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Uncaught Exception occurred in Thread[JavaFX Application Thread,5,main] #5446

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juejung opened this issue Oct 14, 2019 · 27 comments · Fixed by #5451
Closed

Uncaught Exception occurred in Thread[JavaFX Application Thread,5,main] #5446

juejung opened this issue Oct 14, 2019 · 27 comments · Fixed by #5451
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bug Confirmed bugs or reports that are very likely to be bugs entry-editor
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@juejung
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juejung commented Oct 14, 2019

JabRef version
JabRef 5.0.0-dev--2019-10-14----824b10363
Linux 5.0.0-31-generic amd64
Java 12.0.2
on Linux 18.04 installed from .deb file downloaded from https://builds.jabref.org/master/jabref_5.0.0-1_amd64.deb

Steps to reproduce the behavior:

  1. Open JabRef with .bib file
  2. Double click on entry to open entry editor
  3. Exception is thrown
Log File
java.lang.NullPointerException
  at org.jabref/org.jabref.gui.fieldeditors.FieldEditors.getSuggestionProvider(Unknown Source)
  at org.jabref/org.jabref.gui.fieldeditors.FieldEditors.getForField(Unknown Source)
  at org.jabref/org.jabref.gui.entryeditor.FieldsEditorTab.setupPanel(Unknown Source)
  at org.jabref/org.jabref.gui.entryeditor.FieldsEditorTab.bindToEntry(Unknown Source)
  at org.jabref/org.jabref.gui.entryeditor.EntryEditorTab.notifyAboutFocus(Unknown Source)
  at org.jabref/org.jabref.gui.entryeditor.EntryEditor.lambda$new$0(Unknown Source)
  at org.jabref.merged.module/org.fxmisc.easybind.EasyBind.lambda$subscribe$12(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.binding.ExpressionHelper$SingleChange.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module/javafx.beans.property.ReadOnlyObjectPropertyBase.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module/javafx.beans.property.ReadOnlyObjectWrapper.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module/javafx.beans.property.ObjectPropertyBase.markInvalid(Unknown Source)
  at org.jabref.merged.module/javafx.beans.property.ObjectPropertyBase.set(Unknown Source)
  at org.jabref.merged.module/javafx.scene.control.SelectionModel.setSelectedItem(Unknown Source)
  at org.jabref.merged.module/javafx.scene.control.TabPane$TabPaneSelectionModel.select(Unknown Source)
  at org.jabref.merged.module/javafx.scene.control.TabPane$TabPaneSelectionModel.select(Unknown Source)
  at org.jabref.merged.module/javafx.scene.control.TabPane$TabPaneSelectionModel.findNearestAvailableTab(Unknown Source)
  at org.jabref.merged.module/javafx.scene.control.TabPane$TabPaneSelectionModel.lambda$new$0(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.collections.ListListenerHelper$Generic.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module/javafx.collections.ObservableListBase.fireChange(Unknown Source)
  at org.jabref.merged.module/javafx.collections.ListChangeBuilder.commit(Unknown Source)
  at org.jabref.merged.module/javafx.collections.ListChangeBuilder.endChange(Unknown Source)
  at org.jabref.merged.module/javafx.collections.ObservableListBase.endChange(Unknown Source)
  at org.jabref.merged.module/javafx.collections.ModifiableObservableListBase.add(Unknown Source)
  at org.jabref/org.jabref.gui.entryeditor.EntryEditor.recalculateVisibleTabs(Unknown Source)
  at org.jabref/org.jabref.gui.entryeditor.EntryEditor.setEntry(Unknown Source)
  at org.jabref/org.jabref.gui.BasePanel.lambda$createMainTable$21(Unknown Source)
  at java.base/java.util.Optional.ifPresent(Unknown Source)
  at org.jabref/org.jabref.gui.BasePanel.lambda$createMainTable$22(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.collections.ListListenerHelper$Generic.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module/javafx.collections.ObservableListBase.fireChange(Unknown Source)
  at org.jabref.merged.module/javafx.collections.ListChangeBuilder.commit(Unknown Source)
  at org.jabref.merged.module/javafx.collections.ListChangeBuilder.endChange(Unknown Source)
  at org.jabref.merged.module/javafx.collections.ObservableListBase.endChange(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.scene.control.SelectedItemsReadOnlyObservableList.lambda$new$1(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.collections.ListListenerHelper$Generic.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(Unknown Source)
  at org.jabref.merged.module/javafx.collections.ObservableListBase.fireChange(Unknown Source)
  at org.jabref.merged.module/javafx.collections.ListChangeBuilder.commit(Unknown Source)
  at org.jabref.merged.module/javafx.collections.ListChangeBuilder.endChange(Unknown Source)
  at org.jabref.merged.module/javafx.collections.ObservableListBase.endChange(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.scene.control.ReadOnlyUnbackedObservableList._endChange(Unknown Source)
  at org.jabref.merged.module/javafx.scene.control.MultipleSelectionModelBase$SelectedIndicesList._endChange(Unknown Source)
  at org.jabref.merged.module/javafx.scene.control.ControlUtils.updateSelectedIndices(Unknown Source)
  at org.jabref.merged.module/javafx.scene.control.TableView$TableViewArrayListSelectionModel.fireCustomSelectedCellsListChangeEvent(Unknown Source)
  at org.jabref.merged.module/javafx.scene.control.TableView$TableViewArrayListSelectionModel.clearAndSelect(Unknown Source)
  at org.jabref.merged.module/javafx.scene.control.TableView$TableViewSelectionModel.clearAndSelect(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.scene.control.behavior.TableCellBehaviorBase.simpleSelect(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.scene.control.behavior.TableCellBehaviorBase.doSelect(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.scene.control.behavior.CellBehaviorBase.mousePressed(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.scene.control.inputmap.InputMap.handle(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(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.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.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.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.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.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.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.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$MouseHandler.process(Unknown Source)
  at org.jabref.merged.module/javafx.scene.Scene.processMouseEvent(Unknown Source)
  at org.jabref.merged.module/javafx.scene.Scene$ScenePeerListener.mouseEvent(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
  at java.base/java.security.AccessController.doPrivileged(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)
  at org.jabref.merged.module/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(Unknown Source)
  at org.jabref.merged.module/com.sun.glass.ui.View.handleMouseEvent(Unknown Source)
  at org.jabref.merged.module/com.sun.glass.ui.View.notifyMouse(Unknown Source)
  at org.jabref.merged.module/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
  at org.jabref.merged.module/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source)
  at java.base/java.lang.Thread.run(Unknown Source)

