Unable to upload any dicom object after upgrade to 5.24.2 #3638

jason1122g · 2022-04-06T08:51:29Z

jason1122g
Apr 6, 2022

Describe the bug
Cannot upload any dicom after upgrade to 5.24.2 from 5.11.0
We have also migrated the db from MariaDB to PostgreSQL via pgloader

Expected behavior
It should be able to upload dicom objects

Additional context

We cannot reproduce the issue stably
This issue might be related to the data size because it usually appears in the env already containing many dicom objects
The upgrade procedure is same as the description in wiki pages (https://github.com/dcm4che/dcm4chee-arc-light/wiki/Upgrade-on-Docker)

Our environment is composed of the following docker images:

dcm4che/slapd-dcm4chee:2.4.57-24.2
dcm4che/keycloak:15.0.2
dcm4che/postgres-dcm4chee:13.3-24
dcm4che/dcm4chee-arc-psql:5.24.2-secure-ui

Whenever we want to upload any dicom objects, the following wildfly error logs appear:

INFO  [org.dcm4che3.net.Association] (EE-ManagedExecutorService-default-Thread-5663) DCM4CHEE<-AE_TITLE_MAC(204): processing 166:C-STORE-RQ[pcid=1, prior=0
  cuid=1.2.840.10008.5.1.4.1.1.4 - MR Image Storage
  iuid=1.3.46.670589.11.38198.5.0.3692.2020032709212886785 - ?
  tsuid=1.2.840.10008.1.2 - Implicit VR Little Endian] failed. Caused by:   : org.dcm4che3.net.service.DicomServiceException: javax.ejb.EJBTransactionRolledbackException: javax.transaction.RollbackException: ARJUNA016053: Could not commit transaction.
    at deployment.dcm4chee-arc-ear-5.24.2-psql.ear.dcm4chee-arc-store-5.24.2.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.store(StoreServiceImpl.java:212)
    at deployment.dcm4chee-arc-ear-5.24.2-psql.ear.dcm4chee-arc-store-5.24.2.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.store(StoreServiceImpl.java:179)
    at deployment.dcm4chee-arc-ear-5.24.2-psql.ear.dcm4chee-arc-store-5.24.2.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl$Proxy$_$$_WeldClientProxy.store(Unknown Source)
    at deployment.dcm4chee-arc-ear-5.24.2-psql.ear//org.dcm4chee.arc.store.scp.CStoreSCP.store(CStoreSCP.java:36)
    at org.dcm4che.net@5.24.2//org.dcm4che3.net.service.BasicCStoreSCP.onDimseRQ(BasicCStoreSCP.java:72)
    at jdk.internal.reflect.GeneratedMethodAccessor103.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.jboss.weld.core@3.1.7.SP1//org.jboss.weld.bean.proxy.AbstractBeanInstance.invoke(AbstractBeanInstance.java:38)
    at org.jboss.weld.core@3.1.7.SP1//org.jboss.weld.bean.proxy.ProxyMethodHandler.invoke(ProxyMethodHandler.java:106)
    at deployment.dcm4chee-arc-ear-5.24.2-psql.ear//org.dcm4che3.net.service.DicomService$1523545383$Proxy$_$$_WeldClientProxy.onDimseRQ(Unknown Source)
    at org.dcm4che.net@5.24.2//org.dcm4che3.net.service.DicomServiceRegistry.onDimseRQ(DicomServiceRegistry.java:86)
    at org.dcm4che.net@5.24.2//org.dcm4che3.net.ApplicationEntity.onDimseRQ(ApplicationEntity.java:474)
    at org.dcm4che.net@5.24.2//org.dcm4che3.net.Association.onDimseRQ(Association.java:755)
    at org.dcm4che.net@5.24.2//org.dcm4che3.net.PDUDecoder.decodeDIMSE(PDUDecoder.java:466)
    at org.dcm4che.net@5.24.2//org.dcm4che3.net.Association.handlePDataTF(Association.java:738)
    at org.dcm4che.net@5.24.2//org.dcm4che3.net.State$4.onPDataTF(State.java:108)
    at org.dcm4che.net@5.24.2//org.dcm4che3.net.Association.onPDataTF(Association.java:734)
    at org.dcm4che.net@5.24.2//org.dcm4che3.net.PDUDecoder.nextPDU(PDUDecoder.java:177)
    at org.dcm4che.net@5.24.2//org.dcm4che3.net.Association$2.run(Association.java:571)
    at org.jboss.as.ee@24.0.1.Final//org.jboss.as.ee.concurrent.ControlPointUtils$ControlledRunnable.run(ControlPointUtils.java:125)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at org.glassfish.javax.enterprise.concurrent//org.glassfish.enterprise.concurrent.internal.ManagedFutureTask.run(ManagedFutureTask.java:117)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.lang.Thread.run(Thread.java:829)
