Field right-click 'Protect terms' resulting in error #4958

alfureu · 2019-05-07T11:19:49Z

JabRef 5.0-dev--snapshot--2019-05-06--master--c168c4978
Windows 10 10.0 amd64
Java 1.8.0_172

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

Steps to reproduce the behavior:

Add author field, ie: Directorate-General for Research and Innovation
Right-click and select Protect terms > Add {} around selected text
Error (see screenshot)
Even if the {} brackets are manually added, it is ignored in the main list

Log File

java.lang.IllegalStateException: Task must only be used from the FX Application Thread
  at javafx.concurrent.Task.checkThread(Task.java:1218)
  at javafx.concurrent.Task.isRunning(Task.java:985)
  at org.controlsfx.control.textfield.AutoCompletionBinding.onUserInputChanged(AutoCompletionBinding.java:333)
  at org.controlsfx.control.textfield.AutoCompletionBinding.setUserInput(AutoCompletionBinding.java:135)
  at org.jabref.gui.autocompleter.AutoCompletionTextInputBinding.setUserInputText(AutoCompletionTextInputBinding.java:136)
  at org.jabref.gui.autocompleter.AutoCompletionTextInputBinding.lambda$new$1074(AutoCompletionTextInputBinding.java:54)
  at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:361)
  at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81)
  at javafx.scene.control.TextInputControl$TextProperty.fireValueChangedEvent(TextInputControl.java:1389)
  at javafx.scene.control.TextInputControl$TextProperty.markInvalid(TextInputControl.java:1393)
  at javafx.scene.control.TextInputControl$TextProperty.controlContentHasChanged(TextInputControl.java:1332)
  at javafx.scene.control.TextInputControl$TextProperty.access$1600(TextInputControl.java:1300)
  at javafx.scene.control.TextInputControl.lambda$new$162(TextInputControl.java:139)
  at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:137)
  at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81)
  at javafx.scene.control.TextField$TextFieldContent.insert(TextField.java:87)
  at javafx.scene.control.TextInputControl.replaceText(TextInputControl.java:1204)
  at javafx.scene.control.TextInputControl.filterAndSet(TextInputControl.java:1171)
  at javafx.scene.control.TextInputControl.access$900(TextInputControl.java:79)
  at javafx.scene.control.TextInputControl$TextProperty.doSet(TextInputControl.java:1410)
  at javafx.scene.control.TextInputControl$TextProperty.set(TextInputControl.java:1323)
  at javafx.scene.control.TextInputControl$TextProperty.set(TextInputControl.java:1300)
  at javafx.beans.property.StringProperty.setValue(StringProperty.java:65)
  at javafx.beans.property.StringProperty.setValue(StringProperty.java:57)
  at com.sun.javafx.binding.BidirectionalBinding$TypedGenericBidirectionalBinding.changed(BidirectionalBinding.java:601)
  at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:361)
  at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81)
  at javafx.beans.property.StringPropertyBase.fireValueChangedEvent(StringPropertyBase.java:103)
  at javafx.beans.property.StringPropertyBase.markInvalid(StringPropertyBase.java:110)
  at javafx.beans.property.StringPropertyBase.set(StringPropertyBase.java:144)
  at javafx.beans.property.StringPropertyBase.set(StringPropertyBase.java:49)
  at javafx.beans.property.StringProperty.setValue(StringProperty.java:65)
  at javafx.beans.property.StringProperty.setValue(StringProperty.java:57)
  at org.jabref.gui.util.BindingsHelper$BidirectionalBinding.updateLocked(BindingsHelper.java:234)
  at org.jabref.gui.util.BindingsHelper$BidirectionalBinding.changedB(BindingsHelper.java:227)
  at com.sun.javafx.binding.ExpressionHelper$SingleChange.fireValueChangedEvent(ExpressionHelper.java:182)
  at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81)
  at javafx.beans.binding.ObjectBinding.invalidate(ObjectBinding.java:172)
  at com.sun.javafx.binding.BindingHelperObserver.invalidated(BindingHelperObserver.java:51)
  at com.sun.javafx.collections.MapListenerHelper$Generic.fireValueChangedEvent(MapListenerHelper.java:320)
  at com.sun.javafx.collections.MapListenerHelper.fireValueChangedEvent(MapListenerHelper.java:72)
  at com.sun.javafx.collections.ObservableMapWrapper.callObservers(ObservableMapWrapper.java:115)
  at com.sun.javafx.collections.ObservableMapWrapper.put(ObservableMapWrapper.java:169)
  at org.jabref.model.entry.BibEntry.setField(BibEntry.java:413)
  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$192(BibDatabaseWriter.java:60)
  at java.util.Optional.ifPresent(Unknown Source)
  at org.jabref.logic.exporter.BibDatabaseWriter.applySaveActions(BibDatabaseWriter.java:57)
  at org.jabref.logic.exporter.BibDatabaseWriter.savePartOfDatabase(BibDatabaseWriter.java:172)
  at org.jabref.logic.exporter.BibDatabaseWriter.saveDatabase(BibDatabaseWriter.java:143)
  at org.jabref.logic.autosaveandbackup.BackupManager.performBackup(BackupManager.java:124)
  at java.util.Optional.ifPresent(Unknown Source)
  at org.jabref.logic.autosaveandbackup.BackupManager.lambda$new$132(BackupManager.java:49)
  at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
  at java.util.concurrent.FutureTask.run(Unknown Source)
  at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
  at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
  at java.lang.Thread.run(Unknown Source)

