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.
Diff:
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