Moved Journal Abbreviation from Quality Menu to Cleanup Entries Dialog

[GDeane]

Closes #11791
This change moves the Journal Abbreviation behavior from the Quality Menu into the Cleanup Entries Dialog as follows:

The JabRef documentation will need to be updated. A new issue has been created to do this here

Before Changes

After Changes

Summary

This pull request implements the steps outlined in this issue refinement

Specifically, all journal‐abbreviation tasks (both abbreviate and unabbreviate) from separate menu commands have been moved into the “Clean up entries” dialog. This allows the user to pick how they want to handle journal names—no change, abbreviate, or unabbreviate—directly inside the Cleanup dialog rather than from separate menu items.

Key changes:

• Journal‐related combo box in the Cleanup dialog. You can choose:
  1. No changes (default)
  2. Abbreviate (default)
  3. Abbreviate (dotless)
  4. Abbreviate (shortest unique)
  5. Unabbreviate
• Added two new cleanup classes:
  • AbbreviateJournalCleanup (replaces old UndoableAbbreviator)
  • UnabbreviateJournalCleanup (replaces old UndoableUnabbreviator)
• Removed the old "Abbreviate" and "Unabbreviate" items from the Quality menu, as well as old references in the code to UndoableAbbreviator, UndoableUnabbreviator, and the old keybindings for them.
• Added tests in AbbreviateJournalCleanupTest and UnabbreviateJournalCleanupTest, along with changes to JournalAbbreviationRepositoryTest so the coverage is the same as before but uses the new cleanup approach.

Notable Design Details

To perform this change, the functionality in UndoableAbbreviator (and UndoableUnabbreviator) had to be adapted to the org.jabref.logic.cleanup.CleanupJob interface. I discovered while figuring out an implementation that org.jabref.logic.cleanup.AbbreviateJournalCleanup (and org.jabref.logic.cleanup.AbbreviateJournalCleanup) both needed access to a JournalAbbreviationRepository object. Many of the changes in this PR are related to this dependency being passed down from org.jabref.gui.frame.MainMenu and org.jabref.gui.frame.MainToolBar. This issue is further described at this comment and this comment

It was suggested here that the journal abbreviation menu items instead be added to the field formatters in the UI, and implemented as a Formatter. The reason this was not done is because all the formatters act as stateless transformations, and are instantiated without any parameters (see org.jabref.logic.formatter.Formatters). Journal Abbreviation is notably not stateless, as it needs access to JournalAbbreviationRepository. Theoretically, this could be overcome with dependency injection into the logic layer, but I believe that violates the architecture.

How To Test

IMPORTANT NOTE: When testing and switching from running JabRef on this branch to running JabRef on the main branch, I had an unhandled exception because a new enum constant (e.g. UNABBREVIATE) persisted in the user preferences, but the code on main doesn't define this constant:

The only workaround I have found for this is to go in JabRef to File -> Preferences -> Reset Preferences and then hit save.

1. Open the “Clean up entries” dialog (Quality → “Clean up entries”).
2. Select a group of entries with different journal names.
3. In “Journal‐related,” pick Abbreviate (default) or Unabbreviate, then apply cleanup.
4. Observe that the journal fields have become either abbreviated or unabbreviated accordingly.
5. If you open the Cleanup dialog again, your choice in the combo box should persist in subsequent sessions (provided you store your preferences).

Additionally:

• Try “Abbreviate (dotless)” or “Abbreviate (shortest unique)” on a few entries with known abbreviations (like “Physical Review Letters” → “PRL”).
• Run the tests at org.jabref.logic.cleanup.AbbreviateJournalCleanupTest, org.jabref.logic.cleanup.UnabbreviateJournalCleanupTest, and org.jabref.logic.journals.JournalAbbreviationRepositoryTest

Mandatory checks

• I own the copyright of the code submitted and I license it under the MIT license
• Change in CHANGELOG.md described in a way that is understandable for the average user (if change is visible to the user)
• Tests created for changes (if applicable)
• Manually tested changed features in running JabRef (always required)
• Screenshots added in PR description (if change is visible to the user)
• 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.

[GDeane]

This is kind of concerning. I don't know why it's taking 50 minutes:

I did close some of its comments which I judged invalid as they popped up. I dunno if that caused this

[koppor]

This refs #11305 (comment)

[trag-bot]

@trag-bot didn't find any issues in the code! ✅✨