Grouper Users - Open Discussion List

[Baron Fujimoto <>]

We had this problem about a year ago, and unfortunately we never did
manage to figure it out. We're working on our infrastructure again now,
and so we find ourselves confronted with it again.

We're running Grouper 2.2.2. I believe it's fully patched
(grouper_v2_2_2_api_patch_11).  Our DBA had cloned (exported/imported) the
DBs from a source MySQL host to a new MySQL host. However, when we
configure Grouper to point ot the cloned DBs, we get the following errors
(for example when trying to run gsh):

=====
Couldnt startup grouper: Problem in HibernateSession: HibernateSession 
(5c77ba8f): notNew, notReadonly, READ_WRITE_NEW, activeTransaction, session 
(66273da0),
Exception in save: edu.internet2.middleware.grouper.Membership, 
ByObjectStatic, query: ', cacheable: null, cacheRegion: null, entityName: 
ImmediateMembershipEntry, tx type: null,
Problem in HibernateSession: HibernateSession (30364216): new, notReadonly, 
READ_WRITE_NEW, notActiveTransaction, session (66273da0)
edu.internet2.middleware.grouper.internal.dao.GrouperDAOException: Problem in 
HibernateSession: HibernateSession (5c77ba8f): notNew, notReadonly, 
READ_WRITE_NEW, activeTransaction, session (66273da0),
Exception in save: edu.internet2.middleware.grouper.Membership, 
ByObjectStatic, query: ', cacheable: null, cacheRegion: null, entityName: 
ImmediateMembershipEntry, tx type: null,
Problem in HibernateSession: HibernateSession (30364216): new, notReadonly, 
READ_WRITE_NEW, notActiveTransaction, session (66273da0)
...
Caused by: org.hibernate.exception.ConstraintViolationException: Could not 
execute JDBC batch update,
Exception in save: edu.internet2.middleware.grouper.Membership, 
edu.internet2.middleware.grouper.hibernate.ByObject@6ede46f6
...
Caused by: java.sql.BatchUpdateException: Duplicate entry 
'56a628646e5949bf89868455caa72adb-39e8f222fa1d434f87d40cc4f063371' for key 
'membership_uniq_idx'
=====

I'm told that when the DBs are cloned it includes all
tables/views/constraints/foreignkeys.

I didn't find any actual duplicates in either the original or copy of the
DBs using the command,

"select owner_id, member_id, field_id from grouper_memberships group by 
owner_id, member_id, field_id having count(*) > 1"

Nor are there nulls as reported by,

"select owner_id, member_id, field_id from grouper_memberships where owner_id 
= null or member_id = null or field_id = null;"

If I search with the the value of the entry reported in the error msg, e.g.

"SELECT * FROM grouper_memberships where owner_id like 
'56a628646e5949bf89868455caa72adb';"

I get the same results for both the original and the copy of the DB.

id,member_id,owner_id,field_id,owner_group_id,owner_stem_id,owner_attr_def_id,via_composite_id,enabled,enabled_timestamp,disabled_timestamp,mship_type,creator_id,create_time,hibernate_version_number,context_id
7e137eca43ac4a65a2b83b7e857f29b8,39e8f222fa1d434f87d40cc4f0633717,56a628646e5949bf89868455caa72adb,5d5dce817f7e411799fc5f5e6328a28c,NULL,NULL,56a628646e5949bf89868455caa72adb,NULL,T,NULL,NULL,immediate,a166b283e3124910a9f0661eae5b2b8e,1460748581132,0,NULL
968d28bd7585499f97bc0b291e47dc87,39e8f222fa1d434f87d40cc4f0633717,56a628646e5949bf89868455caa72adb,cda43f2141844e7aaaa79dfc0c119757,NULL,NULL,56a628646e5949bf89868455caa72adb,NULL,T,NULL,NULL,immediate,a166b283e3124910a9f0661eae5b2b8e,1460748581148,0,NULL
28c6bdfa8132434baf008d51b22b46dd,a166b283e3124910a9f0661eae5b2b8e,56a628646e5949bf89868455caa72adb,0239be70f97243f690e1372cecd634dd,NULL,NULL,56a628646e5949bf89868455caa72adb,NULL,T,NULL,NULL,immediate,a166b283e3124910a9f0661eae5b2b8e,1460748581112,0,79c0d83dbb71409e88330a971899016c

We see this problem with every Grouper DB we've copied, so I assume it
must be something systemic. Any suggestions would be greatly appreciated.
I'm at a loss at this point.

