Fix journal abbbrev checker for curly braces by Siedlerchr · Pull Request #9504 · JabRef/jabref

Siedlerchr · 2022-12-28T16:48:47Z

Escape any curly braces
Also use latex free fields

Change in CHANGELOG.md described in a way that is understandable for the average user (if applicable)
Tests created for changes (if applicable)
Manually tested changed features in running JabRef (always required)
Screenshots added in PR description (for UI changes)
Checked developer's documentation: Is the information available and up to date? If not, I outlined it in this pull request.
Checked documentation: Is the information available and up to date? If not, I created an issue at https://github.com/JabRef/user-documentation/issues or, even better, I submitted a pull request to the documentation repository.

Escape any curly braces Also use latex free fields Fixes #9475 Fixes #9503

HoussemNasri · 2022-12-28T18:05:21Z

I was able to reproduce even after this pr. Also, try to hold the up or down keyboard arrow to move past entries and you'll notice a major lag in UI (it wasn't introduced here). Apparently, some heavy operation is being executed on the UI thread whenever an entry is ~~selected~~ selected for the first time.

Edit:
The lag is caused by Pattern.compile

jabref/buildSrc/src/copied/java/org/jabref/logic/journals/JournalAbbreviationRepository.java

Lines 106 to 109 in 690f837

    
               foundKey = abbreviationToFull.keySet().stream() 
        
                                            .filter(s -> Pattern.compile(joined).matcher(s).find()) 
        
                                            .collect(Collectors.joining()); 
        
