Move journal abbreaviation actions to the "Cleanup entries" dialog

[BOgdAnSAM-sudo]

User description

Closes #11791.

Moved the functionality of org.jabref.gui.journals.UndoableAbbreviator and org.jabref.gui.journals.UndoableUnabbreviator to org.jabref.logic.cleanup.AbbreviateJournalCleanup and org.jabref.logic.cleanup.UnabbreviateJournalCleanup respectivly. Added "Journal-related" tab to "Clean up entries" dialog. Added the journal abbreviations actions to the "Cleanup entries" dialog.

Some code was used from #12835.

Before

After

Steps to test

1. Chose entry with journal field.
2. Open "Quality" menu.
3. Notice that "Abbreviate journal names" and "Unabbreviate journal names" options are now removed.
4. Open "Clean up entries" dialog.
5. Notice that new tab "Journal-related" was added.
6. In "Journal-related" tab click on "Manage journal abbreviations" combobox and choose desired options.
7. After pressing "Clean up" button selected actions should be done: abbreviate in case of "Abbreviate (default)", "Abbreviate (dotless)", "Abbreviate (shortest unique)"; uabbreviate in case of "Unabbreviate"; no changes in case of "No changes".

Mandatory checks

• I own the copyright of the code submitted and I license it under the MIT license
• I manually tested my changes in running JabRef (always required)
• I added JUnit tests for changes (if applicable)
• I added screenshots in the PR description (if change is visible to the user)
• I described the change in CHANGELOG.md in a way that is understandable for the average user (if change is visible to the user)
• I checked the user 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 updating file(s) in https://github.com/JabRef/user-documentation/tree/main/en.

Proposed user documentation changes JabRef/user-documentation#613.

---

PR Type

Enhancement

---

Description

• Moved journal abbreviation actions from Quality menu to Cleanup dialog

• Added new "Journal-related" tab with abbreviation/unabbreviation options

• Refactored UndoableAbbreviator and UndoableUnabbreviator to cleanup jobs

• Moved AbbreviationType from GUI to logic package for better separation

• Updated cleanup worker to support journal field abbreviation operations

---

Diagram Walkthrough

flowchart LR
  A["Quality Menu<br/>Abbreviate/Unabbreviate"] -->|Removed| B["Cleanup Dialog"]
  C["UndoableAbbreviator<br/>UndoableUnabbreviator"] -->|Refactored to| D["AbbreviateJournalCleanup<br/>UnabbreviateJournalCleanup"]
  E["GUI Package<br/>AbbreviationType"] -->|Moved to| F["Logic Package<br/>AbbreviationType"]
  B -->|New Tab| G["Journal-related Panel<br/>with ComboBox Options"]
  D -->|Integrated into| H["CleanupWorker"]

Loading

File Walkthrough

	Relevant files
Enhancement	22 files JabRefGUI.java Add journal abbreviation repository to GUI initialization +4/-2      StandardActions.java Remove journal abbreviation menu actions from standard actions +0/-7      CleanupAction.java Add journal abbreviation repository parameter to cleanup action +7/-2      CleanupDialog.java Add journal-related panel to cleanup dialog tabs                  +10/-5    CleanupDialogViewModel.java Add journal abbreviation repository to cleanup view model +8/-3      CleanupJournalRelatedPanel.java New panel for journal abbreviation cleanup options              +82/-0    CleanupJournalRelatedViewModel.java New view model for journal cleanup preferences                      +33/-0    CleanupSingleAction.java Add journal abbreviation repository to single entry cleanup +6/-2      EntryEditor.java Pass journal abbreviation repository to cleanup action      +1/-1      JabRefFrame.java Add journal abbreviation repository field and initialization +9/-3      MainMenu.java Remove journal abbreviation menu items and update cleanup action +6/-14    MainToolBar.java Add journal abbreviation repository to toolbar cleanup button +5/-2      AbbreviateAction.java Remove deprecated abbreviate action class                                +0/-138  UndoableUnabbreviator.java Remove deprecated unabbreviator class                                        +0/-76    KeyBinding.java Remove abbreviation and unabbreviation key bindings            +0/-2      AbbreviateJournalCleanup.java New cleanup job for journal abbreviation                                  +35/-26  CleanupPreferences.java Add journal abbreviation cleanup step enums                            +9/-2      CleanupWorker.java Integrate journal abbreviation cleanup jobs                            +15/-1    UnabbreviateJournalCleanup.java New cleanup job for journal unabbreviation                              +85/-0    AbbreviationType.java Move abbreviation type from GUI to logic package                  +1/-1      JabRefCliPreferences.java Exclude journal abbreviation from default cleanup jobs      +5/-1      CleanupJournalRelatedPanel.fxml New FXML layout for journal cleanup panel                                +25/-0
Tests	7 files KeyBindingRepositoryTest.java Update test to use different key binding                                  +3/-3      KeyBindingsTabModelTest.java Update tests to use merge entries instead of abbreviate    +16/-16  KeyBindingViewModelTest.java Update test to use different key binding                                  +4/-4      JournalAbbreviationRepositoryTest.java Refactor tests to use new cleanup job classes                        +32/-37  AbbreviateJournalCleanupTest.java Add comprehensive tests for abbreviate journal cleanup      +307/-0  CleanupWorkerTest.java Update cleanup worker test with journal abbreviation repository +2/-1      UnabbreviateJournalCleanupTest.java Add comprehensive tests for unabbreviate journal cleanup  +183/-0
Documentation	9 files JabRef_de.properties Add German translation for journal-related tab                      +2/-1      JabRef_en.properties Add English translation for journal-related tab                    +1/-0      JabRef_es.properties Add Spanish translation for journal-related tab                    +3/-2      JabRef_fr.properties Add French translation for journal-related tab                      +1/-0      JabRef_it.properties Add Italian translation for journal-related tab                    +1/-0      JabRef_pl.properties Add Polish translation for journal-related tab                      +1/-0      JabRef_pt_BR.properties Add Portuguese translation for journal-related tab              +1/-0      JabRef_zh_CN.properties Add Chinese translation for journal-related tab                    +2/-1      CHANGELOG.md Document journal abbreviation feature relocation                  +2/-0
Additional files	2 files Project.xml +1/-1      csl-locales +1/-1

