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Home » Modeling » EMF » [CDO] Repository initialization for mysql databse backend
[CDO] Repository initialization for mysql databse backend [message #1821822] Thu, 20 February 2020 15:56 Go to next message
Robert Schulk is currently offline Robert SchulkFriend
Messages: 112
Registered: July 2015
Senior Member
We (successfully) used the mysql datbase backend with the following cdo version:
		<unit id="org.eclipse.emf.cdo.sdk.feature.group" version="4.5.0.v20160607-1511"/>
		<unit id="org.eclipse.net4j.db.mysql.feature.group" version="4.2.300.v20160301-1326"/>
		<unit id="org.eclipse.net4j.feature.group" version="4.5.0.v20160607-1254"/>


Now, we updated to this version:
		<unit id="org.eclipse.emf.cdo.sdk.feature.group" version="5.0.0.v20180530-1201"/>
		<unit id="org.eclipse.net4j.db.mysql.feature.group" version="4.2.500.v20180529-1130"/>
		<unit id="org.eclipse.net4j.feature.group" version="4.7.0.v20180530-1201"/>


Since then, I am not able to start a repository.
It fails with this stacktrace:
java.lang.NullPointerException
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.removeClassMapping(AbstractMappingStrategy.java:561)
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.mapClasses(AbstractMappingStrategy.java:533)
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.mapPackageInfos(AbstractMappingStrategy.java:515)
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.mapPackageUnits(AbstractMappingStrategy.java:502)
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.removeMapping(AbstractMappingStrategy.java:490)
	at org.eclipse.emf.cdo.server.internal.db.DBStoreAccessor.doRollback(DBStoreAccessor.java:809)
	at org.eclipse.emf.cdo.spi.server.StoreAccessorBase.rollback(StoreAccessorBase.java:189)
	at org.eclipse.emf.cdo.internal.server.TransactionCommitContext.rollback(TransactionCommitContext.java:1362)
	at org.eclipse.emf.cdo.internal.server.TransactionCommitContext.handleException(TransactionCommitContext.java:808)
	at org.eclipse.emf.cdo.internal.server.TransactionCommitContext.write(TransactionCommitContext.java:746)
	at org.eclipse.emf.cdo.spi.server.InternalCommitContext$1.runLoop(InternalCommitContext.java:49)
	at org.eclipse.emf.cdo.spi.server.InternalCommitContext$1.runLoop(InternalCommitContext.java:1)
	at org.eclipse.net4j.util.om.monitor.ProgressDistributor.run(ProgressDistributor.java:95)
	at org.eclipse.emf.cdo.internal.server.Repository.commitUnsynced(Repository.java:1206)
	at org.eclipse.emf.cdo.internal.server.Repository.commit(Repository.java:1199)
	at org.eclipse.emf.cdo.server.internal.net4j.protocol.CommitTransactionIndication.indicatingCommit(CommitTransactionIndication.java:316)
	at org.eclipse.emf.cdo.server.internal.net4j.protocol.CommitTransactionIndication.indicating(CommitTransactionIndication.java:102)
	at org.eclipse.emf.cdo.server.internal.net4j.protocol.CDOServerIndicationWithMonitoring.indicating(CDOServerIndicationWithMonitoring.java:118)
	at org.eclipse.net4j.signal.IndicationWithMonitoring.indicating(IndicationWithMonitoring.java:87)
	at org.eclipse.net4j.signal.IndicationWithResponse.doExtendedInput(IndicationWithResponse.java:100)
	at org.eclipse.net4j.signal.Signal.doInput(Signal.java:380)
	at org.eclipse.net4j.signal.IndicationWithResponse.execute(IndicationWithResponse.java:73)
	at org.eclipse.net4j.signal.IndicationWithMonitoring.execute(IndicationWithMonitoring.java:66)
	at org.eclipse.net4j.signal.Signal.runSync(Signal.java:286)
	at org.eclipse.net4j.signal.Signal.run(Signal.java:165)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)


Could this be a bug, or do I need to change some configuration?
Re: [CDO] Repository initialization for mysql databse backend [message #1821849 is a reply to message #1821822] Fri, 21 February 2020 06:32 Go to previous messageGo to next message
Eike Stepper is currently offline Eike StepperFriend
Messages: 6561
Registered: July 2009
Senior Member
Hi Robert,

Your stack trace doesn't match the current sources anymore. When you upgrade, why don't you upgrade to the latest version of CDO?

