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[grouper-users] can't start Grouper after patches applied


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  • From: Ben Beecher <>
  • To:
  • Subject: [grouper-users] can't start Grouper after patches applied
  • Date: Fri, 9 Feb 2018 12:07:32 -0500
  • Ironport-phdr: 9a23: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
I installed patches on our dev Grouper system with no problems. Here is our current patch level:
API patches 0 to 88 are installed
UI patches 0 to 35 are installed
WS patches 0 to 11 are installed
PSPNG patches 0 to 16 are installed
PSP patches 0 to 1 are installed

I installed the same patches on one of our production Grouper hosts but I get this error when Grouper tries to start:

edu.internet2.middleware.grouper.exception.AttributeDefNameAddException: Cannot create attribute def name: , stem name: etc:attribute:loaderMetadata, attrDefName extension: grouperLoaderMetadataLastFullMillisSince1970, uuid: null, Problem create child attributeDef: 
Caused by: java.sql.BatchUpdateException: ORA-00001: unique constraint (GROUPER.ATTRIBUTE_DEF_NAME_NAME_IDX) violated

Log messages are attached. Any idea how to fix this? I need to get this working ASAP.

Ben
sources.xml read from:
/var/tomcat/grouperprod/webapps/grouper/WEB-INF/classes/sources.xml
sources configured in: sources.xml
sources.xml groupersource id: g:gsa
sources.xml groupersource id: grouperEntities
sources.xml jdbc source id: idm:
grouper@jdbc:oracle:thin:@//idmsysproddb01.cc.columbia.edu:1527/idmprod1.cc.columbia.edu
sources.xml jdbc source id: externalUsers:
GrouperJdbcConnectionProvider
Grouper warning: jarfile mismatch, expecting name: 'log4j.jar' size:
LinkedHashSet size: 1: [0]: 489883
manifest version: 1.2.17. However the jar detected is:
/var/tomcat/grouperprod/webapps/grouper-ws/WEB-INF/lib/apache-log4j-extras-1.2.17.jar,
name: apache-log4j-extras-1.2.17.jar size: 448794 manifest version: null
Grouper note: auto-created attributeDefName:
etc:attribute:attestation:attestationCalculatedDaysLeft
Grouper note: auto-created attributeDefName:
etc:attribute:attestation:attestationHasAttestation
Grouper warning: jarfile mismatch, expecting name: 'log4j.jar' size:
LinkedHashSet size: 1: [0]: 489883
manifest version: 1.2.17. However the jar detected is:
/var/tomcat/grouperprod/webapps/grouper/WEB-INF/lib/apache-log4j-extras-1.2.17.jar,
name: apache-log4j-extras-1.2.17.jar size: 448794 manifest version: null
Grouper note: auto-created attributeDefName:
etc:attribute:loaderMetadata:loaderMetadata
Grouper note: auto-created attributeDefName:
etc:attribute:loaderMetadata:grouperLoaderMetadataLoaded
Grouper note: auto-created attributeDefName:
etc:attribute:loaderMetadata:grouperLoaderMetadataGroupId
Couldnt startup grouper: Cannot create attribute def name: , stem name:
etc:attribute:loaderMetadata, attrDefName extension:
grouperLoaderMetadataLastFullMillisSince1970, uuid: null, Problem create
child attributeDef:
Stem[displayName=etc:attribute:loaderMetadata,name=etc:attribute:loaderMetadata,uuid=95090d2db734468ba6ac5f3ac71eea88,creator=08619efecf9a4d59bb5944ace654af09,modifier=08619efecf9a4d59bb5944ace654af09],
child:
AttributeDefName[name=etc:attribute:loaderMetadata:grouperLoaderMetadataLastFullMillisSince1970,uuid=f98b39545a8346f0b85099ec92dcec74],
Problem in HibernateSession: HibernateSession (5c020a55): notNew,
notReadonly, READ_WRITE_NEW, activeTransaction, session (65325598),
Problem in HibernateSession: HibernateSession (49d8460b): new, notReadonly,
READ_WRITE_NEW, notActiveTransaction, session (65325598)
Grouper note: auto-created attributeDefName:
etc:attribute:loaderMetadata:grouperLoaderMetadataLastFullMillisSince1970
edu.internet2.middleware.grouper.exception.AttributeDefNameAddException:
Cannot create attribute def name: , stem name: etc:attribute:loaderMetadata,
attrDefName extension: grouperLoaderMetadataLastFullMillisSince1970, uuid:
null, Problem create child attributeDef:
Stem[displayName=etc:attribute:loaderMetadata,name=etc:attribute:loaderMetadata,uuid=95090d2db734468ba6ac5f3ac71eea88,creator=08619efecf9a4d59bb5944ace654af09,modifier=08619efecf9a4d59bb5944ace654af09],
child:
AttributeDefName[name=etc:attribute:loaderMetadata:grouperLoaderMetadataLastFullMillisSince1970,uuid=f98b39545a8346f0b85099ec92dcec74],
Problem in HibernateSession: HibernateSession (5c020a55): notNew,