           }

Exception

java.util.regex.PatternSyntaxException: Illegal/unsupported escape sequence near index 48 Proceedings[\.\s]*of[\.\s]*the[\.\s]*4$\{\}^\{\mbox\{th\}\}$[\.\s]*Central-European[\.\s]*Workshop[\.\s]*on[\.\s]*Services[\.\s]*and[\.\s]*their[\.\s]*Composition,[\.\s]*ZEUS-2012,[\.\s]*Bamberg,[\.\s]*Germany,[\.\s]*February[\.\s]*23-24,[\.\s]*2012[\.\s]* ^ at java.base/java.util.regex.Pattern.error(Pattern.java:2038) at java.base/java.util.regex.Pattern.escape(Pattern.java:2618) at java.base/java.util.regex.Pattern.atom(Pattern.java:2296) at java.base/java.util.regex.Pattern.sequence(Pattern.java:2169) at java.base/java.util.regex.Pattern.expr(Pattern.java:2079) at java.base/java.util.regex.Pattern.compile(Pattern.java:1793) at java.base/java.util.regex.Pattern.(Pattern.java:1440) at java.base/java.util.regex.Pattern.compile(Pattern.java:1079) at org.jabref@100.0.0/org.jabref.logic.journals.JournalAbbreviationRepository.lambda$findDottedAbbrFromDotless$2(JournalAbbreviationRepository.java:109) at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:178) at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133) at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845) at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509) at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499) at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:921) at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:682) at org.jabref@100.0.0/org.jabref.logic.journals.JournalAbbreviationRepository.findDottedAbbrFromDotless(JournalAbbreviationRepository.java:110) at org.jabref@100.0.0/org.jabref.logic.journals.JournalAbbreviationRepository.isAbbreviatedName(JournalAbbreviationRepository.java:83) at org.jabref@100.0.0/org.jabref.logic.integrity.AbbreviationChecker.checkValue(AbbreviationChecker.java:23) at org.jabref@100.0.0/org.jabref.gui.fieldeditors.AbstractEditorViewModel.lambda$new$0(AbstractEditorViewModel.java:43) at de.saxsys.mvvmfx.validation/de.saxsys.mvvmfx.utils.validation.FunctionBasedValidator.lambda$new$1(FunctionBasedValidator.java:74) at de.saxsys.mvvmfx.validation/de.saxsys.mvvmfx.utils.validation.FunctionBasedValidator.validate(FunctionBasedValidator.java:102) at de.saxsys.mvvmfx.validation/de.saxsys.mvvmfx.utils.validation.FunctionBasedValidator.lambda$new$0(FunctionBasedValidator.java:57) at javafx.base@19/com.sun.javafx.binding.ExpressionHelper$Generic.fireValueChangedEvent(ExpressionHelper.java:360) at javafx.base@19/com.sun.javafx.binding.ExpressionHelper.fireValueChangedEvent(ExpressionHelper.java:80) at javafx.base@19/javafx.beans.property.StringPropertyBase.fireValueChangedEvent(StringPropertyBase.java:104) at javafx.base@19/javafx.beans.property.StringPropertyBase.markInvalid(StringPropertyBase.java:111) at javafx.base@19/javafx.beans.property.StringPropertyBase.set(StringPropertyBase.java:145) at javafx.base@19/javafx.beans.property.StringPropertyBase.set(StringPropertyBase.java:50) at javafx.base@19/javafx.beans.property.StringProperty.setValue(StringProperty.java:71) at javafx.base@19/javafx.beans.property.StringProperty.setValue(StringProperty.java:57) at org.jabref@100.0.0/org.jabref.gui.util.BindingsHelper.bindBidirectional(BindingsHelper.java:80) at org.jabref@100.0.0/org.jabref.gui.util.BindingsHelper.bindBidirectional(BindingsHelper.java:70) at org.jabref@100.0.0/org.jabref.gui.fieldeditors.AbstractEditorViewModel.bindToEntry(AbstractEditorViewModel.java:62) at org.jabref@100.0.0/org.jabref.gui.fieldeditors.SimpleEditor.bindToEntry(SimpleEditor.java:56) at org.jabref@100.0.0/org.jabref.gui.entryeditor.FieldsEditorTab.setupPanel(FieldsEditorTab.java:122) at org.jabref@100.0.0/org.jabref.gui.entryeditor.FieldsEditorTab.bindToEntry(FieldsEditorTab.java:204) at org.jabref@100.0.0/org.jabref.gui.entryeditor.EntryEditorTab.notifyAboutFocus(EntryEditorTab.java:42) at org.jabref@100.0.0/org.jabref.gui.entryeditor.EntryEditor.setEntry(EntryEditor.java:342) at java.base/java.util.Optional.ifPresent(Optional.java:178) at org.jabref@100.0.0/org.jabref.gui.LibraryTab.lambda$createMainTable$10(LibraryTab.java:517) at javafx.base@19/com.sun.javafx.collections.ListListenerHelper$Generic.fireValueChangedEvent(ListListenerHelper.java:329) at javafx.base@19/com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(ListListenerHelper.java:73) at javafx.base@19/javafx.collections.ObservableListBase.fireChange(ObservableListBase.java:239) at javafx.base@19/javafx.collections.ListChangeBuilder.commit(ListChangeBuilder.java:482) at javafx.base@19/javafx.collections.ListChangeBuilder.endChange(ListChangeBuilder.java:541) at javafx.base@19/javafx.collections.ObservableListBase.endChange(ObservableListBase.java:211) at javafx.controls@19/com.sun.javafx.scene.control.SelectedItemsReadOnlyObservableList.lambda$new$0(SelectedItemsReadOnlyObservableList.java:91) at