<< Journal abbreviations with dot >>

icamps · June 1, 2022, 2:28pm

Hello,

When using journals abbreviations, I got always the abbreviations without the final dots afters each abbreviation.

Is it possible to change this to “force” the addition of dots after each abbreviated word?

For example, for the journal “Computer Physics Communications” I got “Comput Phys Commun” instead of “Comput. Phys. Commun.”

Regards,

Camps

ThiloteE · June 6, 2022, 11:25am

Hello

You can use custom abbreviations under options > preferences > Journal Abbreviations.

You could look up the folder of JabRef’s default list, copy / paste it and then change the second file to your liking. Then import the new file into JabRef via options > preferences > Journal Abbreviations.

For some reason I can’t just add a new abbreviation, but maybe that is because the JabRef default list can’t and is not supposed to be modified?

I have never used a custom abbreviation file before, so I would be happy, if you could report your findings back

Siedlerchr · June 6, 2022, 2:42pm

Hi,

the best way to change/fix abbreviations globally is here GitHub - JabRef/abbrv.jabref.org: A repository of abbreviations for references, e.g., for conferences, journals, institutes, etc.
Then they will make it into the next release.

icamps · June 23, 2022, 2:37pm

I created the file with all journals abbreviations with dots.

When added to JabRef, it take some time to process but after saving the preferences, closing and opened again, JabRef continue to use the built-in list (without dots).

Also, after adding a full journal name and click to change to abbreviations, I got a bunch of errors:


java.lang.RuntimeException: java.lang.reflect.InvocationTargetException
	at org.jabref.merged.module@5.6.60000/javafx.fxml.FXMLLoader$MethodHandler.invoke(Unknown Source)
	at org.jabref.merged.module@5.6.60000/javafx.fxml.FXMLLoader$ControllerMethodEventHandler.handle(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/javafx.event.Event.fireEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/javafx.scene.Node.fireEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/javafx.scene.control.Button.fire(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.scene.control.behavior.ButtonBehavior.mouseReleased(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.scene.control.inputmap.InputMap.handle(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventUtil.fireEventImpl(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.event.EventUtil.fireEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/javafx.event.Event.fireEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/javafx.scene.Scene$MouseHandler.process(Unknown Source)
	at org.jabref.merged.module@5.6.60000/javafx.scene.Scene.processMouseEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/javafx.scene.Scene$ScenePeerListener.mouseEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.tk.quantum.GlassViewEventHandler$MouseEventNotification.run(Unknown Source)
	at java.base/java.security.AccessController.doPrivileged(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleMouseEvent$2(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleMouseEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.glass.ui.View.handleMouseEvent(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.glass.ui.View.notifyMouse(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.glass.ui.gtk.GtkApplication._runLoop(Native Method)
	at org.jabref.merged.module@5.6.60000/com.sun.glass.ui.gtk.GtkApplication.lambda$runLoop$11(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)
Caused by: java.lang.reflect.InvocationTargetException
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
	at java.base/java.lang.reflect.Method.invoke(Unknown Source)
	at com.sun.javafx.reflect.Trampoline.invoke(Unknown Source)
	at jdk.internal.reflect.GeneratedMethodAccessor5.invoke(Unknown Source)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
	at java.base/java.lang.reflect.Method.invoke(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.reflect.MethodUtil.invoke(Unknown Source)
	at org.jabref.merged.module@5.6.60000/com.sun.javafx.fxml.MethodHelper.invoke(Unknown Source)
	... 87 more
Caused by: org.h2.mvstore.MVStoreException: Reading from file sun.nio.ch.FileChannelImpl@499f6e9b failed at 14125750 (length -1), read 0, remaining 1536 [2.1.212/1]
	at org.jabref.merged.module@5.6.60000/org.h2.mvstore.DataUtils.newMVStoreException(Unknown Source)
	at org.jabref.merged.module@5.6.60000/org.h2.mvstore.DataUtils.readFully(Unknown Source)
	at org.jabref.merged.module@5.6.60000/org.h2.mvstore.FileStore.readFully(Unknown Source)
	at org.jabref.merged.module@5.6.60000/org.h2.mvstore.Chunk.readBufferForPage(Unknown Source)
	at org.jabref.merged.module@5.6.60000/org.h2.mvstore.MVStore.readPage(Unknown Source)
	at org.jabref.merged.module@5.6.60000/org.h2.mvstore.MVMap.readPage(Unknown Source)
	at org.jabref.merged.module@5.6.60000/org.h2.mvstore.Page$NonLeaf.getChildPage(Unknown Source)
	at org.jabref.merged.module@5.6.60000/org.h2.mvstore.Page.get(Unknown Source)
	at org.jabref.merged.module@5.6.60000/org.h2.mvstore.MVMap.get(Unknown Source)
	at org.jabref.merged.module@5.6.60000/org.h2.mvstore.MVMap.get(Unknown Source)
	at org.jabref.merged.module@5.6.60000/org.h2.mvstore.MVMap.containsKey(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.logic.journals.JournalAbbreviationRepository.isKnownName(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.gui.fieldeditors.JournalEditorViewModel.toggleAbbreviation(Unknown Source)
	at org.jabref@5.6.60000/org.jabref.gui.fieldeditors.JournalEditor.toggleAbbreviation(Unknown Source)
	... 97 more
Caused by: java.nio.channels.ClosedChannelException
	at java.base/sun.nio.ch.FileChannelImpl.ensureOpen(Unknown Source)
	at java.base/sun.nio.ch.FileChannelImpl.read(Unknown Source)
	... 110 more

Siedlerchr · June 23, 2022, 3:07pm

@icamps Thanks for the log file. It seems the problem is related to the database JabRef uses to store these abbrevs. Something is interrupting the reading of the file.

Would it be possible to provide the journal abbrevs with dots somewhere for us to reproduce?

icamps · June 24, 2022, 11:52am

Hi @Siedlerchr , here is the link with my abbrevs: lamodel.unifal-mg.edu.br/downloads/journalList_dots.csv

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<< Journal abbreviations with dot >>

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