Grouper Users - Open Discussion List

[Shilen Patel <>]

So the owner_id column in the view comes from the grouper_group_set 
table.  If you query this table for owner_id=null and look at the 
create_time, were the rows created about the same time or were they 
created over several days or weeks or more?  Were they created during 
your upgrade from 1.5 or sometime after?   Did you run any special load 
job during the time?  I'm just trying to get an idea of how the issue 
occurred.

In any case, to fix the owner_id column....

update grouper_group_set set owner_id = owner_group_id where owner_id is 
null and owner_group_id is not null;
update grouper_group_set set owner_id = owner_stem_id where owner_id is 
null and owner_stem_id is not null;
update grouper_group_set set owner_id = owner_attr_def_id where owner_id 
is null and owner_attr_def_id is not null;

Then set a not null constraint on owner_id and if anything tries to add 
a null value, you'll get an error before bad data gets added.

Thanks!

-- Shilen


On 12/4/10 11:00 AM, Colin Hudler wrote:
> I ran that query.  The owner_id does match the others, but they are null :-/
>
> There's others that are null also.  I think you are right about the db
> inconsistency.
>
> SQL>  select
> owner_id,owner_group_id,owner_attr_def_id,owner_group_id,owner_stem_id
> from grouper_memberships_all_v where
> immediate_membership_id='00554d01d4eb451e93305b898f81adf3' and
> group_set_id='55d3a30ada5040febdd7ac5ddc504ae5';
>
> OWNER_ID                                 OWNER_GROUP_ID
>             OWNER_ATTR_DEF_ID                        OWNER_GROUP_ID
>                        OWNER_STEM_ID
> ----------------------------------------
> ----------------------------------------
> ----------------------------------------
> ----------------------------------------
> ----------------------------------------
>
> 865e18c2d5eb4314a7fe9ea2fb493bc2
>             865e18c2d5eb4314a7fe9ea2fb493bc2
>
> SQL>  select count(*) from grouper_memberships_all_v where owner_id is null;
>
>     COUNT(*)
> ----------
>          303
>
>
> On 12/4/10 8:44 AM, Shilen Patel wrote:
>    
> > I think you can get that error if the database has inconsistent data. If
> > the full stack trace shows a call to the hibernate flush(), that's
> > possibly the issue. Can you run the following query?
> >
> > select * from grouper_memberships_all_v where
> > immediate_membership_id='00554d01d4eb451e93305b898f81adf3' and
> > group_set_id='55d3a30ada5040febdd7ac5ddc504ae5'
> >
> > Does the owner_id column match either owner_attr_def_id, owner_group_id,
> > or owner_stem_id? If not, then that's the problem. Otherwise, can you
> > send me the result of that query so I can see what else might be wrong?
> >
> > Thanks!
> >
> > -- Shilen
> >
> > On 12/4/10 8:05 AM, Shilen Patel wrote:
> >      
> > > Hi Colin,
> > >
> > > For the second issue, can you send me the complete stack trace?
> > >
> > > Thanks!
> > >
> > > -- Shilen
> > >
> > > On 12/3/10 2:44 PM, Colin Hudler wrote:
> > >        
> > > > Greetings,
> > > >
> > > > Today I am troubleshooting a multi-symptom problem with grouper 1.6.2
> > > > running on oracle 11g. I know of nothing that happened or changed in
> > > > the last two days to cause this (we've been running smoothly until now).
> > > > Sorry for vomiting these stack traces here; I hope it helps someone to
> > > > see the direction of the problem. I also hope that the problems are
> > > > related, because they all showed up around the same time. When browsing
> > > > to a particular group-of-groups in the UI this error is logged:
> > > >
> > > > 2010-12-03 13:21:17,695: [TP-Processor23] ERROR
> > > > GrouperCapableAction.execute(?) -<  chudler
> > > > 485E91D737D48700834238215E9B8B65-0110 840a2034d00a41608b9ec2436cd5c142
> > > > 21882177X ucmcdb>  - java.lang.RuntimeException: Too many results: 42672
> > > > at
> > > > edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MembershipDAO.findAllByGroupOwnerOptions(Hib3MembershipDAO.java:630)
> > > >
> > > > at
> > > > edu.internet2.middleware.grouper.MembershipFinder.findMemberships(MembershipFinder.java:81)
> > > >
> > > > at
> > > > edu.internet2.middleware.grouper.ui.actions.PopulateGroupMembersAction.grouperExecute(Unknown
> > > >
> > > > Source)
> > > > at