javafx.base@19/com.sun.javafx.collections.ListListenerHelper$Generic.fireValueChangedEvent(ListListenerHelper.java:329) at javafx.base@19/com.sun.javafx.collections.ListListenerHelper.fireValueChangedEvent(ListListenerHelper.java:73) at javafx.base@19/javafx.collections.ObservableListBase.fireChange(ObservableListBase.java:239) at javafx.base@19/javafx.collections.ListChangeBuilder.commit(ListChangeBuilder.java:482) at javafx.base@19/javafx.collections.ListChangeBuilder.endChange(ListChangeBuilder.java:541) at javafx.base@19/javafx.collections.ObservableListBase.endChange(ObservableListBase.java:211) at javafx.controls@19/com.sun.javafx.scene.control.ReadOnlyUnbackedObservableList._endChange(ReadOnlyUnbackedObservableList.java:64) at javafx.controls@19/javafx.scene.control.MultipleSelectionModelBase$SelectedIndicesList._endChange(MultipleSelectionModelBase.java:918) at javafx.controls@19/javafx.scene.control.ControlUtils.updateSelectedIndices(ControlUtils.java:218) at javafx.controls@19/javafx.scene.control.TableView$TableViewArrayListSelectionModel.fireCustomSelectedCellsListChangeEvent(TableView.java:3032) at javafx.controls@19/javafx.scene.control.TableView$TableViewArrayListSelectionModel.clearAndSelect(TableView.java:2482) at javafx.controls@19/javafx.scene.control.TableView$TableViewSelectionModel.clearAndSelect(TableView.java:1968) at javafx.controls@19/com.sun.javafx.scene.control.behavior.TableViewBehaviorBase.selectCell(TableViewBehaviorBase.java:875) at javafx.controls@19/com.sun.javafx.scene.control.behavior.TableViewBehaviorBase.selectNextRow(TableViewBehaviorBase.java:838) at javafx.controls@19/com.sun.javafx.scene.control.behavior.TableViewBehaviorBase.lambda$new$12(TableViewBehaviorBase.java:156) at javafx.controls@19/com.sun.javafx.scene.control.inputmap.InputMap.handle(InputMap.java:274) at javafx.base@19/com.sun.javafx.event.CompositeEventHandler$NormalEventHandlerRecord.handleBubblingEvent(CompositeEventHandler.java:247) at javafx.base@19/com.sun.javafx.event.CompositeEventHandler.dispatchBubblingEvent(CompositeEventHandler.java:80) at javafx.base@19/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:234) at javafx.base@19/com.sun.javafx.event.EventHandlerManager.dispatchBubblingEvent(EventHandlerManager.java:191) at javafx.base@19/com.sun.javafx.event.CompositeEventDispatcher.dispatchBubblingEvent(CompositeEventDispatcher.java:59) at javafx.base@19/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:58) at javafx.base@19/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base@19/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base@19/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base@19/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base@19/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base@19/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base@19/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base@19/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base@19/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base@19/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base@19/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base@19/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base@19/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base@19/com.sun.javafx.event.BasicEventDispatcher.dispatchEvent(BasicEventDispatcher.java:56) at javafx.base@19/com.sun.javafx.event.EventDispatchChainImpl.dispatchEvent(EventDispatchChainImpl.java:114) at javafx.base@19/com.sun.javafx.event.EventUtil.fireEventImpl(EventUtil.java:74) at javafx.base@19/com.sun.javafx.event.EventUtil.fireEvent(EventUtil.java:54) at javafx.base@19/javafx.event.Event.fireEvent(Event.java:198) at javafx.graphics@19/javafx.scene.Scene$KeyHandler.process(Scene.java:4113) at javafx.graphics@19/javafx.scene.Scene.processKeyEvent(Scene.java:2159) at javafx.graphics@19/javafx.scene.Scene$ScenePeerListener.keyEvent(Scene.java:2627) at javafx.graphics@19/com.sun.javafx.tk.quantum.GlassViewEventHandler$KeyEventNotification.run(GlassViewEventHandler.java:218) at javafx.graphics@19/com.sun.javafx.tk.quantum.GlassViewEventHandler$KeyEventNotification.run(GlassViewEventHandler.java:150) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at javafx.graphics@19/com.sun.javafx.tk.quantum.GlassViewEventHandler.lambda$handleKeyEvent$1(GlassViewEventHandler.java:250) at javafx.graphics@19/com.sun.javafx.tk.quantum.QuantumToolkit.runWithoutRenderLock(QuantumToolkit.java:424) at javafx.graphics@19/com.sun.javafx.tk.quantum.GlassViewEventHandler.handleKeyEvent(GlassViewEventHandler.java:249) at javafx.graphics@19/com.sun.glass.ui.View.handleKeyEvent(View.java:542) at javafx.graphics@19/com.sun.glass.ui.View.notifyKey(View.java:966) at javafx.graphics@19/com.sun.glass.ui.win.WinApplication._runLoop(Native Method) at javafx.graphics@19/com.sun.glass.ui.win.WinApplication.lambda$runLoop$3(WinApplication.java:184) at java.base/java.lang.Thread.run(Thread.java:833)