notReadonly, READ_WRITE_NEW, activeTransaction, session (65325598),
Problem in HibernateSession: HibernateSession (49d8460b): new, notReadonly,
READ_WRITE_NEW, notActiveTransaction, session (65325598)
at edu.internet2.middleware.grouper.Stem$6.callback(Stem.java:2523)
at
edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:700)
at
edu.internet2.middleware.grouper.Stem.internal_addChildAttributeDefName(Stem.java:2462)
at
edu.internet2.middleware.grouper.Stem.addChildAttributeDefName(Stem.java:560)
at
edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkAttribute(GrouperCheckConfig.java:1719)
at
edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkAttribute(GrouperCheckConfig.java:1699)
at
edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkAttributes(GrouperCheckConfig.java:2054)
at
edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkConfig(GrouperCheckConfig.java:478)
at
edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperStartup.java:256)
at
edu.internet2.middleware.grouper.ui.GrouperUiFilter.init(GrouperUiFilter.java:836)
at
org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279)
at
org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260)
at
org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:105)
at
org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4950)
at
org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5652)
at
org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at
org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1700)
at
org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1690)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: edu.internet2.middleware.grouper.internal.dao.GrouperDAOException:
Problem create child attributeDef:
Stem[displayName=etc:attribute:loaderMetadata,name=etc:attribute:loaderMetadata,uuid=95090d2db734468ba6ac5f3ac71eea88,creator=08619efecf9a4d59bb5944ace654af09,modifier=08619efecf9a4d59bb5944ace654af09],
child:
AttributeDefName[name=etc:attribute:loaderMetadata:grouperLoaderMetadataLastFullMillisSince1970,uuid=f98b39545a8346f0b85099ec92dcec74],
Problem in HibernateSession: HibernateSession (5c020a55): notNew,
notReadonly, READ_WRITE_NEW, activeTransaction, session (65325598)
at
edu.internet2.middleware.grouper.internal.dao.hib3.Hib3StemDAO.createChildAttributeDefName(Hib3StemDAO.java:1910)
at edu.internet2.middleware.grouper.Stem$6.callback(Stem.java:2500)
... 21 more
Caused by: edu.internet2.middleware.grouper.internal.dao.GrouperDAOException:
Problem in HibernateSession: HibernateSession (5c020a55): notNew,
notReadonly, READ_WRITE_NEW, activeTransaction, session (65325598)
at
edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_hibernateSessionCatch(HibernateSession.java:588)
at
edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:710)
at
edu.internet2.middleware.grouper.internal.dao.hib3.Hib3StemDAO.createChildAttributeDefName(Hib3StemDAO.java:1881)
... 22 more
Caused by: org.hibernate.exception.ConstraintViolationException: could not
execute batch,
Exception in save: edu.internet2.middleware.grouper.attr.AttributeDefName,
edu.internet2.middleware.grouper.hibernate.ByObject@3627e8f
at
org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:112)
at
org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)
at
org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:109)
at
org.hibernate.engine.jdbc.batch.internal.BatchingBatch.performExecution(BatchingBatch.java:119)
at
org.hibernate.engine.jdbc.batch.internal.BatchingBatch.doExecuteBatch(BatchingBatch.java:97)
at
org.hibernate.engine.jdbc.batch.internal.AbstractBatchImpl.execute(AbstractBatchImpl.java:147)
at
org.hibernate.engine.jdbc.internal.JdbcCoordinatorImpl.executeBatch(JdbcCoordinatorImpl.java:214)
at
org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:589)
at
org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:434)
at
org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:337)
at
org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:39)
at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1224)
at
edu.internet2.middleware.grouper.hibernate.ByObject.save(ByObject.java:221)
at
edu.internet2.middleware.grouper.internal.dao.hib3.Hib3StemDAO$7.callback(Hib3StemDAO.java:1891)
at
edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:700)
... 23 more
Caused by: java.sql.BatchUpdateException: ORA-00001: unique constraint
(GROUPER.ATTRIBUTE_DEF_NAME_NAME_IDX) violated

