Grouper Users - Open Discussion List

[Bryan Wooten <>]

Vivek,

 

We are not using the default embedded DB.

 

We have set grouper.hibernate.properties to use our Oracle DB here:

 

/opt/grouper/grouper.ws-2.3.0/grouper-ws-scim/targetBuiltin/grouper-ws-scim/WEB-INF/classes

 

But yeah the error seems to indicate it is trying to use the embedded DB:

 

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',

       

Thanks,

 

 

Bryan Wooten

 

 

 

From: Vivek Sachdeva <>
Sent: Wednesday, June 13, 2018 10:27 AM
To: Bryan Wooten <>
Cc:
Subject: [Ext] Re: [grouper-users] RE: Still having trouble getting WS-SCIM to work.

 

******************************************************
WARNING: Stop. Think. Read. This is an external email.
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Hi Bryan,

 

This happens mostly when grouper is not able to connect to the database. Are you using default embedded database Hsql?

 

Thanks,

Vivek

 

On Tue, Jun 12, 2018 at 1:04 PM, Bryan Wooten <> wrote:

All,

 

After letting the ws-scim tomee idle for a while we now get this error.

 

We ran gsh –registry –check and it said everything is correct. Gsh can find users and groups as can the ui.

 

Again, any help appreciated.

 

ype Exception report

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

description The server encountered an internal error that prevented it from fulfilling this request.

exception

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',

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

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

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

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

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

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

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

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

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

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

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

edu.internet2.middleware.grouper.ws.scim.TierFilter.retrieveSubjectFromRemoteUser(TierFilter.java:79)

        edu.internet2.middleware.grouper.ws.scim.TierFilter.doFilter(TierFilter.java:116)

note The full stack trace of the root cause is available in the Apache Tomcat (TomEE)/8.5.2 (7.0.0) logs.

 

 

 

 

Bryan Wooten

 

 

 

From: <> On Behalf Of Bryan Wooten
Sent: Tuesday, June 12, 2018 9:51 AM
To:
Subject: [Ext] [grouper-users] Still having trouble getting WS-SCIM to work.

 

******************************************************
WARNING: Stop. Think. Read. This is an external email.
******************************************************

We have made some progress, but we had to make 2 manual changes after the install.

 

1.       We had to manually add ojdbc_g.jar to the lib directory

2.       Add some ehcache.xml we found on some Grouper github location

 

We are using tomcat Basic Auth for now. We are logging in as GrouperSystem (setup in tomcat-users.xml)

 

When we try an hit /grouper-ws-scim/v2/Schemas/

 

Everything was installed with the installer and we have verified our grouper.hibernate.properties are set correctly.

 

We see this stack trace grouper_error.log: Any suggestions? Thanks.

 

2018-06-12 09:14:31,032: [http-nio-9090-exec-1] FATAL Hib3DAO.initHibernateIfNotInitted(236) -  - unable to initialize hibernate: Unable to create requested service [org.hibernate.cache.spi.R

egionFactory]

org.hibernate.service.spi.ServiceException: Unable to create requested service [org.hibernate.cache.spi.RegionFactory]

        at org.hibernate.service.internal.AbstractServiceRegistryImpl.createService(AbstractServiceRegistryImpl.java:244)

        at org.hibernate.service.internal.AbstractServiceRegistryImpl.initializeService(AbstractServiceRegistryImpl.java:208)

        at org.hibernate.service.internal.AbstractServiceRegistryImpl.getService(AbstractServiceRegistryImpl.java:189)

        at org.hibernate.boot.internal.MetadataBuilderImpl$MetadataBuildingOptionsImpl.<init>(MetadataBuilderImpl.java:663)

        at org.hibernate.boot.internal.MetadataBuilderImpl.<init>(MetadataBuilderImpl.java:127)

        at org.hibernate.boot.MetadataSources.getMetadataBuilder(MetadataSources.java:135)

        at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:655)

        at org.hibernate.cfg.Configuration.buildSessionFactory(Configuration.java:724)

        at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3DAO.initHibernateIfNotInitted(Hib3DAO.java:223)

        at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3DAO.session(Hib3DAO.java:322)

        at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3DAOFactory.getSession(Hib3DAOFactory.java:186)

        at edu.internet2.middleware.grouper.hibernate.HibernateSession.<init>(HibernateSession.java:241)

        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.ByCriteriaStatic.list(ByCriteriaStatic.java:303)

        at edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.retrieveDdlsFromDb(GrouperDdlUtils.java:1957)

        at edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.retrieveDdlsFromCache(GrouperDdlUtils.java:1520)

        at edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.retrieveObjectNames(GrouperDdlUtils.java:1794)

        at edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.bootstrapHelper(GrouperDdlUtils.java:438)

        at edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.bootstrap(GrouperDdlUtils.java:340)

        at edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperStartup.java:251)

        at edu.internet2.middleware.grouper.subj.SubjectResolverFactory.getInstance(SubjectResolverFactory.java:58)

        at edu.internet2.middleware.grouper.SubjectFinder.getResolver(SubjectFinder.java:878)

        at edu.internet2.middleware.grouper.SubjectFinder.findRootSubject(SubjectFinder.java:863)

