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#275 Exception in DBManagerHibernate#getCreationUserName while importing large dataset

any future version
open
nobody
None
5
2017-06-01
2017-04-18
Philipp Mewes
No

While importing a large dataset, an error occurs after one third of the data is imported. The dialog displays finished, but an error-message "An error occuredwhile trying to communiate with the database: Fetching username of Dataset creator failed" is shown.
This error is thrown by DBManagerHibernate#getCreationUserName and may be caused by:

  1. an incomplete transaction before the fetch of the username, this may also be caused by asynchronous execution
  2. the value of the username is null
  3. the database crashed or timed out
  4. the database does not act strictly transactional

The bug could not reproduced with a machine using the same OS- and Java-version, as well as the same database-system. For this reason there may be a problem with the database-configuration.

Discussion

  • Philipp Mewes

    Philipp Mewes - 2017-04-18
    • Description has changed:

    Diff:

    --- old
+++ new
@@ -1,8 +1,8 @@
 While importing a large dataset, an error occurs after one third of the data is imported. The dialog displays finished, but an error-message "An error occuredwhile trying to communiate with the database: Fetching username of Dataset creator failed" is shown.
 This error is thrown by `DBManagerHibernate#getCreationUserName` and may be caused by:
-* an incomplete transaction before the fetch of the username, this may also be caused by asynchronous execution
-* the value of the username is `null`
-* the database crashed or timed out
-* the database does not act strictly transactional
+1. an incomplete transaction before the fetch of the username, this may also be caused by asynchronous execution
+2. the value of the username is `null`
+3. the database crashed or timed out
+4. the database does not act strictly transactional

 The bug could not reproduced with a machine using the same OS- and Java-version, as well as the same database-system. For this reason there may be a problem with the database-configuration.
     

  • Till Schäfer

    Till Schäfer - 2017-04-18
    • summary: Error while importing large dataset --> Exception in DBManagerHibernate#getCreationUserName while importing large dataset
     

  • Karsten Klein

    Karsten Klein - 2017-06-01

    With a similar, large sdf file I receive a bunch of errors, starting with a CDKexception for smiles generation and ending with an UTF8 issue

    Jun 01, 2017 3:21:53 PM edu.udo.scaffoldhunter.model.util.CanonicalSmilesGenerator createSMILES
    SCHWERWIEGEND: Smiles generation failed
    org.openscience.cdk.exception.CDKException: Unsupported bond order: UNSET
    at org.openscience.cdk.smiles.CDKToBeam.toBeamEdgeLabel(CDKToBeam.java:270)
    at org.openscience.cdk.smiles.CDKToBeam.toBeamEdge(CDKToBeam.java:240)
    at org.openscience.cdk.smiles.CDKToBeam.toBeamGraph(CDKToBeam.java:149)
    at org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:369)
    at org.openscience.cdk.smiles.SmilesGenerator.create(SmilesGenerator.java:325)
    at edu.udo.scaffoldhunter.model.util.CanonicalSmilesGenerator.createSMILES(CanonicalSmilesGenerator.java:92)
    at edu.udo.scaffoldhunter.model.util.CanonicalSmilesGenerator.createSMILES(CanonicalSmilesGenerator.java:67)
    at edu.udo.scaffoldhunter.model.dataimport.MergeIterator.getNextMolecule(MergeIterator.java:562)
    at edu.udo.scaffoldhunter.model.dataimport.MergeIterator.next(MergeIterator.java:315)
    at edu.udo.scaffoldhunter.model.db.DbManagerHibernate.mergeMoleculesIntoDBbySMILES(DbManagerHibernate.java:2663)
    at edu.udo.scaffoldhunter.model.dataimport.Importer$MergeWorker.doInBackground(Importer.java:454)
    at edu.udo.scaffoldhunter.model.dataimport.Importer$MergeWorker.doInBackground(Importer.java:401)
    at edu.udo.scaffoldhunter.gui.util.SwingWorker$1.call(SwingWorker.java:308)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at edu.udo.scaffoldhunter.gui.util.SwingWorker$2.run(SwingWorker.java:315)
    at edu.udo.scaffoldhunter.gui.util.SwingWorker.run(SwingWorker.java:354)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)

