Automatically set file links throws java error that is not shown to the user in the GUI

[joelostblom]

When I click Automatically set file links, JabRef shows the progress bar for a long time (close to a minute) and then a small toast message says that it is done, but no links are found. The event log inside JabRef does not show anything, but when I check the terminal from which I launch JabRef, I see the java error ERROR AutoSetFileLinksUtil Problem finding files.

I figured this is because I don't have permission to access a folder on my system, but it took me a while to figure this out because I was launching jabref via my systems menu and neither the toast message or the event log showed that anything was awry. It was only when I launched from the terminal that I could figure out what was going on. It would be nice to somehow inform the user in the GUI that there has been an error.

Full error:

$ jabref
Picked up _JAVA_OPTIONS: -Dawt.useSystemAAFontSettings=on
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...

(JabRef:70588): Gdk-WARNING **: 11:51:12.817: XSetErrorHandler() called with a GDK error trap pushed. Don't do that.
ERROR AutoSetFileLinksUtil Problem finding files
 java.io.IOException: Problem in finding files
        at org.jabref/org.jabref.logic.util.io.CiteKeyBasedFileFinder.findFilesByExtension(Unknown Source)
        at org.jabref/org.jabref.logic.util.io.CiteKeyBasedFileFinder.findAssociatedFiles(Unknown Source)
        at org.jabref/org.jabref.gui.externalfiles.AutoSetFileLinksUtil.findAssociatedNotLinkedFiles(Unknown Source)
        at org.jabref/org.jabref.gui.externalfiles.AutoSetFileLinksUtil.linkAssociatedFiles(Unknown Source)
        at org.jabref/org.jabref.gui.externalfiles.AutoLinkFilesAction$1.call(Unknown Source)
        at org.jabref/org.jabref.gui.externalfiles.AutoLinkFilesAction$1.call(Unknown Source)
        at org.jabref.merged.module/javafx.concurrent.Task$TaskCallable.call(Unknown Source)
        at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
        at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
        at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
        at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
        at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
        at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.io.UncheckedIOException: java.nio.file.AccessDeniedException: /home/joel/gnupg2/crls.d
        at java.base/java.nio.file.FileTreeIterator.fetchNextIfNeeded(Unknown Source)
        at java.base/java.nio.file.FileTreeIterator.hasNext(Unknown Source)
        at java.base/java.util.Iterator.forEachRemaining(Unknown Source)
        at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source)
        at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source)
        at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source)
        at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(Unknown Source)
        at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source)
        at java.base/java.util.stream.ReferencePipeline.collect(Unknown Source)
        ... 13 more
Caused by: java.nio.file.AccessDeniedException: /home/joel/gnupg2/crls.d
        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.newDirectoryStream(Unknown Source)
        at java.base/java.nio.file.Files.newDirectoryStream(Unknown Source)
        at java.base/java.nio.file.FileTreeWalker.visit(Unknown Source)
        at java.base/java.nio.file.FileTreeWalker.next(Unknown Source)
        ... 22 more

I installed jabref via the AUR package jabref-latest:

JabRef 5.0-beta.382--2020-01-28--0b53d4b
Linux 5.4.14-arch1-1 amd64 
Java 13.0.2

[tobiasdiez]

The problem that errors are not shown in the error console but only in the terminal is a consequence of #5437
Nonetheless, in this particular case, I agree that the user should be properly informed about the error using an error dialog.

[rubenLindstrom]

Hi! @tobiasdiez
We're a team of 5 students currently attempting to make our first open source contribution, and chose this issue!

We're unfamiliar with JabRef, and are currently unable to recreate this issue. Could you please provide us a step by step for how to recreate it, so we can attempt to solve it?

All recommendations and tips are of course welcome!

Thanks!

[IfIWantedTo]

Hi @joelostblom, I am currently working on this as my first issue. Since I am very new to JabRef I don't quite know my way around yet. It would help me alot if you could give me directions on how to recreate the error. Only if you have the time and energy to do so of course.

[github-actions]

This issue has been inactive for half a year. Since JabRef is constantly evolving this issue may not be relevant any longer and it will be closed in two weeks if no further activity occurs.

As part of an effort to ensure that the JabRef team is focusing on important and valid issues, we would like to ask if you could update the issue if it still persists. This could be in the following form:

• If there has been a longer discussion, add a short summary of the most important points as a new comment (if not yet existing).
• Provide further steps or information on how to reproduce this issue.
• Upvote the initial post if you like to see it implemented soon. Votes are not the only metric that we use to determine the requests that are implemented, however, they do factor into our decision-making process.
• If all information is provided and still up-to-date, then just add a short comment that the issue is still relevant.

Thank you for your contribution!