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Library has been modified => Crash #5124

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j0hannes opened this issue Jul 14, 2019 · 7 comments
Closed
1 task done

Library has been modified => Crash #5124

j0hannes opened this issue Jul 14, 2019 · 7 comments

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@j0hannes
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JabRef version 5.0-dev on Arch

Jabref tells me that "The library has been modified by another program." even if this is not the case. If I choose "Review changes", I see one entry for "Metadata change" and several hundreds of "Added entry". Clicking on "Metadata change" in the list shows "Metadata change" on the right where we usually differences are depicted. Clicking on any of the "Added entry" just gives no description. Accepting the "changes" will immediately lead to a new notification of changes, which, when accepted, give a null pointer exception.

Steps to reproduce the behavior:

  1. use Jabref
  2. problem will eventually occur after waking up from sleep mode or even spontaneously
Exception
java.lang.NullPointerException
  at javafx.collections.ListChangeBuilder.finalizeSubChange(ListChangeBuilder.java:552)
  at javafx.collections.ListChangeBuilder.finalizeSubChangeArray(ListChangeBuilder.java:546)
  at javafx.collections.ListChangeBuilder.commit(ListChangeBuilder.java:524)
  at javafx.collections.ListChangeBuilder.endChange(ListChangeBuilder.java:541)
  at javafx.collections.ObservableListBase.endChange(ObservableListBase.java:205)
  at javafx.collections.ModifiableObservableListBase.addAll(ModifiableObservableListBase.java:102)
  at javafx.collections.FXCollections$SynchronizedList.addAll(FXCollections.java:1049)
  at org.jabref.model.database.BibDatabase.insertEntries(BibDatabase.java:232)
  at org.jabref.model.database.BibDatabase.insertEntry(BibDatabase.java:206)
  at org.jabref.model.database.BibDatabase.insertEntry(BibDatabase.java:194)
  at org.jabref.gui.collab.EntryAddChangeViewModel.makeChange(EntryAddChangeViewModel.java:25)
  at org.jabref.gui.collab.ChangeDisplayDialog.lambda$new$393(ChangeDisplayDialog.java:58)
  at javafx.scene.control.Dialog.impl_setResultAndClose(Dialog.java:1026)
  at javafx.scene.control.DialogPane.lambda$createButton$3(DialogPane.java:777)
  at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
  at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
  at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
  at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
  at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
  at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
  at javafx.event.Event.fireEvent(Event.java:198)
  at javafx.scene.Node.fireEvent(Node.java:8413)
  at javafx.scene.control.Button.fire(Button.java:185)
  at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:182)
  at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(BehaviorSkinBase.java:96)
  at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(BehaviorSkinBase.java:89)
  at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
  at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
  at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
  at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
  at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
  at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
  at javafx.event.Event.fireEvent(Event.java:198)
  at javafx.scene.Scene$MouseHandler.process(Scene.java:3757)
  at javafx.scene.Scene$MouseHandler.access$1500(Scene.java:3485)
  at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1762)
  at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2494)
  at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:394)
  at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:295)
  at java.security.AccessController.doPrivileged(Native Method)
  at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:432)
  at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:389)
  at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:431)
  at com.sun.glass.ui.View.handleMouseEvent(View.java:555)
  at com.sun.glass.ui.View.notifyMouse(View.java:937)
  at com.sun.glass.ui.gtk.GtkApplication.enterNestedEventLoopImpl(Native Method)
  at com.sun.glass.ui.gtk.GtkApplication._enterNestedEventLoop(GtkApplication.java:211)
  at com.sun.glass.ui.Application.enterNestedEventLoop(Application.java:511)
  at com.sun.glass.ui.EventLoop.enter(EventLoop.java:107)
  at com.sun.javafx.tk.quantum.QuantumToolkit.enterNestedEventLoop(QuantumToolkit.java:590)
  at javafx.stage.Stage.showAndWait(Stage.java:474)
  at javafx.scene.control.HeavyweightDialog.showAndWait(HeavyweightDialog.java:162)
  at javafx.scene.control.Dialog.showAndWait(Dialog.java:341)
  at org.jabref.gui.collab.DatabaseChangePane.lambda$onDatabaseChanged$176(DatabaseChangePane.java:38)
  at org.controlsfx.control.action.Action.handle(Action.java:419)
  at org.controlsfx.control.action.Action.handle(Action.java:64)
  at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:86)
  at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
  at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
  at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
  at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:49)
  at javafx.event.Event.fireEvent(Event.java:198)
  at javafx.scene.Node.fireEvent(Node.java:8413)
  at javafx.scene.control.Button.fire(Button.java:185)
  at com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(ButtonBehavior.java:182)
  at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(BehaviorSkinBase.java:96)
  at com.sun.javafx.scene.control.skin.BehaviorSkinBase$1.handle(BehaviorSkinBase.java:89)
  at com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:218)
  at com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80)
  at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:238)
  at com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191)
  at com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56)
  at com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114)
  at com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74)
  at com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54)
  at javafx.event.Event.fireEvent(Event.java:198)
  at javafx.scene.Scene$MouseHandler.process(Scene.java:3757)
  at javafx.scene.Scene$MouseHandler.access$1500(Scene.java:3485)
  at javafx.scene.Scene.impl_processMouseEvent(Scene.java:1762)
  at javafx.scene.Scene$ScenePeerListener.mouseEvent(Scene.java:2494)
  at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:394)
  at com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(GlassViewEventHandler.java:295)
  at java.security.AccessController.doPrivileged(Native Method)
  at com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(GlassViewEventHandler.java:432)
  at com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:389)
  at com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(GlassViewEventHandler.java:431)
  at com.sun.glass.ui.View.handleMouseEvent(View.java:555)
  at com.sun.glass.ui.View.notifyMouse(View.java:937)
  at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
  at com.sun.glass.ui.gtk.GtkApplication.lambda$null$5(GtkApplication.java:139)
  at java.lang.Thread.run(Thread.java:748)
@AEgit
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AEgit commented Jul 14, 2019

