Cannot add TeX macros to text fields

[wujastyk]

JabRef 5.0-dev--snapshot--2019-01-25--master--aa3657cac
Linux 4.15.0-43-generic amd64
Java 1.8.0_201

Steps to reproduce:

1. Trying to add a LaTeX command - \emph{} - in the Title field of the Editor
2. The typed text is deleted, with some other chars from the title text, and an error message pops up.

This is a general problem over all text fields.

Detail information:

Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Opening: /tmp/jabref8908283084044077187.bib
Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Could not generate BibEntry citation. The CSL engine could not create a preview for your item.
Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Opening: /tmp/jabref8908283084044077187.bib
Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Opening: /tmp/jabref8908283084044077187.bib
Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Opening: /tmp/jabref8908283084044077187.bib
Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Opening: /tmp/jabref8908283084044077187.bib
Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Opening: /tmp/jabref8908283084044077187.bib
Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Opening: /tmp/jabref8908283084044077187.bib
Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Opening: /tmp/jabref8908283084044077187.bib
Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Opening: /tmp/jabref8509673933137157696.bib
Opening: /home/dom/Dropbox/localtexmf/bibtex/bib/biblio4-utf8.bib
Uncaught exception occurred in Thread[pool-6-thread-1,5,main]
Uncaught exception occurred in Thread[JavaFX Application Thread,5,main]
Opening: /tmp/jabref8908283084044077187.bib
Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Opening: /tmp/jabref8908283084044077187.bib
Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib
Uncaught exception occurred in Thread[JavaFX Application Thread,5,main]
Uncaught exception occurred in Thread[pool-6-thread-1,5,main]

[Siedlerchr]

Hm seems to be a linux issue apparently, on windows I cannot reproduce this.
Could you please copy the whole stacktrace from the error log?

[wujastyk]

Is this the stacktrace? jabref-testversion 11:35:47.030 [JavaFX Application Thread] INFO org.jabref.logic.importer.OpenDatabase - Opening: /home/dom/Dropbox/localtexmf/bibtex/bib/biblio4-utf8.bib 11:35:48.289 [JavaFX Application Thread] INFO org.jabref.logic.importer.OpenDatabase - Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib 11:35:57.193 [JabRef LowPriorityCachedThreadPool] INFO org.jabref.logic.importer.OpenDatabase - Opening: /tmp/jabref3118246704378959765.bib 11:35:57.213 [JabRef LowPriorityCachedThreadPool] INFO org.jabref.logic.importer.OpenDatabase - Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib ANTLR Tool version 4.5.3 used for code generation does not match the current runtime version 4.7.2ANTLR Runtime version 4.5.3 used for parser compilation does not match the current runtime version 4.7.2ANTLR Tool version 4.5.3 used for code generation does not match the current runtime version 4.7.2ANTLR Runtime version 4.5.3 used for parser compilation does not match the current runtime version 4.7.2ANTLR Tool version 4.5.3 used for code generation does not match the current runtime version 4.7.2ANTLR Runtime version 4.5.3 used for parser compilation does not match the current runtime version 4.7.2ANTLR Tool version 4.5.3 used for code generation does not match the current runtime version 4.7.2ANTLR Runtime version 4.5.3 used for parser compilation does not match the current runtime version 4.7.211:36:48.501 [JabRef LowPriorityCachedThreadPool] INFO org.jabref.logic.importer.OpenDatabase - Opening: /tmp/jabref3118246704378959765.bib 11:36:48.518 [JabRef LowPriorityCachedThreadPool] INFO org.jabref.logic.importer.OpenDatabase - Opening: /home/dom/Dropbox/Projects/HSSA/issue 7 Fabrizio Speziale/paper/speziale2019.bib

…

-- Professor Dominik Wujastyk <http://ualberta.academia.edu/DominikWujastyk> , Singhmar Chair in Classical Indian Society and Polity , Department of History and Classics <http://historyandclassics.ualberta.ca/> , University of Alberta, Canada . South Asia at the U of A: sas.ualberta.ca

On Sat, 26 Jan 2019 at 11:24, Christoph ***@***.***> wrote: Hm seems to be a linux issue apparently, on windows I cannot reproduce this. Could you please copy the whole stacktrace from the error log? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4616 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAuhhiuW6w5jCN_ZfoAbXsA77ac51uNkks5vHJ1ZgaJpZM4aUS0u> .