The latest release is currently http://download.eclipse.org/modeling/emf/cdo/drops/R20191211-0144 and the latest integration build is always in http://download.eclipse.org/modeling/emf/cdo/updates/integration/weekly/latest

Even though I can't map your stack trace to the sources exactly it suggests that a client already sent a commit request to the server, which fails somewhere in TransactionCommitContext.write(). I suspect that this commit included new model packages that couldn't be completely mapped to the database. During the subsequent rollback the server attempted to drop the new tables that were created until the point of failure. The logged NPE comes from the rollback/error handling code and unfortunately hides the original error message. For the further analysis it is essential that the stack trace matches the sources. I could try to find the right Git commit but first I'd like to understand why you're not using the latest version.


Re: [CDO] Repository initialization for mysql databse backend [message #1821850 is a reply to message #1821849] Fri, 21 February 2020 06:34 Go to previous messageGo to next message
Eike Stepper is currently offline Eike StepperFriend
Messages: 6561
Registered: July 2009
Senior Member
Oh, and why do you say that you're not able to start a repository? The stack trace suggests that the server is started and a client is connected and committing...

Re: [CDO] Repository initialization for mysql databse backend [message #1821856 is a reply to message #1821850] Fri, 21 February 2020 07:40 Go to previous messageGo to next message
Robert Schulk is currently offline Robert SchulkFriend
Messages: 112
Registered: July 2015
Senior Member
Sorry, that was not accurately phrased. The error happens during our server initialization routine.
More specifically, when activating the security manager like this:

        InternalSecurityManager securityMngr = (InternalSecurityManager) SecurityManagerUtil.createSecurityManager("/security", IPluginContainer.INSTANCE);
        securityMngr.addCommitHandler((CommitHandler) container.getElement("org.eclipse.emf.cdo.server.security.commitHandlers", "annotation", null));
        securityMngr.setRepository((InternalRepository) repository);
        LifecycleUtil.activate(securityMngr); //<<<<<<<<<<<<<<<<<<<<<<mysql exception here (but not with h2)


We cannot upgrade yet to the newest cdo version because of https://bugs.eclipse.org/bugs/show_bug.cgi?id=560280
But I updated the target to get the current stacktrace:

<unit id="org.eclipse.emf.cdo.sdk.feature.group" version="5.2.0.v20200218-1854"/>
<unit id="org.eclipse.net4j.db.mysql.feature.group" version="4.3.0.v20191214-1959"/>
<unit id="org.eclipse.net4j.feature.group" version="4.9.0.v20200108-0001"/>


!ENTRY org.eclipse.emf.cdo.server.security 1 0 2020-02-21 08:14:02.559
!MESSAGE Security realm created in /security
[WARN] Problem while rolling back the transaction
java.lang.NullPointerException
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.removeClassMapping(AbstractMappingStrategy.java:573)
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.mapClasses(AbstractMappingStrategy.java:545)
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.mapPackageInfos(AbstractMappingStrategy.java:527)
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.mapPackageUnits(AbstractMappingStrategy.java:514)
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.removeMapping(AbstractMappingStrategy.java:502)
	at org.eclipse.emf.cdo.server.internal.db.DBStoreAccessor.doRollback(DBStoreAccessor.java:825)
	at org.eclipse.emf.cdo.spi.server.StoreAccessorBase.rollback(StoreAccessorBase.java:197)
	at org.eclipse.emf.cdo.internal.server.TransactionCommitContext.rollback(TransactionCommitContext.java:1549)
	at org.eclipse.emf.cdo.internal.server.TransactionCommitContext.handleException(TransactionCommitContext.java:880)
	at org.eclipse.emf.cdo.internal.server.TransactionCommitContext.write(TransactionCommitContext.java:816)
	at org.eclipse.emf.cdo.spi.server.InternalCommitContext$1.runLoop(InternalCommitContext.java:49)
	at org.eclipse.emf.cdo.spi.server.InternalCommitContext$1.runLoop(InternalCommitContext.java:1)
	at org.eclipse.net4j.util.om.monitor.ProgressDistributor.run(ProgressDistributor.java:95)
	at org.eclipse.emf.cdo.internal.server.Repository.commitUnsynced(Repository.java:1283)
	at org.eclipse.emf.cdo.internal.server.Repository.commit(Repository.java:1276)
	at org.eclipse.emf.cdo.server.internal.net4j.protocol.CommitTransactionIndication.indicatingCommit(CommitTransactionIndication.java:318)
	at org.eclipse.emf.cdo.server.internal.net4j.protocol.CommitTransactionIndication.indicating(CommitTransactionIndication.java:103)
	at org.eclipse.emf.cdo.server.internal.net4j.protocol.CDOServerIndicationWithMonitoring.indicating(CDOServerIndicationWithMonitoring.java:118)
	at org.eclipse.net4j.signal.IndicationWithMonitoring.indicating(IndicationWithMonitoring.java:87)
	at org.eclipse.net4j.signal.IndicationWithResponse.doExtendedInput(IndicationWithResponse.java:100)
	at org.eclipse.net4j.signal.Signal.doInput(Signal.java:381)
	at org.eclipse.net4j.signal.IndicationWithResponse.execute(IndicationWithResponse.java:73)
	at org.eclipse.net4j.signal.IndicationWithMonitoring.execute(IndicationWithMonitoring.java:66)
	at org.eclipse.net4j.signal.Signal.runSync(Signal.java:287)
	at org.eclipse.net4j.signal.Signal.run(Signal.java:166)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)


