Feature/14361 enable parameters for cli by CodeRishiX · Pull Request #14500 · JabRef/jabref

CodeRishiX · 2025-12-03T04:19:16Z

Added customizable parameters to JabKit's citationkeys generate command. Users can now configure citation key generation settings via CLI parameters, matching the customization options available in the JabRef GUI.

Implemented all CitationKeyPatternPreferences options as CLI parameters.

Steps to test

Verify CLI options:

./gradlew :jabkit:run --args="citationkeys generate --help"

output :
Shows all citation key options
Confirms subcommand hierarchy

Verify functionality:

./gradlew :jabkit:run --args="citationkeys generate --input=C:/git-repositories/jabref/jablib/src/main/resources/Chocolate.bib --pattern='[author][year]' --transliterate --warn-before-overwrite --suffix=ALWAYS --regex='[^a-zA-Z0-9]' --regex-replacement='' --keyword-delimiter='_'"

No GUI settings are modified — this only affects the current CLI run

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.

calixtus · 2025-12-03T07:59:42Z

jabkit/src/main/java/org/jabref/toolkit/commands/GenerateCitationKeys.java

+    @Option(names = "--output", description = "The output .bib file.")
    private Path outputFile;

+    @Option(


Please implement as a subcommand. We need to keep some hierarchy to keep JabRef and all of its features manageable.

Okay thanks for suggesting .

@calixtus
Thanks again for the guidance. I followed your suggestion and tried to update the hierarchy accordingly. Could you please check if it looks correct now and let me know if I should adjust anything before I continue adding the remaining parts?

@CodeRishiX Did you update the screenshot in the PR description?

calixtus · 2025-12-03T08:01:15Z

README.md

@@ -1,4 +1,4 @@
-# JabRef Bibliography Management [![APIdia](https://apidia.net/java/JabRef/main/badge.svg)](https://apidia.net/java/JabRef/main)
+  # JabRef Bibliography Management [![APIdia](https://apidia.net/java/JabRef/main/badge.svg)](https://apidia.net/java/JabRef/main)


This change seems unrelated to your PR. Please undo.

calixtus · 2025-12-03T08:01:38Z

jabkit/src/main/java/org/jabref/toolkit/commands/GenerateCitationKeys.java

        CitationKeyGenerator keyGenerator = new CitationKeyGenerator(
                databaseContext,
-                argumentProcessor.cliPreferences.getCitationKeyPatternPreferences());
+                prefs);


We do not use abbreviations.

calixtus · 2025-12-03T08:02:03Z

jabkit/src/main/java/org/jabref/toolkit/commands/GenerateCitationKeys.java

            System.out.println(Localization.lang("Regenerating citation keys according to metadata."));
        }

+        var prefs = argumentProcessor.cliPreferences.getCitationKeyPatternPreferences();


We do not use abbreviations.

…ubcommand

koppor · 2025-12-04T11:28:41Z

README.md


 For any inquiries, feel free to [contact ProductMap.ai](https://product-map.ai).
+
+<!-- markdownlint-disable-file MD060 -->


This change seems to be OK - https://github.com/DavidAnson/markdownlint/blob/main/doc/Rules.md#md060---table-column-style

koppor · 2025-12-04T11:29:11Z

jabkit/src/main/java/org/jabref/toolkit/commands/CitationKeyCommands.java

+
+@Command(
+        name = "citationkeys",
+        description = "Manage citation key operations.",


I think, this is not a good text. Maybe just remove it.

koppor · 2025-12-04T11:30:10Z

test.bib

@@ -0,0 +1,12 @@
+@article{dummy,


Please use src/main/resources/Chocolate.bib instead of putting a .bib file in the root of the repository.

…est.bib, undo README changes

CodeRishiX · 2025-12-06T16:58:38Z

@koppor @calixtus Fixed all review comments as suggested - removed CitationKeyCommands description, deleted test.bib, and resolved README changes.

koppor

Some comments; I don't know What is left todo - the PR is flagged as "draft"

koppor · 2025-12-07T22:41:51Z

jabkit/src/main/java/org/jabref/toolkit/commands/CitationKeyCommands.java

+
+    @Override
+    public void run() {
+        System.out.println("Testing");


This indicates that the PR is sitll draft

jabkit/src/main/java/org/jabref/toolkit/commands/GenerateCitationKeys.java

koppor · 2025-12-07T22:45:07Z

Not fully optimized yet.

Please work on this. See the screenshot at #14361.

…escription.

…egex, delimiter, etc.)

CodeRishiX · 2025-12-12T17:03:48Z

@calixtus @koppor
Hi!
I’ve implemented all parameters of CitationKeyPatternPreferences in the CLI except the per-entry-type patterns.