[Siedlerchr]

Yes a part from it, but it seem like in the Error Dialog you got a more detailed exception stacktrace (the one you selected in your screenshot). Best option is to paste it here, and then select it, and press insert code (formats it fitting)

PS: Thanks for intensively testing JabRef dev and reporting the errors! We value your effort in testing! 🥇

[wujastyk]

Now I'm getting this repeatedly as I work; about every five or ten minutes. I don't know the cause of this error message, or if it's related to the previous report about TeX macros in fields. java.lang.IllegalStateException: Not on FX application thread; currentThread = pool-9-thread-1 at com.sun.javafx.tk.Toolkit.checkFxUserThread(Toolkit.java:279) at com.sun.javafx.tk.quantum.QuantumToolkit.checkFxUserThread(QuantumToolkit.java:423) at javafx.scene.Parent$2.onProposedChange(Parent.java:367) at com.sun.javafx.collections.VetoableListDecorator.setAll(VetoableListDecorator.java:113) at com.sun.javafx.collections.VetoableListDecorator.setAll(VetoableListDecorator.java:108) at com.sun.javafx.scene.control.skin.LabeledSkinBase.updateChildren(LabeledSkinBase.java:580) at com.sun.javafx.scene.control.skin.LabeledSkinBase.handleControlPropertyChanged(LabeledSkinBase.java:181) at com.sun.javafx.scene.control.skin.ButtonSkin.handleControlPropertyChanged(ButtonSkin.java:71) at com.sun.javafx.scene.control.skin.BehaviorSkinBase.lambda$registerChangeListener$105(BehaviorSkinBase.java:197) at com.sun.javafx.scene.control.MultiplePropertyChangeListenerHandler$1.changed(MultiplePropertyChangeListenerHandler.java:55) at javafx.beans.value.WeakChangeListener.changed(WeakChangeListener.java:89) at com.sun.javafx.binding.ExpressionHelper$SingleChange.fireValueChangedEvent(ExpressionHelper.java:182) at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) at javafx.beans.property.ObjectPropertyBase.fireValueChangedEvent(ObjectPropertyBase.java:105) at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:112) at javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:146) at javafx.css.StyleableObjectProperty.set(StyleableObjectProperty.java:82) at javafx.beans.property.ObjectProperty.setValue(ObjectProperty.java:69) at javafx.scene.control.Labeled.setGraphic(Labeled.java:423) at org.jabref.gui.actions.ActionFactory.lambda$configureIconButton$435(ActionFactory.java:86) at java.util.Optional.ifPresent(Optional.java:159) at org.jabref.gui.actions.ActionFactory.configureIconButton(ActionFactory.java:82) at org.jabref.gui.entryeditor.EntryEditor.setupToolBar(EntryEditor.java:397) at org.jabref.gui.entryeditor.EntryEditor.setEntry(EntryEditor.java:363) at org.jabref.gui.BasePanel.lambda$null$173(BasePanel.java:726) at java.util.Optional.ifPresent(Optional.java:159) at org.jabref.gui.BasePanel.lambda$createMainTable$174(BasePanel.java:724) at com.sun.javafx.collections.ListListenerHelper$Generic.fireValueChangedEvent(ListListenerHelper.java:329) at com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(ListListenerHelper.java:73) at com.sun.javafx.scene.control.ReadOnlyUnbackedObservableList.callObservers(ReadOnlyUnbackedObservableList.java:75) at javafx.scene.control.TableView$TableViewArrayListSelectionModel.handleSelectedCellsListChangeEvent(TableView.java:3073) at javafx.scene.control.TableView$TableViewArrayListSelectionModel.lambda$new$70(TableView.java:2056) at