The initial exception in TransactionCommitContext.java:816
org.eclipse.net4j.db.DBException: java.sql.SQLException: Table definition has changed, please retry transaction

Re: [CDO] Repository initialization for mysql databse backend [message #1821860 is a reply to message #1821856] Fri, 21 February 2020 09:16 Go to previous messageGo to next message
Eike Stepper is currently offline Eike StepperFriend
Messages: 6561
Registered: July 2009
Senior Member
Ok, the stack trace matches my source now. But it's still not the original exception. Can you please run the server once more, this time with these Debug Options:

index.php/fa/37424/0/

That should write the original exception and its stack trace to the log.

BTW., https://bugs.eclipse.org/bugs/show_bug.cgi?id=560280 should be fixed, now ;-)
  • Attachment: Unbenannt.PNG
    (Size: 24.25KB, Downloaded 111 times)


Re: [CDO] Repository initialization for mysql databse backend [message #1821861 is a reply to message #1821860] Fri, 21 February 2020 09:37 Go to previous messageGo to next message
Robert Schulk is currently offline Robert SchulkFriend
Messages: 112
Registered: July 2015
Senior Member
Thats great news about 560280 :). Will try with the next weekly build.
This is the stacktrace with debugging enabled:

!ENTRY org.eclipse.emf.cdo.server.security 1 0 2020-02-21 10:34:27.273
!MESSAGE Security realm created in /security
net4j-thread-3 [debug] Writing transaction: Transaction[2:1]
net4j-thread-3 [debug.transaction] null
org.eclipse.net4j.db.DBException: java.sql.SQLException: Table definition has changed, please retry transaction
	at org.eclipse.emf.cdo.server.internal.db.mapping.horizontal.NonAuditListTableMapping.getCurrentIndexOffset(NonAuditListTableMapping.java:290)
	at org.eclipse.emf.cdo.server.internal.db.mapping.horizontal.NonAuditListTableMapping.access$0(NonAuditListTableMapping.java:263)
	at org.eclipse.emf.cdo.server.internal.db.mapping.horizontal.NonAuditListTableMapping$ListDeltaWriter.getCurrentIndexOffset(NonAuditListTableMapping.java:348)
	at org.eclipse.emf.cdo.server.internal.db.mapping.horizontal.AbstractBasicListTableMapping$AbstractListDeltaWriter.optimizeListIndexes(AbstractBasicListTableMapping.java:468)
	at org.eclipse.emf.cdo.server.internal.db.mapping.horizontal.AbstractBasicListTableMapping$AbstractListDeltaWriter.writeListDeltas(AbstractBasicListTableMapping.java:214)
	at org.eclipse.emf.cdo.server.internal.db.mapping.horizontal.NonAuditListTableMapping.processDelta(NonAuditListTableMapping.java:227)
	at org.eclipse.emf.cdo.server.internal.db.mapping.horizontal.HorizontalNonAuditClassMapping$FeatureDeltaWriter.visit(HorizontalNonAuditClassMapping.java:602)
	at org.eclipse.emf.cdo.internal.common.revision.delta.CDOListFeatureDeltaImpl.accept(CDOListFeatureDeltaImpl.java:614)
	at org.eclipse.emf.cdo.internal.common.revision.delta.CDORevisionDeltaImpl.accept(CDORevisionDeltaImpl.java:389)
	at org.eclipse.emf.cdo.internal.common.revision.delta.CDORevisionDeltaImpl.accept(CDORevisionDeltaImpl.java:371)
	at org.eclipse.emf.cdo.server.internal.db.mapping.horizontal.HorizontalNonAuditClassMapping$FeatureDeltaWriter.doProcess(HorizontalNonAuditClassMapping.java:561)
	at org.eclipse.emf.cdo.server.internal.db.mapping.horizontal.AbstractHorizontalClassMapping$AbstractFeatureDeltaWriter.process(AbstractHorizontalClassMapping.java:1227)
	at org.eclipse.emf.cdo.server.internal.db.mapping.horizontal.HorizontalNonAuditClassMapping.writeRevisionDelta(HorizontalNonAuditClassMapping.java:511)
	at org.eclipse.emf.cdo.server.internal.db.DBStoreAccessor.writeRevisionDelta(DBStoreAccessor.java:579)
	at org.eclipse.emf.cdo.server.internal.db.DBStoreAccessor.writeRevisionDeltas(DBStoreAccessor.java:565)
	at org.eclipse.emf.cdo.spi.server.StoreAccessor.doWrite(StoreAccessor.java:109)
	at org.eclipse.emf.cdo.server.internal.db.DBStoreAccessor.doWrite(DBStoreAccessor.java:940)
	at org.eclipse.emf.cdo.spi.server.StoreAccessorBase.write(StoreAccessorBase.java:144)
	at org.eclipse.emf.cdo.internal.server.TransactionCommitContext.writeAccessor(TransactionCommitContext.java:1800)
	at org.eclipse.emf.cdo.internal.server.TransactionCommitContext.write(TransactionCommitContext.java:807)
	at org.eclipse.emf.cdo.spi.server.InternalCommitContext$1.runLoop(InternalCommitContext.java:49)
	at org.eclipse.emf.cdo.spi.server.InternalCommitContext$1.runLoop(InternalCommitContext.java:1)
	at org.eclipse.net4j.util.om.monitor.ProgressDistributor.run(ProgressDistributor.java:95)
	at org.eclipse.emf.cdo.internal.server.Repository.commitUnsynced(Repository.java:1283)
	at org.eclipse.emf.cdo.internal.server.Repository.commit(Repository.java:1276)
	at org.eclipse.emf.cdo.server.internal.net4j.protocol.CommitTransactionIndication.indicatingCommit(CommitTransactionIndication.java:318)
