Grouper Users - Open Discussion List

[Shilen Patel <>]

FWIW, I've seen that uniqueResult exception be a red herring in the past.  In some cases, it's been a hibernate problem.  In case it turns out that there aren't duplicate rows, I'd check the logs to see if there's an underlying exception.

This may be an indication that it's reading the old hibernate jar instead of the new.

Grouper warning: jarfile mismatch, expecting name: 'hibernate-commons-annotations-5.0.0.Final.jar' size: 75113 manifest version: 5.0.0.Final.  However the jar detected is: /opt/grouper/grouper.api-2.1.5/lib/grouper/hibernate.jar, name: hibernate.jar size: 7018087 manifest version: 3.6.7.Final

Thanks!

- Shilen

From: <Hyzer>, Chris <>
Date: Friday, June 10, 2016 at 12:36 AM
To: Satya Mohapatra <>, Grouper Users <>
Subject: [grouper-users] RE: grouper registry upgrade 2.1.5 -> 2.3.o problem

Seems like there are multiple entries in grouper_members table when there shouldn’t be.

 

Does this return multiple rows?

 

select gms.member_id, count(1) from grouper_memberships gms, grouper_members gm where

GMS.MEMBER_ID = GM.ID and GM.SUBJECT_ID = 'GrouperSystem' and GM.SUBJECT_SOURCE = 'g:isa'

group by gms.member_id ;

 

If so is there one with no memberships, and if so can you delete it and try again?

 

Thanks

chris

 

From: [] On Behalf Of Satya Mohapatra
Sent: Tuesday, June 07, 2016 9:12 PM
To: Grouper Users <>
Subject: [grouper-users] grouper registry upgrade 2.1.5 -> 2.3.o problem

 

Hi,

 

I am trying to upgrade a 2.1.5 grouper system to 2.3.0.  I am using the native upgrader provided by grouper.  I believe the error is occurring while the registry is being upgraded.  I also think the *jar mismatch could be a red herring. 

Any help would be greatly appreciated.

 

Thanks,

 

---

Satya Mohapatra, ସତ୍ୟମହାପାତ୍ର, सत्यमहापात्र, 

 LIGO Laboratory, MIT

 

 

 

Copying records from change log temp to change log with command:

  /opt/grouper/grouper/bin/gsh.sh /opt/grouper_auto_upgrade_from_2.1.5_to_2.3.0/grouper.apiBinary-2.3.0/gshChangeLogTempToChangeLog.gsh

 

stderr: Grouper ddl object type 'Grouper' has dbVersion: 0 and java version: 30

Grouper ddl object type 'Subject' has dbVersion: 0 and java version: 1

Grouper database schema DDL requires updates

(should run script manually and carefully, in sections, verify data before drop statements, backup/export important data before starting, follow change log on confluence, dont run exact same script in multiple envs - generate a new one for each env),

script file is:

/opt/grouper/grouper.api-2.1.5/ddlScripts/grouperDdl_20160607_18_03_46_214.sql

Note: this script was not executed due to option passed in

To run script via gsh, carefully review it, then run this:

gsh -registry -runsqlfile /opt/grouper/grouper.api-2.1.5/ddlScripts/grouperDdl_20160607_18_03_46_214.sql

Grouper warning: jarfile mismatch, expecting name: 'ehcache-core-2.4.3.jar' size: 1006424 manifest version: null.  However the jar detected is: /opt/grouper/grouper.api-2.1.5/lib/grouper/ehcache.jar, name: ehcache.jar size: 1838291 manifest version: 2.4.5

Grouper warning: jarfile mismatch, expecting name: 'grouperClient.jar' size: 4341330 manifest version: 2.3.0.  However the jar detected is: /opt/grouper/grouper.api-2.1.5/lib/grouper/grouperClient.jar, name: grouperClient.jar size: 4332468 manifest version: 2.3.0

Grouper warning: jarfile mismatch, expecting name: 'hibernate-commons-annotations-5.0.0.Final.jar' size: 75113 manifest version: 5.0.0.Final.  However the jar detected is: /opt/grouper/grouper.api-2.1.5/lib/grouper/hibernate.jar, name: hibernate.jar size: 7018087 manifest version: 3.6.7.Final

Couldnt startup grouper: Database schema ddl is not up to date, or has issues, check logs and config ddl in grouper.properties and run: gsh -registry -check,