CitationKeyPatternPreferences supports type-specific patterns , but JabKit’s GlobalCitationKeyPatterns currently applies only a single default pattern and does not support per-entry-type overrides.

public class GlobalCitationKeyPatterns extends AbstractCitationKeyPatterns {

public GlobalCitationKeyPatterns(CitationKeyPattern defaultPattern) {
    this.defaultPattern = defaultPattern;
}

public static GlobalCitationKeyPatterns fromPattern(String pattern) {
    return new GlobalCitationKeyPatterns(new CitationKeyPattern(pattern));
}

@Override
public CitationKeyPattern getLastLevelCitationKeyPattern(EntryType entryType) {
    return defaultPattern;
}

Because of this mismatch, I’ve kept keyPatterns unchanged for now until your guidance.

Thanks!

koppor · 2025-12-17T10:05:17Z

jabkit/src/main/java/org/jabref/toolkit/commands/JabKit.java

                DoiToBibtex.class,
                Fetch.class,
                GenerateBibFromAux.class,
-                GenerateCitationKeys.class,


This should be noted in "Removed" in CHANGELOG.md

CodeRishiX · 2025-12-17T14:02:26Z

I wonder why there is not any banner displayed?

Hi @calixtus I’m not fully sure what you mean by the missing banner here. Do you expect the standard JabKit startup banner to be shown for citationkeys generate, or some explicit output indicating that the command is running/completed? Just want to confirm before implementing. Thanks!

koppor · 2025-12-19T11:48:23Z

I wonder why there is not any banner displayed?

No banner is OK --> #14664

…nKeys

koppor · 2025-12-19T20:25:03Z

CHANGELOG.md


 ### Removed

+- We removed `generate-citation-keys` as a standalone command in JabKit. Use `citationkeys generate` instead. [#14361](https://github.com/JabRef/jabref/issues/14361)


Link the PR here, because it is not in the issue.

koppor · 2025-12-19T20:25:56Z

jabkit/src/main/java/org/jabref/toolkit/commands/GenerateCitationKeys.java

+    @Option(names = "--output", description = "The output .bib file.")
    private Path outputFile;

+    @Option(


@CodeRishiX Did you update the screenshot in the PR description?

koppor · 2025-12-19T20:27:15Z

jabkit/src/main/java/org/jabref/toolkit/commands/GenerateCitationKeys.java

+                    avoidOverwrite != null ? avoidOverwrite : existingPreferences.shouldAvoidOverwriteCiteKey(),
+                    warnBeforeOverwrite != null ? warnBeforeOverwrite : existingPreferences.shouldWarnBeforeOverwriteCiteKey(),
+                    generateBeforeSaving != null ? generateBeforeSaving : existingPreferences.shouldGenerateCiteKeysBeforeSaving(),
+                    suffix != null ? suffix : existingPreferences.getKeySuffix(),


Keep key -- variable should be keySuffix. See other lines. They are consistent (somehow)

koppor · 2025-12-19T20:27:27Z

jabkit/src/main/java/org/jabref/toolkit/commands/GenerateCitationKeys.java

+                    transliterate != null ? transliterate : existingPreferences.shouldTransliterateFieldsForCitationKey(),
+                    avoidOverwrite != null ? avoidOverwrite : existingPreferences.shouldAvoidOverwriteCiteKey(),
+                    warnBeforeOverwrite != null ? warnBeforeOverwrite : existingPreferences.shouldWarnBeforeOverwriteCiteKey(),
+                    generateBeforeSaving != null ? generateBeforeSaving : existingPreferences.shouldGenerateCiteKeysBeforeSaving(),


Be consistent left and right.

…d options

…ture/14361-enable-parameters-for-cli

calixtus

Minor tweaks to codestyle and handling of command with no subcommand.

addressed

Siedlerchr · 2025-12-21T23:01:36Z

jabkit/src/main/java/org/jabref/toolkit/commands/GenerateCitationKeys.java

+                keyPatternRegex != null ? keyPatternRegex : existingPreferences.getKeyPatternRegex(),
+                keyPatternReplacement != null ? keyPatternReplacement : existingPreferences.getKeyPatternReplacement(),
+                unwantedCharacters != null ? unwantedCharacters : existingPreferences.getUnwantedCharacters(),
+                existingPreferences.getKeyPatterns(),


is this correct?

Yes, looks correct to me. keypatterns cannot be overridden in the commandline. would be a funny commandline.

Yes, looks correct to me. keypatterns cannot be overridden in the commandline. would be a funny commandline.

But it was wished in the issue

Offer each element of CitationKeyPatternPreferences as parameter in the CLI for org.jabref.toolkit.commands.GenerateCitationKeys

Reason: Use on server-side.

Yes, looks correct to me. keypatterns cannot be overridden in the commandline. would be a funny commandline.

But it was wished in the issue

Offer each element of CitationKeyPatternPreferences as parameter in the CLI for org.jabref.toolkit.commands.GenerateCitationKeys

Reason: Use on server-side.

@koppor I agree , maybe this matches the limitation I mentioned in my comment two weeks ago about keyPatterns and GlobalCitationKeyPatterns,

Yes, looks correct to me. keypatterns cannot be overridden in the commandline. would be a funny commandline.

