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Jabref freezes after merging of entries #3294

@g-mos

Description

@g-mos

JabRef version JabRef-4.1-dev--snapshot--2017-10-10--fix3235--a43057b72.jar on Ubuntu 16.04

I had a bibliography entry and I tried to update its info based on the doi. After I choose what to keep from which side the program freezes on the replace original entry. This has happened also before on previous 4.0 / 4.1 versions, but its the first time I have the dump file.
Additionally, irrelevant of the log file the db is a shared database also backed up on a local file.

Log File AI: INFO 12-10-2017 20:54, 20: Configuration file has been successfully found as resource 20:54:11.904 [AWT-EventQueue-0] INFO org.jabref.logic.importer.OpenDatabase - Opening: /xxx/xxx/xxx/Jabref.bib File: grouptree.fxml not found, attempting with camel case File: grouptree.css not found, attempting with camel case log4j:WARN No appenders could be found for logger (io.netty.util.internal.logging.InternalLoggerFactory). log4j:WARN Please initialize the log4j system properly. log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info. 21:02:17.214 [pool-3-thread-4] WARN org.jabref.logic.net.URLDownload - Fix SSL exceptions by accepting ALL certificates Oct 12, 2017 9:09:52 PM com.google.common.eventbus.EventBus$LoggingHandler handleException SEVERE: Exception thrown by subscriber method listen(org.jabref.model.entry.event.EntryChangedEvent) on subscriber org.jabref.gui.entryeditor.EntryEditor[,0,460,1605x406,layout=java.awt.BorderLayout,alignmentX=0.0,alignmentY=0.0,border=,flags=9,maximumSize=,minimumSize=,preferredSize=] when dispatching event: org.jabref.model.entry.event.FieldChangedEvent@42a4643b java.lang.IllegalStateException: Not on FX application thread; currentThread = AWT-EventQueue-0 at com.sun.javafx.tk.Toolkit.checkFxUserThread(Toolkit.java:236) at com.sun.javafx.tk.quantum.QuantumToolkit.checkFxUserThread(QuantumToolkit.java:423) at javafx.scene.Parent$2.onProposedChange(Parent.java:367) at com.sun.javafx.collections.VetoableListDecorator$VetoableSubListDecorator.clear(VetoableListDecorator.java:529) at com.sun.javafx.binding.ContentBinding$ListContentBinding.onChanged(ContentBinding.java:114) at org.reactfx.collection.ChangeListenerWrapper.onChange(LiveList.java:439) at org.reactfx.collection.ChangeListenerWrapper.onChange(LiveList.java:417) at org.reactfx.util.ListNotifications.lambda$takeHead$0(NotificationAccumulator.java:317) at org.reactfx.ObservableBase.notifyObservers(ObservableBase.java:68) at org.reactfx.ObservableBase.notifyObservers(ObservableBase.java:57) at org.reactfx.collection.MappedList.sourceChanged(MappedList.java:41) at org.reactfx.util.ListNotifications.lambda$takeHead$0(NotificationAccumulator.java:317) at org.reactfx.ObservableBase.notifyObservers(ObservableBase.java:68) at org.reactfx.collection.MemoizationListImpl$MemoizedView.publishNotifications(MemoizationList.java:58) at org.reactfx.collection.MemoizationListImpl$MemoizedView.access$300(MemoizationList.java:30) at org.reactfx.collection.MemoizationListImpl.sourceChanged(MemoizationList.java:89) at org.reactfx.util.ListNotifications.lambda$takeHead$0(NotificationAccumulator.java:317) at org.reactfx.ObservableBase.notifyObservers(ObservableBase.java:68) at org.reactfx.ObservableBase.notifyObservers(ObservableBase.java:57) at org.reactfx.collection.MappedList.sourceChanged(MappedList.java:41) at org.reactfx.util.ListNotifications.lambda$takeHead$0(NotificationAccumulator.java:317) at org.reactfx.ObservableBase.notifyObservers(ObservableBase.java:68) at org.reactfx.SuspendableBase.resume(SuspendableBase.java:64) at org.reactfx.CloseableOnceGuard.close(Guard.java:49) at org.reactfx.MultiGuard.close(Guard.java:83) at org.reactfx.Suspendable$1.resumeSource(Suspendable.java:118) at org.reactfx.Suspendable$1.suspendSource(Suspendable.java:104) at org.reactfx.util.NonAccumulativeStreamNotifications.lambda$head$0(NotificationAccumulator.java:134) at org.reactfx.ObservableBase.notifyObservers(ObservableBase.java:68) at org.reactfx.ObservableBase.notifyObservers(ObservableBase.java:57) at