    at org.glassfish.javax.enterprise.concurrent//org.glassfish.enterprise.concurrent.ManagedThreadFactoryImpl$ManagedThread.run(ManagedThreadFactoryImpl.java:227)
Caused by: javax.ejb.EJBTransactionRolledbackException: javax.transaction.RollbackException: ARJUNA016053: Could not commit transaction.
    at org.jboss.as.ejb3@24.0.1.Final//org.jboss.as.ejb3.tx.CMTTxInterceptor.endTransaction(CMTTxInterceptor.java:117)
    at org.jboss.as.ejb3@24.0.1.Final//org.jboss.as.ejb3.tx.CMTTxInterceptor.invokeInOurTx(CMTTxInterceptor.java:284)
    at org.jboss.as.ejb3@24.0.1.Final//org.jboss.as.ejb3.tx.CMTTxInterceptor.required(CMTTxInterceptor.java:390)
    at org.jboss.as.ejb3@24.0.1.Final//org.jboss.as.ejb3.tx.CMTTxInterceptor.processInvocation(CMTTxInterceptor.java:160)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:422)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.InterceptorContext$Invocation.proceed(InterceptorContext.java:509)
    at org.jboss.weld.core@3.1.7.SP1//org.jboss.weld.module.ejb.AbstractEJBRequestScopeActivationInterceptor.aroundInvoke(AbstractEJBRequestScopeActivationInterceptor.java:81)
    at org.jboss.as.weld.common@24.0.1.Final//org.jboss.as.weld.ejb.EjbRequestScopeActivationInterceptor.processInvocation(EjbRequestScopeActivationInterceptor.java:89)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:422)
    at org.jboss.as.ejb3@24.0.1.Final//org.jboss.as.ejb3.component.interceptors.CurrentInvocationContextInterceptor.processInvocation(CurrentInvocationContextInterceptor.java:41)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:422)
    at org.jboss.as.ejb3@24.0.1.Final//org.jboss.as.ejb3.component.invocationmetrics.WaitTimeInterceptor.processInvocation(WaitTimeInterceptor.java:47)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:422)
    at org.jboss.as.ejb3@24.0.1.Final//org.jboss.as.ejb3.security.SecurityContextInterceptor.processInvocation(SecurityContextInterceptor.java:100)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:422)
    at org.jboss.as.ejb3@24.0.1.Final//org.jboss.as.ejb3.deployment.processors.StartupAwaitInterceptor.processInvocation(StartupAwaitInterceptor.java:22)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:422)
    at org.jboss.as.ejb3@24.0.1.Final//org.jboss.as.ejb3.component.interceptors.ShutDownInterceptorFactory$1.processInvocation(ShutDownInterceptorFactory.java:64)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:422)
    at org.jboss.as.ejb3@24.0.1.Final//org.jboss.as.ejb3.component.interceptors.LoggingInterceptor.processInvocation(LoggingInterceptor.java:67)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:422)
    at org.jboss.as.ee@24.0.1.Final//org.jboss.as.ee.component.NamespaceContextInterceptor.processInvocation(NamespaceContextInterceptor.java:50)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:422)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.ContextClassLoaderInterceptor.processInvocation(ContextClassLoaderInterceptor.java:60)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:422)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.InterceptorContext.run(InterceptorContext.java:438)
    at org.wildfly.security.elytron-base@1.16.1.Final//org.wildfly.security.manager.WildFlySecurityManager.doChecked(WildFlySecurityManager.java:633)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.AccessCheckingInterceptor.processInvocation(AccessCheckingInterceptor.java:57)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.InterceptorContext.proceed(InterceptorContext.java:422)
    at org.jboss.invocation@1.6.0.Final//org.jboss.invocation.ChainedInterceptor.processInvocation(ChainedInterceptor.java:53)
