Convert MSC code Cleanup to Formatter #13233

JustinHennis1 · 2025-06-03T02:44:10Z

Removed Cleanup functionality for MSC Code conversion. Added formatter at bottom of preset panel because formatters handle single-field conversion.

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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.

… URL object

…to ktooltip updates from jabref main

…to ktooltip pulling changes from main to local

…till in progress

…iptions, bug: error when trying to cleanup when editor is open

…er and special characters were added

…rors in other files

…till in progress

…to ktooltip Pulling changes from main

… Test cases

jablib/src/main/java/org/jabref/logic/formatter/bibtexfields/ConvertMSCCodesFormatter.java

JustinHennis1 · 2025-06-04T04:29:30Z

@koppor I think it's ready for review

koppor

Please revet changes in sub modules - see https://devdocs.jabref.org/code-howtos/faq.html#submodules

CHANGELOG.md

jablib/src/main/java/org/jabref/logic/formatter/bibtexfields/ConvertMSCCodesFormatter.java

koppor · 2025-06-05T02:20:54Z

jablib/src/main/java/org/jabref/logic/formatter/bibtexfields/ConvertMSCCodesFormatter.java

+            return result.toString();
+        }
+        // text contains comma separated codes
+        String[] codeList = result.toString().split(",");


Use org.jabref.model.entry.KeywordList#parse(java.lang.String, java.lang.Character, java.lang.Character) and then work on KeywordList

Reason: Better data structure and adheres to user configuration (keyword delimiter) and escpaings.

See at other usages of the parser and how to pass the prefernces

At first, I thought:

Suggested change

String[] codeList = result.toString().split(",");

String[] codeList = text.toString().split(",");

but this is wrong, because no escaping treatment etc.

jablib/src/main/java/org/jabref/logic/formatter/bibtexfields/ConvertMSCCodesFormatter.java

koppor · 2025-06-07T19:31:35Z

jablib/src/main/java/org/jabref/logic/cleanup/FieldFormatterCleanups.java

@@ -87,6 +90,13 @@ public FieldFormatterCleanups(boolean enabled, List<FieldFormatterCleanup> actio
        this.actions = Objects.requireNonNull(actions);
    }

+    public FieldFormatterCleanups(boolean enabled, List<FieldFormatterCleanup> actions, BibEntryPreferences preferences) {


Needs to be reviewed in IDE - why this general method is needed - until now, this was not needed - and the formatter worked.

I had no way to retrieve BibEntryPreferences so that I could call getKeywordSeperator. This is used to inject preferences so that the formatter can use a dynamic delimiter.

If there is another method of retrieving BibEntryPreferences pleases lmk.

Why is getInstance() deprecated for JabrefCLIPreferences Class? Isn't the point of this class to allow preferences to be accessible globally. @koppor

I feel like it defeats the purpose to implement a Singleton design that isn't easily accessible. 😅

Preferences are indeed singleton but nonetheless you should avoid calling get instance as it creates a tight coupling between the two classes and hinders testing.
That's why you should pass or inject them via constructor so you can still mock them

Thanks for clarifying. @Siedlerchr

That said, do you think my approach was correct?

Creating a new constructor for FieldFormatterCleanups
In JabrefCliPreferences, passing BibEntryPreferences to this constructor
Finally, passing those preferences down to the formatter to get the keyword separator.

Where is your method used? I did I do a mistake at checking out your branch?

I think, in this case, it is OK to use Injector.instantiateModelOrService(CliPreferences.class) and then get your preferences for that.

Do this at the latest point in time - and do not initialize a default value ,

Note that you already have

Character dlim = preferences.getKeywordSeparator();

At this place, use this injector "magic".

Add a javadoc comment to the class that it relies to on Injector.instantiateModelOrService(CliPreferences.class), and add a reason. Maybe "because routing through this dependency causes too much changes."

Where is your method used? I did I do a mistake at checking out your branch?

My fault, I think I forgot to change this (I was testing setter vs constructor injection), I put it in this method of JabRefCliPreferences initially.

koppor · 2025-06-07T19:33:19Z

@JustinHennis1 Could you try to revert the change in the sub module - see https://devdocs.jabref.org/code-howtos/faq.html#submodules

Which git client did you use? Maybe, we can search for a bug report there and ask all developers of JabRef to give a +1 there. (the bug is that ignore = all is not handled by the git client)

JustinHennis1 · 2025-06-07T19:50:39Z

@JustinHennis1 Could you try to revert the change in the sub module - see https://devdocs.jabref.org/code-howtos/faq.html#submodules

Which git client did you use? Maybe, we can search for a bug report there and ask all developers of JabRef to give a +1 there. (the bug is that ignore = all is not handled by the git client)

I'm using Git CMD on my Windows Laptop. I just merged main back into my fork, did that fix it?

koppor · 2025-06-11T07:40:37Z

I'm using Git CMD on my Windows Laptop. I just merged main back into my fork, did that fix it?