Full logs:
=====
$ ./gsh
Using GROUPER_HOME: /home/grouper/grouper/grouper.apiBinary-2.2.2/bin/..
Using GROUPER_CONF: /home/grouper/grouper/grouper.apiBinary-2.2.2/bin/../conf
Using JAVA: /usr/java/latest/bin/java
using MEMORY: 64m-750m
Grouper starting up: version: 2.2.2, build date: null, env: grouper-test
grouper.properties read from: 
/home/grouper/grouper/grouper.apiBinary-2.2.2/conf/grouper.properties
Grouper current directory is: 
/home/grouper/grouper/grouper.apiBinary-2.2.2/bin
log4j.properties read from:   
/home/grouper/grouper/grouper.apiBinary-2.2.2/conf/log4j.properties
Grouper is logging to file:   
/home/grouper/grouper/logs/grouper-api_error.log, at min level WARN for 
package: edu.internet2.middleware.grouper, based on log4j.properties
grouper.hibernate.properties: 
/home/grouper/grouper/grouper.apiBinary-2.2.2/conf/grouper.hibernate.properties
grouper.hibernate.properties: 
grpr_admin@jdbc:mysql://dbfoo.hawaii.edu:3306/grprfoo?CharSet=utf8&useUnicode=true&characterEncoding=utf8
sources.xml read from:        
/home/grouper/grouper/grouper.apiBinary-2.2.2/conf/sources.xml
sources.xml ldap source id:   UH test LDAP: 
cn=*****@ldaps://ldapfoo.hawaii.edu:636
sources.xml groupersource id: g:gsa
sources.xml groupersource id: grouperEntities
Couldnt startup grouper: Problem in HibernateSession: HibernateSession 
(5c77ba8f): notNew, notReadonly, READ_WRITE_NEW, activeTransaction, session 
(66273da0),
Exception in save: edu.internet2.middleware.grouper.Membership, 
ByObjectStatic, query: ', cacheable: null, cacheRegion: null, entityName: 
ImmediateMembershipEntry, tx type: null,
Problem in HibernateSession: HibernateSession (30364216): new, notReadonly, 
READ_WRITE_NEW, notActiveTransaction, session (66273da0)
edu.internet2.middleware.grouper.internal.dao.GrouperDAOException: Problem in 
HibernateSession: HibernateSession (5c77ba8f): notNew, notReadonly, 
READ_WRITE_NEW, activeTransaction, session (66273da0),
Exception in save: edu.internet2.middleware.grouper.Membership, 
ByObjectStatic, query: ', cacheable: null, cacheRegion: null, entityName: 
ImmediateMembershipEntry, tx type: null,
Problem in HibernateSession: HibernateSession (30364216): new, notReadonly, 
READ_WRITE_NEW, notActiveTransaction, session (66273da0)
    at 
edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_hibernateSessionCatch(HibernateSession.java:575)
    at 
edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:697)
    at 
edu.internet2.middleware.grouper.hibernate.ByObjectStatic.save(ByObjectStatic.java:468)
    at 
edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MembershipDAO.save(Hib3MembershipDAO.java:2053)
    at 
edu.internet2.middleware.grouper.Membership.internal_addImmediateMembership(Membership.java:2748)
    at 
edu.internet2.middleware.grouper.privs.GrouperNonDbAttrDefAdapter$1.callback(GrouperNonDbAttrDefAdapter.java:243)
    at 
edu.internet2.middleware.grouper.GrouperSession.callbackGrouperSession(GrouperSession.java:974)
    at 
edu.internet2.middleware.grouper.privs.GrouperNonDbAttrDefAdapter.grantPriv(GrouperNonDbAttrDefAdapter.java:228)
    at 
edu.internet2.middleware.grouper.privs.AttributeDefWrapper.grantPrivilege(AttributeDefWrapper.java:147)
    at 
edu.internet2.middleware.grouper.privs.AttributeDefResolverDecorator.grantPrivilege(AttributeDefResolverDecorator.java:144)
    at 
edu.internet2.middleware.grouper.privs.AttributeDefResolverDecorator.grantPrivilege(AttributeDefResolverDecorator.java:144)
    at 
edu.internet2.middleware.grouper.privs.CachingAttrDefResolver.grantPrivilege(CachingAttrDefResolver.java:179)
    at 
