NullPointerException when deleting many entries

1. Load up a bibliography file with about 1,000 references.
2. Select all the entries.
3. Press the Delete key.
4. Confirm, if prompted.

22:18:58.081 [AWT-EventQueue-0] ERROR org.jabref.FallbackExceptionHandler - Uncaught exception occurred in Thread[AWT-EventQueue-0,6,main]
java.lang.NullPointerException: null
	at com.sun.javafx.text.PrismTextLayout.layout(PrismTextLayout.java:1209) ~[jfxrt.jar:?]
	at com.sun.javafx.text.PrismTextLayout.ensureLayout(PrismTextLayout.java:223) ~[jfxrt.jar:?]
	at com.sun.javafx.text.PrismTextLayout.getBounds(PrismTextLayout.java:246) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.getLogicalBounds(Text.java:358) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.getYRendering(Text.java:1069) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.access$4400(Text.java:95) ~[jfxrt.jar:?]
	at javafx.scene.text.Text$TextAttribute$11.computeValue(Text.java:1785) ~[jfxrt.jar:?]
	at javafx.scene.text.Text$TextAttribute$11.computeValue(Text.java:1777) ~[jfxrt.jar:?]
	at javafx.beans.binding.ObjectBinding.get(ObjectBinding.java:153) ~[jfxrt.jar:?]
	at javafx.beans.binding.ObjectExpression.getValue(ObjectExpression.java:50) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase.get(ObjectPropertyBase.java:132) ~[jfxrt.jar:?]
	at com.sun.javafx.scene.control.skin.TextFieldSkin.lambda$new$412(TextFieldSkin.java:233) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:137) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase.fireValueChangedEvent(ObjectPropertyBase.java:105) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:112) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase.access$000(ObjectPropertyBase.java:51) ~[jfxrt.jar:?]
	at javafx.beans.property.ObjectPropertyBase$Listener.invalidated(ObjectPropertyBase.java:233) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:137) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) ~[jfxrt.jar:?]
	at javafx.beans.binding.ObjectBinding.invalidate(ObjectBinding.java:172) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.impl_geomChanged(Text.java:769) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.needsTextLayout(Text.java:194) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.needsFullTextLayout(Text.java:189) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.access$200(Text.java:95) ~[jfxrt.jar:?]
	at javafx.scene.text.Text$2.invalidated(Text.java:389) ~[jfxrt.jar:?]
	at javafx.beans.property.StringPropertyBase.markInvalid(StringPropertyBase.java:109) ~[jfxrt.jar:?]
	at javafx.beans.property.StringPropertyBase.access$000(StringPropertyBase.java:49) ~[jfxrt.jar:?]
	at javafx.beans.property.StringPropertyBase$Listener.invalidated(StringPropertyBase.java:230) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:137) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) ~[jfxrt.jar:?]
	at javafx.beans.binding.StringBinding.invalidate(StringBinding.java:171) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.BindingHelperObserver.invalidated(BindingHelperObserver.java:51) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:349) ~[jfxrt.jar:?]
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) ~[jfxrt.jar:?]
	at javafx.scene.control.TextInputControl$TextProperty.fireValueChangedEvent(TextInputControl.java:1389) ~[jfxrt.jar:?]
	at javafx.scene.control.TextInputControl$TextProperty.markInvalid(TextInputControl.java:1393) ~[jfxrt.jar:?]
	at javafx.scene.control.TextInputControl$TextProperty.set(TextInputControl.java:1324) ~[jfxrt.jar:?]
	at javafx.scene.control.TextInputControl.setText(TextInputControl.java:349) ~[jfxrt.jar:?]
	at org.jabref.gui.search.GlobalSearchBar.clearSearch(GlobalSearchBar.java:328) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.search.GlobalSearchBar.performSearch(GlobalSearchBar.java:356) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.BasePanel$SearchListener.listen(BasePanel.java:2101) ~[JabRef-4.3.1.jar:?]
