Opening a PDF blocks JabRef (under Ubuntu/Linux)

[ytzemih]

JabRef 5.0-beta.419--2020-02-12--3859620
Linux 5.4.19-050419-generic amd64
Java 13.0.2

• I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists

Steps to reproduce the behavior:

1. Click on the symbol to open a PDF linked to a bib entry (or use F4 or use the "Open menu" command from the context menu).
2. The PDF viewer (in my case MasterPDFEditor is associated with application/pdf) opens.
3. JabRef can only be used after the PDF viewer is closed again (in the screenshot JabRef is not properly rendered because the whole application is blocked).

I first thought this only happens in my i3/Gnome Flashback environment. But switching to plain Ubuntu 19.10 Gnome desktop, exactly the same behaviour can be observed.

This phenomenon didn't appear for me (with highly similar settings) in JabRef 4.x.

I am seeing this exception on the console after closing JabRef, though this might not result from having called an external program (I suppose):

Log File

Exception in Application stop method ERROR FallbackExceptionHandler Uncaught exception occurred in Thread[main,5,main] java.lang.RuntimeException: Exception in Application stop method at org.jabref.merged.module/com.sun.javafx.application.LauncherImpl.launchApplication1(Unknown Source) at org.jabref.merged.module/com.sun.javafx.application.LauncherImpl.lambda$launchApplication$2(Unknown Source) at java.base/java.lang.Thread.run(Unknown Source) Caused by: java.lang.IllegalAccessError: class kong.unirest.JsonObjectMapper (in module org.jabref.merged.module) cannot access class com.google.gson.Gson (in module com.google.gson) because module org.jabref.merged.module does not read module com.google.gson at org.jabref.merged.module/kong.unirest.JsonObjectMapper.(Unknown Source) at org.jabref.merged.module/kong.unirest.Config.(Unknown Source) at org.jabref.merged.module/kong.unirest.Unirest.(Unknown Source) at org.jabref/org.jabref.Globals.stopBackgroundTasks(Unknown Source) at org.jabref/org.jabref.JabRefMain.stop(Unknown Source) at org.jabref.merged.module/com.sun.javafx.application.LauncherImpl.lambda$launchApplication1$10(Unknown Source) at org.jabref.merged.module/com.sun.javafx.application.PlatformImpl.lambda$runAndWait$12(Unknown Source) at org.jabref.merged.module/com.sun.javafx.application.PlatformImpl.lambda$runLater$10(Unknown Source) at java.base/java.security.AccessController.doPrivileged(Unknown Source) at org.jabref.merged.module/com.sun.javafx.application.PlatformImpl.lambda$runLater$11(Unknown Source) at org.jabref.merged.module/com.sun.glass.ui.InvokeLaterDispatcher$Future.run(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) ... 1 more

[Siedlerchr]

@tobiasdiez You recently added this gson to the module info. Do we need to add it to the gradle file somehow?

[AEgit]

Might be a duplicate of (or connected to):
#5882

[ytzemih]

@AEgit, can be. However, in my case, I can work with the PDF and once I close the reader, JabRef continues to work perfectly. Also, in the meanwhile, CPU load is not going up. It merely looks like a blocking system call (external process call) to me, instead of a non-blocking call.

[Siedlerchr]

Have you tried opening with another pdf editor as default?

[ytzemih]

Yep, just done that with 5 different applications that can open PDF (via changing the mime-type through the Nautilus file manager):

1. It works (i.e. it open asynchronously) with Evince (default Ubuntu viewer) and with Firefox.
2. It doesn't work (i.e. it opens blocking) with MasterPDFEditor, Zathura (another PDF viewer), and LibreOffice.

The three apps in 2 must have something in common in the way they are called via JabRef based on the mime-type settings.

[Siedlerchr]

@ytzemih I tried a simple addition to the existing code, redirecting the process output. Could you please test this version here?
https://builds.jabref.org/pull/5945/merge/

[ytzemih]

@Siedlerchr, thx. Installed JabRef 5.0-pull-5945-merge.421--2020-02-13--6cddf64.
Unfortunately, nothing has changed. Actually, it got worse: Now, only Firefox works, but Zathura, LibreOffice, MasterPDFEditor, and Evince open in a blocking mode. Can there be an interference with Java 13.0.2 being part of JabRef (as by the credentials) and openjdk version "11.0.6" 2020-01-14 installed in my system?

[ytzemih]

Adding another screenshot to show that the problem also arises when using the context menu in the File field of the General tab to open the PDF.

In that case, my whole desktop environment is blocked. The only way to get out is Ctrl-Q to quit Evince. Maybe that helps further pinpointing the problem.

[Siedlerchr]

Thanks for the hint. I will try to wrap this in a new Thread this evening

[Siedlerchr]

Could you please try again with the new version? https://builds.jabref.org/pull/5945/merge/

[Siedlerchr]

The gson error should also be fixed in this branch + master

[AEgit]

JabRef 5.0-beta.421--2020-02-14--ec93ad3
Linux 5.3.0-28-generic amd64
Java 13.0.2

I am afraid, as far as I can tell, this issue persists (and this one persists as well: #5882).

[ytzemih]

JabRef 5.0-beta.421--2020-02-14--ec93ad3
Linux 5.4.19-050419-generic amd64
Java 13.0.2

Good news, gson error/exception is gone, no more Zombie jobs left.

Bad news: Can confirm @AEgit , opening still blocks for me.

[Siedlerchr]

@ytzemih Could you please test again with the new version from today? https://builds.jabref.org/pull/5945/merge/

[ytzemih]

@Siedlerchr Done. I can't reproduce the error anymore. Open file is now non-blocking. Thanks for the fix.

[AEgit]

JabRef 5.0-beta.432--2020-02-19--c768697
Linux 5.3.0-40-generic amd64
Java 13.0.2

Cannot confirm for the current master version. Since I am now pretty confident that this issue is a duplicate of #5882, you can find my error report here:
#5882 (comment)

[ytzemih]

@AEgit I tested it only with
JabRef 5.0-pull-5945-merge.440--2020-02-19--fcaeef1
Linux 5.4.19-050419-generic amd64
Java 13.0.2