edu.internet2.middleware.grouper.privs.AttributeDefResolverDecorator.grantPrivilege(AttributeDefResolverDecorator.java:144)
    at 
edu.internet2.middleware.grouper.privs.ValidatingAttrDefResolver.grantPrivilege(ValidatingAttrDefResolver.java:116)
    at 
edu.internet2.middleware.grouper.attr.AttributeDefPrivilegeDelegate$2.callback(AttributeDefPrivilegeDelegate.java:453)
    at 
edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:687)
    at 
edu.internet2.middleware.grouper.attr.AttributeDefPrivilegeDelegate.internal_grantPriv(AttributeDefPrivilegeDelegate.java:441)
    at 
edu.internet2.middleware.grouper.attr.AttributeDefPrivilegeDelegate.grantPriv(AttributeDefPrivilegeDelegate.java:295)
    at 
edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkAttributes(GrouperCheckConfig.java:2242)
    at 
edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkConfig(GrouperCheckConfig.java:433)
    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)
Caused by: org.hibernate.exception.ConstraintViolationException: Could not 
execute JDBC batch update,
Exception in save: edu.internet2.middleware.grouper.Membership, 
edu.internet2.middleware.grouper.hibernate.ByObject@6ede46f6
    at 
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:96)
    at 
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
    at 
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:275)
    at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:268)
    at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:184)
    at 
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)
    at 
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:51)
    at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1216)
    at 
edu.internet2.middleware.grouper.hibernate.ByObject.save(ByObject.java:214)
    at 
edu.internet2.middleware.grouper.hibernate.ByObjectStatic$7.callback(ByObjectStatic.java:481)
    at 
edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:687)
    ... 21 more
Caused by: java.sql.BatchUpdateException: Duplicate entry 
'56a628646e5949bf89868455caa72adb-39e8f222fa1d434f87d40cc4f063371' for key 
'membership_uniq_idx'
    at 
com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:1269)
    at 
com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:955)
    at 
com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeBatch(NewProxyPreparedStatement.java:1723)
    at 
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:70)
    at 
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:268)
    ... 29 more
Exception in thread "main" 
edu.internet2.middleware.grouper.internal.dao.GrouperDAOException: Problem in 
HibernateSession: HibernateSession (5c77ba8f): notNew, notReadonly, 
READ_WRITE_NEW, activeTransaction, session (66273da0),
Exception in save: edu.internet2.middleware.grouper.Membership, 
ByObjectStatic, query: ', cacheable: null, cacheRegion: null, entityName: 
ImmediateMembershipEntry, tx type: null,
Problem in HibernateSession: HibernateSession (30364216): new, notReadonly, 
READ_WRITE_NEW, notActiveTransaction, session (66273da0)
    at 
edu.internet2.middleware.grouper.hibernate.HibernateSession._internal_hibernateSessionCatch(HibernateSession.java:575)
    at 
edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:697)
    at 
edu.internet2.middleware.grouper.hibernate.ByObjectStatic.save(ByObjectStatic.java:468)
    at 
edu.internet2.middleware.grouper.internal.dao.hib3.Hib3MembershipDAO.save(Hib3MembershipDAO.java:2053)
    at 
edu.internet2.middleware.grouper.Membership.internal_addImmediateMembership(Membership.java:2748)
    at 
