Grouper Users - Open Discussion List

[Scott Koranda <>]

Hi,

> What version doesn't have a problem?  1.4.1?

No, the working version is also a CVS checkout since the 1.4.1
release. I did a checkout in order to pick up a bug you fixed
having to do with the infinite recursion we were seeing
through the UI.

I should also add that in order to use InnoDB tables with
MySQL I followed the usual steps to create a grouperDdl_*.sql
file, moved it to grouperWithInnoDB.sql and edited by hand
changing the table types to be InnoDB. Then I used gsh.sh like
this:

./bin/gsh.sh -registry -runsqlfile 
/opt/grouper/grouper-api-1_4_BRANCH/grouper/ddlScripts/grouperWithInnoDB.sql

> 
> The change log has upgrade instructions, though Im not sure any of them are 
> crucial or should cause your error:
> 
> https://wiki.internet2.edu/confluence/display/GrouperWG/Grouper+change+log+v1.4
> 
> Can you send me your log file?

Sent to Chris privately.

> 
> /opt/grouper/grouper-api-1_4_BRANCH/grouper/logs/grouper_error.log
>  
> And what does this query return?
> 
> select object_name, db_version from grouper_ddl

mysql> SELECT object_name, db_version FROM grouper_ddl;
+-------------+------------+
| object_name | db_version |
+-------------+------------+
| Subject     |          1 |
| Grouper     |         13 |
+-------------+------------+
2 rows in set (0.00 sec)