	at org.eclipse.emf.cdo.server.internal.net4j.protocol.CommitTransactionIndication.indicating(CommitTransactionIndication.java:103)
	at org.eclipse.emf.cdo.server.internal.net4j.protocol.CDOServerIndicationWithMonitoring.indicating(CDOServerIndicationWithMonitoring.java:118)
	at org.eclipse.net4j.signal.IndicationWithMonitoring.indicating(IndicationWithMonitoring.java:87)
	at org.eclipse.net4j.signal.IndicationWithResponse.doExtendedInput(IndicationWithResponse.java:100)
	at org.eclipse.net4j.signal.Signal.doInput(Signal.java:381)
	at org.eclipse.net4j.signal.IndicationWithResponse.execute(IndicationWithResponse.java:73)
	at org.eclipse.net4j.signal.IndicationWithMonitoring.execute(IndicationWithMonitoring.java:66)
	at org.eclipse.net4j.signal.Signal.runSync(Signal.java:287)
	at org.eclipse.net4j.signal.Signal.run(Signal.java:166)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Caused by: java.sql.SQLException: Table definition has changed, please retry transaction
	at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:965)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3978)
	at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3914)
	at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2530)
	at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2683)
	at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2495)
	at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1903)
	at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:2011)
	at org.eclipse.net4j.internal.db.DBPreparedStatement.executeQuery(DBPreparedStatement.java:128)
	at org.eclipse.emf.cdo.server.internal.db.mapping.horizontal.NonAuditListTableMapping.getCurrentIndexOffset(NonAuditListTableMapping.java:278)
	... 37 more
net4j-thread-3 [debug] Rolling back transaction: Transaction[2:1]
[WARN] Problem while rolling back the transaction
java.lang.NullPointerException
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.removeClassMapping(AbstractMappingStrategy.java:573)
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.mapClasses(AbstractMappingStrategy.java:545)
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.mapPackageInfos(AbstractMappingStrategy.java:527)
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.mapPackageUnits(AbstractMappingStrategy.java:514)
	at org.eclipse.emf.cdo.server.internal.db.mapping.AbstractMappingStrategy.removeMapping(AbstractMappingStrategy.java:502)
	at org.eclipse.emf.cdo.server.internal.db.DBStoreAccessor.doRollback(DBStoreAccessor.java:825)
	at org.eclipse.emf.cdo.spi.server.StoreAccessorBase.rollback(StoreAccessorBase.java:197)
	at org.eclipse.emf.cdo.internal.server.TransactionCommitContext.rollback(TransactionCommitContext.java:1549)
	at org.eclipse.emf.cdo.internal.server.TransactionCommitContext.handleException(TransactionCommitContext.java:880)
	at org.eclipse.emf.cdo.internal.server.TransactionCommitContext.write(TransactionCommitContext.java:816)
	at org.eclipse.emf.cdo.spi.server.InternalCommitContext$1.runLoop(InternalCommitContext.java:49)
	at org.eclipse.emf.cdo.spi.server.InternalCommitContext$1.runLoop(InternalCommitContext.java:1)
	at org.eclipse.net4j.util.om.monitor.ProgressDistributor.run(ProgressDistributor.java:95)
	at org.eclipse.emf.cdo.internal.server.Repository.commitUnsynced(Repository.java:1283)
	at org.eclipse.emf.cdo.internal.server.Repository.commit(Repository.java:1276)
	at org.eclipse.emf.cdo.server.internal.net4j.protocol.CommitTransactionIndication.indicatingCommit(CommitTransactionIndication.java:318)
	at org.eclipse.emf.cdo.server.internal.net4j.protocol.CommitTransactionIndication.indicating(CommitTransactionIndication.java:103)
	at org.eclipse.emf.cdo.server.internal.net4j.protocol.CDOServerIndicationWithMonitoring.indicating(CDOServerIndicationWithMonitoring.java:118)
	at org.eclipse.net4j.signal.IndicationWithMonitoring.indicating(IndicationWithMonitoring.java:87)
	at org.eclipse.net4j.signal.IndicationWithResponse.doExtendedInput(IndicationWithResponse.java:100)
	at org.eclipse.net4j.signal.Signal.doInput(Signal.java:381)
	at org.eclipse.net4j.signal.IndicationWithResponse.execute(IndicationWithResponse.java:73)
	at org.eclipse.net4j.signal.IndicationWithMonitoring.execute(IndicationWithMonitoring.java:66)
	at org.eclipse.net4j.signal.Signal.runSync(Signal.java:287)
	at org.eclipse.net4j.signal.Signal.run(Signal.java:166)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
	at java.lang.Thread.run(Thread.java:748)
Re: [CDO] Repository initialization for mysql databse backend [message #1821877 is a reply to message #1821861] Fri, 21 February 2020 14:26 Go to previous messageGo to next message
Eike Stepper is currently offline Eike StepperFriend
Messages: 6561
Registered: July 2009
Senior Member
Robert Schulk wrote on Fri, 21 February 2020 10:37
Thats great news about 560280 :). Will try with the next weekly build.