at
oracle.jdbc.driver.OraclePreparedStatement.executeBatch(OraclePreparedStatement.java:17952)
at
oracle.jdbc.driver.OracleStatementWrapper.executeBatch(OracleStatementWrapper.java:785)
at
com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeBatch(NewProxyPreparedStatement.java:2544)
at
org.hibernate.engine.jdbc.batch.internal.BatchingBatch.performExecution(BatchingBatch.java:110)
... 34 more
Feb 09, 2018 11:34:37 AM org.apache.catalina.core.StandardContext filterStart
SEVERE: Exception starting filter GrouperUi
edu.internet2.middleware.grouper.exception.AttributeDefNameAddException:
Cannot create attribute def name: , stem name: etc:attribute:loaderMetadata,
attrDefName extension: grouperLoaderMetadataLastFullMillisSince1970, uuid:
null, Problem create child attributeDef:
Stem[displayName=etc:attribute:loaderMetadata,name=etc:attribute:loaderMetadata,uuid=95090d2db734468ba6ac5f3ac71eea88,creator=08619efecf9a4d59bb5944ace654af09,modifier=08619efecf9a4d59bb5944ace654af09],
child:
AttributeDefName[name=etc:attribute:loaderMetadata:grouperLoaderMetadataLastFullMillisSince1970,uuid=f98b39545a8346f0b85099ec92dcec74],
Problem in HibernateSession: HibernateSession (5c020a55): notNew,
notReadonly, READ_WRITE_NEW, activeTransaction, session (65325598),
Problem in HibernateSession: HibernateSession (49d8460b): new, notReadonly,
READ_WRITE_NEW, notActiveTransaction, session (65325598)
at edu.internet2.middleware.grouper.Stem$6.callback(Stem.java:2523)
at
edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:700)
at
edu.internet2.middleware.grouper.Stem.internal_addChildAttributeDefName(Stem.java:2462)
at
edu.internet2.middleware.grouper.Stem.addChildAttributeDefName(Stem.java:560)
at
edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkAttribute(GrouperCheckConfig.java:1719)
at
edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkAttribute(GrouperCheckConfig.java:1699)
at
edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkAttributes(GrouperCheckConfig.java:2054)
at
edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkConfig(GrouperCheckConfig.java:478)
at
edu.internet2.middleware.grouper.misc.GrouperStartup.startup(GrouperStartup.java:256)
at
edu.internet2.middleware.grouper.ui.GrouperUiFilter.init(GrouperUiFilter.java:836)
at
org.apache.catalina.core.ApplicationFilterConfig.initFilter(ApplicationFilterConfig.java:279)
at
org.apache.catalina.core.ApplicationFilterConfig.getFilter(ApplicationFilterConfig.java:260)
at
org.apache.catalina.core.ApplicationFilterConfig.<init>(ApplicationFilterConfig.java:105)
at
org.apache.catalina.core.StandardContext.filterStart(StandardContext.java:4950)
at
org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5652)
at
org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:145)
at
org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1700)
at
org.apache.catalina.core.ContainerBase$StartChild.call(ContainerBase.java:1690)
at java.util.concurrent.FutureTask.run(FutureTask.java:262)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:745)
Caused by: edu.internet2.middleware.grouper.internal.dao.GrouperDAOException:
Problem create child attributeDef:
Stem[displayName=etc:attribute:loaderMetadata,name=etc:attribute:loaderMetadata,uuid=95090d2db734468ba6ac5f3ac71eea88,creator=08619efecf9a4d59bb5944ace654af09,modifier=08619efecf9a4d59bb5944ace654af09],