Siedlerchr · 2022-12-28T18:18:05Z

I think the key problem is the integrity checker is not using latex free fields. I noticed that lag as well

Siedlerchr · 2022-12-28T19:21:14Z

I converted the checker to an entry based checker and this also has the advantage that it's not executed when the entry is created. Only for the integrity check.
I first try to use the latex free field, if this still contains illegal chars I continue with ignoring the exception

Siedlerchr · 2022-12-31T15:15:07Z

the original fix for the conversion is still buggy. the Regex is too greedy and will return too much

koppor · 2023-01-01T20:26:56Z

Apparently, some heavy operation is being executed on the UI thread whenever an entry is ~~selected~~ selected for the first time

This surely is #9172

Co-authored-by: Christoph <siedlerkiller@gmail.com> Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>

# Conflicts: # CHANGELOG.md

koppor · 2023-01-01T21:12:35Z

META: Working on fixing this clearly shows why code comments are useful. Especially, the usage of Pattern.compile should have been documented (this is a very expensive operation!). -- The general idea should have been documented in the code @K5qu4r3d.

Co-authored-by: Christoph <siedlerkiller@gmail.com>

This reverts commit 626e41a.

koppor · 2023-01-01T23:29:46Z

Current state:

remote: error: File src/main/resources/journals/journalList.mv is 332.14 MB; this exceeds GitHub's file size limit of 100.00 MB

Ideas:

Make JabRef distribution size to 500 MB ^^(and enforce git-lfs)
Re-add *.csv in the repository and have JabRef generate the .mv files if the .mv file is older than any *.csv file
Switch back to "String" and have the Abbreviations in-memory

koppor · 2023-01-02T00:24:54Z

I implemented another idea - store complete object once in MVStore and create the HashMaps on load

Old size: ~15MB
New size: ~38MB

koppor · 2023-01-02T00:45:34Z

New menu (MEDLINE -> dotless)

koppor · 2023-01-02T10:30:07Z

For custom abbreviations working, JabRef needs a restart. Also an issue at v5.8.

* upstream/main: (29 commits) Use Set instead of List for custom journal abbreviations (JabRef#9515) Delete snap.yml (JabRef#9526) New Crowdin updates (JabRef#9523) Fix not on fx thread error when downloading file (JabRef#9522) Fix downloading in case of circular redirect (JabRef#9519) Typo: sucess -> success (JabRef#9520) New Crowdin updates (JabRef#9517) Add CHANGELOG.md entry for 9472 Fix journal abbbrev checker for curly braces (JabRef#9504) Remove journal_abbreviations_ieee_strings.csv from journal lists (JabRef#9511) Bump mockito-core from 4.10.0 to 4.11.0 (JabRef#9513) Bump lucene-core from 9.4.1 to 9.4.2 (JabRef#9512) Bump checkstyle from 10.5.0 to 10.6.0 (JabRef#9514) Create a better solution for define multi line fields (JabRef#9456) Check links once a month Really ignore CHANGELOG.md in link check Fix spaces Add missing dots Squashed 'buildres/csl/csl-styles/' changes from 84dba23..43566f2 try to repack deb file (JabRef#9506) ... # Conflicts: # CHANGELOG.md # src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java

* upstream/main: (244 commits) Use Set instead of List for custom journal abbreviations (JabRef#9515) Delete snap.yml (JabRef#9526) New Crowdin updates (JabRef#9523) Fix not on fx thread error when downloading file (JabRef#9522) Fix downloading in case of circular redirect (JabRef#9519) Typo: sucess -> success (JabRef#9520) New Crowdin updates (JabRef#9517) Add CHANGELOG.md entry for 9472 Fix journal abbbrev checker for curly braces (JabRef#9504) Remove journal_abbreviations_ieee_strings.csv from journal lists (JabRef#9511) Bump mockito-core from 4.10.0 to 4.11.0 (JabRef#9513) Bump lucene-core from 9.4.1 to 9.4.2 (JabRef#9512) Bump checkstyle from 10.5.0 to 10.6.0 (JabRef#9514) Create a better solution for define multi line fields (JabRef#9456) Check links once a month Really ignore CHANGELOG.md in link check Fix spaces Add missing dots Squashed 'buildres/csl/csl-styles/' changes from 84dba23..43566f2 try to repack deb file (JabRef#9506) ...