        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.ws.scim.TierFilter.retrieveSubjectFromRemoteUser(TierFilter.java:79)

        at edu.internet2.middleware.grouper.ws.scim.TierFilter.doFilter(TierFilter.java:116)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:192)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)

        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)

        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:108)

        at org.apache.tomee.catalina.OpenEJBValve.invoke(OpenEJBValve.java:44)

        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:632)

        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)

        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)

        at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)

        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)

        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:349)

        at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:1102)

        at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)

        at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:788)

        at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1485)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)

        at java.lang.Thread.run(Thread.java:748)

Caused by: org.hibernate.HibernateException: could not instantiate RegionFactory [edu.internet2.middleware.grouper.cache.GrouperEhcacheRegionFactory]

        at org.hibernate.cache.internal.RegionFactoryInitiator.initiateService(RegionFactoryInitiator.java:84)

        at org.hibernate.cache.internal.RegionFactoryInitiator.initiateService(RegionFactoryInitiator.java:29)

        at org.hibernate.boot.registry.internal.StandardServiceRegistryImpl.initiateService(StandardServiceRegistryImpl.java:88)

        at org.hibernate.service.internal.AbstractServiceRegistryImpl.createService(AbstractServiceRegistryImpl.java:234)

        ... 46 more

Caused by: org.hibernate.boot.registry.selector.spi.StrategySelectionException: Unable to resolve name [edu.internet2.middleware.grouper.cache.GrouperEhcacheRegionFactory] as strategy [org.hibernate.cache.spi.RegionFactory]

        at org.hibernate.boot.registry.selector.internal.StrategySelectorImpl.selectStrategyImplementor(StrategySelectorImpl.java:113)

        at org.hibernate.cache.internal.RegionFactoryInitiator.initiateService(RegionFactoryInitiator.java:71)

        ... 49 more

2018-06-12 09:14:31,034: [http-nio-9090-exec-1] ERROR GrouperDdlUtils.retrieveDdlsFromCache(1533) -  - maybe the grouper_ddl table isnt there... if that is the reason its ok.  info level logging will show underlying reason.unable to initialize hibernate: Unable to create requested service [org.hibernate.cache.spi.RegionFactory],

Problem in HibernateSession: null,

Exception in list: (class edu.internet2.middleware.grouper.app.loader.db.Hib3GrouperDdl), ByCriteriaStatic, persistentClass: 'class edu.internet2.middleware.grouper.app.loader.db.Hib3GrouperDdl', criterions: null', cacheable: null, cacheRegion: null, entityName: null, tx type: null

2018-06-12 09:14:31,094: [http-nio-9090-exec-1] ERROR GrouperDdlUtils.bootstrapHelper(486) -  - Grouper ddl object type 'Grouper' has dbVersion: 0 and java version: 30

2018-06-12 09:14:51,608: [http-nio-9090-exec-1] ERROR GrouperStartup.startup(299) -  - Couldnt startup grouper: Problem in HibernateSession: null

java.lang.NullPointerException: Problem in HibernateSession: null

        at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3DAO.session(Hib3DAO.java:323)

        at edu.internet2.middleware.grouper.internal.dao.hib3.Hib3DAOFactory.getSession(Hib3DAOFactory.java:186)

        at edu.internet2.middleware.grouper.hibernate.HibernateSession.<init>(HibernateSession.java:241)

        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.BySqlStatic.select(BySqlStatic.java:138)

        at edu.internet2.middleware.grouper.hibernate.BySqlStatic.select(BySqlStatic.java:124)

        at edu.internet2.middleware.grouper.ddl.GrouperDdl.addTableIndices(GrouperDdl.java:13233)

        at edu.internet2.middleware.grouper.ddl.GrouperDdl.access$3700(GrouperDdl.java:103)

        at edu.internet2.middleware.grouper.ddl.GrouperDdl$25.updateVersionFromPrevious(GrouperDdl.java:1836)

        at edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.upgradeDatabaseVersion(GrouperDdlUtils.java:2104)

        at edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.bootstrapHelper(GrouperDdlUtils.java:631)

        at edu.internet2.middleware.grouper.ddl.GrouperDdlUtils.bootstrap(GrouperDdlUtils.java:340)

        at edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperStartup.java:251)

        at edu.internet2.middleware.grouper.subj.SubjectResolverFactory.getInstance(SubjectResolverFactory.java:58)

        at edu.internet2.middleware.grouper.SubjectFinder.getResolver(SubjectFinder.java:878)

        at edu.internet2.middleware.grouper.SubjectFinder.findRootSubject(SubjectFinder.java:863)

        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.ws.scim.TierFilter.retrieveSubjectFromRemoteUser(TierFilter.java:79)

        at edu.internet2.middleware.grouper.ws.scim.TierFilter.doFilter(TierFilter.java:116)

        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:192)

        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:165)

        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198)

        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:108)

        at org.apache.tomee.catalina.OpenEJBValve.invoke(OpenEJBValve.java:44)

        at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:632)

        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140)

        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79)

        at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:620)

        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87)

        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:349)

        at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:1102)

        at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66)

        at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:788)

        at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1485)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)

        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)

        at java.lang.Thread.run(Thread.java:748)

 

 

 

Bryan Wooten