The text was updated successfully, but these errors were encountered:

Siedlerchr · 2019-05-10T10:16:13Z

Threading problem in Cleanup/setFields. I think we had simliar issues already with the cleanup dialog and could solve this somewhow.

Siedlerchr · 2019-05-10T13:10:16Z

@DOFfactory It seems like you have save actions enabled. Do you maybe have Latex2Unicode formatting enabled as save actions?
Please look at the LIbrary-> Library Propertes menu and post the list of save actions

alfureu · 2019-05-10T13:15:02Z

Hi @Siedlerchr, you are right, whenever I create a biblatex library, I usually set up the user-specific library for the respective library (instead of one single library location), and I also click at the Save actions - Enable save actions > Recommended for biblatex.

This last action automatically enables the all-text-fields: Latex to Unicode option. While I can disable it, I think it is a useful conversion, and it should be rather Latex to UTF-8 instead and not firing an error mentioned in my 1st post.

Siedlerchr · 2019-05-10T13:19:33Z

@DOFfactory Okay thanks! Now I could reproduce the error.
Regarding the protected terms: This is a known issue with the Latex2Unicode conversion:
#4152

alfureu · 2019-05-10T13:35:59Z

Thanks. Sorry, I was not aware of the fact that it has been already reported. Something similar happens also if one copy&pastes a text from the website directly to the Abstract field.

Siedlerchr · 2019-05-10T13:38:57Z

@DOFfactory This are two different issues. The error reported from your log comes from the save actions and is defintively a bug. And the same underlying error for every other field.

The other issue you noticed is that the braces of corporate authors vanish. That is the issue #4152