    Jun 01, 2017 3:22:11 PM org.hibernate.engine.jdbc.spi.SqlExceptionHelper logExceptions
    WARNUNG: SQL Error: 1366, SQLState: 22001
    Jun 01, 2017 3:22:11 PM org.hibernate.engine.jdbc.spi.SqlExceptionHelper logExceptions
    SCHWERWIEGEND: Data truncation: Incorrect string value: '\xEF\xBF\xBD" y...' for column 'string' at row 1
    Jun 01, 2017 3:22:11 PM edu.udo.scaffoldhunter.model.db.DbManagerHibernate mergeMoleculesIntoDBbySMILES
    SCHWERWIEGEND: An error occured during merging.
    org.hibernate.exception.DataException: could not execute statement
    Stacktrace:
    org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:69)
    org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49)
    org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:126)
    org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:112)
    org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:211)
    org.hibernate.id.IdentityGenerator$GetGeneratedKeysDelegate.executeAndExtract(IdentityGenerator.java:96)
    org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:58)
    org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3032)
    org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3558)
    org.hibernate.action.internal.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:98)
    org.hibernate.engine.spi.ActionQueue.execute(ActionQueue.java:490)
    org.hibernate.engine.spi.ActionQueue.addResolvedEntityInsertAction(ActionQueue.java:195)
    org.hibernate.engine.spi.ActionQueue.addInsertAction(ActionQueue.java:179)
    org.hibernate.engine.spi.ActionQueue.addAction(ActionQueue.java:214)
    org.hibernate.event.internal.AbstractSaveEventListener.addInsertAction(AbstractSaveEventListener.java:324)
    org.hibernate.event.internal.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:288)
    org.hibernate.event.internal.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:194)
    org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:125)
    org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:209)
    org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:194)
    org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:114)
    org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:90)
    org.hibernate.internal.SessionImpl.fireSaveOrUpdate(SessionImpl.java:684)
    org.hibernate.internal.SessionImpl.saveOrUpdate(SessionImpl.java:676)
    org.hibernate.engine.spi.CascadingActions$5.cascade(CascadingActions.java:235)
    org.hibernate.engine.internal.Cascade.cascadeToOne(Cascade.java:350)
    org.hibernate.engine.internal.Cascade.cascadeAssociation(Cascade.java:293)
    org.hibernate.engine.internal.Cascade.cascadeProperty(Cascade.java:161)
    org.hibernate.engine.internal.Cascade.cascade(Cascade.java:118)
    org.hibernate.event.internal.AbstractSaveEventListener.cascadeBeforeSave(AbstractSaveEventListener.java:432)
    org.hibernate.event.internal.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:265)
    org.hibernate.event.internal.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:194)
    org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:125)
    org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:209)
    org.hibernate.event.internal.DefaultSaveEventListener.saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:55)
    org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:194)
    org.hibernate.event.internal.DefaultSaveEventListener.performSaveOrUpdate(DefaultSaveEventListener.java:49)
    org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:90)
    org.hibernate.internal.SessionImpl.fireSave(SessionImpl.java:715)
    org.hibernate.internal.SessionImpl.save(SessionImpl.java:707)
    org.hibernate.internal.SessionImpl.save(SessionImpl.java:702)
    sun.reflect.GeneratedMethodAccessor19.invoke(Unknown Source)
    sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    java.lang.reflect.Method.invoke(Unknown Source)
    org.hibernate.context.internal.ThreadLocalSessionContext$TransactionProtectionWrapper.invoke(ThreadLocalSessionContext.java:356)
    com.sun.proxy.$Proxy2.save(Unknown Source)
    edu.udo.scaffoldhunter.model.db.DbManagerHibernate.mergeMoleculesIntoDBbySMILES(DbManagerHibernate.java:2702)
    edu.udo.scaffoldhunter.model.dataimport.Importer$MergeWorker.doInBackground(Importer.java:454)
    edu.udo.scaffoldhunter.model.dataimport.Importer$MergeWorker.doInBackground(Importer.java:401)
    edu.udo.scaffoldhunter.gui.util.SwingWorker$1.call(SwingWorker.java:308)
    java.util.concurrent.FutureTask.run(Unknown Source)
    edu.udo.scaffoldhunter.gui.util.SwingWorker$2.run(SwingWorker.java:315)
    edu.udo.scaffoldhunter.gui.util.SwingWorker.run(SwingWorker.java:354)
    java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    java.lang.Thread.run(Unknown Source)