com.sun.javafx.collections.ListListenerHelper$SingleChange.fireValueChangedEvent(ListListenerHelper.java:164) at com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(ListListenerHelper.java:73) at javafx.collections.ObservableListBase.fireChange(ObservableListBase.java:233) at javafx.collections.ListChangeBuilder.commit(ListChangeBuilder.java:482) at javafx.collections.ListChangeBuilder.endChange(ListChangeBuilder.java:541) at javafx.collections.ObservableListBase.endChange(ObservableListBase.java:205) at javafx.collections.transformation.SortedList.sourceChanged(SortedList.java:111) at javafx.collections.transformation.TransformationList.lambda$getListener$1(TransformationList.java:106) at javafx.collections.WeakListChangeListener.onChanged(WeakListChangeListener.java:88) at com.sun.javafx.collections.ListListenerHelper$SingleChange.fireValueChangedEvent(ListListenerHelper.java:164) at com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(ListListenerHelper.java:73) at javafx.collections.ObservableListBase.fireChange(ObservableListBase.java:233) at javafx.collections.ListChangeBuilder.commit(ListChangeBuilder.java:482) at javafx.collections.ListChangeBuilder.endChange(ListChangeBuilder.java:541) at javafx.collections.ObservableListBase.endChange(ObservableListBase.java:205) at javafx.collections.ModifiableObservableListBase.add(ModifiableObservableListBase.java:155) at java.util.AbstractList.add(AbstractList.java:108) at com.sun.javafx.scene.control.SelectedCellsMap.add(SelectedCellsMap.java:118) at javafx.scene.control.TableView$TableViewArrayListSelectionModel.select(TableView.java:2456) at javafx.scene.control.TableView$TableViewArrayListSelectionModel.updateDefaultSelection(TableView.java:2929) at javafx.scene.control.TableView$TableViewArrayListSelectionModel.lambda$new$72(TableView.java:2119) at javafx.collections.WeakListChangeListener.onChanged(WeakListChangeListener.java:88) at com.sun.javafx.collections.ListListenerHelper$Generic.fireValueChangedEvent(ListListenerHelper.java:329) at com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(ListListenerHelper.java:73) at javafx.collections.ObservableListBase.fireChange(ObservableListBase.java:233) at javafx.collections.transformation.SortedList.sourceChanged(SortedList.java:114) at javafx.collections.transformation.TransformationList.lambda$getListener$1(TransformationList.java:106) at javafx.collections.WeakListChangeListener.onChanged(WeakListChangeListener.java:88) at com.sun.javafx.collections.ListListenerHelper$SingleChange.fireValueChangedEvent(ListListenerHelper.java:164) at com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(ListListenerHelper.java:73) at javafx.collections.ObservableListBase.fireChange(ObservableListBase.java:233) at javafx.collections.transformation.FilteredList.refilter(FilteredList.java:333) at javafx.collections.transformation.FilteredList.access$000(FilteredList.java:50) at javafx.collections.transformation.FilteredList$1.invalidated(FilteredList.java:102) at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:111) at javafx.beans.property.ObjectPropertyBase.access$000(ObjectPropertyBase.java:51) at javafx.beans.property.ObjectPropertyBase$Listener.invalidated(ObjectPropertyBase.java:233) at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:137) at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) at javafx.beans.binding.ObjectBinding.invalidate(ObjectBinding.java:172) at