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Saving file throws exception #6102

Closed
Tracked by #8750
ilippert opened this issue Mar 11, 2020 · 11 comments · Fixed by #9067
Closed
Tracked by #8750

Saving file throws exception #6102

ilippert opened this issue Mar 11, 2020 · 11 comments · Fixed by #9067
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@koppor
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bug Confirmed bugs or reports that are very likely to be bugs export / save
Milestone
v5.8

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@ilippert
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ilippert commented Mar 11, 2020 •
edited by stefan-kolb
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I saved my file, and got this exception. I cannot repeat this.

JabRef 5.0--2020-03-09--6bff936
Linux 5.5.8-200.fc31.x86_64 amd64
Java 13.0.2

Inspired by the discussion at #4877 I like to contribute the fact that my file system is a LVM partition with a cache.

Caused by: java.nio.file.NoSuchFileException: /home/ilippert/Documents/Studies/Publications&Products/Resources/Literature-bibtex.bib.tmp -> /home/ilippert/Documents/Studies/Publications&Products/Resources/Literature-bibtex.bib at
Log File org.jabref.logic.exporter.SaveException: Problems saving: at org.jabref/org.jabref.gui.exporter.SaveDatabaseAction.saveDatabase(Unknown Source) at org.jabref/org.jabref.gui.exporter.SaveDatabaseAction.doSave(Unknown Source) at org.jabref/org.jabref.gui.exporter.SaveDatabaseAction.save(Unknown Source) at org.jabref/org.jabref.gui.exporter.SaveDatabaseAction.save(Unknown Source) at org.jabref/org.jabref.gui.exporter.SaveAction.execute(Unknown Source) at org.jabref/org.jabref.gui.actions.JabRefAction.lambda$new$2(Unknown Source) at org.jabref.merged.module/org.controlsfx.control.action.Action.handle(Unknown Source) at org.jabref.merged.module/org.controlsfx.control.action.Action.handle(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source) at org.jabref.merged.module/javafx.event.Event.fireEvent(Unknown Source) at org.jabref.merged.module/javafx.scene.control.MenuItem.fire(Unknown Source) at org.jabref.merged.module/com.sun.javafx.scene.control.ControlAcceleratorSupport.lambda$doAcceleratorInstall$1(Unknown Source) at org.jabref.merged.module/com.sun.javafx.scene.KeyboardShortcutsHandler.processAccelerators(Unknown Source) at org.jabref.merged.module/com.sun.javafx.scene.KeyboardShortcutsHandler.dispatchBubblingEvent(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source) at org.jabref.merged.module/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source) at org.jabref.merged.module/javafx.event.Event.fireEvent(Unknown Source) at org.jabref.merged.module/javafx.scene.Scene$KeyHandler.process(Unknown Source) at org.jabref.merged.module/javafx.scene.Scene.processKeyEvent(Unknown Source) at org.jabref.merged.module/javafx.scene.Scene$ScenePeerListener.keyEvent(Unknown Source) at org.jabref.merged.module/com.sun.javafx.tk.quantum.GlassViewEventHandler$KeyEventNotification.run(Unknown Source) at org.jabref.merged.module/com.sun.javafx.tk.quantum.GlassViewEventHandler$KeyEventNotification.run(Unknown Source) at java.base/java.security.AccessController.doPrivileged(Unknown Source) at org.jabref.merged.module/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleKeyEvent$1(Unknown Source) at org.jabref.merged.module/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source) at org.jabref.merged.module/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleKeyEvent(Unknown Source) at org.jabref.merged.module/com.sun.glass.ui.View.handleKeyEvent(Unknown Source) at org.jabref.merged.module/com.sun.glass.ui.View.notifyKey(Unknown Source) at org.jabref.merged.module/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method) at org.jabref.merged.module/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) Caused by: java.nio.file.NoSuchFileException: /home/ilippert/Documents/Studies/Publications&Products/Resources/Literature-bibtex.bib.tmp -> /home/ilippert/Documents/Studies/Publications&Products/Resources/Literature-bibtex.bib at java.base/sun.nio.fs.UnixException.translateToIOException(Unknown Source) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown Source) at java.base/sun.nio.fs.UnixCopyFile.move(Unknown Source) at java.base/sun.nio.fs.UnixFileSystemProvider.move(Unknown Source) at java.base/java.nio.file.Files.move(Unknown Source) at org.jabref/org.jabref.logic.exporter.AtomicFileOutputStream.close(Unknown Source) at java.base/sun.nio.cs.StreamEncoder.implClose(Unknown Source) at java.base/sun.nio.cs.StreamEncoder.close(Unknown Source) at java.base/java.io.OutputStreamWriter.close(Unknown Source) at org.jabref/org.jabref.logic.exporter.BibDatabaseWriter.savePartOfDatabase(Unknown Source) at org.jabref/org.jabref.logic.exporter.BibDatabaseWriter.saveDatabase(Unknown Source) ... 42 more
@koppor
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koppor commented Mar 12, 2020

