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Can't save bibliography after a false "modified by another program" message. #7909

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wujastyk opened this issue Jul 14, 2021 · 4 comments · Fixed by #9067
Closed
1 task done

Can't save bibliography after a false "modified by another program" message. #7909

wujastyk opened this issue Jul 14, 2021 · 4 comments · Fixed by #9067

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@wujastyk
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wujastyk commented Jul 14, 2021 •
edited by calixtus
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JabRef 5.3--2021-07-12--b6a287f
Linux 5.4.0-77-generic amd64
Java 16.0.1
JavaFX 16+8

Steps to reproduce the behavior:

  1. edited an entry
  2. tried to save file
  3. got the error message in the snapshot below. The library was not modified by another program! I was just working in JabRef.

image

Log File 
java.lang.NullPointerException: Cannot invoke "org.jabref.gui.mergeentries.MergeEntries.getMergeEntry()" because "this.mergePanel" is null
  at org.jabref@5.3.16/org.jabref.gui.collab.EntryChangeViewModel.makeChange(Unknown Source)
  at org.jabref@5.3.16/org.jabref.gui.collab.ChangeDisplayDialog.lambda$new$2(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.control.Dialog.setResultAndClose(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.control.DialogPane.lambda$createButton$3(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.event.Event.fireEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.Node.fireEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.control.Button.fire(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.scene.control.inputmap.InputMap.handle(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.event.Event.fireEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.Scene$MouseHandler.process(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.Scene.processMouseEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.Scene$ScenePeerListener.mouseEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
  at java.base/java.security.AccessController.doPrivileged(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.glass.ui.View.handleMouseEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.glass.ui.View.notifyMouse(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.glass.ui.gtk.GtkApplication.enterNestedEventLoopImpl(Native Method)
  at org.jabref.merged.module@5.3.16/com.sun.glass.ui.gtk.GtkApplication._enterNestedEventLoop(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.glass.ui.Application.enterNestedEventLoop(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.glass.ui.EventLoop.enter(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.tk.quantum.QuantumToolkit.enterNestedEventLoop(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.stage.Stage.showAndWait(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.control.HeavyweightDialog.showAndWait(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.control.Dialog.showAndWait(Unknown Source)
  at org.jabref@5.3.16/org.jabref.gui.JabRefDialogService.showCustomDialogAndWait(Unknown Source)
  at org.jabref@5.3.16/org.jabref.gui.collab.DatabaseChangePane.lambda$onDatabaseChanged$1(Unknown Source)
  at org.jabref.merged.module@5.3.16/org.controlsfx.control.action.Action.handle(Unknown Source)
  at org.jabref.merged.module@5.3.16/org.controlsfx.control.action.Action.handle(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.event.Event.fireEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.Node.fireEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.control.Button.fire(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.scene.control.inputmap.InputMap.handle(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.event.Event.fireEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.Scene$MouseHandler.process(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.Scene.processMouseEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/javafx.scene.Scene$ScenePeerListener.mouseEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
  at java.base/java.security.AccessController.doPrivileged(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.glass.ui.View.handleMouseEvent(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.glass.ui.View.notifyMouse(Unknown Source)
  at org.jabref.merged.module@5.3.16/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
  at org.jabref.merged.module@5.3.16/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source)
  at java.base/java.lang.Thread.run(Unknown Source)
@S1r0hub
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S1r0hub commented Oct 25, 2021

Got this problem as well and found another related issue: #4877
In my case it had to do with line breaks in comments but some report similar behaviour for other attribute fields.

Try to set Options -> Preferences -> File -> Newline separator from CR/LF to LF.
After that, consider to restart JabRef. This worked for me and maybe it does for you as well.

@Siedlerchr
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Thanks for the analysis, I think this gives us some hints!

@damnms
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damnms commented Oct 26, 2021 •
edited
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same problem here jabref-5.3.60000-1.x86_64 fedora

when ever i change the .bib file outside of jabref, i get this exception, very annoying :/

@Siedlerchr
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Fixed by #9067

@ThiloteE ThiloteE mentioned this issue Aug 17, 2022
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AtomicFileOutputStream does not overwrite file if exception occurred during write JabRef/jabref
4 participants
@Siedlerchr @wujastyk @S1r0hub @damnms