    Jun 01, 2017 3:22:12 PM edu.udo.scaffoldhunter.gui.util.ProgressWorker done
    WARNUNG: Executing worker failed:
    java.util.concurrent.ExecutionException: edu.udo.scaffoldhunter.model.db.DatabaseException: An error occured during merging.
    at java.util.concurrent.FutureTask.report(Unknown Source)
    at java.util.concurrent.FutureTask.get(Unknown Source)
    at edu.udo.scaffoldhunter.gui.util.SwingWorker.get(SwingWorker.java:576)
    at edu.udo.scaffoldhunter.gui.util.ProgressWorker.done(ProgressWorker.java:159)
    at edu.udo.scaffoldhunter.gui.util.SwingWorker$4.run(SwingWorker.java:713)
    at edu.udo.scaffoldhunter.gui.util.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:858)
    at edu.udo.scaffoldhunter.gui.util.AccumulativeRunnable.run(AccumulativeRunnable.java:113)
    at edu.udo.scaffoldhunter.gui.util.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:880)
    at javax.swing.Timer.fireActionPerformed(Unknown Source)
    at javax.swing.Timer$DoPostEvent.run(Unknown Source)
    at java.awt.event.InvocationEvent.dispatch(Unknown Source)
    at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    at java.awt.EventQueue.access$500(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.WaitDispatchSupport$2.run(Unknown Source)
    at java.awt.WaitDispatchSupport$4.run(Unknown Source)
    at java.awt.WaitDispatchSupport$4.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.WaitDispatchSupport.enter(Unknown Source)
    at java.awt.Dialog.show(Unknown Source)
    at java.awt.Component.show(Unknown Source)
    at java.awt.Component.setVisible(Unknown Source)
    at java.awt.Window.setVisible(Unknown Source)
    at java.awt.Dialog.setVisible(Unknown Source)
    at edu.udo.scaffoldhunter.model.dataimport.Importer.runImport(Importer.java:302)
    at edu.udo.scaffoldhunter.gui.datasetmanagement.DatasetManagement.newDatasetDialog(DatasetManagement.java:103)
    at edu.udo.scaffoldhunter.gui.datasetmanagement.DatasetAndTreeManagerDialog$NewDatasetAction.actionPerformed(DatasetAndTreeManagerDialog.java:536)
    at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
    at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
    at java.awt.Component.processMouseEvent(Unknown Source)
    at javax.swing.JComponent.processMouseEvent(Unknown Source)
    at java.awt.Component.processEvent(Unknown Source)
    at java.awt.Container.processEvent(Unknown Source)
    at java.awt.Component.dispatchEventImpl(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Window.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    at java.awt.EventQueue.access$500(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.awt.EventQueue$4.run(Unknown Source)
    at java.awt.EventQueue$4.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.WaitDispatchSupport$2.run(Unknown Source)
    at java.awt.WaitDispatchSupport$4.run(Unknown Source)
    at java.awt.WaitDispatchSupport$4.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.WaitDispatchSupport.enter(Unknown Source)
    at java.awt.Dialog.show(Unknown Source)
    at java.awt.Component.show(Unknown Source)
    at java.awt.Component.setVisible(Unknown Source)
    at java.awt.Window.setVisible(Unknown Source)
    at java.awt.Dialog.setVisible(Unknown Source)
    at edu.udo.scaffoldhunter.gui.datasetmanagement.DatasetManagement.showDatasetAndTreeManager(DatasetManagement.java:83)
    at edu.udo.scaffoldhunter.gui.dialogs.SessionDialog$ManageDatasetsAction.actionPerformed(SessionDialog.java:581)
    at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
    at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
    at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source)
    at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
    at java.awt.Component.processMouseEvent(Unknown Source)
    at javax.swing.JComponent.processMouseEvent(Unknown Source)
    at java.awt.Component.processEvent(Unknown Source)
    at java.awt.Container.processEvent(Unknown Source)
    at java.awt.Component.dispatchEventImpl(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
    at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
    at java.awt.Container.dispatchEventImpl(Unknown Source)
    at java.awt.Window.dispatchEventImpl(Unknown Source)
    at java.awt.Component.dispatchEvent(Unknown Source)