Problem in HibernateSession: null,

Exception in uniqueResult: (class edu.internet2.middleware.grouper.Member), ByHqlStatic, query: 'from Member as m where      m.subjectIdDb       = :sid    and  m.subjectSourceIdDb = :source and  m.subjectTypeId   = :type', cacheable: true, cacheRegion: edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.FindBySubject, tx type: null, tx type: nullBind var[0]: 'Param (class java.lang.String): 'sid'->'GrouperSystem', Bind var[1]: 'Param (class java.lang.String): 'type'->'application'Bind var[2]: 'Param (class java.lang.String): 'source'->'g:isa',

java.lang.RuntimeException: Database schema ddl is not up to date, or has issues, check logs and config ddl in grouper.properties and run: gsh -registry -check,

Problem in HibernateSession: null,

Exception in uniqueResult: (class edu.internet2.middleware.grouper.Member), ByHqlStatic, query: 'from Member as m where      m.subjectIdDb       = :sid    and  m.subjectSourceIdDb = :source and  m.subjectTypeId   = :type', cacheable: true, cacheRegion: edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.FindBySubject, tx type: null, tx type: nullBind var[0]: 'Param (class java.lang.String): 'sid'->'GrouperSystem', Bind var[1]: 'Param (class java.lang.String): 'type'->'application'Bind var[2]: 'Param (class java.lang.String): 'source'->'g:isa',

            at edu.internet2.middleware.grouper.hibernate.HibernateSession.<init>(HibernateSession.java:176)

            at edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_hibernateSession(HibernateSession.java:467)

            at edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:659)

            at edu.internet2.middleware.grouper.hibernate.ByHqlStatic.uniqueResult(ByHqlStatic.java:339)

            at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.findBySubject(Hib3MemberDAO.java:296)

            at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.findBySubject(Hib3MemberDAO.java:202)

            at edu.internet2.middleware.grouper.MemberFinder.internal_findOrCreateBySubject(MemberFinder.java:401)

            at edu.internet2.middleware.grouper.MemberFinder.internal_findBySubject(MemberFinder.java:318)

            at edu.internet2.middleware.grouper.GrouperSession.start(GrouperSession.java:487)

            at edu.internet2.middleware.grouper.GrouperSession.startRootSession(GrouperSession.java:427)

            at edu.internet2.middleware.grouper.GrouperSession.startRootSession(GrouperSession.java:445)

            at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkGroups(GrouperCheckConfig.java:475)

            at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkConfig(GrouperCheckConfig.java:435)

            at edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperStartup.java:256)

            at edu.internet2.middleware.grouper.app.gsh.GrouperShell.main(GrouperShell.java:151)

            at edu.internet2.middleware.grouper.app.gsh.GrouperShellWrapper.main(GrouperShellWrapper.java:31)

Exception in thread "main" java.lang.RuntimeException: Database schema ddl is not up to date, or has issues, check logs and config ddl in grouper.properties and run: gsh -registry -check,

Problem in HibernateSession: null,

Exception in uniqueResult: (class edu.internet2.middleware.grouper.Member), ByHqlStatic, query: 'from Member as m where      m.subjectIdDb       = :sid    and  m.subjectSourceIdDb = :source and  m.subjectTypeId   = :type', cacheable: true, cacheRegion: edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.FindBySubject, tx type: null, tx type: nullBind var[0]: 'Param (class java.lang.String): 'sid'->'GrouperSystem', Bind var[1]: 'Param (class java.lang.String): 'type'->'application'Bind var[2]: 'Param (class java.lang.String): 'source'->'g:isa',

            at edu.internet2.middleware.grouper.hibernate.HibernateSession.<init>(HibernateSession.java:176)

            at edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_hibernateSession(HibernateSession.java:467)

            at edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:659)

            at edu.internet2.middleware.grouper.hibernate.ByHqlStatic.uniqueResult(ByHqlStatic.java:339)

            at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.findBySubject(Hib3MemberDAO.java:296)

            at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.findBySubject(Hib3MemberDAO.java:202)

            at edu.internet2.middleware.grouper.MemberFinder.internal_findOrCreateBySubject(MemberFinder.java:401)

            at edu.internet2.middleware.grouper.MemberFinder.internal_findBySubject(MemberFinder.java:318)

            at edu.internet2.middleware.grouper.GrouperSession.start(GrouperSession.java:487)

            at edu.internet2.middleware.grouper.GrouperSession.startRootSession(GrouperSession.java:427)

            at edu.internet2.middleware.grouper.GrouperSession.startRootSession(GrouperSession.java:445)

            at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkGroups(GrouperCheckConfig.java:475)

            at edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkConfig(GrouperCheckConfig.java:435)

            at edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperStartup.java:256)

            at edu.internet2.middleware.grouper.app.gsh.GrouperShell.main(GrouperShell.java:151)

            at edu.internet2.middleware.grouper.app.gsh.GrouperShellWrapper.main(GrouperShellWrapper.java:31)