Could the file be saved at the end or is it corrupted?

@ilippert
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ilippert commented Mar 12, 2020 via email

@stefan-kolb stefan-kolb added the bug Confirmed bugs or reports that are very likely to be bugs label Mar 14, 2020
@stefan-kolb stefan-kolb mentioned this issue Mar 14, 2020
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@ilippert
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ilippert commented Apr 15, 2020 •
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I have not experienced the issue for a long time anymore

JabRef 5.1--2020-04-14--e86d415
Linux 5.5.15-200.fc31.x86_64 amd64
Java 14.0.1

@ilippert ilippert mentioned this issue May 9, 2020
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@ilippert ilippert mentioned this issue Jul 12, 2020
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@ilippert
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these days I have been seeing the phenomenon again - the same as in #4877 (comment) I guess?

@Siedlerchr
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Siedlerchr commented Jul 12, 2020 •
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The problem lies here:

jabref/src/main/java/org/jabref/logic/exporter/AtomicFileOutputStream.java

Line 196 in 4e220f6

Files.move(temporaryFile, targetFile, StandardCopyOption.ATOMIC_MOVE, StandardCopyOption.REPLACE_EXISTING);

And I finally found the root cause. It's a threading problem when you have austosave enabled and at the same time manually hit save.
The Autosave Backup manager also calls the writer.close method, through a different path.
The problem is that the backup manager invokes this method in

jabref/src/main/java/org/jabref/logic/exporter/BibDatabaseWriter.java

Line 221 in 7cc5747

writer.close();

We somehow need a way to lock that or cancel the save operation when already one is active. The other problem is that always a new object instance of the Writer or Save Action is created. I tried some locking in the cleanup
@koppor @tobiasdiez any ideas?
File based locking will not work on unix.

@tobiasdiez
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What about writing to a unique temporary file (in the users temporary file folder, with some random name)? Then you don't need to worry about locking etc (since the move command is atomic).

Moreover, I think, it's time to finally remove the BackupManager stuff...simply make a copy of the bib file upon loading a library (and say keep the last 10 versions). We run into so many problems with the backup stuff and it's a pretty old concept anyway.

@ilippert
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I see mozilla and others simply writing to /tmp/ - i do not know whether that is possible for all unixes. but it would make sense to me.

in case the BackupManager is to keep x versions, I would say: let the user define x. I suggest so because many users will have already other backup/versioning software and might constrain x to 1; and other might like a higher number of backup versions.

@Siedlerchr Siedlerchr added this to the v5.1 milestone Jul 17, 2020
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@tobiasdiez The backup manager is not that problem it's the autosave manager.
change anything in a field. Autosave is triggered. Now hit a manual save repeatedly
The autosave manager also calls the writer.close in the savePartOfDatabase which then triggers the file moving. However, as it's a move, the original file is already moved.

I also discovered an issue with the FileOutputStream locking. Trying to check that

@tobiasdiez
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Yeah I understand, that's why I suggested that every write process should have their own temporary file.