    at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    at java.awt.EventQueue.access$500(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.awt.EventQueue$4.run(Unknown Source)
    at java.awt.EventQueue$4.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.WaitDispatchSupport$2.run(Unknown Source)
    at java.awt.WaitDispatchSupport$4.run(Unknown Source)
    at java.awt.WaitDispatchSupport$4.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.WaitDispatchSupport.enter(Unknown Source)
    at java.awt.Dialog.show(Unknown Source)
    at java.awt.Component.show(Unknown Source)
    at java.awt.Component.setVisible(Unknown Source)
    at java.awt.Window.setVisible(Unknown Source)
    at java.awt.Dialog.setVisible(Unknown Source)
    at edu.udo.scaffoldhunter.gui.GUIController.showSessionDialog(GUIController.java:698)
    at edu.udo.scaffoldhunter.gui.GUIController.createStartingState(GUIController.java:542)
    at edu.udo.scaffoldhunter.gui.GUIController.access$200(GUIController.java:99)
    at edu.udo.scaffoldhunter.gui.GUIController$1Start$1.finished(GUIController.java:163)
    at edu.udo.scaffoldhunter.gui.GUIController$1Start$1.finished(GUIController.java:155)
    at edu.udo.scaffoldhunter.util.ProgressSupport.finished(ProgressSupport.java:62)
    at edu.udo.scaffoldhunter.gui.util.ProgressWorker$5.run(ProgressWorker.java:135)
    at edu.udo.scaffoldhunter.gui.util.ProgressWorker.finished(ProgressWorker.java:139)
    at edu.udo.scaffoldhunter.gui.util.ProgressWorker.done(ProgressWorker.java:198)
    at edu.udo.scaffoldhunter.gui.util.SwingWorker$4.run(SwingWorker.java:713)
    at edu.udo.scaffoldhunter.gui.util.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:858)
    at edu.udo.scaffoldhunter.gui.util.AccumulativeRunnable.run(AccumulativeRunnable.java:113)
    at edu.udo.scaffoldhunter.gui.util.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:880)
    at javax.swing.Timer.fireActionPerformed(Unknown Source)
    at javax.swing.Timer$DoPostEvent.run(Unknown Source)
    at java.awt.event.InvocationEvent.dispatch(Unknown Source)
    at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
    at java.awt.EventQueue.access$500(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.awt.EventQueue$3.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
    at java.awt.EventQueue.dispatchEvent(Unknown Source)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
    at java.awt.EventDispatchThread.run(Unknown Source)
    Caused by: edu.udo.scaffoldhunter.model.db.DatabaseException: An error occured during merging.
    at edu.udo.scaffoldhunter.model.db.DbManagerHibernate.mergeMoleculesIntoDBbySMILES(DbManagerHibernate.java:2715)
    at edu.udo.scaffoldhunter.model.dataimport.Importer$MergeWorker.doInBackground(Importer.java:454)
    at edu.udo.scaffoldhunter.model.dataimport.Importer$MergeWorker.doInBackground(Importer.java:401)
    at edu.udo.scaffoldhunter.gui.util.SwingWorker$1.call(SwingWorker.java:308)
    at java.util.concurrent.FutureTask.run(Unknown Source)
    at edu.udo.scaffoldhunter.gui.util.SwingWorker$2.run(SwingWorker.java:315)
    at edu.udo.scaffoldhunter.gui.util.SwingWorker.run(SwingWorker.java:354)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
    at java.lang.Thread.run(Unknown Source)
    Caused by: org.hibernate.exception.DataException: could not execute statement
    at org.hibernate.exception.internal.SQLExceptionTypeDelegate.convert(SQLExceptionTypeDelegate.java:69)
    at org.hibernate.exception.internal.StandardSQLExceptionConverter.convert(StandardSQLExceptionConverter.java:49)
    at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:126)
    at org.hibernate.engine.jdbc.spi.SqlExceptionHelper.convert(SqlExceptionHelper.java:112)
    at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:211)
    at org.hibernate.id.IdentityGenerator$GetGeneratedKeysDelegate.executeAndExtract(IdentityGenerator.java:96)
    at org.hibernate.id.insert.AbstractReturningDelegate.performInsert(AbstractReturningDelegate.java:58)
    at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3032)
    at org.hibernate.persister.entity.AbstractEntityPersister.insert(AbstractEntityPersister.java:3558)
    at org.hibernate.action.internal.EntityIdentityInsertAction.execute(EntityIdentityInsertAction.java:98)