    at org.jboss.as.ee@24.0.1.Final//org.jboss.as.ee.component.ViewService$View.invoke(ViewService.java:198)
    at org.jboss.as.ee@24.0.1.Final//org.jboss.as.ee.component.ViewDescription$1.processInvocation(ViewDescription.java:191)
    at org.jboss.as.ee@24.0.1.Final//org.jboss.as.ee.component.ProxyInvocationHandler.invoke(ProxyInvocationHandler.java:81)
    at deployment.dcm4chee-arc-ear-5.24.2-psql.ear.dcm4chee-arc-store-5.24.2.jar//org.dcm4chee.arc.store.impl.StoreServiceEJB$$$view10.updateDB(Unknown Source)
    at jdk.internal.reflect.GeneratedMethodAccessor92.invoke(Unknown Source)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:566)
    at org.jboss.weld.core@3.1.7.SP1//org.jboss.weld.util.reflection.Reflections.invokeAndUnwrap(Reflections.java:410)
    at org.jboss.weld.core@3.1.7.SP1//org.jboss.weld.module.ejb.EnterpriseBeanProxyMethodHandler.invoke(EnterpriseBeanProxyMethodHandler.java:134)
    at org.jboss.weld.core@3.1.7.SP1//org.jboss.weld.bean.proxy.EnterpriseTargetBeanInstance.invoke(EnterpriseTargetBeanInstance.java:56)
    at org.jboss.weld.core@3.1.7.SP1//org.jboss.weld.module.ejb.InjectionPointPropagatingEnterpriseTargetBeanInstance.invoke(InjectionPointPropagatingEnterpriseTargetBeanInstance.java:68)
    at org.jboss.weld.core@3.1.7.SP1//org.jboss.weld.bean.proxy.ProxyMethodHandler.invoke(ProxyMethodHandler.java:106)
    at deployment.dcm4chee-arc-ear-5.24.2-psql.ear.dcm4chee-arc-store-5.24.2.jar//org.dcm4chee.arc.store.impl.StoreServiceEJB$Proxy$_$$_Weld$EnterpriseProxy$.updateDB(Unknown Source)
    at deployment.dcm4chee-arc-ear-5.24.2-psql.ear.dcm4chee-arc-store-5.24.2.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.updateDB(StoreServiceImpl.java:256)
    at deployment.dcm4chee-arc-ear-5.24.2-psql.ear.dcm4chee-arc-store-5.24.2.jar//org.dcm4chee.arc.store.impl.StoreServiceImpl.store(StoreServiceImpl.java:205)
    ... 27 more
Caused by: javax.transaction.RollbackException: ARJUNA016053: Could not commit transaction.
    at org.jboss.jts//com.arjuna.ats.internal.jta.transaction.arjunacore.TransactionImple.commitAndDisassociate(TransactionImple.java:1307)
    at org.jboss.jts//com.arjuna.ats.internal.jta.transaction.arjunacore.BaseTransaction.commit(BaseTransaction.java:128)
    at org.jboss.jts.integration//com.arjuna.ats.jbossatx.BaseTransactionManagerDelegate.commit(BaseTransactionManagerDelegate.java:94)
    at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.LocalTransaction.commitAndDissociate(LocalTransaction.java:78)
    at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.ContextTransactionManager.commit(ContextTransactionManager.java:71)
    at org.jboss.as.ejb3@24.0.1.Final//org.jboss.as.ejb3.tx.CMTTxInterceptor.endTransaction(CMTTxInterceptor.java:91)
    ... 71 more
    Suppressed: javax.transaction.RollbackException: WFTXN0061: Transaction is marked rollback-only
        at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.AbstractTransaction.setRollbackOnly(AbstractTransaction.java:96)
        at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.LocalTransaction.setRollbackOnly(LocalTransaction.java:159)
        at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.ContextTransactionManager.setRollbackOnly(ContextTransactionManager.java:94)
        at org.hibernate@5.3.20.Final//org.hibernate.resource.transaction.backend.jta.internal.JtaTransactionAdapterTransactionManagerImpl.markRollbackOnly(JtaTransactionAdapterTransactionManagerImpl.java:100)
        at org.hibernate@5.3.20.Final//org.hibernate.resource.transaction.backend.jta.internal.JtaTransactionCoordinatorImpl$TransactionDriverControlImpl.markRollbackOnly(JtaTransactionCoordinatorImpl.java:456)
        at org.hibernate@5.3.20.Final//org.hibernate.engine.transaction.internal.TransactionImpl.markRollbackOnly(TransactionImpl.java:206)