---

[qodo-free-for-open-source-projects]

PR Compliance Guide 🔍

Below is a summary of compliance checks for this PR:

Security Compliance
🟢	No security concerns identified No security vulnerabilities detected by AI analysis. Human verification advised for critical code.
Ticket Compliance
🟢	🎫 #11791 🟢 Add an option to abbreviate journal titles in the Cleanup operation dialog Add an option to expand (unabbreviate) journal titles in the Cleanup operation dialog Help users enforce their convention of using abbreviated or unabbreviated journal titles through a cleanup operation
Codebase Duplication Compliance
⚪	Codebase context is not defined Follow the guide to enable codebase context checks.
Custom Compliance
🟢	Generic: Comprehensive Audit Trails Objective: To create a detailed and reliable record of critical system actions for security analysis and compliance. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Meaningful Naming and Self-Documenting Code Objective: Ensure all identifiers clearly express their purpose and intent, making code self-documenting Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Robust Error Handling and Edge Case Management Objective: Ensure comprehensive error handling that provides meaningful context and graceful degradation Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Error Handling Objective: To prevent the leakage of sensitive system information through error messages while providing sufficient detail for internal debugging. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Secure Logging Practices Objective: To ensure logs are useful for debugging and auditing without exposing sensitive information like PII, PHI, or cardholder data. Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
	Generic: Security-First Input Validation and Data Handling Objective: Ensure all data inputs are validated, sanitized, and handled securely to prevent vulnerabilities Status: Passed Learn more about managing compliance generic rules or creating your own custom rules
Update

Compliance status legend

🟢 - Fully Compliant
🟡 - Partial Compliant
🔴 - Not Compliant
⚪ - Requires Further Human Verification
🏷️ - Compliance label

[qodo-free-for-open-source-projects]

PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Impact
Possible issue	✅ Prevent unintended data loss on restore Suggestion Impact: The commit directly implements the suggestion by adding a blank check for the fjournal field and moving the newText assignment earlier in the method. This prevents the method from overwriting the journal field with an empty value when fjournal is blank. code diff: + String newText = entry.getField(AMSField.FJOURNAL).orElse(""); + if (newText.isBlank()) { + return List.of(); + } + List<FieldChange> changes = new ArrayList<>(); String origText = entry.getField(field).orElse(""); - String newText = entry.getField(AMSField.FJOURNAL).orElse(""); In restoreFromFJournal, add a check to ensure the fjournal field is not blank before proceeding to prevent accidental data loss in the journal field. jablib/src/main/java/org/jabref/logic/cleanup/UnabbreviateJournalCleanup.java [67-84] private List<FieldChange> restoreFromFJournal(BibEntry entry, Field field) { if ((StandardField.JOURNAL != field && StandardField.JOURNALTITLE != field) || !entry.hasField(AMSField.FJOURNAL)) { + return List.of(); + } + + String newText = entry.getField(AMSField.FJOURNAL).orElse(""); + if (newText.isBlank()) { return List.of(); } List<FieldChange> changes = new ArrayList<>(); String origText = entry.getField(field).orElse(""); - String newText = entry.getField(AMSField.FJOURNAL).orElse(""); entry.setField(AMSField.FJOURNAL, ""); changes.add(new FieldChange(entry, AMSField.FJOURNAL, newText, "")); entry.setField(field, newText); changes.add(new FieldChange(entry, field, origText, newText)); return changes; } [Suggestion processed] Suggestion importance[1-10]: 8 __ Why: The suggestion identifies a critical bug where an empty fjournal field could incorrectly clear an existing journal field, leading to data loss. This is a significant correctness issue.	Medium
High-level	Refactor cleanup jobs for better composition Refactor the journal abbreviation cleanup jobs to operate on a single field instead of multiple hardcoded fields. This change will improve modularity and allow for more flexible composition in the future. Examples: jablib/src/main/java/org/jabref/logic/cleanup/AbbreviateJournalCleanup.java [34-42] public List<FieldChange> cleanup(BibEntry entry) { List<FieldChange> allChanges = new ArrayList<>(); allChanges.addAll(abbreviateField(entry, StandardField.JOURNAL)); allChanges.addAll(abbreviateField(entry, StandardField.JOURNALTITLE)); return allChanges; } jablib/src/main/java/org/jabref/logic/cleanup/UnabbreviateJournalCleanup.java [27-35] @Override public List<FieldChange> cleanup(BibEntry entry) { List<FieldChange> allChanges = new ArrayList<>(); allChanges.addAll(unabbreviate(entry, StandardField.JOURNAL)); allChanges.addAll(unabbreviate(entry, StandardField.JOURNALTITLE)); return allChanges; } Solution Walkthrough: Before: public class AbbreviateJournalCleanup implements CleanupJob { @Override public List<FieldChange> cleanup(BibEntry entry) { List<FieldChange> allChanges = new ArrayList<>(); // Hardcoded fields allChanges.addAll(abbreviateField(entry, StandardField.JOURNAL)); allChanges.addAll(abbreviateField(entry, StandardField.JOURNALTITLE)); return allChanges; } // ... } After: public class AbbreviateFieldCleanup implements CleanupJob { private final Field field; // ... constructor ... @Override public List<FieldChange> cleanup(BibEntry entry) { return abbreviateField(entry, this.field); } // ... } // In CleanupWorker or similar factory: // jobs.add(new AbbreviateFieldCleanup(StandardField.JOURNAL, ...)); // jobs.add(new AbbreviateFieldCleanup(StandardField.JOURNALTITLE, ...)); Suggestion importance[1-10]: 6 __ Why: The suggestion correctly identifies a design limitation where the new cleanup jobs hardcode multiple fields, reducing flexibility and reusability, which is a valid point for improving the architecture.	Low
General	✅ Localize user-facing strings in UI Suggestion Impact: The commit directly implements the suggestion by adding the Localization import (line 5) and wrapping all five user-facing strings in the toString method with Localization.lang() calls (lines 14, 17, 20, 23, 26), exactly as suggested. code diff: +import org.jabref.logic.l10n.Localization; import com.airhacks.afterburner.views.ViewLoader; import org.jspecify.annotations.NonNull; @@ -42,15 +43,15 @@ case null -> ""; case ABBREVIATE_DEFAULT -> - "Abbreviate (default)"; + Localization.lang("Abbreviate (default)"); case ABBREVIATE_DOTLESS -> - "Abbreviate (dotless)"; + Localization.lang("Abbreviate (dotless)"); case ABBREVIATE_SHORTEST_UNIQUE -> - "Abbreviate (shortest unique)"; + Localization.lang("Abbreviate (shortest unique)"); case UNABBREVIATE -> - "Unabbreviate"; + Localization.lang("Unabbreviate"); case ABBREVIATION_NO_CHANGES -> - "No changes"; + Localization.lang("No changes"); Localize the user-facing strings in the toString method of the StringConverter by wrapping them with Localization.lang(). jabgui/src/main/java/org/jabref/gui/cleanup/CleanupJournalRelatedPanel.java [38-57] public String toString(CleanupPreferences.CleanupStep object) { return switch (object) { case null -> ""; case ABBREVIATE_DEFAULT -> - "Abbreviate (default)"; + Localization.lang("Abbreviate (default)"); case ABBREVIATE_DOTLESS -> - "Abbreviate (dotless)"; + Localization.lang("Abbreviate (dotless)"); case ABBREVIATE_SHORTEST_UNIQUE -> - "Abbreviate (shortest unique)"; + Localization.lang("Abbreviate (shortest unique)"); case UNABBREVIATE -> - "Unabbreviate"; + Localization.lang("Unabbreviate"); case ABBREVIATION_NO_CHANGES -> - "No changes"; + Localization.lang("No changes"); default -> object.toString(); }; } [To ensure code accuracy, apply this suggestion manually] Suggestion importance[1-10]: 6 __ Why: The suggestion correctly points out that user-facing strings in the new CleanupJournalRelatedPanel class should be localized for internationalization, which is a standard practice in the project.	Low
Learned best practice	Verify semantic change in documentation The comment was changed from "iff" (if and only if) to "if", but this changes the semantic meaning. "iff" is a mathematical term indicating bidirectional implication, while "if" only indicates one direction. Verify whether the original "iff" was intentional and correct. jablib/src/main/java/org/jabref/logic/cleanup/CleanupDialogViewModel.java [138-142] /** * Runs the cleanup on the entry and records the change. * - * @return true if entry was modified + * @return true iff entry was modified */ [To ensure code accuracy, apply this suggestion manually] Suggestion importance[1-10]: 6 __ Why: Relevant best practice - Correct typographical errors in documentation, code comments, configuration files, and user-facing strings. This includes fixing misspellings in variable names, method names, documentation text, changelog entries, and localization strings to maintain code quality and professionalism.	Low
	✅ Fix typo in changelog entry Suggestion Impact: The suggestion was directly implemented. The commit changed "journal abbreviation" to "journal abbreviations" in the CHANGELOG.md file, exactly as suggested. code diff: -- We moved journal abbreviation from the "Quality" menu to the "Clean up entries" dialog [#11791](https://github.com/JabRef/jabref/issues/11791) +- We moved journal abbreviations from the "Quality" menu to the "Clean up entries" dialog [#11791](https://github.com/JabRef/jabref/issues/11791) The word "abbreviation" should be pluralized to "abbreviations" to match the feature name and maintain consistency with the rest of the codebase where "journal abbreviations" is used. CHANGELOG.md [20] -- We moved journal abbreviation from the "Quality" menu to the "Clean up entries" dialog [#11791](https://github.com/JabRef/jabref/issues/11791) +- We moved journal abbreviations from the "Quality" menu to the "Clean up entries" dialog [#11791](https://github.com/JabRef/jabref/issues/11791) [Suggestion processed] Suggestion importance[1-10]: 5 __ Why: Relevant best practice - Correct typographical errors in documentation, code comments, configuration files, and user-facing strings. This includes fixing misspellings in variable names, method names, documentation text, changelog entries, and localization strings to maintain code quality and professionalism.	Low
Update