@tobiasdiez tobiasdiez added this to the v5.0 milestone Oct 14, 2019
@Siedlerchr Siedlerchr added the bug Confirmed bugs or reports that are very likely to be bugs label Oct 14, 2019
@Siedlerchr
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Could confirm this under windows, too:

  1. Create a new biblatex library
  2. Paste a doi
  3. Double click to open the entry editor

@AEgit
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AEgit commented Oct 15, 2019

JabRef 5.0.0-dev--2019-10-14----d2ddff574
Windows 10 10.0 amd64
Java 12.0.2

I can confirm this issue as well.

@j0hannes
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JabRef 5.0.0-dev--2019-10-14----d2ddff574
Linux 5.3.6-arch1-1-arch amd64
Java 12.0.2

@tobiasdiez
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This should be fixed in the latest development version. Could you please check the build from http://builds.jabref.org/master/. Thanks! Please remember to make a backup of your library before trying-out this version.

@j0hannes
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Now Java just crashed when starting Jabref, core dump attached.

hs_err_pid78360.log

Note that "The crash happened outside the Java Virtual Machine in native code."

@Siedlerchr
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Siedlerchr commented Oct 16, 2019

The exception is thrown from some network/proxy detection class in the VM. Do you maybe have an old instance of java or jabref lurking around?

@j0hannes
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I have Java 12.0.2 and the JabRef version from today.

@juejung
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juejung commented Oct 16, 2019

@tobiasdiez Thanks, it works again under:
Ubuntu 18.04 with Gnome desktop with the latest .deb build.

JabRef 5.0.0-dev--2019-10-16----e36daae20
Linux 5.0.0-31-generic amd64
Java 12.0.2

@j0hannes
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@Siedlerchr, you were right, the problem's gone now.

