Exception when saving files

Help
1

Hi everyone,

I have been using JabRef for a while now. Today I edited a bib file and the following exception happened when saving it:

org.jabref.logic.exporter.SaveException: Problems saving: java.io.FileNotFoundException: /home/fmachado/snap/jabref/1852/pvd.bib.tmp (Permission denied)
at org.jabref@5.8.60000/org.jabref.gui.exporter.SaveDatabaseAction.saveDatabase(Unknown Source)
at org.jabref@5.8.60000/org.jabref.gui.exporter.SaveDatabaseAction.save(Unknown Source)
at org.jabref@5.8.60000/org.jabref.gui.exporter.SaveDatabaseAction.saveAs(Unknown Source)
at org.jabref@5.8.60000/org.jabref.gui.exporter.SaveDatabaseAction.saveAs(Unknown Source)
at java.base/java.util.Optional.ifPresent(Unknown Source)
at org.jabref@5.8.60000/org.jabref.gui.exporter.SaveDatabaseAction.saveAs(Unknown Source)
at org.jabref@5.8.60000/org.jabref.gui.exporter.SaveAction.execute(Unknown Source)
at org.jabref@5.8.60000/org.jabref.gui.actions.JabRefAction.lambda$new$3(Unknown Source)
at org.jabref.merged.module@5.8.60000/org.controlsfx.control.action.Action.handle(Unknown Source)
at org.jabref.merged.module@5.8.60000/org.controlsfx.control.action.Action.handle(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/javafx.event.Event.fireEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/javafx.scene.control.MenuItem.fire(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.doSelect(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.scene.control.ContextMenuContent$MenuItemContainer.lambda$createChildren$12(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/javafx.event.Event.fireEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/javafx.scene.Scene$MouseHandler.process(Unknown Source)
at org.jabref.merged.module@5.8.60000/javafx.scene.Scene.processMouseEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/javafx.scene.Scene$ScenePeerListener.mouseEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
at java.base/java.security.AccessController.doPrivileged(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.glass.ui.View.handleMouseEvent(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.glass.ui.View.notifyMouse(Unknown Source)
at org.jabref.merged.module@5.8.60000/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
at org.jabref.merged.module@5.8.60000/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source)
at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.io.FileNotFoundException: /home/fmachado/snap/jabref/1852/pvd.bib.tmp (Permission denied)
at java.base/java.io.FileOutputStream.open0(Native Method)
at java.base/java.io.FileOutputStream.open(Unknown Source)
at java.base/java.io.FileOutputStream.(Unknown Source)
at java.base/java.io.FileOutputStream.(Unknown Source)
at org.jabref@5.8.60000/org.jabref.logic.exporter.AtomicFileOutputStream.(Unknown Source)
at org.jabref@5.8.60000/org.jabref.logic.exporter.AtomicFileWriter.(Unknown Source)
… 51 more

this is now happening for any new or old file I try to save. I have no idea what is going on, I hope somebody can help me.
Best,
Fabiana

2

Just tried it on my machine with newest (5.8) snap distribution on arch linux and worked.
Java is complaining that a tmp file could not be saved. Is the actual bib file save correctly?

May have something to do with the new backup manager not having the right app / tmp dir configured when using snap

3

Hi,

thanks for the report, Can you try to check if the home folder connection is correctly set up?

4

Hi Christoph, thanks for your reply

the home folder should be correct. It is weird that this is happening out of nowhere and to anything I try to do with JabRef…

5

Hi Carl,

all was working until this morning, now the same error occurs for old bib files and if I try to create new ones from scratch. I am using the program without any problems for almost a year now.

6

We made a new release last friday. Did your snap refresh today? Can you try to roll back with to 5.7 with snap? Can you try the linux portable version of JabRef (should work at least as a workaround - index - powered by h5ai v0.29.0 (https://larsjung.de/h5ai/) )?

7

By reverting to 5.7.6 I get to edit and save existing works, but if I create new ones and try save Jabref quits. I will try the portable version, should I uninstall the snap version before or it is irrelevant?

8

You don’t have to uninstall the snap version, though it might be confusing if you have two JabRef installs on your computer