        at org.hibernate@5.3.20.Final//org.hibernate.internal.AbstractSharedSessionContract.markForRollbackOnly(AbstractSharedSessionContract.java:381)
        at org.hibernate@5.3.20.Final//org.hibernate.internal.ExceptionConverterImpl.handlePersistenceException(ExceptionConverterImpl.java:297)
        at org.hibernate@5.3.20.Final//org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:155)
        at org.hibernate@5.3.20.Final//org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:181)
        at org.hibernate@5.3.20.Final//org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:188)
        at org.hibernate@5.3.20.Final//org.hibernate.internal.SessionImpl.doFlush(SessionImpl.java:1478)
        at org.hibernate@5.3.20.Final//org.hibernate.internal.SessionImpl.managedFlush(SessionImpl.java:512)
        at org.hibernate@5.3.20.Final//org.hibernate.internal.SessionImpl.flushBeforeTransactionCompletion(SessionImpl.java:3310)
        at org.hibernate@5.3.20.Final//org.hibernate.internal.SessionImpl.beforeTransactionCompletion(SessionImpl.java:2506)
        at org.hibernate@5.3.20.Final//org.hibernate.engine.jdbc.internal.JdbcCoordinatorImpl.beforeTransactionCompletion(JdbcCoordinatorImpl.java:447)
        at org.hibernate@5.3.20.Final//org.hibernate.resource.transaction.backend.jta.internal.JtaTransactionCoordinatorImpl.beforeCompletion(JtaTransactionCoordinatorImpl.java:352)
        at org.hibernate@5.3.20.Final//org.hibernate.resource.transaction.backend.jta.internal.synchronization.SynchronizationCallbackCoordinatorNonTrackingImpl.beforeCompletion(SynchronizationCallbackCoordinatorNonTrackingImpl.java:47)
        at org.hibernate@5.3.20.Final//org.hibernate.resource.transaction.backend.jta.internal.synchronization.RegisteredSynchronization.beforeCompletion(RegisteredSynchronization.java:37)
        at org.jboss.as.transactions@24.0.1.Final//org.jboss.as.txn.service.internal.tsr.JCAOrderedLastSynchronizationList.beforeCompletion(JCAOrderedLastSynchronizationList.java:113)
        at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.AbstractTransaction.performConsumer(AbstractTransaction.java:236)
        at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.AbstractTransaction.performConsumer(AbstractTransaction.java:247)
        at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.AbstractTransaction$AssociatingSynchronization.beforeCompletion(AbstractTransaction.java:292)
        at org.jboss.jts//com.arjuna.ats.internal.jta.resources.arjunacore.SynchronizationImple.beforeCompletion(SynchronizationImple.java:76)
        at org.jboss.jts//com.arjuna.ats.arjuna.coordinator.TwoPhaseCoordinator.beforeCompletion(TwoPhaseCoordinator.java:360)
        at org.jboss.jts//com.arjuna.ats.arjuna.coordinator.TwoPhaseCoordinator.end(TwoPhaseCoordinator.java:91)
        at org.jboss.jts//com.arjuna.ats.arjuna.AtomicAction.commit(AtomicAction.java:162)
        at org.jboss.jts//com.arjuna.ats.internal.jta.transaction.arjunacore.TransactionImple.commitAndDisassociate(TransactionImple.java:1295)
        ... 76 more
    Suppressed: javax.transaction.RollbackException: WFTXN0061: Transaction is marked rollback-only
        at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.AbstractTransaction.setRollbackOnly(AbstractTransaction.java:96)
        at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.LocalTransaction.setRollbackOnly(LocalTransaction.java:159)
        at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.ContextTransactionManager.setRollbackOnly(ContextTransactionManager.java:94)
        at org.hibernate@5.3.20.Final//org.hibernate.resource.transaction.backend.jta.internal.JtaTransactionAdapterTransactionManagerImpl.markRollbackOnly(JtaTransactionAdapterTransactionManagerImpl.java:100)
