Saving file throws exception

[ilippert]

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]

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

[ilippert]

It was saved.

…

On 12 March 2020 07:54:18 CET, Oliver Kopp ***@***.***> wrote: Could the file be saved at the end or is it corrupted? -- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: #6102 (comment)

-- Sent from my LineageOS device with K-9 Mail. Please excuse my brevity.

[ilippert]

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]

these days I have been seeing the phenomenon again - the same as in #4877 (comment) I guess?

[Siedlerchr]

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.