@koppor koppor modified the milestones: v5.1, v5.2 Jul 27, 2020
@Siedlerchr Siedlerchr mentioned this issue Sep 1, 2020
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@koppor koppor modified the milestones: v5.2, v5.3 Dec 7, 2020
@koppor koppor modified the milestones: v5.3, v5.4 Jun 7, 2021
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ilippert commented Aug 8, 2021 •
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JabRef 5.3--2021-07-16--c99d61c
Linux 5.13.7-200.fc34.x86_64 amd64
Java 16.0.1
JavaFX 16+8

Let me add this exception I got a moment ago - might be related

Log File org.jabref.logic.exporter.SaveException: Problems saving: java.nio.file.NoSuchFileException: /home/il/Documents/Studies/Publications&Products/Resources/Literature-bibtex.bib.tmp -> /home/il/Documents/Studies/Publications&Products/Resources/Literature-bibtex.bib at org.jabref@5.3.21/org.jabref.gui.exporter.SaveDatabaseAction.saveDatabase(Unknown Source) at org.jabref@5.3.21/org.jabref.gui.exporter.SaveDatabaseAction.save(Unknown Source) at org.jabref@5.3.21/org.jabref.gui.exporter.SaveDatabaseAction.save(Unknown Source) at org.jabref@5.3.21/org.jabref.gui.exporter.SaveDatabaseAction.save(Unknown Source) at org.jabref@5.3.21/org.jabref.gui.exporter.SaveAction.execute(Unknown Source) at org.jabref@5.3.21/org.jabref.gui.actions.JabRefAction.lambda$new$3(Unknown Source) at org.jabref.merged.module@5.3.21/org.controlsfx.control.action.Action.handle(Unknown Source) at org.jabref.merged.module@5.3.21/org.controlsfx.control.action.Action.handle(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source) at org.jabref.merged.module@5.3.21/javafx.event.Event.fireEvent(Unknown Source) at org.jabref.merged.module@5.3.21/javafx.scene.control.MenuItem.fire(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.scene.control.ControlAcceleratorSupport.lambda$doAcceleratorInstall$1(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.scene.KeyboardShortcutsHandler.processAccelerators(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.scene.KeyboardShortcutsHandler.dispatchBubblingEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source) at org.jabref.merged.module@5.3.21/javafx.event.Event.fireEvent(Unknown Source) at org.jabref.merged.module@5.3.21/javafx.scene.Scene$KeyHandler.process(Unknown Source) at org.jabref.merged.module@5.3.21/javafx.scene.Scene.processKeyEvent(Unknown Source) at org.jabref.merged.module@5.3.21/javafx.scene.Scene$ScenePeerListener.keyEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.tk.quantum.GlassViewEventHandler$KeyEventNotification.run(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.tk.quantum.GlassViewEventHandler$KeyEventNotification.run(Unknown Source) at java.base/java.security.AccessController.doPrivileged(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleKeyEvent$1(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleKeyEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.glass.ui.View.handleKeyEvent(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.glass.ui.View.notifyKey(Unknown Source) at org.jabref.merged.module@5.3.21/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method) at org.jabref.merged.module@5.3.21/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) Caused by: java.nio.file.NoSuchFileException: /home/il/Documents/Studies/Publications&Products/Resources/Literature-bibtex.bib.tmp -> /home/il/Documents/Studies/Publications&Products/Resources/Literature-bibtex.bib at java.base/sun.nio.fs.UnixException.translateToIOException(Unknown Source) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown Source) at java.base/sun.nio.fs.UnixCopyFile.move(Unknown Source) at java.base/sun.nio.fs.UnixFileSystemProvider.move(Unknown Source) at java.base/java.nio.file.Files.move(Unknown Source) at org.jabref@5.3.21/org.jabref.logic.exporter.AtomicFileOutputStream.close(Unknown Source) at java.base/sun.nio.cs.StreamEncoder.implClose(Unknown Source) at java.base/sun.nio.cs.StreamEncoder.close(Unknown Source) at java.base/java.io.OutputStreamWriter.close(Unknown Source) at org.jabref@5.3.21/org.jabref.logic.exporter.BibDatabaseWriter.savePartOfDatabase(Unknown Source) at org.jabref@5.3.21/org.jabref.logic.exporter.BibDatabaseWriter.saveDatabase(Unknown Source) ... 42 more

@koppor koppor assigned koppor and unassigned Siedlerchr Aug 16, 2021
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CouldBeThis commented Aug 26, 2021 •
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Hi, I thought I would let you know that I was having a similar error but I managed to fix it.

I was creating a new library. The problem in my case was that I had an emoji (🌱) in path of "main file directory". There is an & still in the directory name with no issue.

(You will think that using emojis in file names is a stupid thing to do but I am a very visual person and having cues makes using the computer much, much easier especially when in the command line. It causes surprisingly few problems but occasionally there is something. Especially with non-native applications.)

