JIRA Common Errors that prevent Gaia to work normally

About the JIRA log file

When JIRA is launched, information, warning errors and others messages are stored in a log file called atlassian-jira.log, which is generally located in the JIRA installation directory (Atlassian\Application Data\JIRA\log on Microsoft Windows). This file is a key hint when trying to understand why Gaia for JIRA is not working. We will produce debug information in this file, should the proper debug parameter is set to on.

However, it may happens that Gaia cannot start, or Gaia cannot run normally because of external errors that occurred and that directly affect the behaviour of Gaia. If JIRA shows specific errors related to, for instance, the database initialization, then, obviously, Gaia won't be able to create any JIRA or Confluence project. The natural conclusion any user would have would directly lead to thinking there are bugs in Gaia. Fortunately, the proper study of the log file helps us/you understand what happened.

If you are not a system administrator, it is not easy to debug, Here are some key elements you may find in the log file, to help you debug Gaia for JIRA (and JIRA as well!)

SQL Errors

When a database is in use (for instance MySQL), it is imperative that it is properly setup and initialized, otherwise no information can be stored into it. Here are some errors you may find, and potential correction paths.

Drivers

2015-02-24 09:02:47,149 localhost-startStop-1 INFO [jira.config.database.SystemDatabaseConfigurationLoader] Reading database configuration from D:\JIRA\dbconfig.xml
2015-02-24 09:02:47,165 localhost-startStop-1 INFO [jira.instrumentation.external.DatabaseExternalGauges] Installing DBCP monitoring instruments: DatabaseExternalGauges.JiraDbcpInstruments[instruments=[DBCP_MAX, DBCP_ACTIVE, DBCP_IDLE],objectName=com.atlassian.jira:name=BasicDataSource]
2015-02-24 09:02:47,274 localhost-startStop-1 INFO [atlassian.jira.startup.JiraStartupLogger] Running JIRA startup checks.2015-02-24 09:02:47,274 localhost-startStop-1 INFO [atlassian.jira.startup.JiraStartupLogger] JIRA pre-database startup checks completed successfully.
2015-02-24 09:02:47,290 localhost-startStop-1 INFO [jira.config.database.DatabaseConfigurationManagerImpl] The database is not yet configured
2015-02-24 09:02:47,290 localhost-startStop-1 INFO [jira.config.database.DatabaseConfigurationManagerImpl] Enqueuing Database Checklist Launcher on post-database-configured-but-pre-database-activated queue
2015-02-24 09:02:47,290 localhost-startStop-1 INFO [jira.config.database.DatabaseConfigurationManagerImpl] The database is not yet configured
2015-02-24 09:02:47,290 localhost-startStop-1 INFO [jira.config.database.DatabaseConfigurationManagerImpl] Enqueuing Post database-configuration launchers on post-database-activated queue
2015-02-24 09:08:08,487 http-bio-80-exec-5 FATAL anonymous 548x21x1 1nqqq5r 0:0:0:0:0:0:0:1 /secure/SetupDatabase.jspa [atlassian.jira.startup.JiraStartupLogger] Driver for the database MySQL not found. Ensure it is installed in the 'lib' directory.
2015-02-24 09:08:08,487 http-bio-80-exec-5 INFO anonymous 548x21x1 1nqqq5r 0:0:0:0:0:0:0:1 /secure/SetupDatabase.jspa [atlassian.jira.startup.JiraStartupLogger] If you are upgrading a standalone distribution of JIRA, this may be due to the fact that JIRA no longer ships with MySQL drivers.

Solution : refer to https://docs.atlassian.com/jira/docs-063/Connecting+JIRA+to+MySQL and to https://confluence.atlassian.com/display/DOC/Database+Setup+For+MySQL for details on how to configure confluence and JIRA and My SQL.
See also this Atlassian answer : https://jira.atlassian.com/browse/JRA-37044

When JIRA has problem to use database drivers, many other problems can occurs that are related to database connector. Here an example for Database test and access denied

2015-02-24 10:14:53,748 http-bio-80-exec-1 ERROR anonymous 614x21x1 bry5v3 0:0:0:0:0:0:0:1 /secure/SetupDatabase.jspa [atlassian.config.bootstrap.DefaultAtlassianBootstrapManager] Could not successfully test your database:
java.sql.SQLException: Access denied for user 'root'@'localhost' (using password: YES)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:996)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3887)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3823)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:870)
...