> > > > edu.internet2.middleware.grouper.ui.actions.GrouperCapableAction$1.callback(Unknown
> > > >
> > > > Source)
> > > > at
> > > > <snip>
> > > > org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:685)
> > > >
> > > > at java.lang.Thread.run(Thread.java:619)
> > > >
> > > > The web interface simply shows the generic error page. Additionally,
> > > > our daily report from grouper-loader generates a different stack trace
> > > > (an oracle error!) while it is syncing flat memberships table:
> > > >
> > > > edu.internet2.middleware.grouper.misc.GrouperReportException: Problem
> > > > generating daily report
> > > > at
> > > > edu.internet2.middleware.grouper.misc.GrouperReport.runReport(GrouperReport.java:400)
> > > >
> > > > at
> > > > edu.internet2.middleware.grouper.app.loader.GrouperLoaderType$2.runJob(GrouperLoaderType.java:215)
> > > >
> > > > at
> > > > edu.internet2.middleware.grouper.app.loader.GrouperLoaderJob.runJob(GrouperLoaderJob.java:344)
> > > >
> > > > at
> > > > edu.internet2.middleware.grouper.app.loader.GrouperLoaderJob.execute(GrouperLoaderJob.java:247)
> > > >
> > > > at org.quartz.core.JobRunShell.run(JobRunShell.java:202)
> > > > at
> > > > org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:529)
> > > >
> > > > Caused by:
> > > > edu.internet2.middleware.grouper.internal.dao.GrouperDAOException:
> > > > Problem in HibernateSession: HibernateSession: isNew: true, isReadonly:
> > > > true, grouperTransactionType: READONLY_NEW,
> > > > Exception in list: (class edu.internet2.middleware.grouper.Membership),
> > > > ByHqlStatic, query: 'select ms from MembershipEntry ms where
> > > > ms.enabledDb='T' and not exists (select 1 from FlatMembership flatMship
> > > > where flatMship.ownerId=ms.ownerId and
> > > > flatMship.memberId=ms.memberUuid and flatMship.fieldId=ms.fieldId) and
> > > > not exists (select 1 from ChangeLogEntryTemp temp, ChangeLogType type
> > > > where temp.string06 = ms.ownerGroupId and temp.string09=ms.fieldId
> > > > and type.actionName='addMembership' and
> > > > type.changeLogCategory='membership' and type.id=temp.changeLogTypeId)
> > > > and not exists (select 1 from ChangeLogEntryTemp temp, ChangeLogType
> > > > type where temp.string07 = ms.ownerId and temp.string10=ms.fieldId
> > > > and type.actionName='addPrivilege' and
> > > > type.changeLogCategory='privilege' and type.id=temp.changeLogTypeId) and
> > > > not exists (select 1 from ChangeLogEntryTemp temp, ChangeLogType type,
> > > > Member m, MembershipEntry ms2 where temp.string09=:fieldId and
> > > > type.actionName='addMembership' and type.changeLogCategory='membership'
> > > > and type.id=temp.changeLogTypeId and m.subjectIdDb=temp.string06 and
> > > > m.subjectSourceIdDb='g:gsa' and ms2.memberUuid = m.uuid and
> > > > ms.ownerId=ms2.ownerId and ms.fieldId = ms2.fieldId and
> > > > ms2.enabledDb='T') order by ms.immediateMembershipId, ms.groupSetId',
> > > > cacheable: false, cacheRegion:
> > > > edu.internet2.middleware.grouper.internal.dao.hib3.Hib3FlatMembershipDAO.FindMissingFlatMemberships,
> > > >
> > > > tx type: null, options: QueryOptions: queryPaging: pageSize: 100000,
> > > > pageNumberOnIndexed: 1, , tx type: nullBind var[0]: 'Param (class
> > > > java.lang.String): 'fieldId'->'8007cdc65bc24e928c13ab7a9ea3fae2',
> > > > at
> > > > edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_hibernateSessionCatch(HibernateSession.java:424)
> > > >
> > > > at
> > > > edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:510)
> > > >
> > > > at
> > > > edu.internet2.middleware.grouper.hibernate.ByHqlStatic.list(ByHqlStatic.java:346)
> > > >
> > > > at
> > > > edu.internet2.middleware.grouper.hibernate.ByHqlStatic.listSet(ByHqlStatic.java:395)
> > > >
> > > > at
> > > > edu.internet2.middleware.grouper.internal.dao.hib3.Hib3FlatMembershipDAO.findMissingFlatMemberships(Hib3FlatMembershipDAO.java:288)
> > > >
> > > > at
> > > > edu.internet2.middleware.grouper.misc.SyncFlatTables.addMissingFlatMemberships(SyncFlatTables.java:341)
> > > >
> > > > at
> > > > edu.internet2.middleware.grouper.misc.SyncFlatTables.syncAllFlatTables(SyncFlatTables.java:158)
> > > >
> > > > at
> > > > edu.internet2.middleware.grouper.misc.GrouperReport.runReport(GrouperReport.java:195)
> > > >
> > > > ... 5 more
