org.hibernate.exception.LockAcquisitionException: could not initialize a collection: [uk.ac.ebi.interpro.scan.model.Protein.matches#1474]

Google Groups | Unknown author | 4 years ago
  1. 0

    IPRScan 5 RC 2 - [org.hibernate.util.JDBCExceptionReporter:234] ERROR

    Google Groups | 4 years ago | Unknown author
    org.hibernate.exception.LockAcquisitionException: could not initialize a collection: [uk.ac.ebi.interpro.scan.model.Protein.matches#1474]
  2. 0

    IPRScan 5 RC2 - [org.hibernate.util.JDBCExceptionReporter:234] ERROR

    Google Groups | 4 years ago | Unknown author
    org.hibernate.exception.LockAcquisitionException: could not initialize a collection: [uk.ac.ebi.interpro.scan.model.Protein.matches#1474]
  3. 0

    Using NOLOCK to eliminate deadlocks for application which has pessimistic locking

    Stack Overflow | 3 years ago | Vineet Bhatia
    org.hibernate.exception.LockAcquisitionException: could not initialize a collection: [com.co.app.domain.Customer.customerBusElemtVals#component[custId,txnId]{txnId=11111111, CustomerId=22222222}]
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  5. 0

    Progress KB - Corticon causing SQL Server deadlocks on reads with "com.corticon.reactor.CcJavaReactor|org.hibernate.exception.LockAcquisitionException" in logs

    progress.com | 1 year ago
    org.hibernate.exception.LockAcquisitionException: could not initialize a collection: [corticoncdo.EAccessionsCDO.RdecisionResultsTableAssoc#583]
  6. 0

    {code} 2013-11-21 21:57:20,657 DEBUG [rescope-details:thread-1] com.atlassian.stash.scm.BaseCommand Executed /usr/bin/git rev-list --format=%H%x02%h%x02%P%x02%p%x02%aN%x02%aE%x02%at%n%B%n%x03 --ignore-missing --stdin -- 2013-11-21 21:57:21,240 WARN [rescope-details:thread-1] o.h.e.jdbc.spi.SqlExceptionHelper SQL Error: 1213, SQLState: 40001 2013-11-21 21:57:21,241 ERROR [rescope-details:thread-1] o.h.e.jdbc.spi.SqlExceptionHelper Deadlock found when trying to get lock; try restarting transaction 2013-11-21 21:57:21,256 WARN [rescope-details:thread-1] c.a.s.i.p.r.DefaultRescopeProcessor 15173: Could not delete empty rescope with ID 296604 org.hibernate.exception.LockAcquisitionException: could not execute statement at org.hibernate.dialect.MySQLDialect$1.convert(MySQLDialect.java:411) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final] at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final] at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:125) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final] at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:110) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final] at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:136) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final] at org.hibernate.hql.spi.TableBasedDeleteHandlerImpl.execute(TableBasedDeleteHandlerImpl.java:163) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final] at org.hibernate.hql.internal.ast.exec.MultiTableDeleteExecutor.execute(MultiTableDeleteExecutor.java:63) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final] at org.hibernate.hql.internal.ast.QueryTranslatorImpl.executeUpdate(QueryTranslatorImpl.java:414) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final] at org.hibernate.engine.query.spi.HQLQueryPlan.performExecuteUpdate(HQLQueryPlan.java:282) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final] at org.hibernate.internal.SessionImpl.executeUpdate(SessionImpl.java:1290) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final] at org.hibernate.internal.QueryImpl.executeUpdate(QueryImpl.java:116) ~[hibernate-core-4.2.5.Final.jar:4.2.5.Final] at com.atlassian.stash.internal.AbstractHibernateDao.deleteById(AbstractHibernateDao.java:53) ~[stash-dao-impl-2.9.1.jar:na] at com.atlassian.stash.internal.AbstractHibernateDao.deleteById(AbstractHibernateDao.java:22) ~[stash-dao-impl-2.9.1.jar:na] at com.sun.proxy.$Proxy155.deleteById(Unknown Source) ~[na:na] at com.atlassian.stash.internal.pull.rescope.DefaultRescopeProcessor$3.doInTransactionWithoutResult(DefaultRescopeProcessor.java:139) ~[stash-service-impl-2.9.1.jar:na] at org.springframework.transaction.support.TransactionCallbackWithoutResult.doInTransaction(TransactionCallbackWithoutResult.java:33) ~[spring-tx-3.2.4.RELEASE.jar:3.2.4.RELEASE] at org.springframework.transaction.support.TransactionTemplate.execute(TransactionTemplate.java:131) ~[spring-tx-3.2.4.RELEASE.jar:3.2.4.RELEASE] at com.atlassian.stash.internal.pull.rescope.DefaultRescopeProcessor.deleteActivity(DefaultRescopeProcessor.java:130) [stash-service-impl-2.9.1.jar:na] at com.atlassian.stash.internal.pull.rescope.DefaultRescopeProcessor.processAll(DefaultRescopeProcessor.java:100) [stash-service-impl-2.9.1.jar:na] at com.atlassian.stash.internal.pull.rescope.DefaultRescopeProcessor.process(DefaultRescopeProcessor.java:77) [stash-service-impl-2.9.1.jar:na] at com.atlassian.stash.internal.pull.rescope.DefaultRescopeProcessor$RescopeCalculator.run(DefaultRescopeProcessor.java:219) [stash-service-impl-2.9.1.jar:na] at com.atlassian.stash.internal.concurrent.StateTransferringExecutor$StateTransferringRunnable.run(StateTransferringExecutor.java:69) [stash-platform-2.9.1.jar:na] at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:439) [na:1.6.0_45] at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303) [na:1.6.0_45] at java.util.concurrent.FutureTask.run(FutureTask.java:138) [na:1.6.0_45] at java.lang.Thread.run(Thread.java:662) [na:1.6.0_45] ... 11 frames trimmed Caused by: com.mysql.jdbc.exceptions.jdbc4.MySQLTransactionRollbackException: Deadlock found when trying to get lock; try restarting transaction at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.6.0_45] at com.mysql.jdbc.Util.handleNewInstance(Util.java:411) ~[mysql-connector-java-5.1.24-bin.jar:na] at com.mysql.jdbc.Util.getInstance(Util.java:386) ~[mysql-connector-java-5.1.24-bin.jar:na] at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1066) ~[mysql-connector-java-5.1.24-bin.jar:na] at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4120) ~[mysql-connector-java-5.1.24-bin.jar:na] at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:4052) ~[mysql-connector-java-5.1.24-bin.jar:na] at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2503) ~[mysql-connector-java-5.1.24-bin.jar:na] at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2664) ~[mysql-connector-java-5.1.24-bin.jar:na] {code}