Although it doesn't look like the others above do such ridiculous things as I do, maybe it'll be some kind of useful hint.

Thanks for the software. :)

org.jabref.logic.exporter.SaveException: Problems saving: java.nio.file.NoSuchFileException: /Volumes/HDD02/Files/� Writing & Research/_JabRef/_BibFiles/Untitled..bib.tmp
	at org.jabref@5.3.60000/org.jabref.gui.exporter.SaveDatabaseAction.saveDatabase(Unknown Source)
	at org.jabref@5.3.60000/org.jabref.gui.exporter.SaveDatabaseAction.save(Unknown Source)
	at org.jabref@5.3.60000/org.jabref.gui.exporter.SaveDatabaseAction.saveAs(Unknown Source)
	at org.jabref@5.3.60000/org.jabref.gui.exporter.SaveDatabaseAction.save(Unknown Source)
	at org.jabref@5.3.60000/org.jabref.gui.exporter.SaveDatabaseAction.save(Unknown Source)
	at org.jabref@5.3.60000/org.jabref.gui.exporter.SaveAction.execute(Unknown Source)
	at org.jabref@5.3.60000/org.jabref.gui.actions.JabRefAction.lambda$new$3(Unknown Source)
	at org.jabref.merged.module@5.3.60000/org.controlsfx.control.action.Action.handle(Unknown Source)
	at org.jabref.merged.module@5.3.60000/org.controlsfx.control.action.Action.handle(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/javafx.event.Event.fireEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/javafx.scene.control.MenuItem.fire(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.scene.control.GlobalMenuAdapter.lambda$bindMenuItemProperties$2(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/javafx.event.Event.fireEvent(Unknown Source)
	at org.jabref.merged.module@5.3.60000/javafx.scene.control.MenuItem.fire(Unknown Source)
	at org.jabref.merged.module@5.3.60000/com.sun.javafx.tk.quantum.GlassSystemMenu$1.action(Unknown Source)
Caused by: java.nio.file.NoSuchFileException: /Volumes/HDD02/Files/� Writing & Research/_JabRef/_BibFiles/Untitled..bib.tmp
	at java.base/sun.nio.fs.UnixException.translateToIOException(Unknown Source)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown Source)
	at java.base/sun.nio.fs.UnixException.rethrowAsIOException(Unknown Source)
	at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(Unknown Source)
	at java.base/java.nio.file.spi.FileSystemProvider.newOutputStream(Unknown Source)
	at java.base/java.nio.file.Files.newOutputStream(Unknown Source)
	at org.jabref@5.3.60000/org.jabref.logic.exporter.AtomicFileOutputStream.<init>(Unknown Source)
	at org.jabref@5.3.60000/org.jabref.logic.exporter.AtomicFileWriter.<init>(Unknown Source)
	... 29 more

JabRef 5.3--2021-07-05--50c96a2
Mac OS X 10.14.6 x86_64
Java 16.0.1
JavaFX 16+8

Edit: I was closing the tabs from solving this problem and noticed noticed one I had opened from a search but didn't get to reading: Problem Saving Library - Help - Forum - JabRef

the real cause is a bit hidden in the log:

You have a missing opening curly brace somewhere in this entry:

Error in field ‘TITLE of entry Urpietal2016’: Unescaped ‘}’ character without opening bracket ends string prematurely. Field value: Dynamic simulation of CO{_2}-injection-induced fault rupture with slip-rate dependent friction coefficient

which sounds similar.

@koppor koppor modified the milestones: v5.4, v6.0 Dec 6, 2021
@koppor koppor modified the milestones: v6.0, v5.6 Feb 18, 2022
@koppor koppor modified the milestones: v5.6, v5.7 Mar 28, 2022
@koppor koppor mentioned this issue May 2, 2022
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14 tasks
@ThiloteE ThiloteE modified the milestones: v5.7, v5.8 Jul 14, 2022
@koppor koppor mentioned this issue Aug 16, 2022
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@koppor koppor moved this to Done in Prioritization Nov 10, 2022
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bug Confirmed bugs or reports that are very likely to be bugs export / save
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v5.8
7 participants
@Siedlerchr @koppor @stefan-kolb @tobiasdiez @ilippert @CouldBeThis @ThiloteE