> > > > Caused by: org.hibernate.exception.SQLGrammarException: could not
> > > > update:
> > > > [MembershipEntry#component[uuid,immediateMembershipId,groupSetId]{groupSetId=55d3a30ada5040febdd7ac5ddc504ae5,
> > > >
> > > > immediateMembershipId=00554d01d4eb451e93305b898f81adf3,
> > > > uuid=00554d01d4eb451e93305b898f81adf3:55d3a30ada5040febdd7ac5ddc504ae5}]
> > > > at
> > > > org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:67)
> > > >
> > > > at
> > > > org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:43)
> > > >
> > > > at
> > > > org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:2430)
> > > >
> > > > at
> > > > org.hibernate.persister.entity.AbstractEntityPersister.updateOrInsert(AbstractEntityPersister.java:2312)
> > > >
> > > > at
> > > > org.hibernate.persister.entity.AbstractEntityPersister.update(AbstractEntityPersister.java:2612)
> > > >
> > > > at
> > > > org.hibernate.action.EntityUpdateAction.execute(EntityUpdateAction.java:96)
> > > >
> > > > <snip>
> > > > edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:500)
> > > >
> > > > ... 11 more
> > > > Caused by: java.sql.SQLException: ORA-01779: cannot modify a column
> > > > which maps to a non key-preserved table
> > > >
> > > > at oracle.jdbc.driver.T4CTTIoer.processError(T4CTTIoer.java:439)
> > > >
> > > >
> > > > I can easily duplicate this with gsh: "new
> > > > SyncFlatTables().sendNotifications(false).syncAllFlatTables();", but
> > > > debugging logs haven't revealed much of use. Finally, "gsh
> > > > -findbadmemberships -all" fails with:
> > > >
> > > > org/hibernate/engine/TwoPhaseLoad.java:104:in `initializeEntity':
> > > > org.hibernate.AssertionFailure: possible non-threadsafe access to the
> > > > session, (NativeException)
> > > > Problem in HibernateSession: HibernateSession: isNew: false, isReadonly:
> > > > false, grouperTransactionType: READ_WRITE_NEW,
> > > > Exception in list: (class [Ljava.lang.Object;), ByHqlStatic, query:
> > > > 'select distinct ms, m from MembershipEntry as ms, Member as m, Field as
> > > > field where ms.ownerGroupId = :owner and
> > > > ms.memberUuid = :member and ms.fieldId = :fuuid and
> > > > ms.memberUuid = m.uuid and ms.enabledDb = 'T'', cacheable: false,
> > > > cacheRegion:
> > > > edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MembershipDAO.FindAllByGroupOwnerAndMemberAndField,
> > > >
> > > > tx type: null, tx type: nullBind var[0]: 'Param (class
> > > > java.lang.String): 'owner'->'7a246c38-b60e-4b11-96e6-67683fe82237', Bind
> > > > var[1]: 'Param (class java.lang.String):
> > > > 'member'->'89fc30292ed14ea091d5e792c24038e8'Bind var[2]: 'Param (class
> > > > java.lang.String): 'fuuid'->'8007cdc65bc24e928c13ab7a9ea3fae2', ,
> > > > Exception in delete: edu.internet2.middleware.grouper.Membership,
> > > > edu.internet2.middleware.grouper.hibernate.ByObject@6f65bb15,
> > > > Problem in HibernateSession: HibernateSession: isNew: false, isReadonly:
> > > > false, grouperTransactionType: READ_WRITE_NEW,
> > > > Exception in delete: edu.internet2.middleware.grouper.Membership,
> > > > ByObjectStatic, query: ', cacheable: null, cacheRegion: null,
> > > > entityName: ImmediateMembershipEntry, tx type: null,
> > > > Problem in HibernateSession: HibernateSession: isNew: false, isReadonly:
> > > > false, grouperTransactionType: READ_WRITE_NEW,
> > > > Problem in HibernateSession: HibernateSession: isNew: true, isReadonly:
> > > > false, grouperTransactionType: READ_WRITE_NEW
> > > > from org/hibernate/loader/Loader.java:854:in
> > > > `initializeEntitiesAndCollections'
> > > > from org/hibernate/loader/Loader.java:729:in `doQuery'
> > > > from org/hibernate/loader/Loader.java:236:in
> > > > `doQueryAndInitializeNonLazyCollections'
> > > > from org/hibernate/loader/Loader.java:2213:in `doList'
> > > > from org/hibernate/loader/Loader.java:2104:in `listIgnoreQueryCache'
> > > > from org/hibernate/loader/Loader.java:2099:in `list'
> > > > from org/hibernate/loader/hql/QueryLoader.java:378:in `list'
> > > > from org/hibernate/hql/ast/QueryTranslatorImpl.java:338:in `list'
> > > > ... 35 levels...
> > > > from run.rb:50
> > > > from run.rb:40:in `each'
> > > > from run.rb:40
> > > >
> > > > Several of our own loader jobs and scripts (using the API) generate the
> > > > same error.
> > > >
> > > >          
> >      
>