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[?:1.8.0_201]
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[?:1.8.0_201]
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[?:1.8.0_201]
	at java.lang.reflect.Method.invoke(Method.java:498) ~[?:1.8.0_201]
	at com.google.common.eventbus.Subscriber.invokeSubscriberMethod(Subscriber.java:87) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber$SynchronizedSubscriber.invokeSubscriberMethod(Subscriber.java:144) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber$1.run(Subscriber.java:72) ~[JabRef-4.3.1.jar:?]
	at com.google.common.util.concurrent.MoreExecutors$DirectExecutor.execute(MoreExecutors.java:398) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Subscriber.dispatchEvent(Subscriber.java:67) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.Dispatcher$PerThreadQueuedDispatcher.dispatch(Dispatcher.java:108) ~[JabRef-4.3.1.jar:?]
	at com.google.common.eventbus.EventBus.post(EventBus.java:212) ~[JabRef-4.3.1.jar:?]
	at org.jabref.model.database.BibDatabase.removeEntry(BibDatabase.java:252) ~[JabRef-4.3.1.jar:?]
	at org.jabref.model.database.BibDatabase.removeEntry(BibDatabase.java:236) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.BasePanel.delete(BasePanel.java:837) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.BasePanel.delete(BasePanel.java:803) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.BasePanel.lambda$setupActions$4(BasePanel.java:401) ~[JabRef-4.3.1.jar:?]
	at org.jabref.gui.BasePanel.runCommand(BasePanel.java:1075) [JabRef-4.3.1.jar:?]
	at org.jabref.gui.JabRefFrame$GeneralAction.actionPerformed(JabRefFrame.java:2054) [JabRef-4.3.1.jar:?]
	at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022) [?:1.8.0_201]
	at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348) [?:1.8.0_201]
	at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) [?:1.8.0_201]
	at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) [?:1.8.0_201]
	at javax.swing.AbstractButton.doClick(AbstractButton.java:376) [?:1.8.0_201]
	at javax.swing.AbstractButton.doClick(AbstractButton.java:356) [?:1.8.0_201]
	at javax.swing.plaf.basic.BasicMenuItemUI$Actions.actionPerformed(BasicMenuItemUI.java:811) [?:1.8.0_201]
	at javax.swing.SwingUtilities.notifyAction(SwingUtilities.java:1668) [?:1.8.0_201]
	at javax.swing.JComponent.processKeyBinding(JComponent.java:2882) [?:1.8.0_201]
	at javax.swing.JMenuBar.processBindingForKeyStrokeRecursive(JMenuBar.java:699) [?:1.8.0_201]
	at javax.swing.JMenuBar.processBindingForKeyStrokeRecursive(JMenuBar.java:706) [?:1.8.0_201]
	at javax.swing.JMenuBar.processBindingForKeyStrokeRecursive(JMenuBar.java:706) [?:1.8.0_201]
	at javax.swing.JMenuBar.processKeyBinding(JMenuBar.java:677) [?:1.8.0_201]
	at javax.swing.KeyboardManager.fireBinding(KeyboardManager.java:307) [?:1.8.0_201]
	at javax.swing.KeyboardManager.fireKeyboardAction(KeyboardManager.java:293) [?:1.8.0_201]
	at javax.swing.JComponent.processKeyBindingsForAllComponents(JComponent.java:2974) [?:1.8.0_201]
	at javax.swing.JComponent.processKeyBindings(JComponent.java:2966) [?:1.8.0_201]
	at javax.swing.JComponent.processKeyEvent(JComponent.java:2845) [?:1.8.0_201]
	at java.awt.Component.processEvent(Component.java:6316) [?:1.8.0_201]
	at java.awt.Container.processEvent(Container.java:2239) [?:1.8.0_201]
	at java.awt.Component.dispatchEventImpl(Component.java:4889) [?:1.8.0_201]
	at java.awt.Container.dispatchEventImpl(Container.java:2297) [?:1.8.0_201]
	at java.awt.Component.dispatchEvent(Component.java:4711) [?:1.8.0_201]
	at java.awt.KeyboardFocusManager.redispatchEvent(KeyboardFocusManager.java:1954) [?:1.8.0_201]
	at java.awt.DefaultKeyboardFocusManager.dispatchKeyEvent(DefaultKeyboardFocusManager.java:835) [?:1.8.0_201]