[koppor]

Our abbreviations are somehow wrong. I did abbreviate and then unabbreviate.

diff --git a/chocolate/Chocolate.bib b/chocolate/Chocolate.bib
index 98de469..86fb9d9 100644
--- a/chocolate/Chocolate.bib
+++ b/chocolate/Chocolate.bib
@@ -96,7 +96,7 @@
 @Article{Tan_2021,
   author       = {Tan, Terence Yew Chin and Lim, Xin Yi and Yeo, Julie Hsiao Hui and Lee, Shaun Wen Huey and Lai, Nai Ming},
   date         = {2021-08},
-  journaltitle = {Nutrients},
+  journaltitle = {Nutrition},
   title        = {The Health Effects of Chocolate and Cocoa: A Systematic Review},
   doi          = {10.3390/nu13092909},
   issn         = {2072-6643},

See https://doi.org/10.3390/nu13092909 --> https://www.mdpi.com/2072-6643/13/9/2909 -->

Note that this happens when abbreviating already:

 @Article{Tan_2021,
   author       = {Tan, Terence Yew Chin and Lim, Xin Yi and Yeo, Julie Hsiao Hui and Lee, Shaun Wen Huey and Lai, Nai Ming},
   date         = {2021-08},
-  journaltitle = {Nutrients},
+  journaltitle = {Nutrition},
   title        = {The Health Effects of Chocolate and Cocoa: A Systematic Review},
   doi          = {10.3390/nu13092909},
   issn         = {2072-6643},
   number       = {9},
   pages        = {2909},
   volume       = {13},
+  fjournal     = {Nutrition},
   publisher    = {MDPI AG},
   readstatus   = {skimmed},
 }

[BOgdAnSAM-sudo]

I tested it on the main branch, the same issue is also present.

[koppor]

I tested it on the main branch, the same issue is also present.

Maybe, you can dig down at github.com/JabRef/abbrv.jabref.org - where this abbreviation comes from.

[koppor]

Roundtrip is not working (yet).

Meaning: First abbreviate then unabbreviate - ampersands not kept.