    Atlassian JIRA | 3 years ago | Alexey Efimov
    org.hibernate.exception.LockAcquisitionException: could not execute statement

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    Root Cause Analysis

    1. org.hibernate.exception.LockAcquisitionException

      could not initialize a collection: [uk.ac.ebi.interpro.scan.model.Protein.matches#1474]

      at org.hibernate.exception.SQLStateConverter.convert()
    2. Hibernate
      AbstractCollectionPersister.initialize
      1. org.hibernate.exception.SQLStateConverter.convert(SQLStateConverter.java:107)
      2. org.hibernate.exception.JDBCExceptionHelper.convert(JDBCExceptionHelper.java:66)
      3. org.hibernate.loader.Loader.loadCollection(Loader.java:2173)
      4. org.hibernate.loader.collection.CollectionLoader.initialize(CollectionLoader.java:62)
      5. org.hibernate.persister.collection.AbstractCollectionPersister.initialize(AbstractCollectionPersister.java:627)
      5 frames
    3. Hibernate
      PersistentSet.add
      1. org.hibernate.event.def.DefaultInitializeCollectionEventListener.onInitializeCollection(DefaultInitializeCollectionEventListener.java:83)
      2. org.hibernate.impl.SessionImpl.initializeCollection(SessionImpl.java:1863)
      3. org.hibernate.collection.AbstractPersistentCollection.initialize(AbstractPersistentCollection.java:369)
      4. org.hibernate.collection.AbstractPersistentCollection.read(AbstractPersistentCollection.java:111)
      5. org.hibernate.collection.AbstractPersistentCollection.readElementExistence(AbstractPersistentCollection.java:167)
      6. org.hibernate.collection.PersistentSet.add(PersistentSet.java:210)
      6 frames
    4. uk.ac.ebi
      FilteredMatchDAOImpl.persist
      1. uk.ac.ebi.interpro.scan.model.Protein.addMatch(Protein.java:267)
      2. uk.ac.ebi.interpro.scan.persistence.SignalPFilteredMatchDAOImpl.persist(SignalPFilteredMatchDAOImpl.java:82)
      3. uk.ac.ebi.interpro.scan.persistence.FilteredMatchDAOImpl.persist(FilteredMatchDAOImpl.java:90)
      3 frames
    5. Java RT
      Method.invoke
      1. sun.reflect.GeneratedMethodAccessor78.invoke(Unknown Source)
      2. sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
      3. java.lang.reflect.Method.invoke(Unknown Source)
      3 frames
    6. Spring AOP
      ReflectiveMethodInvocation.proceed
      1. org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:318)
      2. org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
      3. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
      3 frames
    7. Spring Tx
      TransactionInterceptor.invoke
      1. org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
      1 frame
    8. Spring AOP
      JdkDynamicAopProxy.invoke
      1. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
      2. org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
      2 frames
    9. Unknown
      $Proxy61.persist
      1. $Proxy61.persist(Unknown Source)
      1 frame
    10. uk.ac.ebi
      StepExecutionTransactionImpl.executeInTransaction
      1. uk.ac.ebi.interpro.scan.management.model.implementations.signalp.ParseAndPersistBinaryOutputStep.execute(ParseAndPersistBinaryOutputStep.java:91)
      2. uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:82)
      2 frames
    11. Java RT
      Method.invoke
      1. sun.reflect.GeneratedMethodAccessor72.invoke(Unknown Source)
      2. sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
      3. java.lang.reflect.Method.invoke(Unknown Source)
      3 frames
    12. Spring AOP
      ReflectiveMethodInvocation.proceed
      1. org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:318)
      2. org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:183)
      3. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:150)
      3 frames
    13. Spring Tx
      TransactionInterceptor.invoke
      1. org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:110)
      1 frame
    14. Spring AOP
      JdkDynamicAopProxy.invoke
      1. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:172)
      2. org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:202)
      2 frames
    15. Unknown
      $Proxy90.executeInTransaction
      1. $Proxy90.executeInTransaction(Unknown Source)
      1 frame
    16. uk.ac.ebi
      AmqInterProScanWorker.onMessage
      1. uk.ac.ebi.interpro.scan.jms.activemq.AmqInterProScanWorker.onMessage(AmqInterProScanWorker.java:96)
      1 frame
    17. Spring Framework
      DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run
      1. org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:561)
      2. org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:499)
      3. org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:467)
      4. org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:325)
      5. org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:263)
      6. org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1059)
      7. org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1051)
      8. org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:948)
      8 frames
    18. Java RT
      Thread.run
      1. java.lang.Thread.run(Unknown Source)
      1 frame