	at java.awt.DefaultKeyboardFocusManager.preDispatchKeyEvent(DefaultKeyboardFocusManager.java:1103) [?:1.8.0_201]
	at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(DefaultKeyboardFocusManager.java:974) [?:1.8.0_201]
	at java.awt.DefaultKeyboardFocusManager.dispatchEvent(DefaultKeyboardFocusManager.java:800) [?:1.8.0_201]
	at java.awt.Component.dispatchEventImpl(Component.java:4760) [?:1.8.0_201]
	at java.awt.Container.dispatchEventImpl(Container.java:2297) [?:1.8.0_201]
	at java.awt.Window.dispatchEventImpl(Window.java:2746) [?:1.8.0_201]
	at java.awt.Component.dispatchEvent(Component.java:4711) [?:1.8.0_201]
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760) [?:1.8.0_201]
	at java.awt.EventQueue.access$500(EventQueue.java:97) [?:1.8.0_201]
	at java.awt.EventQueue$3.run(EventQueue.java:709) [?:1.8.0_201]
	at java.awt.EventQueue$3.run(EventQueue.java:703) [?:1.8.0_201]
	at java.security.AccessController.doPrivileged(Native Method) [?:1.8.0_201]
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) [?:1.8.0_201]
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84) [?:1.8.0_201]
	at java.awt.EventQueue$4.run(EventQueue.java:733) [?:1.8.0_201]
	at java.awt.EventQueue$4.run(EventQueue.java:731) [?:1.8.0_201]
	at java.security.AccessController.doPrivileged(Native Method) [?:1.8.0_201]
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74) [?:1.8.0_201]
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:730) [?:1.8.0_201]
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205) [?:1.8.0_201]
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [?:1.8.0_201]
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [?:1.8.0_201]
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [?:1.8.0_201]
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [?:1.8.0_201]
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [?:1.8.0_201]
22:18:58.755 [JavaFX Application Thread] ERROR org.jabref.FallbackExceptionHandler - Uncaught exception occurred in Thread[JavaFX Application Thread,5,main]
java.lang.NullPointerException: null
	at com.sun.javafx.text.PrismTextLayout.getBounds(PrismTextLayout.java:283) ~[jfxrt.jar:?]
	at javafx.scene.text.Text.impl_computeGeomBounds(Text.java:1198) ~[jfxrt.jar:?]
	at javafx.scene.Node.updateGeomBounds(Node.java:3577) ~[jfxrt.jar:?]
	at javafx.scene.Node.getGeomBounds(Node.java:3530) ~[jfxrt.jar:?]
	at javafx.scene.Node.getLocalBounds(Node.java:3478) ~[jfxrt.jar:?]
	at javafx.scene.Node.updateTxBounds(Node.java:3641) ~[jfxrt.jar:?]
	at javafx.scene.Node.getTransformedBounds(Node.java:3424) ~[jfxrt.jar:?]
	at javafx.scene.Node.updateBounds(Node.java:559) ~[jfxrt.jar:?]
	at javafx.scene.Parent.updateBounds(Parent.java:1717) ~[jfxrt.jar:?]
	at javafx.scene.Parent.updateBounds(Parent.java:1717) ~[jfxrt.jar:?]
	at javafx.scene.Scene$ScenePulseListener.pulse(Scene.java:2404) ~[jfxrt.jar:?]
	at com.sun.javafx.tk.Toolkit.lambda$runPulse$34(Toolkit.java:398) ~[jfxrt.jar:?]
	at java.security.AccessController.doPrivileged(Native Method) ~[?:1.8.0_201]
	at com.sun.javafx.tk.Toolkit.runPulse(Toolkit.java:397) ~[jfxrt.jar:?]
	at com.sun.javafx.tk.Toolkit.firePulse(Toolkit.java:424) ~[jfxrt.jar:?]
	at com.sun.javafx.tk.quantum.QuantumToolkit.pulse(QuantumToolkit.java:518) ~[jfxrt.jar:?]
	at com.sun.javafx.tk.quantum.QuantumToolkit.pulse(QuantumToolkit.java:498) ~[jfxrt.jar:?]
	at com.sun.javafx.tk.quantum.QuantumToolkit.pulseFromQueue(QuantumToolkit.java:491) ~[jfxrt.jar:?]
	at com.sun.javafx.tk.quantum.QuantumToolkit.lambda$runToolkit$291(QuantumToolkit.java:319) ~[jfxrt.jar:?]
	at com.sun.glass.ui.InvokeLaterDispatcher$Future.run(InvokeLaterDispatcher.java:95) ~[jfxrt.jar:?]
	at com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method) ~[jfxrt.jar:?]
	at com.sun.glass.ui.gtk.GtkApplication.lambda$null$203(GtkApplication.java:139) ~[jfxrt.jar:?]
	at java.lang.Thread.run(Thread.java:748) [?:1.8.0_201]