I am working on it.

diff --git a/chocolate/Chocolate.bib b/chocolate/Chocolate.bib
index 98de469..86fb9d9 100644
--- a/chocolate/Chocolate.bib
+++ b/chocolate/Chocolate.bib
@@ -27,7 +27,7 @@
 @Article{Ding_2006,
   author       = {Ding, Eric L and Hutfless, Susan M and Ding, Xin and Girotra, Saket},
   date         = {2006-01},
-  journaltitle = {Nutrition \& Metabolism},
+  journaltitle = {Nutrition & Metabolism},
   title        = {Chocolate and Prevention of Cardiovascular Disease: A Systematic Review},
   doi          = {10.1186/1743-7075-3-2},
   issn         = {1743-7075},
@@ -52,7 +52,7 @@
 @Article{Katz_2011,
   author       = {Katz, David L. and Doughty, Kim and Ali, Ather},
   date         = {2011-11},
-  journaltitle = {Antioxidants \& Redox Signaling},
+  journaltitle = {Antioxidants & Redox Signaling},
   title        = {Cocoa and Chocolate in Human Health and Disease},
   doi          = {10.1089/ars.2010.3697},
   issn         = {1557-7716},
@@ -96,7 +96,7 @@
 @Article{Tan_2021,
   author       = {Tan, Terence Yew Chin and Lim, Xin Yi and Yeo, Julie Hsiao Hui and Lee, Shaun Wen Huey and Lai, Nai Ming},
   date         = {2021-08},
-  journaltitle = {Nutrients},
+  journaltitle = {Nutrition},
   title        = {The Health Effects of Chocolate and Cocoa: A Systematic Review},
   doi          = {10.3390/nu13092909},
   issn         = {2072-6643},
@@ -150,7 +150,7 @@
 @Article{Hooper_2012,
   author       = {Hooper, Lee and Kay, Colin and Abdelhamid, Asmaa and Kroon, Paul A and Cohn, Jeffrey S and Rimm, Eric B and Cassidy, Aedín},
   date         = {2012-03},
-  journaltitle = {The American Journal of Clinical Nutrition},
+  journaltitle = {American Journal of Clinical Nutrition},
   title        = {Effects of chocolate, cocoa, and flavan-3-ols on cardiovascular health: a systematic review and meta-analysis of randomized trials},
   doi          = {10.3945/ajcn.111.023457},
   issn         = {0002-9165},
@@ -207,7 +207,7 @@
 @Article{LunaOstos_2024,
   author       = {Luna Ostos, Luisa Marcela and Roche, Lindsey and Coroama, Vlad and Finkbeiner, Matthias},
   date         = {2024-01},
-  journaltitle = {The International Journal of Life Cycle Assessment},
+  journaltitle = {International Journal of Life Cycle Assessment},
   title        = {Social life cycle assessment in the chocolate industry: A Colombian case study with Luker Chocolate},
   doi          = {10.1007/s11367-023-02261-y},
   issn         = {1614-7502},

[BOgdAnSAM-sudo]

I tested it on the main branch, the same issue is also present.

Maybe, you can dig down at github.com/JabRef/abbrv.jabref.org - where this abbreviation comes from.

This abbreviation seems to be coming from one of those lines

https://github.com/JabRef/abbrv.jabref.org/blob/91f15ce2f885b735149fd65bdfcc869b1ea22fa1/journals/journal_abbreviations_lifescience.csv#L7055

https://github.com/JabRef/abbrv.jabref.org/blob/91f15ce2f885b735149fd65bdfcc869b1ea22fa1/journals/journal_abbreviations_entrez.csv#L12535

[BOgdAnSAM-sudo]

FindAbbreviationFuzzyMatched finds most similar abbreaviation and returns it, "Nutrition" is similar to "Nutrients", so "Nutrition" is returned.

jabref/jablib/src/main/java/org/jabref/logic/journals/JournalAbbreviationRepository.java

Lines 141 to 143 in 369d068

	if (abbreviation.isEmpty()) {
	abbreviation = findAbbreviationFuzzyMatched(journal);
	}

[koppor]

@BOgdAnSAM-sudo You could improve the tests in a follow-up PR. See 39b064a for the "template"

[BOgdAnSAM-sudo]

@BOgdAnSAM-sudo You could improve the tests in a follow-up PR. See 39b064a for the "template"

I'll do it today or tomorrow.

[koppor]

@BOgdAnSAM-sudo You could improve the tests in a follow-up PR. See 39b064a for the "template"

I'll do it today or tomorrow.

Thank you! Base on upstream/main. I want this PR to be in - otherwise, we loose context 😅.