Thanks,

Scott


> 
> Thanks!
> Chris
> 
> 
> > -----Original Message-----
> > From: Scott Koranda 
> > [mailto:]
> > Sent: Sunday, April 19, 2009 3:28 PM
> > To: Grouper Users Mailing List
> > Subject: [grouper-users] debugging with new grouper.jar and ddl errors
> > 
> > Hi,
> > 
> > I have a testbed running the Grouper API built from the
> > GROUPER_1_4_BRANCH. I am having some problems with ldappc and
> > wanted to try to debug them.
> > 
> > My strategy was to checkout a new version of the CVS
> > repository for the GROUPER_1_4_BRANCH, make a slight
> > modification to the code and build a new jar. Then put the new
> > jar into place.
> > 
> > I cannot, however, create a new jar and put it into place even
> > if I do not make any modifications to the code.
> > 
> > Here in detail is what I am doing:
> > 
> > -bash-3.2$ cvs 
> > -d:pserver::/home/cvs/i2mi
> > export -r GROUPER_1_4_BRANCH grouper
> > 
> > <snip long co details>
> > 
> > -bash-3.2$ cd grouper
> > -bash-3.2$ ant dist
> > 
> > <snip long build log>
> > 
> > BUILD SUCCESSFUL
> > Total time: 18 seconds
> > 
> > -bash-3.2$ cp dist/lib/grouper.jar /opt/grouper/grouper-api-
> > 1_4_BRANCH/grouper/dist/lib/grouper.jar
> > -bash-3.2$ cd /opt/grouper/grouper-api-1_4_BRANCH/grouper
> > -bash-3.2$ ./bin/gsh.sh -ldappc -subject GrouperSystem -groups -
> > memberships -configManager /opt/grouper/ldappc/grouper/conf/ldappc.xml
> > Using GROUPER_HOME: /opt/grouper/grouper-api-1_4_BRANCH/grouper
> > Using GROUPER_CONF: /opt/grouper/grouper-api-1_4_BRANCH/grouper/conf
> > Using JAVA: java
> > using MEMORY: 64m-512m
> > Grouper starting up: version: 1.4.2, build date: 2009/04/19 14:15:03,
> > env: production
> > grouper.properties read from: /opt/grouper/grouper-api-
> > 1_4_BRANCH/grouper/conf/grouper.properties
> > Grouper current directory is: /opt/grouper/grouper-api-
> > 1_4_BRANCH/grouper
> > log4j.properties read from:   /opt/grouper/grouper-api-
> > 1_4_BRANCH/grouper/conf/log4j.properties
> > Grouper is logging to file:   /opt/grouper/grouper-api-
> > 1_4_BRANCH/grouper/logs/grouper_error.log, at min level WARN for
> > package: edu.internet2.middleware.grouper, based on log4j.properties
> > grouper.hibernate.properties: /opt/grouper/grouper-api-
> > 1_4_BRANCH/grouper/conf/grouper.hibernate.properties
> > grouper.hibernate.properties:
> > grouper@jdbc:mysql://oregano.phys.uwm.edu:3306/grouper?useSSL=true
> > sources.xml read from:        /opt/grouper/grouper-api-
> > 1_4_BRANCH/grouper/conf/sources.xml
> > sources.xml groupersource id: g:gsa
> > sources.xml jndi source id:   ligo:
> > cn=admin,dc=ligo,dc=org@ldaps://oregano.phys.uwm.edu
> > Grouper ddl object type 'Grouper' has dbVersion: 0 and java version: 13
> > 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-
> > 1_4_BRANCH/grouper/ddlScripts/grouperDdl_20090419_14_25_32_076.sql
> > 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.FindBy
> > Subject, 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.FindBy
> > Subject, 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>(Hibe
> > rnateSession.java:67)
> >     at
> > edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_h
> > ibernateSession(HibernateSession.java:254)
> >     at
> > edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHib
> > ernateSession(HibernateSession.java:383)
> >     at
> > edu.internet2.middleware.grouper.hibernate.ByHqlStatic.uniqueResult(ByH
> > qlStatic.java:295)
> >     at
> > edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.findBy
> > Subject(Hib3MemberDAO.java:141)
> >     at
> > edu.internet2.middleware.grouper.MemberFinder.internal_findOrCreateBySu
> > bject(MemberFinder.java:225)
> >     at
> > edu.internet2.middleware.grouper.MemberFinder.internal_findBySubject(Me
> > mberFinder.java:198)
> >     at
> > edu.internet2.middleware.grouper.GrouperSession.start(GrouperSession.ja
> > va:272)
> >     at
> > edu.internet2.middleware.grouper.GrouperSession.startRootSession(Groupe
> > rSession.java:222)
> >     at
> > edu.internet2.middleware.grouper.GrouperSession.startRootSession(Groupe
> > rSession.java:240)
> >     at
> > edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkGroups(Gr
> > ouperCheckConfig.java:439)
> >     at
> > edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkConfig(Gr
> > ouperCheckConfig.java:410)
> >     at
> > edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperSta
> > rtup.java:82)
> >     at
> > edu.internet2.middleware.grouper.internal.dao.hib3.Hib3DAO.<clinit>(Hib
> > 3DAO.java:64)
> >     at
> > edu.internet2.middleware.grouper.internal.dao.hib3.Hib3DAOFactory.getGr
> > oup(Hib3DAOFactory.java:56)
> >     at
> > edu.internet2.middleware.grouper.GrouperSourceAdapter.getSubject(Groupe
> > rSourceAdapter.java:121)
> >     at
> > edu.internet2.middleware.grouper.subj.SourcesXmlResolver.find(SourcesXm
> > lResolver.java:91)
> >     at
> > edu.internet2.middleware.grouper.subj.CachingResolver.find(CachingResol
> > ver.java:74)
> >     at
> > edu.internet2.middleware.grouper.subj.ValidatingResolver.find(Validatin
> > gResolver.java:67)
> >     at
> > edu.internet2.middleware.grouper.SubjectFinder.findById(SubjectFinder.j
> > ava:100)
> >     at
> > edu.internet2.middleware.ldappc.GrouperSubjectRetriever.findSubjectById
> > (GrouperSubjectRetriever.java:50)
> >     at
> > edu.internet2.middleware.ldappc.GrouperSessionControl.startSession(Grou
> > perSessionControl.java:75)
> >     at
> > edu.internet2.middleware.ldappc.GrouperProvisioner.provision(GrouperPro
> > visioner.java:155)
> >     at
> > edu.internet2.middleware.ldappc.LdappcGrouperProvisioner.provisionGroup
> > s(LdappcGrouperProvisioner.java:119)
> >     at
> > edu.internet2.middleware.ldappc.LdappcProvisionControl.run(LdappcProvis