[AEgit]

Please report which operating system, JabRef version and Java version you are using.
Help -> About JabRef -> Copy Version

• Arch Linux (Manjaro)
• JabRef 4.3.1 (latest build)

It may be an older version of Java (like 8u40), which I can confirm this later.

[AEgit]

Please try the latest development version:
https://builds.jabref.org/master/

Do not forget to create a backup of your JabRef literature database, before installing the development version (since it still has some known bugs).

$ ./JabRef 
Error: could not find libjava.so
Error: Could not find Java SE Runtime Environment.
$ command -v java
/opt/jdk/bin/java
$ java -version
java version "1.8.0_201"
Java(TM) SE Runtime Environment (build 1.8.0_201-b09)
Java HotSpot(TM) 64-Bit Server VM (build 25.201-b09, mixed mode)
$ echo $JAVA_HOME
/opt/jdk
$ echo $PATH
/opt/context/tex/texmf-linux-64/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/opt/jdk/bin
$ locate -i libjava.so
/opt/jdk-12.0.1/lib/libjava.so
/opt/jdk1.8.0_201/jre/lib/amd64/libjava.so
$ ls -lad /opt/jdk*
lrwxrwxrwx 1 user user   12 Jun 25 18:49 /opt/jdk -> jdk1.8.0_201
drwxr-xr-x 8 user user 4096 Jun 25 17:34 /opt/jdk-12.0.1
drwxr-xr-x 7 user user 4096 Dec 15  2018 /opt/jdk1.8.0_201
$ export LD_LIBRARY_PATH=$JAVA_HOME/jre/lib/amd64
$ echo $LD_LIBRARY_PATH
/opt/jdk/jre/lib/amd64
$ ls $LD_LIBRARY_PATH/libjava.*
/opt/jdk/jre/lib/amd64/libjava.so
$ ./JabRef 
Error: could not find libjava.so
Error: Could not find Java SE Runtime Environment.

Is there a standalone JAR file available?

[koppor]

Refs #5410 - maybe, this is fixed by the refactorings by @NorwayMaple

[koppor]

@davejarvis We have a linux archive available at http://builds.jabref.org/master/ - just unzip it. - I don't quite see above whether you did that. We do not ship a fat jar anymore since from Java 11 on the JRE should be adapted to the application (and we ship the JRE)

[abepolk]

Refs #5410 - maybe, this is fixed by the refactorings by @NorwayMaple

The only difference my refactorings would change is that GlobalSearchBar.performSearch would be executed only once rather than 1000 times. Not sure if this would help.

mkdir -p $HOME/archives
cd $HOME/archives
wget http://builds.jabref.org/master/JabRef-portable_linux.tar.gz
cd $HOME/bin
tar xf ~/archives/JabRef-portable_linux.tar.gz
cd JabRef/bin
$ ./JabRef 
Error: could not find libjava.so
Error: Could not find Java SE Runtime Environment.

[Siedlerchr]

Thank you for reporting this issue. We think, that is already fixed in our development version and consequently the change will be included in the next release.

We would like to ask you to use a development build from https://builds.jabref.org/master and report back if it works for you. Please remember to make a backup of your library before trying-out this version.