Network errors

This kind of errors occurs when using JIRA in a network environment where a proxy between local JIRA installation and the internet connection is present:

UrlPortMismatchException

2015-02-24 14:13:19,736 http-bio-8080-exec-4 ERROR anonymous 853x113x1 1mznhhr 172.16.130.159,172.16.1.60 /plugins/servlet/gadgets/dashboard-diagnostics [dashboard.internal.diagnostics.DiagnosticsServlet] DIAGNOSTICS: FAILED
com.atlassian.gadgets.dashboard.internal.diagnostics.UrlPortMismatchException: Detected URL port, '8080', does not match expected port, '80'
at com.atlassian.gadgets.dashboard.internal.diagnostics.Diagnostics.checkExpectedPort(Diagnostics.java:87)
at com.atlassian.gadgets.dashboard.internal.diagnostics.Diagnostics.check(Diagnostics.java:38)
at com.atlassian.gadgets.dashboard.internal.diagnostics.DiagnosticsServlet.executeDiagnostics(DiagnosticsServlet.java:97)
at com.atlassian.gadgets.dashboard.internal.diagnostics.DiagnosticsServlet.doPost(DiagnosticsServlet.java:65)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
...

For a solution to this error visit https://confluence.atlassian.com/display/JIRAKB/Unable+to+View+Dashboard+'UrlPortMismatchException'+Due+to+Apache+Tomcat+Connector

UrlHostnameMismatchException

2015-02-24 14:36:51,908 http-bio-8080-exec-13 ERROR anonymous 876x738x1 1nfi72o 172.16.130.159,0:0:0:0:0:0:0:1 /plugins/servlet/gadgets/dashboard-diagnostics [dashboard.internal.diagnostics.DiagnosticsServlet] DIAGNOSTICS: FAILED
com.atlassian.gadgets.dashboard.internal.diagnostics.UrlHostnameMismatchException: Detected URL hostname, 'servername.company.com', does not match expected hostname, 'jira.company.com'
at com.atlassian.gadgets.dashboard.internal.diagnostics.Diagnostics.checkExpectedHostname(Diagnostics.java:76)
at com.atlassian.gadgets.dashboard.internal.diagnostics.Diagnostics.check(Diagnostics.java:37)
at com.atlassian.gadgets.dashboard.internal.diagnostics.DiagnosticsServlet.executeDiagnostics(DiagnosticsServlet.java:97)
at com.atlassian.gadgets.dashboard.internal.diagnostics.DiagnosticsServlet.doPost(DiagnosticsServlet.java:65)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at com.atlassian.plugin.servlet.DelegatingPluginServlet.service(DelegatingPluginServlet.java:42)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
...

For solution to this error visit https://confluence.atlassian.com/display/JIRAKB/HostName+Mismatch%3A+UrlHostnameMismatchException

Error looking up attributes for highestCommittedUSN

2015-03-01 01:17:36,909 atlassian-scheduler-quartz1.clustered_Worker-2 ERROR ServiceRunner [com.atlassian.scheduler.JobRunnerResponse] Unable to synchronise directory
com.atlassian.crowd.exception.OperationFailedException: Error looking up attributes for highestCommittedUSN
at com.atlassian.crowd.directory.MicrosoftActiveDirectory.fetchHighestCommittedUSN(MicrosoftActiveDirectory.java:807)
at com.atlassian.crowd.directory.ldap.cache.UsnChangedCacheRefresher.synchroniseChanges(UsnChangedCacheRefresher.java:118)
at com.atlassian.crowd.directory.DbCachingRemoteDirectory.synchroniseCache(DbCachingRemoteDirectory.java:999)
at com.atlassian.crowd.manager.directory.DirectorySynchroniserImpl.synchronise(DirectorySynchroniserImpl.java:75)
at com.atlassian.jira.crowd.embedded.JiraDirectorySynchroniser.synchronizeDirectory(JiraDirectorySynchroniser.java:96)
at com.atlassian.jira.crowd.embedded.JiraDirectorySynchroniser.runJob(JiraDirectorySynchroniser.java:60)
at com.atlassian.scheduler.core.JobLauncher.runJob(JobLauncher.java:135)
...

Visit this link https://confluence.atlassian.com/pages/viewpage.action?pageId=244352186 for detail on Active directory and JIRA

Sending message errors

2015-03-27 14:28:59,730 Sending mailitem com.atlassian.support.tools.salext.mail.SupportRequestMailQueueItem@ddfb4ad ERROR ServiceRunner Mail Queue Service [tools.salext.mail.AbstractSupportMailQueueItem] Error sending message 'Not able to link confluence pages with JIRA', see stack trace below for details.
2015-03-27 14:29:19,583 Sending mailitem com.atlassian.support.tools.salext.mail.SupportRequestMailQueueItem@ddfb4ad WARN ServiceRunner Mail Queue Service [tools.salext.mail.AbstractSupportMailQueueItem] Sending message via mail server servername.company.com

To see all the problems related to mail sending visit https://confluence.atlassian.com/display/CONFKB/Mail+Troubleshooting for a list of articles