The diff doesn't show any changes, thus this worked :)

…to ktooltip

jablib/src/test/java/org/jabref/logic/formatter/bibtexfields/ConvertMSCCodesFormatterTest.java

JustinHennis1 · 2025-06-12T00:17:47Z

@koppor

👋 Hey, I completed the following:

made changes so that we use Injector to instantiate JabrefCliPreferences in the ConvertMSCCodesFormatter.
changed ConvertMSCCodesFormatterTest back to using the default constructor.
added comments in JabrefCliPreferences specifying why constructor was made public as well as the reason for the changes (without being made public, a java.lang access exception is thrown)

trag-bot · 2025-06-12T17:59:34Z

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

JustinHennis1 and others added 30 commits April 8, 2025 22:38

added msc codes, keyword tooltip feature

0f77aba

keyword tooltip feature#423, changelog updated

9cec66b

Merge branch 'main' into ktooltip

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uses getResource to find json/loadMscCodesFromJson overloaded to take…

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… URL object

Merge branch 'ktooltip' of https://github.com/JustinHennis1/jabref in…

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…to ktooltip updates from jabref main

printstacktrace removed from MscCodeUtils

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Switched from File to Path.of in loadMscFromJson

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Merge branch 'JabRef:main' into ktooltip

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checkstyle compliance

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Merge branch 'ktooltip' of https://github.com/JustinHennis1/jabref in…

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…to ktooltip pulling changes from main to local

fixed markdown check

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Added logic for MSC code conversion cleanup. Actual cleanup() logic s…

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…till in progress

added secondary cleanup to convert keywords in entries to their descr…

1ab572d

…iptions, bug: error when trying to cleanup when editor is open

MSC code cleanup functional, msc_codes.json cleaned for comma delimit…

a1d0c92

…er and special characters were added

Cleaned msc json for extra commas

475c3b9

Tests updated for msc code conversion

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Passes Checkstyle and RewriteDryRun, cleanup mentioned in changelog

965a564

Markup check

903f2e1

MSC cleanup test modified because conversion is async,Fixed syntax er…

87203b1

…rors in other files

loadMSCCodes is wrapped in Optional, Custom Exception created

53b47a6

loadMSCCodeFromJson: empty optional returned, cstyle compliant

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Merge branch 'main' into ktooltip

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localizations added, most tests pass, javafx issue with cleanuptest s…

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…till in progress

Merge branch 'ktooltip' of https://github.com/JustinHennis1/jabref in…

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…to ktooltip Pulling changes from main

JavaFX initializes once for tests

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Tests Pass Local, Using Platform class to check JavaFX initialized in…

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… Test cases

Features and Tests work, one caveat issue w/ JavaFX

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Merge branch 'main' into ktooltip

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Merge branch 'main' into ktooltip

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Language Localizations added, FF principle fixes

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JustinHennis1 and others added 5 commits May 26, 2025 17:23

Merge branch 'main' into ktooltip

99cb9d3

Removed Cleanup, Added Single Action Formatter

e41c3b7

Merge remote-tracking branch 'upstream/main' into ktooltip

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merged main and updated conflicts

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removed unused import

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JustinHennis1 added 2 commits June 3, 2025 13:50

Update CHANGELOG.md

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Merge branch 'main' into ktooltip

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koppor requested changes Jun 5, 2025

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Update ConvertMSCCodesFormatter

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fix test, remove debug statements

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koppor reviewed Jun 7, 2025

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Merge branch 'main' into ktooltip

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JustinHennis1 added 3 commits June 11, 2025 04:45

Uses Injector in Formatter

afc3e1b

Merge branch 'ktooltip' of https://github.com/JustinHennis1/jabref in…

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Fix test, unused import

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JustinHennis1 added 2 commits June 11, 2025 05:11

Merge branch 'main' into ktooltip

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Merge branch 'main' into ktooltip

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JustinHennis1 requested a review from koppor June 12, 2025 03:51

Merge branch 'main' into ktooltip

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	String[] codeList = result.toString().split(",");
	String[] codeList = text.toString().split(",");

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Convert MSC code Cleanup to Formatter #13233

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JustinHennis1 commented Jun 4, 2025

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JustinHennis1 Jun 11, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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koppor commented Jun 7, 2025

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JustinHennis1 commented Jun 7, 2025

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koppor commented Jun 11, 2025

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JustinHennis1 commented Jun 12, 2025

👋 Hey, I completed the following:

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JustinHennis1 commented Jun 3, 2025 •

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