Fixes #4958

homocomputeris · 2019-06-13T20:07:37Z

Latest Git version
JabRef 5.0-dev
Linux 5.1.8-zen1-1-zen amd64
Java 1.8.0_212

java.lang.IllegalStateException: Task must only be used from the FX Application Thread
	at javafx.concurrent.Task.checkThread(Task.java:1218)
	at javafx.concurrent.Task.isRunning(Task.java:985)
	at org.controlsfx.control.textfield.AutoCompletionBinding.onUserInputChanged(AutoCompletionBinding.java:333)
	at org.controlsfx.control.textfield.AutoCompletionBinding.setUserInput(AutoCompletionBinding.java:135)
	at org.jabref.gui.autocompleter.AutoCompletionTextInputBinding.setUserInputText(AutoCompletionTextInputBinding.java:136)
	at org.jabref.gui.autocompleter.AutoCompletionTextInputBinding.lambda$new$394(AutoCompletionTextInputBinding.java:54)
	at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:361)
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81)
	at javafx.scene.control.TextInputControl$TextProperty.fireValueChangedEvent(TextInputControl.java:1389)
	at javafx.scene.control.TextInputControl$TextProperty.markInvalid(TextInputControl.java:1393)
	at javafx.scene.control.TextInputControl$TextProperty.controlContentHasChanged(TextInputControl.java:1332)
	at javafx.scene.control.TextInputControl$TextProperty.access$1600(TextInputControl.java:1300)
	at javafx.scene.control.TextInputControl.lambda$new$0(TextInputControl.java:139)
	at com.sun.javafx.binding.ExpressionHelper$SingleInvalidation.fireValueChangedEvent(ExpressionHelper.java:137)
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81)
	at javafx.scene.control.TextField$TextFieldContent.insert(TextField.java:87)
	at javafx.scene.control.TextInputControl.replaceText(TextInputControl.java:1204)
	at javafx.scene.control.TextInputControl.filterAndSet(TextInputControl.java:1171)
	at javafx.scene.control.TextInputControl.access$900(TextInputControl.java:79)
	at javafx.scene.control.TextInputControl$TextProperty.doSet(TextInputControl.java:1410)
	at javafx.scene.control.TextInputControl$TextProperty.set(TextInputControl.java:1323)
	at javafx.scene.control.TextInputControl$TextProperty.set(TextInputControl.java:1300)
	at javafx.beans.property.StringProperty.setValue(StringProperty.java:65)
	at javafx.beans.property.StringProperty.setValue(StringProperty.java:57)
	at com.sun.javafx.binding.BidirectionalBinding$TypedGenericBidirectionalBinding.changed(BidirectionalBinding.java:601)
	at com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:361)
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81)
	at javafx.beans.property.StringPropertyBase.fireValueChangedEvent(StringPropertyBase.java:103)
	at javafx.beans.property.StringPropertyBase.markInvalid(StringPropertyBase.java:110)
	at javafx.beans.property.StringPropertyBase.set(StringPropertyBase.java:144)
	at javafx.beans.property.StringPropertyBase.set(StringPropertyBase.java:49)
	at javafx.beans.property.StringProperty.setValue(StringProperty.java:65)
	at javafx.beans.property.StringProperty.setValue(StringProperty.java:57)
	at org.jabref.gui.util.BindingsHelper$BidirectionalBinding.updateLocked(BindingsHelper.java:234)
	at org.jabref.gui.util.BindingsHelper$BidirectionalBinding.changedB(BindingsHelper.java:227)
	at com.sun.javafx.binding.ExpressionHelper$SingleChange.fireValueChangedEvent(ExpressionHelper.java:182)
	at com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:81)
	at javafx.beans.binding.ObjectBinding.invalidate(ObjectBinding.java:172)
	at com.sun.javafx.binding.BindingHelperObserver.invalidated(BindingHelperObserver.java:51)
	at com.sun.javafx.collections.MapListenerHelper$Generic.fireValueChangedEvent(MapListenerHelper.java:320)
	at com.sun.javafx.collections.MapListenerHelper.fireValueChangedEvent(MapListenerHelper.java:72)
	at com.sun.javafx.collections.ObservableMapWrapper.callObservers(ObservableMapWrapper.java:115)
	at com.sun.javafx.collections.ObservableMapWrapper.put(ObservableMapWrapper.java:169)
	at org.jabref.model.entry.BibEntry.setField(BibEntry.java:413)
	at org.jabref.model.cleanup.FieldFormatterCleanup.cleanupSingleField(FieldFormatterCleanup.java:63)
	at org.jabref.model.cleanup.FieldFormatterCleanup.cleanup(FieldFormatterCleanup.java:34)
	at org.jabref.logic.cleanup.CleanupWorker.cleanup(CleanupWorker.java:31)
	at org.jabref.gui.cleanup.CleanupAction.doCleanup(CleanupAction.java:90)
	at org.jabref.gui.cleanup.CleanupAction.cleanup(CleanupAction.java:133)
	at org.jabref.gui.cleanup.CleanupAction.lambda$action$708(CleanupAction.java:65)
	at org.jabref.gui.util.BackgroundTask$2.call(BackgroundTask.java:55)
	at org.jabref.gui.util.BackgroundTask$2.call(BackgroundTask.java:52)
	at org.jabref.gui.util.DefaultTaskExecutor$1.call(DefaultTaskExecutor.java:122)
	at javafx.concurrent.Task$TaskCallable.call(Task.java:1423)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	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)