        at org.hibernate@5.3.20.Final//org.hibernate.resource.transaction.backend.jta.internal.JtaTransactionCoordinatorImpl$TransactionDriverControlImpl.markRollbackOnly(JtaTransactionCoordinatorImpl.java:456)
        at org.hibernate@5.3.20.Final//org.hibernate.resource.transaction.backend.jta.internal.JtaTransactionCoordinatorImpl.beforeCompletion(JtaTransactionCoordinatorImpl.java:359)
        at org.hibernate@5.3.20.Final//org.hibernate.resource.transaction.backend.jta.internal.synchronization.SynchronizationCallbackCoordinatorNonTrackingImpl.beforeCompletion(SynchronizationCallbackCoordinatorNonTrackingImpl.java:47)
        at org.hibernate@5.3.20.Final//org.hibernate.resource.transaction.backend.jta.internal.synchronization.RegisteredSynchronization.beforeCompletion(RegisteredSynchronization.java:37)
        at org.jboss.as.transactions@24.0.1.Final//org.jboss.as.txn.service.internal.tsr.JCAOrderedLastSynchronizationList.beforeCompletion(JCAOrderedLastSynchronizationList.java:113)
        at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.AbstractTransaction.performConsumer(AbstractTransaction.java:236)
        at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.AbstractTransaction.performConsumer(AbstractTransaction.java:247)
        at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.AbstractTransaction$AssociatingSynchronization.beforeCompletion(AbstractTransaction.java:292)
        at org.jboss.jts//com.arjuna.ats.internal.jta.resources.arjunacore.SynchronizationImple.beforeCompletion(SynchronizationImple.java:76)
        at org.jboss.jts//com.arjuna.ats.arjuna.coordinator.TwoPhaseCoordinator.beforeCompletion(TwoPhaseCoordinator.java:360)
        at org.jboss.jts//com.arjuna.ats.arjuna.coordinator.TwoPhaseCoordinator.end(TwoPhaseCoordinator.java:91)
        at org.jboss.jts//com.arjuna.ats.arjuna.AtomicAction.commit(AtomicAction.java:162)
        at org.jboss.jts//com.arjuna.ats.internal.jta.transaction.arjunacore.TransactionImple.commitAndDisassociate(TransactionImple.java:1295)
        ... 76 more
Caused by: javax.persistence.PersistenceException: org.hibernate.exception.ConstraintViolationException: could not execute statement
    at org.hibernate@5.3.20.Final//org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:154)
    at org.hibernate@5.3.20.Final//org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:181)
    at org.hibernate@5.3.20.Final//org.hibernate.internal.ExceptionConverterImpl.convert(ExceptionConverterImpl.java:188)
    at org.hibernate@5.3.20.Final//org.hibernate.internal.SessionImpl.doFlush(SessionImpl.java:1478)
    at org.hibernate@5.3.20.Final//org.hibernate.internal.SessionImpl.managedFlush(SessionImpl.java:512)
    at org.hibernate@5.3.20.Final//org.hibernate.internal.SessionImpl.flushBeforeTransactionCompletion(SessionImpl.java:3310)
    at org.hibernate@5.3.20.Final//org.hibernate.internal.SessionImpl.beforeTransactionCompletion(SessionImpl.java:2506)
    at org.hibernate@5.3.20.Final//org.hibernate.engine.jdbc.internal.JdbcCoordinatorImpl.beforeTransactionCompletion(JdbcCoordinatorImpl.java:447)
    at org.hibernate@5.3.20.Final//org.hibernate.resource.transaction.backend.jta.internal.JtaTransactionCoordinatorImpl.beforeCompletion(JtaTransactionCoordinatorImpl.java:352)
    at org.hibernate@5.3.20.Final//org.hibernate.resource.transaction.backend.jta.internal.synchronization.SynchronizationCallbackCoordinatorNonTrackingImpl.beforeCompletion(SynchronizationCallbackCoordinatorNonTrackingImpl.java:47)
    at org.hibernate@5.3.20.Final//org.hibernate.resource.transaction.backend.jta.internal.synchronization.RegisteredSynchronization.beforeCompletion(RegisteredSynchronization.java:37)