I wonder whether all these issues are related/caused by the same problem:

#5085
#4143

@j0hannes
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Author

I opened a new issue since the other ones I found do neither describe/mention the weird list of "changes" nor the NullPointerException.

@AEgit
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AEgit commented Jul 14, 2019

Yes, I think it is correct to have a separate issue, since the problem you report is not exactly the same as the one mentioned in the other reports. But I wonder whether the issues are connected.

@j0hannes
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Another interesting observation is that every entry now exists several times after accepting the "changes". I think I have to start from scratch and rebuild that library, there's no point in trying to fix this in the current library.

@stefan-kolb
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@JabRef/developers Can anybody reproduce this problem? Otherwise, we need more detailed steps.

@j0hannes
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looks like this:

Screenshot_20190824_164453

@tobiasdiez
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Hopefully, this should be fixed in the latest development version. Could you please check the build from http://builds.jabref.org/master/. Thanks! Please remember to make a backup of your library before trying-out this version.

github-actions bot pushed a commit that referenced this issue Dec 1, 2020
a20406d Added name of the editors of a given edition (#5140)
9881fc5 Ping on push, not PR, document role of dist-updater (#5137)
04668cc Create nouvelles-perspectives-en-sciences-sociales.csl (#5063)
1d94e21 Update bursa-uludag-universitesi-saglik-bilimleri-enstitusu.csl (#5047)
84f3893 Add Harvard style for Metropolia University of Applied Sciences (#5086)
8e43e79 Create opto-electronic-advances.csl (#5135)
36e4fba Update society-for-american-archaeology.csl (#5124)
69ca360 St. Paul Canon Law new style (#5138)
b490ab0 Update and rename st-paul-university-faculty-of-canon-law.csl to saint-paul-university-faculty-of-canon-law.csl
b498116 There is no en-CA locale
3c35f28 Metadata
7059cca Create tu-dortmund-agvm.csl (#5088)
c321c98 Create new Citation type (#5093)
a7edc8d Update international-organization.csl (#5103)
3d1a052 The AWS load balancer is messing things up (#5133)
ca3839b Fix sort by a single macro (#5136)
5d1a7e8 Update chungara-revista-de-antropologia-chilena.csl (#5123)
cd75d5d ping distribution-updater (#5132)
dcf473a Update wirtschaftsuniversitat-wien-health-care-management.csl (#5125)
a87085e Fix Harvard Praxisforschung Editors (#5130)
d4176ca Switch automated tests to Github Actions (#5111)
726d0d8 Radiology, MPP, CORR -- small fixes: https://forums.zotero.org/discussion/85883/doi-radiology#latest https://forums.zotero.org/discussion/51058/style-request-molecular-plant-pathology#latest https://forums.zotero.org/discussion/85678/citing-style-clinical-orthopaedics-and-related-research#latest
e23db68 Update to la-trobe-university-harvard style (#5119)
c54b278 Create wirtschaftsuniversitat-wien-health-care-management.csl (#5110)
62fb019 Create austral-entomology.csl (#5118)
afa328c Update iso690-author-date-en.csl (#5113)
5468dce Update iso690-author-date-fr-no-abstract.csl (#5112)
98af86c Update iso690-numeric-fr.csl (#5115)
09f84c4 Update iso690-author-date-fr.csl (#5114)
178a9e4 Fix current biology to superscript
1fa5ce7 Create droit-belge-centre-de-droit-prive-ulb.csl (#5107)
3a6a4bc Fix file modes (#5106)
48f50e5 Create chungara-revista-de-antropologia-chilena.csl (#5096)
1e848f8 Create the-journal-of-the-indian-law-institute.csl (#5100)
856524c Create molecular-biology.csl (#5101)
eeebbf4 Create harvard-harper-adams-university.csl (#5104)
d90993d Fix tests
d4037bf WIP: St Paul Canon Law style

git-subtree-dir: src/main/resources/csl-styles
git-subtree-split: a20406d
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