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Re: [grouper-users] grouper registry upgrade 2.1.5 -> 2.3.o problem


Chronological Thread 
  • From: Satya Mohapatra <>
  • To: Brett Bieber <>
  • Cc: Grouper Users <>
  • Subject: Re: [grouper-users] grouper registry upgrade 2.1.5 -> 2.3.o problem
  • Date: Thu, 9 Jun 2016 21:38:18 +0000
  • Accept-language: en-US
Hi Brett,

We are also using MqSQL database. 

Best,

---
Satya Mohapatra, ସତ୍ୟ ମହାପାତ୍ର, सत्य महापात्र, 
 LIGO Laboratory, MIT






On Jun 9, 2016, at 1:43 PM, Brett Bieber <> wrote:

Hi Satya, 

This looks very familiar to the error we encountered with our 2.2.2 -> 2.3.0 upgrade. In our case, we had to revert to a database dump which took a considerable amount of time to restore to, and we haven't built up the courage to attempt the upgrade again.

Can I ask what database system you're using? We're using MySQL/MariaDB.

-Brett


On Tue, Jun 7, 2016 at 8:12 PM Satya Mohapatra <> wrote:
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, ସତ୍ୟ ମହାପାତ୍ର, सत्य महापात्र, 
 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)






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