com.sun.javafx.binding.BindingHelperObserver.invalidated(BindingHelperObserver.java:51) at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:349) at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81) at javafx.beans.property.ObjectPropertyBase.fireValueChangedEvent(ObjectPropertyBase.java:105) at javafx.beans.property.ObjectPropertyBase.markInvalid(ObjectPropertyBase.java:112) at javafx.beans.property.ObjectPropertyBase.set(ObjectPropertyBase.java:146) at javafx.beans.property.ObjectProperty.setValue(ObjectProperty.java:69) at org.jabref.gui.StateManager.setSearchQuery(StateManager.java:95) at org.jabref.gui.search.GlobalSearchBar.performSearch(GlobalSearchBar.java:323) at org.jabref.gui.BasePanel$SearchListener.listen(BasePanel.java:1374) at sun.reflect.GeneratedMethodAccessor36.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at com.google.common.eventbus.Subscriber.invokeSubscriberMethod(Subscriber.java:87) at com.google.common.eventbus.Subscriber$SynchronizedSubscriber.invokeSubscriberMethod(Subscriber.java:144) at com.google.common.eventbus.Subscriber$1.run(Subscriber.java:72) at com.google.common.util.concurrent.DirectExecutor.execute(DirectExecutor.java:30) at com.google.common.eventbus.Subscriber.dispatchEvent(Subscriber.java:67) at com.google.common.eventbus.Dispatcher$PerThreadQueuedDispatcher.dispatch(Dispatcher.java:108) at com.google.common.eventbus.EventBus.post(EventBus.java:212) at org.jabref.model.database.BibDatabase.relayEntryChangeEvent(BibDatabase.java:582) at sun.reflect.GeneratedMethodAccessor30.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at com.google.common.eventbus.Subscriber.invokeSubscriberMethod(Subscriber.java:87) at com.google.common.eventbus.Subscriber$SynchronizedSubscriber.invokeSubscriberMethod(Subscriber.java:144) at com.google.common.eventbus.Subscriber$1.run(Subscriber.java:72) at com.google.common.util.concurrent.DirectExecutor.execute(DirectExecutor.java:30) at com.google.common.eventbus.Subscriber.dispatchEvent(Subscriber.java:67) at com.google.common.eventbus.Dispatcher$PerThreadQueuedDispatcher.dispatch(Dispatcher.java:108) at com.google.common.eventbus.EventBus.post(EventBus.java:212) at org.jabref.model.entry.BibEntry.setField(BibEntry.java:427) at org.jabref.model.cleanup.FieldFormatterCleanup.cleanupSingleField(FieldFormatterCleanup.java:63) at org.jabref.model.cleanup.FieldFormatterCleanup.cleanupAllTextFields(FieldFormatterCleanup.java:88) at org.jabref.model.cleanup.FieldFormatterCleanup.cleanup(FieldFormatterCleanup.java:32) at org.jabref.model.cleanup.FieldFormatterCleanups.applyAllActions(FieldFormatterCleanups.java:71) at org.jabref.model.cleanup.FieldFormatterCleanups.applySaveActions(FieldFormatterCleanups.java:61) at org.jabref.logic.exporter.BibDatabaseWriter.lambda$applySaveActions$1176(BibDatabaseWriter.java:60) at java.util.Optional.ifPresent(Optional.java:159) at org.jabref.logic.exporter.BibDatabaseWriter.applySaveActions(BibDatabaseWriter.java:57) at org.jabref.logic.exporter.BibDatabaseWriter.savePartOfDatabase(BibDatabaseWriter.java:172) at org.jabref.logic.exporter.BibDatabaseWriter.saveDatabase(BibDatabaseWriter.java:143) at org.jabref.logic.autosaveandbackup.BackupManager.performBackup(BackupManager.java:124) at java.util.Optional.ifPresent(Optional.java:159) at org.jabref.logic.autosaveandbackup.BackupManager.lambda$new$1149(BackupManager.java:49) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