Build http://download.eclipse.org/modeling/emf/cdo/drops/I20200221-0544 with the fix is available now.

Regarding the Mysql issue, I spend a few hours today in order to get everything running with Mysql 8. A nightmare. New APIs even in the connector. I'll try to have more time for this next week. Then I'll hopefully be able to execute our test suite for Mysql...


Re: [CDO] Repository initialization for mysql databse backend [message #1821890 is a reply to message #1821877] Fri, 21 February 2020 16:02 Go to previous messageGo to next message
Robert Schulk is currently offline Robert SchulkFriend
Messages: 112
Registered: July 2015
Senior Member
Mysql8 would be even better, of course!

But I guess most people who used the mysql backend are still on mysql 5.7 (like in our case).
So maybe the fix there is rather simple?
Re: [CDO] Repository initialization for mysql databse backend [message #1822640 is a reply to message #1821890] Tue, 10 March 2020 16:19 Go to previous messageGo to next message
Robert Schulk is currently offline Robert SchulkFriend
Messages: 112
Registered: July 2015
Senior Member
I created this bugzilla:
https://bugs.eclipse.org/bugs/show_bug.cgi?id=560986
Re: [CDO] Repository initialization for mysql databse backend [message #1823117 is a reply to message #1822640] Thu, 19 March 2020 16:25 Go to previous message
Robert Schulk is currently offline Robert SchulkFriend
Messages: 112
Registered: July 2015
Senior Member
For future reference: this problem does not seem to be associated to the security manager. A normal commit also seems to trigger the problem.
Also, there is another bug referring to it:
https://bugs.eclipse.org/bugs/show_bug.cgi?id=546872

I closed the bug 560986 as a duplicate.
Also, I could extend the proposed solution for 546872 which seems to fix the problem for mysql5.7.
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