edu.internet2.middleware.grouper.privs.GrouperNonDbAttrDefAdapter$1.callback(GrouperNonDbAttrDefAdapter.java:243)
    at 
edu.internet2.middleware.grouper.GrouperSession.callbackGrouperSession(GrouperSession.java:974)
    at 
edu.internet2.middleware.grouper.privs.GrouperNonDbAttrDefAdapter.grantPriv(GrouperNonDbAttrDefAdapter.java:228)
    at 
edu.internet2.middleware.grouper.privs.AttributeDefWrapper.grantPrivilege(AttributeDefWrapper.java:147)
    at 
edu.internet2.middleware.grouper.privs.AttributeDefResolverDecorator.grantPrivilege(AttributeDefResolverDecorator.java:144)
    at 
edu.internet2.middleware.grouper.privs.AttributeDefResolverDecorator.grantPrivilege(AttributeDefResolverDecorator.java:144)
    at 
edu.internet2.middleware.grouper.privs.CachingAttrDefResolver.grantPrivilege(CachingAttrDefResolver.java:179)
    at 
edu.internet2.middleware.grouper.privs.AttributeDefResolverDecorator.grantPrivilege(AttributeDefResolverDecorator.java:144)
    at 
edu.internet2.middleware.grouper.privs.ValidatingAttrDefResolver.grantPrivilege(ValidatingAttrDefResolver.java:116)
    at 
edu.internet2.middleware.grouper.attr.AttributeDefPrivilegeDelegate$2.callback(AttributeDefPrivilegeDelegate.java:453)
    at 
edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:687)
    at 
edu.internet2.middleware.grouper.attr.AttributeDefPrivilegeDelegate.internal_grantPriv(AttributeDefPrivilegeDelegate.java:441)
    at 
edu.internet2.middleware.grouper.attr.AttributeDefPrivilegeDelegate.grantPriv(AttributeDefPrivilegeDelegate.java:295)
    at 
edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkAttributes(GrouperCheckConfig.java:2242)
    at 
edu.internet2.middleware.grouper.misc.GrouperCheckConfig.checkConfig(GrouperCheckConfig.java:433)
    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)
Caused by: org.hibernate.exception.ConstraintViolationException: Could not 
execute JDBC batch update,
Exception in save: edu.internet2.middleware.grouper.Membership, 
edu.internet2.middleware.grouper.hibernate.ByObject@6ede46f6
    at 
org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:96)
    at 
org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
    at 
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:275)
    at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:268)
    at org.hibernate.engine.ActionQueue.executeActions(ActionQueue.java:184)
    at 
org.hibernate.event.def.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:321)
    at 
org.hibernate.event.def.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:51)
    at org.hibernate.impl.SessionImpl.flush(SessionImpl.java:1216)
    at 
edu.internet2.middleware.grouper.hibernate.ByObject.save(ByObject.java:214)
    at 
edu.internet2.middleware.grouper.hibernate.ByObjectStatic$7.callback(ByObjectStatic.java:481)
    at 
edu.internet2.middleware.grouper.hibernate.HibernateSession.callbackHibernateSession(HibernateSession.java:687)
    ... 21 more
Caused by: java.sql.BatchUpdateException: Duplicate entry 
'56a628646e5949bf89868455caa72adb-39e8f222fa1d434f87d40cc4f063371' for key 
'membership_uniq_idx'
    at 
com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:1269)
    at 
com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:955)
    at 
com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeBatch(NewProxyPreparedStatement.java:1723)
    at 
org.hibernate.jdbc.BatchingBatcher.doExecuteBatch(BatchingBatcher.java:70)
    at 
org.hibernate.jdbc.AbstractBatcher.executeBatch(AbstractBatcher.java:268)
    ... 29 more

-- 
Baron Fujimoto 
<>
 :: UH Information Technology Services
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