    at org.hibernate.engine.spi.ActionQueue.execute(ActionQueue.java:490)
    at org.hibernate.engine.spi.ActionQueue.addResolvedEntityInsertAction(ActionQueue.java:195)
    at org.hibernate.engine.spi.ActionQueue.addInsertAction(ActionQueue.java:179)
    at org.hibernate.engine.spi.ActionQueue.addAction(ActionQueue.java:214)
    at org.hibernate.event.internal.AbstractSaveEventListener.addInsertAction(AbstractSaveEventListener.java:324)
    at org.hibernate.event.internal.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:288)
    at org.hibernate.event.internal.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:194)
    at org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:125)
    at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:209)
    at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:194)
    at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.performSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:114)
    at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:90)
    at org.hibernate.internal.SessionImpl.fireSaveOrUpdate(SessionImpl.java:684)
    at org.hibernate.internal.SessionImpl.saveOrUpdate(SessionImpl.java:676)
    at org.hibernate.engine.spi.CascadingActions$5.cascade(CascadingActions.java:235)
    at org.hibernate.engine.internal.Cascade.cascadeToOne(Cascade.java:350)
    at org.hibernate.engine.internal.Cascade.cascadeAssociation(Cascade.java:293)
    at org.hibernate.engine.internal.Cascade.cascadeProperty(Cascade.java:161)
    at org.hibernate.engine.internal.Cascade.cascade(Cascade.java:118)
    at org.hibernate.event.internal.AbstractSaveEventListener.cascadeBeforeSave(AbstractSaveEventListener.java:432)
    at org.hibernate.event.internal.AbstractSaveEventListener.performSaveOrReplicate(AbstractSaveEventListener.java:265)
    at org.hibernate.event.internal.AbstractSaveEventListener.performSave(AbstractSaveEventListener.java:194)
    at org.hibernate.event.internal.AbstractSaveEventListener.saveWithGeneratedId(AbstractSaveEventListener.java:125)
    at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.saveWithGeneratedOrRequestedId(DefaultSaveOrUpdateEventListener.java:209)
    at org.hibernate.event.internal.DefaultSaveEventListener.saveWithGeneratedOrRequestedId(DefaultSaveEventListener.java:55)
    at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.entityIsTransient(DefaultSaveOrUpdateEventListener.java:194)
    at org.hibernate.event.internal.DefaultSaveEventListener.performSaveOrUpdate(DefaultSaveEventListener.java:49)
    at org.hibernate.event.internal.DefaultSaveOrUpdateEventListener.onSaveOrUpdate(DefaultSaveOrUpdateEventListener.java:90)
    at org.hibernate.internal.SessionImpl.fireSave(SessionImpl.java:715)
    at org.hibernate.internal.SessionImpl.save(SessionImpl.java:707)
    at org.hibernate.internal.SessionImpl.save(SessionImpl.java:702)
    at sun.reflect.GeneratedMethodAccessor19.invoke(Unknown Source)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
    at java.lang.reflect.Method.invoke(Unknown Source)
    at org.hibernate.context.internal.ThreadLocalSessionContext$TransactionProtectionWrapper.invoke(ThreadLocalSessionContext.java:356)
    at com.sun.proxy.$Proxy2.save(Unknown Source)
    at edu.udo.scaffoldhunter.model.db.DbManagerHibernate.mergeMoleculesIntoDBbySMILES(DbManagerHibernate.java:2702)
    ... 9 more
    Caused by: com.mysql.jdbc.MysqlDataTruncation: Data truncation: Incorrect string value: '\xEF\xBF\xBD" y...' for column 'string' at row 1
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3591)
    at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3525)
    at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1986)
    at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2140)
    at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2626)
    at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:2111)
    at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2407)
    at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2325)
    at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:2310)
    at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.executeUpdate(ResultSetReturnImpl.java:208)
    ... 51 more

     

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