org.reactfx.ProperEventStream.emit(ProperEventStream.java:18) at org.reactfx.EventStreams$3.lambda$observeInputs$0(EventStreams.java:105) at org.reactfx.value.ChangeListenerWrapper.accept(Val.java:786) at org.reactfx.util.AbstractReducingStreamNotifications.lambda$head$0(NotificationAccumulator.java:248) at org.reactfx.ObservableBase.notifyObservers(ObservableBase.java:68) at org.reactfx.ObservableBase.notifyObservers(ObservableBase.java:57) at org.reactfx.value.ValBase.invalidate(ValBase.java:32) at org.reactfx.SuspendableBoolean.release(SuspendableBoolean.java:24) at org.reactfx.CloseableOnceGuard.close(Guard.java:49) at org.reactfx.Suspendable.suspendWhile(Suspendable.java:49) at org.fxmisc.richtext.model.GenericEditableStyledDocumentBase.update(GenericEditableStyledDocumentBase.java:222) at org.reactfx.util.Tuple3.exec(Tuple3.java:43) at org.fxmisc.richtext.model.GenericEditableStyledDocumentBase.replace(GenericEditableStyledDocumentBase.java:129) at org.fxmisc.richtext.model.SimpleEditableStyledDocument.replace(SimpleEditableStyledDocument.java:7) at org.fxmisc.richtext.GenericStyledArea.replace(GenericStyledArea.java:1302) at org.fxmisc.richtext.GenericStyledArea.replaceText(GenericStyledArea.java:1297) at org.fxmisc.richtext.model.EditActions.clear(EditActions.java:140) at org.jabref.gui.entryeditor.SourceTab.updateSourcePane(SourceTab.java:74) at org.jabref.gui.entryeditor.EntryEditor.listen(EntryEditor.java:237) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at com.google.common.eventbus.Subscriber.invokeSubscriberMethod(Subscriber.java:91) at com.google.common.eventbus.Subscriber$SynchronizedSubscriber.invokeSubscriberMethod(Subscriber.java:150) at com.google.common.eventbus.Subscriber$1.run(Subscriber.java:76) at com.google.common.util.concurrent.MoreExecutors$DirectExecutor.execute(MoreExecutors.java:399) at com.google.common.eventbus.Subscriber.dispatchEvent(Subscriber.java:71) at com.google.common.eventbus.Dispatcher$PerThreadQueuedDispatcher.dispatch(Dispatcher.java:116) at com.google.common.eventbus.EventBus.post(EventBus.java:217) at org.jabref.model.entry.BibEntry.setField(BibEntry.java:429) at org.jabref.model.entry.BibEntry.setField(BibEntry.java:448) at org.jabref.gui.mergeentries.MergeFetchedEntryDialog$ReplaceAction.actionPerformed(MergeFetchedEntryDialog.java:137) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252) at java.awt.Component.processMouseEvent(Component.java:6533) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6298) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4889) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2746) at java.awt.Component.dispatchEvent(Component.java:4711) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) at java.awt.EventQueue$4.run(EventQueue.java:731) at java.awt.EventQueue$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:109) at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:184) at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:229) at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:227) at java.security.AccessController.doPrivileged(Native Method) at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:227) at java.awt.Dialog.show(Dialog.java:1084) at java.awt.Component.show(Component.java:1671) at java.awt.Component.setVisible(Component.java:1623) at java.awt.Window.setVisible(Window.java:1014) at java.awt.Dialog.setVisible(Dialog.java:1005) at org.jabref.gui.mergeentries.FetchAndMergeWorker.done(FetchAndMergeWorker.java:67) at javax.swing.SwingWorker$5.run(SwingWorker.java:737) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:832) at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:112) at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:842) at javax.swing.Timer.fireActionPerformed(Timer.java:313) at javax.swing.Timer$DoPostEvent.run(Timer.java:245) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue$3.run(EventQueue.java:709) at java.awt.EventQueue$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) at java.awt.EventQueue.dispatchEvent(EventQueue.java:726) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

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