…

On Sat, 26 Jan 2019 at 12:44, Christoph ***@***.***> wrote: Yes a part from it, but it seem like in the Error Dialog you got a more detailed exception stacktrace (the one you selected in your screenshot). Best option is to paste it here, and then select it, and press insert code (formats it fitting) PS: Thanks for intensively testing JabRef dev and reporting the errors! We value your effort in testing! 🥇 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4616 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAuhhspW2D6wgcpyRDCDM0D8GQU1Nf0Rks5vHLAlgaJpZM4aUS0u> .

[Siedlerchr]

Okay, it seems you have some save actions configured and I think you have the Latex2Unicode save action configured which does a cleanup every time you save or the auto save is triggered. That would also explain the thing about the tex macro.
And you seem to have a search open which gets notified because a field content changed.

Open your bib file with an editor and search for saveActions, should be somewhere defined at the end of the bib file, check if there is the value disabled or `enabled´.
If it's enabled try to change it to disabled.

I think I found the error for the search. Will try to create a verison you can test.,

Probably looks like this:

@Comment{jabref-meta: saveActions:disabled;
date[normalize_date]
pages[normalize_page_numbers]
month[normalize_month]
all-text-fields[latex_to_unicode]
title[html_to_unicode]
;}

[Siedlerchr]

You should also remove the normalize date formatter, it's going nuts in your db. Refs #2753

[wujastyk]

Thanks for spotting that about "save actions." JabRef 5.0-dev--snapshot--2019-01-27--master--8076f847a Linux 4.15.0-43-generic amd64 Java 1.8.0_201 If I go to Library/Library Properties, I get a screen with many expected menu entries absent. This is what I see: [image: Screenshot from 2019-01-27 19-18-48.png] The end of my main bib file (biblio4-utf8.bib) looks like this (before editing): @comment{jabref-meta: databaseType:biblatex;} @comment{jabref-meta: saveActions:disabled; date[normalize_date] pages[normalize_page_numbers] month[normalize_month] all-text-fields[latex_to_unicode] title[html_to_unicode] ;} @comment{jabref-meta: saveOrderConfig:specified;bibtexkey;false;author;false;date;false;} @comment{jabref-entrytype: Manuscript: req[collection;location;library;shelfmark;shortlibrary;shorthand;shortcollection] opt[annotation;owner;pagetotal;pagination;catalog;columns;origin;bookpagination;layer;scribe;pages;contents;dating;support]} Since it says "disabled" it should not be causing a problem, is that right? You also said You should also remove the normalize date formatter, it's going nuts in your db. Refs #2753 <#2753> but I don't know how to do that. Are you talking about "date[normalize_date]" in the saveActions section? If so, since that's "disabled", it shouldn't be causing a problem? Thank you *very* much for looking into these issues! Dominik

…

On Sat, 26 Jan 2019 at 13:50, Christoph ***@***.***> wrote: Okay, it seems you have some save actions configured and I think you have the Latex2Unicode save action configured which does a cleanup every time you save or the auto save is triggered. That would also explain the thing about the tex macro. And you seem to have a search open which gets notified because a field content changed. Open your bib file with an editor and search for saveActions, should be somewhere defined at the end of the bib file, check if there is the value disabled or `enabled´. If it's enabled try to change it to disabled. I think I found the error for the search. Will try to create a verison you can test., Probably looks like this: @comment{jabref-meta: saveActions:disabled; date[normalize_date] pages[normalize_page_numbers] month[normalize_month] all-text-fields[latex_to_unicode] title[html_to_unicode] ;} — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4616 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAuhhj70GQLlC-NJaAdLApFs0S1BwXC0ks5vHL-lgaJpZM4aUS0u> .

[Siedlerchr]

but I don't know how to do that. Are you talking about "date[normalize_date]" in the saveActions section? If so, since that's "disabled", it shouldn't be causing a problem?

Yes that is odd. I will try to check that in my copy. Could also be related to the auto save feautre.

The newest master version (from yesterday) should no longer throw the error you encountered.
Regarding the library properties missing fields/things: In #4617 I am in the process of converting the library properties to javafx as well so that schould be then shown correctly.

[wujastyk]

The TeX-macro-in-field problem is fixed as of today, as you said. Thank you!

…

On Mon, 28 Jan 2019 at 00:37, Christoph ***@***.***> wrote: but I don't know how to do that. Are you talking about "date[normalize_date]" in the saveActions section? If so, since that's "disabled", it shouldn't be causing a problem? Yes that is odd. I will try to check that in my copy. Could also be related to the auto save feautre. The newest master version (from yesterday) should no longer throw the error you encountered. Regarding the library properties missing fields/things: In #4617 <#4617> I am in the process of converting the library properties to javafx as well so that schould be then shown correctly. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#4616 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAuhhhZa6LkkPYckRvqO-aHuskIpWPLHks5vHqiwgaJpZM4aUS0u> .