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Error creating admin account during Jira install

EthanML
EthanML
Contributor
December 4, 2012

I'm in the middle of doing a fresh install of Jira 4.1.2 (to use for migration and upgrading from another Jira later on) and this has happened a couple of times now.

I set up the Standalone Jira fine initially, then I connect it to an external database, which seems to work fine as well. I shutdown and start up the Jira again and it goes back to Setup, which i take it is meant to happen.

This goes fine until the step where you create the administrator account. When I try and continue from this step i get this error and stacktrace:

(this is running on a Linux server using a MySQL db)

==============================================================

Cause:
com.atlassian.util.concurrent.LazyReference$InitializationException: java.lang.RuntimeException: org.ofbiz.core.entity.GenericDataSourceException: SQL Exception while executing the following:SELECT ID, groupname FROM groupbase ORDER BY groupname ASC (Table 'jiradb.groupbase' doesn't exist)

com.atlassian.util.concurrent.LazyReference$InitializationException: java.lang.RuntimeException: org.ofbiz.core.entity.GenericDataSourceException: SQL Exception while executing the following:SELECT ID, groupname FROM groupbase ORDER BY groupname ASC (Table 'jiradb.groupbase' doesn't exist)
	at com.atlassian.util.concurrent.LazyReference.getInterruptibly(LazyReference.java:152)
	at com.atlassian.util.concurrent.LazyReference.get(LazyReference.java:115)
	at com.atlassian.jira.user.osuser.JiraOFBizAccessProvider$CachingAccessProvider.list(JiraOFBizAccessProvider.java:219)
	at com.atlassian.jira.user.osuser.JiraOFBizAccessProvider.handles(JiraOFBizAccessProvider.java:73)
	at com.opensymphony.user.UserManager.getProvider(UserManager.java:269)
	at com.opensymphony.user.UserManager.getEntity(UserManager.java:257)
	at com.opensymphony.user.UserManager.getGroup(UserManager.java:173)
	at com.atlassian.core.user.GroupUtils.getGroupSafely(GroupUtils.java:96)
	at com.atlassian.jira.web.action.setup.Setup2.getOrCreateGroup(Setup2.java:131)
	at com.atlassian.jira.web.action.setup.Setup2.doExecute(Setup2.java:97)
	at webwork.action.ActionSupport.execute(ActionSupport.java:165)
	at com.atlassian.jira.action.JiraActionSupport.execute(JiraActionSupport.java:54)
	at webwork.dispatcher.GenericDispatcher.executeAction(GenericDispatcher.java:139)
	at com.atlassian.jira.web.dispatcher.JiraServletDispatcher.service(JiraServletDispatcher.java:171)
	at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.core.filters.HeaderSanitisingFilter.doFilter(HeaderSanitisingFilter.java:44)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:55)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:41)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.jira.web.filters.accesslog.AccessLogFilter.executeRequest(AccessLogFilter.java:99)
	at com.atlassian.jira.web.filters.accesslog.AccessLogFilter.doFilter(AccessLogFilter.java:83)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.jira.security.xsrf.XsrfTokenAdditionRequestFilter.doFilter(XsrfTokenAdditionRequestFilter.java:50)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)
	at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55)
	at com.atlassian.jira.web.filters.SitemeshExcludePathFilter.doFilter(SitemeshExcludePathFilter.java:40)
	at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:55)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:41)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.seraph.filter.SecurityFilter.doFilter(SecurityFilter.java:219)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.security.auth.trustedapps.filter.TrustedApplicationsFilter.doFilter(TrustedApplicationsFilter.java:98)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.seraph.filter.BaseLoginFilter.doFilter(BaseLoginFilter.java:140)
	at com.atlassian.jira.web.filters.JiraLoginFilter.doFilter(JiraLoginFilter.java:70)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter$1.doFilter(DelegatingPluginFilter.java:66)
	at com.atlassian.oauth.serviceprovider.internal.servlet.OAuthFilter.doFilter(OAuthFilter.java:69)
	at com.atlassian.plugin.servlet.filter.DelegatingPluginFilter.doFilter(DelegatingPluginFilter.java:74)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:42)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:55)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:41)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.util.profiling.filters.ProfilingFilter.doFilter(ProfilingFilter.java:99)
	at com.atlassian.jira.web.filters.JIRAProfilingFilter.doFilter(JIRAProfilingFilter.java:16)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.jira.web.filters.ActionCleanupDelayFilter.doFilter(ActionCleanupDelayFilter.java:59)
	at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.jira.web.filters.RequestCleanupFilter.doFilter(RequestCleanupFilter.java:53)
	at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.johnson.filters.AbstractJohnsonFilter.doFilter(AbstractJohnsonFilter.java:72)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:350)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.gzipfilter.GzipFilter.doFilterInternal(GzipFilter.java:81)
	at com.atlassian.gzipfilter.GzipFilter.doFilter(GzipFilter.java:51)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.plugin.servlet.filter.IteratingFilterChain.doFilter(IteratingFilterChain.java:46)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:55)
	at com.atlassian.plugin.servlet.filter.ServletFilterModuleContainerFilter.doFilter(ServletFilterModuleContainerFilter.java:41)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.core.filters.cache.AbstractCachingFilter.doFilter(AbstractCachingFilter.java:33)
	at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.core.filters.encoding.AbstractEncodingFilter.doFilter(AbstractEncodingFilter.java:41)
	at com.atlassian.core.filters.AbstractHttpFilter.doFilter(AbstractHttpFilter.java:31)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at com.atlassian.jira.startup.JiraStartupChecklistFilter.doFilter(JiraStartupChecklistFilter.java:86)
	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:128)
	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
	at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:567)
	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
	at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:849)
	at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:583)
	at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:454)
	at java.lang.Thread.run(Thread.java:722)
Caused by: java.lang.RuntimeException: org.ofbiz.core.entity.GenericDataSourceException: SQL Exception while executing the following:SELECT ID, groupname FROM groupbase ORDER BY groupname ASC (Table 'jiradb.groupbase' doesn't exist)
	at com.atlassian.jira.user.osuser.JiraOFBizAccessProvider$OfbizAccessProvider$OfbizGroups.get(JiraOFBizAccessProvider.java:497)
	at com.atlassian.jira.user.osuser.JiraOFBizAccessProvider$OfbizAccessProvider$OfbizGroups.get(JiraOFBizAccessProvider.java:484)
	at com.atlassian.jira.user.osuser.JiraOFBizAccessProvider$CachingAccessProvider$GroupsCache.create(JiraOFBizAccessProvider.java:293)
	at com.atlassian.jira.user.osuser.JiraOFBizAccessProvider$CachingAccessProvider$GroupsCache.create(JiraOFBizAccessProvider.java:288)
	at com.atlassian.util.concurrent.LazyReference$1.call(LazyReference.java:79)
	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
	at java.util.concurrent.FutureTask.run(FutureTask.java:166)
	at com.atlassian.util.concurrent.LazyReference.getInterruptibly(LazyReference.java:146)
	... 110 more
Caused by: org.ofbiz.core.entity.GenericDataSourceException: SQL Exception while executing the following:SELECT ID, groupname FROM groupbase ORDER BY groupname ASC (Table 'jiradb.groupbase' doesn't exist)
	at org.ofbiz.core.entity.jdbc.SQLProcessor.executeQuery(SQLProcessor.java:596)
	at org.ofbiz.core.entity.GenericDAO.selectListIteratorByCondition(GenericDAO.java:1076)
	at org.ofbiz.core.entity.GenericDAO.selectByAnd(GenericDAO.java:621)
	at org.ofbiz.core.entity.GenericHelperDAO.findByAnd(GenericHelperDAO.java:134)
	at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:792)
	at org.ofbiz.core.entity.GenericDelegator.findByAnd(GenericDelegator.java:777)
	at org.ofbiz.core.entity.GenericDelegator.findAll(GenericDelegator.java:715)
	at com.atlassian.jira.user.osuser.JiraOFBizAccessProvider$OfbizAccessProvider$OfbizGroups.get(JiraOFBizAccessProvider.java:491)
	... 117 more