child:
AttributeDefName[name=etc:attribute:loaderMetadata:grouperLoaderMetadataLastFullMillisSince1970,uuid=f98b39545a8346f0b85099ec92dcec74],
Problem in HibernateSession: HibernateSession (5c020a55): notNew,
notReadonly, READ_WRITE_NEW, activeTransaction, session (65325598)
at
edu.internet2.middleware.grouper.internal.dao.hib3.Hib3StemDAO.createChildAttributeDefName(Hib3StemDAO.java:1910)
at edu.internet2.middleware.grouper.Stem$6.callback(Stem.java:2500)
... 21 more
Caused by: edu.internet2.middleware.grouper.internal.dao.GrouperDAOException:
Problem in HibernateSession: HibernateSession (5c020a55): notNew,
notReadonly, READ_WRITE_NEW, activeTransaction, session (65325598)
at
edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_hibernateSessionCatch(HibernateSession.java:588)
at
edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:710)
at
edu.internet2.middleware.grouper.internal.dao.hib3.Hib3StemDAO.createChildAttributeDefName(Hib3StemDAO.java:1881)
... 22 more
Caused by: org.hibernate.exception.ConstraintViolationException: could not
execute batch,
Exception in save: edu.internet2.middleware.grouper.attr.AttributeDefName,
edu.internet2.middleware.grouper.hibernate.ByObject@3627e8f
at
org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:112)
at
org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)
at
org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:109)
at
org.hibernate.engine.jdbc.batch.internal.BatchingBatch.performExecution(BatchingBatch.java:119)
at
org.hibernate.engine.jdbc.batch.internal.BatchingBatch.doExecuteBatch(BatchingBatch.java:97)
at
org.hibernate.engine.jdbc.batch.internal.AbstractBatchImpl.execute(AbstractBatchImpl.java:147)
at
org.hibernate.engine.jdbc.internal.JdbcCoordinatorImpl.executeBatch(JdbcCoordinatorImpl.java:214)
at
org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:589)
at
org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:434)
at
org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:337)
at
org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:39)
at org.hibernate.internal.SessionImpl.flush(SessionImpl.java:1224)
at
edu.internet2.middleware.grouper.hibernate.ByObject.save(ByObject.java:221)
at
edu.internet2.middleware.grouper.internal.dao.hib3.Hib3StemDAO$7.callback(Hib3StemDAO.java:1891)
at
edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:700)
... 23 more
Caused by: java.sql.BatchUpdateException: ORA-00001: unique constraint
(GROUPER.ATTRIBUTE_DEF_NAME_NAME_IDX) violated

at
oracle.jdbc.driver.OraclePreparedStatement.executeBatch(OraclePreparedStatement.java:17952)
at
oracle.jdbc.driver.OracleStatementWrapper.executeBatch(OracleStatementWrapper.java:785)
at
com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeBatch(NewProxyPreparedStatement.java:2544)
at
org.hibernate.engine.jdbc.batch.internal.BatchingBatch.performExecution(BatchingBatch.java:110)
... 34 more

Feb 09, 2018 11:34:37 AM org.apache.catalina.core.StandardContext
startInternal
SEVERE: One or more Filters failed to start. Full details will be found in
the appropriate container log file
Feb 09, 2018 11:34:37 AM org.apache.catalina.core.StandardContext
startInternal
SEVERE: Context [/grouper] startup failed due to previous errors

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