    at org.jboss.as.transactions@24.0.1.Final//org.jboss.as.txn.service.internal.tsr.JCAOrderedLastSynchronizationList.beforeCompletion(JCAOrderedLastSynchronizationList.java:113)
    at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.AbstractTransaction.performConsumer(AbstractTransaction.java:236)
    at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.AbstractTransaction.performConsumer(AbstractTransaction.java:247)
    at org.wildfly.transaction.client@1.1.14.Final//org.wildfly.transaction.client.AbstractTransaction$AssociatingSynchronization.beforeCompletion(AbstractTransaction.java:292)
    at org.jboss.jts//com.arjuna.ats.internal.jta.resources.arjunacore.SynchronizationImple.beforeCompletion(SynchronizationImple.java:76)
    at org.jboss.jts//com.arjuna.ats.arjuna.coordinator.TwoPhaseCoordinator.beforeCompletion(TwoPhaseCoordinator.java:360)
    at org.jboss.jts//com.arjuna.ats.arjuna.coordinator.TwoPhaseCoordinator.end(TwoPhaseCoordinator.java:91)
    at org.jboss.jts//com.arjuna.ats.arjuna.AtomicAction.commit(AtomicAction.java:162)
    at org.jboss.jts//com.arjuna.ats.internal.jta.transaction.arjunacore.TransactionImple.commitAndDisassociate(TransactionImple.java:1295)
    ... 76 more
Caused by: org.hibernate.exception.ConstraintViolationException: could not execute statement
    at org.hibernate@5.3.20.Final//org.hibernate.exception.internal.SQLStateConversionDelegate.convert(SQLStateConversionDelegate.java:112)
    at org.hibernate@5.3.20.Final//org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:42)
    at org.hibernate@5.3.20.Final//org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:113)
    at org.hibernate@5.3.20.Final//org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:99)
    at org.hibernate@5.3.20.Final//org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:178)
    at org.hibernate@5.3.20.Final//org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3192)
    at org.hibernate@5.3.20.Final//org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3706)
    at org.hibernate@5.3.20.Final//org.hibernate.action.internal.EntityInsertAction.execute(EntityInsertAction.java:90)
    at org.hibernate@5.3.20.Final//org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:604)
    at org.hibernate@5.3.20.Final//org.hibernate.engine.spi.ActionQueue.executeActions(ActionQueue.java:478)
    at org.hibernate@5.3.20.Final//org.hibernate.event.internal.AbstractFlushingEventListener.performExecutions(AbstractFlushingEventListener.java:356)
    at org.hibernate@5.3.20.Final//org.hibernate.event.internal.DefaultFlushEventListener.onFlush(DefaultFlushEventListener.java:39)
    at org.hibernate@5.3.20.Final//org.hibernate.internal.SessionImpl.doFlush(SessionImpl.java:1472)
    ... 92 more
Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "idx_17289_primary"
  Detail: Key (pk)=(22715) already exists.
    at org.postgresql@42.2.18//org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2553)
    at org.postgresql@42.2.18//org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2285)
    at org.postgresql@42.2.18//org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:323)
    at org.postgresql@42.2.18//org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:473)
    at org.postgresql@42.2.18//org.postgresql.jdbc.PgStatement.execute(PgStatement.java:393)
    at org.postgresql@42.2.18//org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:164)
    at org.postgresql@42.2.18//org.postgresql.jdbc.PgPreparedStatement.executeUpdate(PgPreparedStatement.java:130)
    at org.jboss.ironjacamar.jdbcadapters@1.4.35.Final//org.jboss.jca.adapters.jdbc.WrappedPreparedStatement.executeUpdate(WrappedPreparedStatement.java:537)
    at org.hibernate@5.3.20.Final//org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:175)
    ... 100 more