But it was wished in the issue

Offer each element of CitationKeyPatternPreferences as parameter in the CLI for org.jabref.toolkit.commands.GenerateCitationKeys

Reason: Use on server-side.

@koppor I agree , maybe this matches the limitation I mentioned in my comment two weeks ago about keyPatterns and GlobalCitationKeyPatterns,

The next contributor will have to think of this. If we dive that deep, we could solve the issue for ourselves. We could then leave out humans and just use AI agents. (And believe me, we are short before doing this 😅).

koppor · 2025-12-23T20:07:38Z

jabkit/src/main/java/org/jabref/toolkit/commands/GenerateCitationKeys.java

+                transliterate != null ? transliterate : existingPreferences.shouldTransliterateFieldsForCitationKey(),
+                avoidOverwrite != null ? avoidOverwrite : existingPreferences.shouldAvoidOverwriteCiteKey(),
+                warnBeforeOverwrite != null ? warnBeforeOverwrite : existingPreferences.shouldWarnBeforeOverwriteCiteKey(),
+                generateBeforeSaving != null ? generateBeforeSaving : existingPreferences.shouldGenerateCiteKeysBeforeSaving(),


The naming is still inconsistent.

CodeRishiX added 2 commits December 3, 2025 09:17

add --pattern option support for citation key generation

4fe7d9d

(cli): add --pattern option support for citation key generation

13d4136

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calixtus reviewed Dec 3, 2025

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JabKit: add citationkeys command and move generate-citation-keys as s…

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…ubcommand

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CodeRishiX added 2 commits December 6, 2025 22:09

Fix review comments: remove CitationKeyCommands description, delete t…

d04412e

…est.bib, undo README changes

Merge branch 'main' into feature/14361-enable-parameters-for-cli

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Fix code style: remove var keyword, rename pattern variable, update d…

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Merge branch 'main' into feature/14361-enable-parameters-for-cli

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calixtus added component: JabKit [cli] component: citationkey-generator labels Dec 12, 2025

CodeRishiX added 2 commits December 12, 2025 22:11

Add citation key generation options to JabKit CLI (pattern, suffix, r…

aadb52c

…egex, delimiter, etc.)

Add citation key generation options to JabKit CLI (pattern, suffix, r…

0370046

…egex, delimiter, etc.)

CodeRishiX added 2 commits December 13, 2025 10:05

Merge branch 'main' into feature/14361-enable-parameters-for-cli

477f3f6

Updated CHANGELOG.md

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CodeRishiX added 3 commits December 18, 2025 22:45

Clean up preferences handling and address review feedback

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Clean up preferences handling and address review feedback

b1b9a12

Update CHANGELOG for version 6.0-alpha.3

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github-actions bot removed the status: changes-required Pull requests that are not yet complete label Dec 18, 2025

Merge branch 'main' into feature/14361-enable-parameters-for-cli

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koppor mentioned this pull request Dec 19, 2025

Add requirement to the banner #14664

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CodeRishiX added 3 commits December 19, 2025 20:36

remove abbreviations and keep naming consistency for GenerateCitatio…

90c5a4f

…nKeys

Merge branch 'main' into feature/14361-enable-parameters-for-cli

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Merge branch 'main' into feature/14361-enable-parameters-for-cli

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Merge branch 'main' into feature/14361-enable-parameters-for-cli

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CodeRishiX and others added 4 commits December 20, 2025 21:35

Refactor GenerateCitationKeys to improve parameter naming consistency

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Merge branch 'main' into feature/14361-enable-parameters-for-cli

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Minor tweaks for consistency in codestyle and handling missing comman…

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…d options

Merge remote-tracking branch 'upstream/main' into fork/CodeRishiX/fea…

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…ture/14361-enable-parameters-for-cli

calixtus approved these changes Dec 21, 2025

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Merged via the queue into JabRef:main with commit 6671728 Dec 21, 2025
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github-actions bot mentioned this pull request Dec 21, 2025

Enable parameters for CLI: generate-citation-keys #14361

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Siedlerchr reviewed Dec 21, 2025

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koppor mentioned this pull request Dec 23, 2025

Enable configuration of citation key patterns at the CLI #14707

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		@@ -1,4 +1,4 @@
		# JabRef Bibliography Management [![APIdia](https://apidia.net/java/JabRef/main/badge.svg)](https://apidia.net/java/JabRef/main)
		# JabRef Bibliography Management [![APIdia](https://apidia.net/java/JabRef/main/badge.svg)](https://apidia.net/java/JabRef/main)


		For any inquiries, feel free to [contact ProductMap.ai](https://product-map.ai).

		<!-- markdownlint-disable-file MD060 -->


		### Removed

		- We removed `generate-citation-keys` as a standalone command in JabKit. Use `citationkeys generate` instead. [#14361](https://github.com/JabRef/jabref/issues/14361)

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CodeRishiX commented Dec 3, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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CodeRishiX commented Dec 6, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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koppor commented Dec 7, 2025

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calixtus Dec 21, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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CodeRishiX commented Dec 3, 2025 •

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