tobiasdiez · 2019-09-09T20:05:28Z

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.

5c376b8 Create karlstad-universitet-kau-harvard-swedish.csl (#5083) 6a62c24 Create ucl-institute-of-education-harvard.csl (#5084) 4d1bbb0 Update ferdinand-porsche-fern-fachhochschule.csl (#5073) 3a9f494 Update cureus.csl (#5087) 181c0dd Create apa-no.csl (#5059) 651ce48 Some fixes for Advanced Functional Materials (#5080) 4e3297a Acta Zoologica Hungarica: Don't demote nd particles c659df7 Create medicina-delle-dipendenze-italian-journal-of-the-addictions.csl (#5078) d243055 Update geografia-fisica-e-dinamica-quaternaria.csl (#5079) 1ee3809 Update mcgill-en.csl (#5076) 949cdc6 Update mcgill-fr.csl (#5075) ee7d4e1 Create chem-catalysis.csl (#5074) ec9faec Switch Molecular Therapy to Cell (#5070) cf6034c Switch Elsevier to their own ad-vancouver (#5072) 78cca13 Updates in research-institute-for-nature-and-forest.csl (#4958) 68b7478 Update journal-of-neolithic-archaeology.csl (#5065) 524ba93 Create offa.csl (#5066) 9713a82 Update associacao-brasileira-de-normas-tecnicas-ufrgs-note-initials-with-ibid (#5067) 44449df Uodate associacao-brasileira-de-normas-tecnicas-ufrgs-initials.csl (#5061) baf9efa Create İstanbul Üniversitesi Sosyal Bilimler Enstitüsü Ali Ekber Çına… (#5064) c5c3531 Fix CORR 853a804 Major Update mcgill-fr.csl to 9th ed. (#5057) d3e2cd9 Update mcgill-en.csl (#5056) git-subtree-dir: src/main/resources/csl-styles git-subtree-split: 5c376b8