Fix journal abbbrev checker for curly braces

2628b59

Escape any curly braces Also use latex free fields Fixes #9475 Fixes #9503

Siedlerchr added the status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers label Dec 28, 2022

Siedlerchr requested a review from HoussemNasri December 28, 2022 16:56

refactor abbreviation checker to latex free entry checker

79e2531

github-actions Bot reviewed Dec 28, 2022

View reviewed changes

Comment thread src/main/java/org/jabref/logic/integrity/AbbreviationChecker.java

Siedlerchr added 2 commits December 28, 2022 20:16

adjust test cases

28915bb

checkstyle

b8d72ce

github-actions Bot reviewed Dec 28, 2022

View reviewed changes

Comment thread src/main/java/org/jabref/logic/journals/JournalAbbreviationRepository.java Outdated

Comment thread src/main/java/org/jabref/logic/journals/JournalAbbreviationRepository.java Outdated

Comment thread src/main/java/org/jabref/logic/journals/JournalAbbreviationRepository.java Outdated

Siedlerchr added 2 commits December 28, 2022 20:22

checkstyle

e4bf0af

Merge branch 'main' into fixJournalAbbrevChecker

6bb8db4

koppor and others added 2 commits January 1, 2023 22:04

Streamline tests and add tests for 9475 and 9503

1a5c777

Co-authored-by: Christoph <siedlerkiller@gmail.com> Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>

Merge remote-tracking branch 'origin/main' into fixJournalAbbrevChecker

c2c590b

# Conflicts: # CHANGELOG.md

koppor and others added 12 commits January 1, 2023 22:40

Rename Medline to Dotless and add translations for the menu actions

54fcbd4

On our way

2779e18

Co-authored-by: Christoph <siedlerkiller@gmail.com>

Add misisng test

630c772

Co-authored-by: Christoph <siedlerkiller@gmail.com>

Try to use full MVMap in groovy script

9399277

Fix path

5801e92

Streamline action

626e41a

Try to commit changes

b6beabe

Revert "Streamline action"

e649c5e

This reverts commit 626e41a.

Try to fix action

155617e

Debug: show branch

ac82d8e

Stay on current branch

f6d743f

Fix action

acf5b91

koppor and others added 8 commits January 2, 2023 01:08

Try to use a single MV store only

623514e

Fix import

38bcf84

CamleCase to dash-case

c7b4267

Fix brace

1b0e431

Update journal abbrev list

540b26a

Remove debug output

ba04c0a

Internalize loading

90f7825

Disable workflow

28bf41d

koppor and others added 4 commits January 2, 2023 01:28

Update CHANGELOG.md

25f517e

Remove initialization hack

b012a08

Update journal abbrev list

5c66561

No need to fetch

f579568

koppor and others added 2 commits January 2, 2023 02:07

Use right WoS file

e61c492

Update journal abbrev list

3b23a41

koppor mentioned this pull request Jan 2, 2023

Remove journal_abbreviations_ieee_strings.csv from journal lists #9511

Merged

6 tasks

Siedlerchr closed this Jan 2, 2023

Siedlerchr reopened this Jan 2, 2023

Siedlerchr and others added 2 commits January 2, 2023 09:45

fix l10n and reorder

70a804f

Merge remote-tracking branch 'origin/main' into fixJournalAbbrevChecker

a6c791d

koppor approved these changes Jan 2, 2023

View reviewed changes

Siedlerchr merged commit 88c9f56 into main Jan 2, 2023

Siedlerchr deleted the fixJournalAbbrevChecker branch January 2, 2023 20:34

koppor mentioned this pull request Jan 6, 2025

Support multiple journal abbreviations lists #12364

Open

marwanemad07 mentioned this pull request Mar 17, 2025

Rewrite journal abbrevation repository #12571

Open

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Fix journal abbbrev checker for curly braces#9504

Fix journal abbbrev checker for curly braces#9504
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