.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$CompleteRefreshTask.run(DependencyWaiterApplicationContextExecutor.java:137)
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: Generic Entity Exception occurred in deleteByAnd (SQL Exception while executing the following:DELETE FROM PUBLIC.clusteredjob WHERE JOB_ID=? (General error: "java.lang.IllegalArgumentException"; SQL statement:

...
...
...
2018-12-12 07:57:26,585 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 285 seconds remaining
2018-12-12 07:57:27,717 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 284 seconds remaining
2018-12-12 07:57:28,736 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 283 seconds remaining
2018-12-12 07:57:29,773 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 282 seconds remaining
2018-12-12 07:57:30,810 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 281 seconds remaining
2018-12-12 07:57:31,866 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 280 seconds remaining
2018-12-12 07:57:32,878 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 279 seconds remaining
2018-12-12 07:57:34,030 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 278 seconds remaining
2018-12-12 07:57:34,458 ThreadPoolAsyncTaskExecutor::Thread 10 INFO [c.atlassian.agile.support]

*********************************************************************************
Atlassian GreenHopper v7.9.0-DAILY20180326142825 #926d98943e28d1b1 built 2018-03-26T07:35:44.582-07:00 - plugin starting...
*********************************************************************************

2018-12-12 07:57:35,052 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 277 seconds remaining
2018-12-12 07:57:36,058 JIRA-Bootstrap INFO [c.a.plugin.util.WaitUntil] Plugins that have yet to be enabled: (2): [com.atlassian.jpo, com.pyxis.greenhopper.jira], 276 seconds remaining
2018-12-12 07:57:36,347 ThreadPoolAsyncTaskExecutor::Thread 3 ERROR [o.e.g.b.e.i.util.concurrent.RunnableTimedExecution] Closing runnable for context NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.jira.plugins.jira-development-integration-plugin, config=osgibundle:/META-INF/spring/*.xml) did not finish in 10000ms; consider taking a snapshot and then shutdown the VM in case the thread still hangs
2018-12-12 07:57:36,350 ThreadPoolAsyncTaskExecutor::Thread 3 ERROR [o.e.g.b.e.internal.support.ExtenderConfiguration] Application context refresh failed (NonValidatingOsgiBundleXmlApplicationContext(bundle=com.atlassian.jira.plugins.jira-development-integration-plugin, config=osgibundle:/META-INF/spring/*.xml))
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'devSummaryUpdateJob': Invocation of init method failed; nested exception is com.atlassian.jira.exception.DataAccessException: org.ofbiz.core.entity.GenericDataSourceException: Generic Entity Exception occurred in deleteByAnd (SQL Exception while executing the following:DELETE FROM PUBLIC.clusteredjob WHERE JOB_ID=? (General error: "java.lang.IllegalArgumentException"; SQL statement:

...
...
...

2018-12-12 07:57:46,752 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] We couldn't start JIRA
2018-12-12 07:57:46,752 JIRA-Bootstrap ERROR [c.a.jira.health.HealthChecks] 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.
See our documentation for more information on contacting our support team and creating a support zip.
2018-12-12 07:57:46,915 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.)]
2018-12-12 07:57:46,960 JIRA-Bootstrap INFO [c.a.jira.startup.LauncherContextListener] Memory Usage:
---------------------------------------------------------------------------------
Heap memory : Used: 485 MiB. Committed: 999 MiB. Max: 1002 MiB
Non-heap memory : Used: 253 MiB. Committed: 274 MiB. Max: 1264 MiB
---------------------------------------------------------------------------------
TOTAL : Used: 738 MiB. Committed: 1273 MiB. Max: 2266 MiB
---------------------------------------------------------------------------------
2018-12-12 07:59:21,158 hipchat-plugin-tasks-executor-0 DEBUG [c.a.activeobjects.osgi.ActiveObjectsServiceFactory] getService bundle [com.atlassian.plugins.base-hipchat-integration-plugin-api]

Nic Brough -Adaptavist-

Rick Lupori_i2x4qu

Thank you very much again. The problem is all the articles I've found that explains how to restore from the activeobjects.xml and entities.xml file in the <jira home>/export folders requires that I restore through the system which won't load for me....https://confluence.atlassian.com/adminjiraserver073/restoring-data-from-an-xml-backup-861253849.html#Restoringdatafromanxmlbackup-restorexmldata . Is there another way? I tried to also do a search for these files in <jira home> folders and could not find them. Can you please point me to an article that could help me restore them?

Thanks, Rick

Nic Brough -Adaptavist-

There's not much we can point you at, it sounds like you are looking at the right docs to do a restore, but you're actually blocked before you get there.

Is this Jira install you're working with a completely clean empty Jira?

Rick Lupori

No it's not. I had a lot of project data information is like to try to restore.

Rick

Rick Lupori_i2x4qu

So I now have the option to create my own database now in the Database Setup screen. Can I select SQL Server and then restore from my backup instead of going through and selecting the "Built In (for evaluation or demonstration)" which created this mess?

Thanks,

Rick

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