And we noticed that the duplicated pk number increase in each turn

Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "idx_17289_primary"
  Detail: Key (pk)=(22751) already exists.

Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "idx_17289_primary"
  Detail: Key (pk)=(22763) already exists.

Caused by: org.postgresql.util.PSQLException: ERROR: duplicate key value violates unique constraint "idx_17289_primary"
  Detail: Key (pk)=(22775) already exists.

This index seems to be related to dicomattrs table
It sets pk as auto increament so that we suspected it might be an issue of sequence
But pgloader did reset the sequence and select nextval('dicomattrs_pk_seq1'); showed a number being much more larger than 227xx

pgsql-# \d+ dicomattrs
                                                Table "public.dicomattrs"
 Column |  Type  | Collation | Nullable |                 Default                 | Storage  | Stats target | Description
--------+--------+-----------+----------+-----------------------------------------+----------+--------------+-------------
 pk     | bigint |           | not null | nextval('dicomattrs_pk_seq1'::regclass) | plain    |              |
 attrs  | bytea  |           | not null |                                         | extended |              |
Indexes:
    "idx_17289_primary" PRIMARY KEY, btree (pk)

We are wondering if there is any missing step which might cause this issue 🤔
Truly appreciated for any help

vrindanayak · 2022-04-07T12:48:00Z

vrindanayak
Apr 7, 2022
Maintainer

Not reproducible - see attached screenshots in upload-dicom-obj-5.24.pdf

Would it be possible to anonymize and share the DICOM object (whose upload fails)?

3 replies

jason1122g Apr 8, 2022
Author

The same DICOM object can be uploaded successfully in newly install 5.24.2 (not upgraded from 5.11.0, install 5.24.2 directly). If we upgrade 5.11.0 to 5.24.2 with only a few of DICOM objects uploaded, it would work without any problem. But we had some 5.11.0 machines (> 60GB in storage) encounter the issue after upgrade to 5.24.2, and those machines became to deny any incoming uploads. So I guess the issue is related to storage size.

By the way, I found a similar discussion in google groups (https://groups.google.com/g/dcm4che/c/xr5FQoiDcEo/m/JpRN4r_YAwAJ)

vrindanayak Apr 8, 2022
Maintainer

That discussion in forum relates to upgrade of Synology PACS which internally pre-packages Dcm4chee archive 5.x. There have been some more discussions in the past related to Synology PACS upgrade issues, but not necessarily related to the open source archive, as we have no information / knowledge of customizations done on top of Dcm4chee Archive 5.x for Synology PACS.
Please check if there is enough space on disk where objects are getting stored. If not, the problem is independent of upload DICOM objects. You would encounter failures even if some modalities try to store objects to archive.

jason1122g Apr 15, 2022
Author

I successfully reproduced the issue! I will try to upgrade to the latest version to see if the issue has already been solved.

jason1122g · 2022-04-22T13:27:30Z

jason1122g
Apr 22, 2022
Author

I could reproduce same error after upgrade to 5.12.0 from 5.11.0, and the unique constraint violation error did not appear before db migration. But after I migrated db from MariaDB to PostgreSQL using pgloader, the violation error appear again. The pgloader might do something incorrectly. I will try not to migrate database and test if it works.

# our pgloader command

load database
   from mysql://user@host/dbname
   into pgsql://user@host/dbname
  alter schema 'dbname' rename to 'public';

1 reply

jason1122g Apr 23, 2022
Author

I found the root cause! We ran pgloader on the already initiated dcm4che database, and according to the default behavior of pgloader, it would drop something before create something, but sequence does not exist in mysql database, so that it would rename existing sequences to something like seq1 instead of recreate or update them.

pgsql-# \d+ dicomattrs
                                                Table "public.dicomattrs"
 Column |  Type  | Collation | Nullable |                 Default                 | Storage  | Stats target | Description
--------+--------+-----------+----------+-----------------------------------------+----------+--------------+-------------
 pk     | bigint |           | not null | nextval('dicomattrs_pk_seq1'::regclass) | plain    |              |
 attrs  | bytea  |           | not null |                                         | extended |              |
Indexes:
    "idx_17289_primary" PRIMARY KEY, btree (pk)

While the tables were updated to use seq1, the dcm4che was still using seq to insert records. If we look into the seq value, it would show an incorrect small number. I tried to drop the database before migrating from mysql to postgresql, and it worked as expected!

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Unable to upload any dicom object after upgrade to 5.24.2 #3638

jason1122g Apr 6, 2022

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