@AEgit
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AEgit commented Oct 17, 2019

JabRef 5.0.0-dev--2019-10-17----e81d58c51
Windows 10 10.0 amd64
Java 12.0.2

Can confirm that the issue is fixed in the current development version.

@YetiXie1994
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how to fix it?

@antonallote
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I am getting this exception still in 2021..

@AEgit
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AEgit commented Feb 13, 2021

You need to report which JabRef version you are using.

@quade-butler
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quade-butler commented May 20, 2021

JabRef 5.2--2020-12-24--6a2a512
Windows 10 10.0 amd64
Java 14.0.2

I am also running into this issue. It is only occurring with one of my libraries and not any others.
LogFile.txt

@AEgit
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AEgit commented May 20, 2021

Have you tried the latest dev build?
https://builds.jabref.org/main/

Remember to make a backup of your JabRef database before installing the current development version.

@quade-butler
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@AEgit I tried the dev build and it appears to be working fine now! Thanks.

@AEgit
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AEgit commented May 20, 2021

Cheers!

@phyzhenli
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This should be fixed in the latest development version. Could you please check the build from http://builds.jabref.org/master/. Thanks! Please remember to make a backup of your library before trying-out this version.

This version is OK.

@petersaly
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Hi All,

I have just installed version JabRef 5.10 as 'phyzhenli' suggested that works. Unfortunately it does not work. The error message sent is:

"Uncaught Exception occurred in Thread[#31,JavaFX Application Thread,5,main]
class java.lang.String cannot be cast to class java.lang.Boolen (java.lang.String and java.lang.Boolen are in module java.base of loader 'bootstrap')"

I use

Ubuntu 2204
JabRef 5.10
openjdk version "11.0.17" 2022-10-18.

JabRef version 5.3 worked fine.

Could anyone suggest a solution?

Thanks.

@ThiloteE
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ThiloteE commented Feb 23, 2023

Ubuntu 2204
JabRef 5.10
openjdk version "11.0.17" 2022-10-18.

@petersaly
JabRef comes with its own bundled version of JDK (if I remember correctly, JabRef 5.10 uses a customized version of jdk 19.xx). Which method did you use to install JabRef? Is this a snap/flatpak/deb or portable version? - See here: https://docs.jabref.org/installation

@Siedlerchr
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Can you past the whole stack trace/the whole content of the error message?
For your other issue https://docs.jabref.org/cite/openofficeintegration#known-issues

@petersaly
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Thank you for answering.

Meanwhile, I upgraded my opendk java to version 17. It was effectless, and it is understandable because ThiloteE writes that JabRef comes with its own bundled java version. It is OK. I did not know this information. Further, I downgraded to JabRef version 5.3, which version worked for me in last summer. However, this time version 5.3 also produced the same error. After that, I re-installed version 5.10.

I install JabRef versions from .deb package via GDebi package installer.

Here, I attach a text file with the details of the error message sent by version 5.10 and a screenshot
MessageDetails.txt
Screenshot_2023-02-24
:

@petersaly
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I have forgotten to write how to reproduce:

  1. Open an .odt or .doc document in LibreOffice
  2. Start Jabref
  3. Connect OpenOpenOffice/LibreOffice document
  4. Select an entry in your bibtex library
  5. Click 'Cite' button (or any other) in the OpenOpenOffice/LibreOffice panel

@ThiloteE
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Try:

The connection from JabRef to Libre Office requires some office related jar-archives to be present. For this, you have to install the package libreoffice-java-common.

in addition, you also could try to

  • reset your preferences
  • try the "Linux portable" from https://www.fosshub.com/JabRef.html. Not even once have I encountered any javafx version issues using the portable version of JabRef.

if the portable version works, we know it has something to do with your system or the gdebi package manager.

@Siedlerchr
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Hi, there seems to be something wrong with the OO style. Can you try to reset your preferences?

@petersaly
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Hi,

The package 'libreoffice-java-common' is installed on my computer.

Before I try the portable version, could give me some instruction how to reset my preferences, please?

@petersaly
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Dear All,

I have found out how to reset preferences: JabRef menu, Options -> the rightmost icon button in the left bottom corner "Reset preferences".

I have reset, and restarted JabRef 5.10. No error message. It works perfectly!

Thank you very much for your time and effort to help me and others.

Best regards,
petersaly

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