55200d0 Create computational-intelligence.csl (JabRef#5102) 6d2efc3 Merge branch 'master' of github.com:citation-style-language/styles 60ab0fb Add Steinbeis SMI d5e0130 Add AAQR Style d964f9b Create bitonline-publikationen.csl (JabRef#5090) 0dc1a56 Add "APA 7th edition" to Norsk APA style titles (JabRef#5098) 3b6aaf7 Update norsk-apa-manual.csl (JabRef#5095) 0139c63 Create technische-universitat-dresden-betriebswirtschaftslehre-rechnungswesen-controlling.csl (JabRef#5034) fdc4497 Update universidade-estadual-de-alagoas-abnt (JabRef#5085) afdc2ea Create revista-espanola-de-nutricion-humana-y-dietetica.csl (JabRef#5082) 939189d Create citation-compass-apa-note-no.csl (JabRef#5060) 414f5e6 brazilian-journal-of-veterinary-research: add bib sorting (JabRef#5091) dbae9d7 Add DOI to Thieme German f4399aa APA: match="any" bugfixes (JabRef#5092) d0cc2c4 Add APA numeric and update BioEssays (JabRef#5089) 5c376b8 Create karlstad-universitet-kau-harvard-swedish.csl (JabRef#5083) 6a62c24 Create ucl-institute-of-education-harvard.csl (JabRef#5084) 4d1bbb0 Update ferdinand-porsche-fern-fachhochschule.csl (JabRef#5073) 3a9f494 Update cureus.csl (JabRef#5087) 181c0dd Create apa-no.csl (JabRef#5059) 651ce48 Some fixes for Advanced Functional Materials (JabRef#5080) 4e3297a Acta Zoologica Hungarica: Don't demote nd particles c659df7 Create medicina-delle-dipendenze-italian-journal-of-the-addictions.csl (JabRef#5078) d243055 Update geografia-fisica-e-dinamica-quaternaria.csl (JabRef#5079) 1ee3809 Update mcgill-en.csl (JabRef#5076) 949cdc6 Update mcgill-fr.csl (JabRef#5075) ee7d4e1 Create chem-catalysis.csl (JabRef#5074) ec9faec Switch Molecular Therapy to Cell (JabRef#5070) cf6034c Switch Elsevier to their own ad-vancouver (JabRef#5072) 78cca13 Updates in research-institute-for-nature-and-forest.csl (JabRef#4958) 68b7478 Update journal-of-neolithic-archaeology.csl (JabRef#5065) 524ba93 Create offa.csl (JabRef#5066) 9713a82 Update associacao-brasileira-de-normas-tecnicas-ufrgs-note-initials-with-ibid (JabRef#5067) 44449df Uodate associacao-brasileira-de-normas-tecnicas-ufrgs-initials.csl (JabRef#5061) baf9efa Create İstanbul Üniversitesi Sosyal Bilimler Enstitüsü Ali Ekber Çına… (JabRef#5064) c5c3531 Fix CORR 853a804 Major Update mcgill-fr.csl to 9th ed. (JabRef#5057) d3e2cd9 Update mcgill-en.csl (JabRef#5056) git-subtree-dir: src/main/resources/csl-styles git-subtree-split: 55200d0

Siedlerchr added entry-editor good first issue An issue intended for project-newcomers. Varies in difficulty. ui labels May 7, 2019

Siedlerchr added bug Confirmed bugs or reports that are very likely to be bugs and removed good first issue An issue intended for project-newcomers. Varies in difficulty. labels May 7, 2019

Siedlerchr mentioned this issue May 14, 2019

Uncaught exception occurred in thread[pool-7-thread-1,5,main] #4972

Closed

Siedlerchr added a commit that referenced this issue May 30, 2019

Fix field formatter throwing exception on autosave

6f045e8

Fixes #4958

Siedlerchr mentioned this issue May 30, 2019

[WIP] Fix field formatter save actions throwing exception on autosave #5010

Closed

6 tasks

r0light mentioned this issue Sep 9, 2019

Wrapper classes for UI Lists etc that ensure updates on JavaFX thread #5289

Merged

6 tasks

tobiasdiez closed this as completed Sep 9, 2019

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Field right-click 'Protect terms' resulting in error #4958

Field right-click 'Protect terms' resulting in error #4958

alfureu commented May 7, 2019

Siedlerchr commented May 10, 2019

Siedlerchr commented May 10, 2019

alfureu commented May 10, 2019

Siedlerchr commented May 10, 2019

alfureu commented May 10, 2019

Siedlerchr commented May 10, 2019

homocomputeris commented Jun 13, 2019

tobiasdiez commented Sep 9, 2019

Field right-click 'Protect terms' resulting in error #4958

Field right-click 'Protect terms' resulting in error #4958

Comments

alfureu commented May 7, 2019

Siedlerchr commented May 10, 2019

Siedlerchr commented May 10, 2019

alfureu commented May 10, 2019

Siedlerchr commented May 10, 2019

alfureu commented May 10, 2019

Siedlerchr commented May 10, 2019

homocomputeris commented Jun 13, 2019

tobiasdiez commented Sep 9, 2019