Referer URL: http://localhost:8080/secure/Setup.jspa

Build Information:
Uptime : N/A
Edition : enterprise
Version : 4.1.2
Build Number : 531
Build Date : Mon Jun 07 00:00:00 IST 2010
Atlassian Partner : null
Installation Type : Standalone
Server ID : Contact your Administrator to discover this property value.

Server Information:
Application Server: Apache Tomcat/6.0.20
Servlet Version: 2.5

==================================================================

As far as I can see it's not finding the table that holds the users or something for some reason.The jiradb I created was new and empty, and it's set to use a user which has been granted 'all privileges' on this database.

Does anyone have any experience with this issue or any suggestions?

Thanks,

Ethan

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Jobin Kuruvilla [Adaptavist]
Jobin Kuruvilla [Adaptavist]
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December 4, 2012

Can you check if the table exists? JIRA should create all the tables during the initial startup.

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EthanML
EthanML
Contributor
December 5, 2012

On further inspection, no the table 'groupbase' doesn't seem to exist for some reason...I can't imagine why it would repeatedly not create this table when all the others seem to have been created fine for some reason.

The table 'userbase' for example, which holds the users I'm trying to create in this step of the install, has been created and is storing the user data i enter at each attempt.

Any ideas? Can I just manually create a blank table with this name, or do i need to set it up with any special properties?

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EthanML
EthanML
Contributor
December 5, 2012

UPDATE: Ok this is weird. I tried creating the table manually through phpMyAdmin, and it says the table 'groupbase' already exists. Yet when I search for that table it comes up with nothing.

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EthanML
EthanML
Contributor
December 5, 2012

Yes I set it up exactly as it said to in that article, or the version of that article for jira 4.1.

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C_ Faysal
C_ Faysal
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December 5, 2012

how did you set up the database?

have you read https://confluence.atlassian.com/display/JIRA/Connecting+JIRA+to+MySQL ?

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C_ Faysal
C_ Faysal
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December 5, 2012

since your setup didn't finished successfully it would be no problem dropping the database and start all over right?

in 4.1 documentation some things seem to differ..

https://confluence.atlassian.com/display/JIRA041/Connecting+JIRA+to+MySQL

maybe you could create the db with the shown command "create database jiradb character set utf8;"

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EthanML
EthanML
Contributor
December 5, 2012

Ok i started from scratch and followed those instructions more closely and I think it seems to have worked this time, what an annoying process that was. Thanks for your help.

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