> > ionControl.java:96)
> >     at edu.internet2.middleware.ldappc.Ldappc.main(Ldappc.java:105)
> >     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >     at
> > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.ja
> > va:57)
> >     at
> > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccesso
> > rImpl.java:43)
> >     at java.lang.reflect.Method.invoke(Method.java:616)
> >     at
> > edu.internet2.middleware.grouper.app.gsh.GrouperShell.handleSpecialCase
> > (GrouperShell.java:167)
> >     at
> > edu.internet2.middleware.grouper.app.gsh.GrouperShell.main(GrouperShell
> > .java:108)
> >     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >     at
> > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.ja
> > va:57)
> >     at
> > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccesso
> > rImpl.java:43)
> >     at java.lang.reflect.Method.invoke(Method.java:616)
> >     at com.dawidweiss.invoker.Invoker.loader(Invoker.java:167)
> >     at com.dawidweiss.invoker.Invoker.main(Invoker.java:303)
> > [com.dawidweiss.invoker.Invoker]
> > edu.internet2.middleware.grouper.app.gsh.GrouperShell has thrown an
> > exception.
> > java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
> >     at
> > edu.internet2.middleware.grouper.app.gsh.GrouperShell.handleSpecialCase
> > (GrouperShell.java:172)
> >     at
> > edu.internet2.middleware.grouper.app.gsh.GrouperShell.main(GrouperShell
> > .java:108)
> >     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >     at
> > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.ja
> > va:57)
> >     at
> > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccesso
> > rImpl.java:43)
> >     at java.lang.reflect.Method.invoke(Method.java:616)
> >     at com.dawidweiss.invoker.Invoker.loader(Invoker.java:167)
> >     at com.dawidweiss.invoker.Invoker.main(Invoker.java:303)
> > Caused by: java.lang.reflect.InvocationTargetException
> >     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >     at
> > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.ja
> > va:57)
> >     at
> > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccesso
> > rImpl.java:43)
> >     at java.lang.reflect.Method.invoke(Method.java:616)
> >     at
> > edu.internet2.middleware.grouper.app.gsh.GrouperShell.handleSpecialCase
> > (GrouperShell.java:167)
> >     ... 7 more
> > Caused by: java.lang.ExceptionInInitializerError
> >     at
> > edu.internet2.middleware.grouper.internal.dao.hib3.Hib3DAO.<clinit>(Hib
> > 3DAO.java:69)
> >     at
> > edu.internet2.middleware.grouper.internal.dao.hib3.Hib3DAOFactory.getGr
> > oup(Hib3DAOFactory.java:56)
> >     at
> > edu.internet2.middleware.grouper.GrouperSourceAdapter.getSubject(Groupe
> > rSourceAdapter.java:121)
> >     at
> > edu.internet2.middleware.grouper.subj.SourcesXmlResolver.find(SourcesXm
> > lResolver.java:91)
> >     at
> > edu.internet2.middleware.grouper.subj.CachingResolver.find(CachingResol
> > ver.java:74)
> >     at
> > edu.internet2.middleware.grouper.subj.ValidatingResolver.find(Validatin
> > gResolver.java:67)
> >     at
> > edu.internet2.middleware.grouper.SubjectFinder.findById(SubjectFinder.j
> > ava:100)
> >     at
> > edu.internet2.middleware.ldappc.GrouperSubjectRetriever.findSubjectById
> > (GrouperSubjectRetriever.java:50)
> >     at
> > edu.internet2.middleware.ldappc.GrouperSessionControl.startSession(Grou
> > perSessionControl.java:75)
> >     at
> > edu.internet2.middleware.ldappc.GrouperProvisioner.provision(GrouperPro
> > visioner.java:155)
> >     at
> > edu.internet2.middleware.ldappc.LdappcGrouperProvisioner.provisionGroup
> > s(LdappcGrouperProvisioner.java:119)
> >     at
> > edu.internet2.middleware.ldappc.LdappcProvisionControl.run(LdappcProvis
> > ionControl.java:96)
> >     at edu.internet2.middleware.ldappc.Ldappc.main(Ldappc.java:105)
> >     ... 12 more
> > Caused by: 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.FindBy
> > Subject, 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>(Hibe
> > rnateSession.java:67)
> >     at
> > edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_h
> > ibernateSession(HibernateSession.java:254)
> >     at
> > edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHib
> > ernateSession(HibernateSession.java:383)
> >     at
> > edu.internet2.middleware.grouper.hibernate.ByHqlStatic.uniqueResult(ByH
> > qlStatic.java:295)
> >     at
> > edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MemberDAO.findBy
> > Subject(Hib3MemberDAO.java:141)
> >     at
> > edu.internet2.middleware.grouper.MemberFinder.internal_findOrCreateBySu
> > bject(MemberFinder.java:225)
> >     at
> > edu.internet2.middleware.grouper.MemberFinder.internal_findBySubject(Me
> > mberFinder.java:198)
> >     at
> > edu.internet2.middleware.grouper.GrouperSession.start(GrouperSession.ja
> > va:272)
> >     at
> > edu.internet2.middleware.grouper.GrouperSession.startRootSession(Groupe
> > rSession.java:222)
> >     at
> > edu.internet2.middleware.grouper.GrouperSession.startRootSession(Groupe
> > rSession.java:240)
> >     at
> > edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkGroups(Gr
> > ouperCheckConfig.java:439)
> >     at
> > edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkConfig(Gr
> > ouperCheckConfig.java:410)
> >     at
> > edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperSta
> > rtup.java:82)
> >     at
> > edu.internet2.middleware.grouper.internal.dao.hib3.Hib3DAO.<clinit>(Hib
> > 3DAO.java:64)
> >     ... 24 more
> > 
> > If I move the new jar out of the way and put the "old" jar
> > back into place then gsh starts up without problems.
> > 
> > How can I prevent or workaround the ddl errors when the new
> > jar is put into place?
> > 
> > Thanks,
> > 
> > Scott