Add Copy markdown to copy citation #13387

tushar-2320 · 2025-06-21T12:35:52Z

Closes #12552
This pr contains the changes by adding the Markdown citation copy in the preview panel.I have added changes StandardAction.java ,RightClickMenu.java,CitationStyleOutputFormat.java,ClipboardContentGenerator.java by adding Markdown format and their style respectively.

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.

tushar-2320 · 2025-06-21T12:43:33Z

hey ,can you just guide If I am in the right direction or not.

calixtus · 2025-06-21T14:02:33Z

You could start by fixing your PR description.

tushar-2320 · 2025-06-22T05:57:59Z

I have made the changes but not able find the fault as I can't see the effect in ui
can anyone review and guide me through this.

koppor · 2025-06-22T06:45:23Z

I have made the changes but not able find the fault as I can't see the effect in ui

fault of the test? -> Ignore that one (its an online download thing and the server is unreliable)
GUI effect -> you should be able to see your changes.

can anyone review and guide me through this.

Please add a CHANGELOG.md entry.

koppor · 2025-06-22T07:03:27Z

Tried out, UI works...

Update The content is a bit strange. I checked the code - it seems, citeproc.java is not used correctly?

\[1\]L\. Wegmeth\, T\. Vente\, and J\. Beel\, “Recommender Systems Algorithm Selection for Ranking Prediction on Implicit Feedback Datasets\,” in *Proceedings of the 18th ACM Conference on Recommender Systems*\, in RecSys ’24\. New York\, NY\, USA\: Association for Computing Machinery\, Oct\. 2024\, pp\. 1163–1167\. doi\: 10\.1145\/3640457\.3691718\.<br />

koppor

After a deeper look, I did not see any wiring in the library https://github.com/michel-kraemer/citeproc-java. Please do so.

koppor · 2025-06-22T07:04:49Z

jablib/src/main/java/org/jabref/logic/citationstyle/CitationStyleOutputFormat.java

@@ -5,7 +5,8 @@
 public enum CitationStyleOutputFormat {

    HTML("html", OS.NEWLINE + "<br>" + OS.NEWLINE),
-    TEXT("text", "");
+    TEXT("text", ""),
+    MARKDOWN("markdown", OS.NEWLINE + "<br>" + OS.NEWLINE);


<br> is not a good line separator in markdown. Just remove it. Two empty lines are ok.

koppor · 2025-06-22T07:08:11Z

jabgui/src/main/java/org/jabref/gui/preview/ClipboardContentGenerator.java

@@ -120,6 +121,13 @@ static ClipboardContent processHtml(List<String> citations) {
        return content;
    }

+    static ClipboardContent processMarkdown(List<String> citations) {
+        String result = String.join(CitationStyleOutputFormat.MARKDOWN.getLineSeparator(), citations);


Where is the convertion to Markdown made?

I think, you need to deal with setOutputFormat somehow michel-kraemer/citeproc-java@66cad6b

…r-issue-12552

koppor

Add a test so that one "sees" a conversion result in the code.

trag-bot · 2025-06-27T05:04:54Z

jabgui/src/main/java/org/jabref/gui/preview/ClipboardContentGenerator.java

+    /**
+     * Insert each citation into HTML.
+     * convert HTML to markdown using flexmark.
+    */


The comment is trivial and simply restates what the code does without providing additional information about the reasoning or important details about the implementation.

jabref-machine · 2025-07-07T21:38:23Z

JUnit tests of jablib are failing. You can see which checks are failing by locating the box "Some checks were not successful" on the pull request page. To see the test output, locate "Tests / Unit tests (pull_request)" and click on it.

You can then run these tests in IntelliJ to reproduce the failing tests locally. We offer a quick test running howto in the section Final build system checks in our setup guide.

trag-bot · 2025-07-19T04:42:44Z

jabgui/src/main/java/org/jabref/gui/preview/ClipboardContentGenerator.java

+     * convert HTML to markdown using flexmark.
+    */
+    @VisibleForTesting
+    static ClipboardContent processMarkdown(List<String> citations) {


The method uses string concatenation for multiline HTML template instead of Java text blocks ("""). This makes the code less readable and maintainable.

…r-issue-12552

Siedlerchr · 2025-07-19T11:39:19Z

jabgui/src/test/java/org/jabref/gui/preview/ClipboardContentGeneratorTest.java

+        String actual = markdown.getString();
+
+        // Print actual output for debugging
+        System.out.println("=== Actual Markdown Output ===");


No need for these, on failure assertEquals will show the diff

subhramit · 2025-07-21T06:55:28Z

jabgui/src/test/java/org/jabref/gui/preview/ClipboardContentGeneratorTest.java

+        // Normalize both strings to ignore whitespace and formatting issues
+        String normalizedActual = actual.replaceAll("\\s+", " ").trim();
+        String normalizedExpected = expected.replaceAll("\\s+", " ").trim();


What are "formatting issues" here specifically?
Given we know the expected string, can we trace where the extra whitespaces might come from in the actual?

actually you are right I think I was getting cautious that is why I was removing whitespaces.
but I understood that it overall fails the point of testing.

…ping.

trag-bot · 2025-07-23T05:06:07Z

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

koppor · 2025-07-23T22:02:37Z

jabgui/src/main/java/org/jabref/gui/preview/ClipboardContentGenerator.java

+     * convert HTML to markdown using flexmark.
+    */
+    @VisibleForTesting
+    static ClipboardContent processMarkdown(List<String> citations) {


You followed @Siedlerchr's recommendation and did not follow mine to use citeproc-java conversion. (michel-kraemer/citeproc-java@66cad6b)

There needs to be AT LEAST a comment, why citeproc-java could not be used.

I was unaware of this, good point

Maybe my comment here #13387 (comment) is of help? Just to try out how to route things to that plugin?

Because it works for all previews! Not just csl. I see no advantage in using citeproc here.

My only point is that find citeproc more configurable than flexmark.
flexmark do that only in one line.
in citeproc I think we have to write a function to do that.

I would do case handling

If CSL use citeproc (specialized!, e.g. DOI linked)

If no CSL, use flexmark

Discussion/changes pending

tushar-panto and others added 3 commits June 21, 2025 18:02

fix:Added copy Markdown to copy citation JabRef#12552.

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Merge branch 'main' into fix-for-issue-12552

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Merge branch 'main' into fix-for-issue-12552

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calixtus marked this pull request as draft June 21, 2025 14:02

Merge branch 'main' into fix-for-issue-12552

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koppor requested changes Jun 22, 2025

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tushar-2320 and others added 6 commits June 22, 2025 16:29

Merge branch 'main' into fix-for-issue-12552

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Merge branch 'main' into fix-for-issue-12552

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fix:Added copy Markdown to copy citation JabRef#12552.

49b035b

Merge branch 'main' into fix-for-issue-12552

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fix:Added copy Markdown to copy citation JabRef#12552.

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Merge remote-tracking branch 'origin/fix-for-issue-12552' into fix-fo…

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…r-issue-12552

tushar-2320 requested a review from koppor June 24, 2025 12:08

koppor requested changes Jun 25, 2025

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fix:Added @VisibleForTesting in method processMarkdown JabRef#12552.

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trag-bot bot reviewed Jun 27, 2025

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calixtus changed the title ~~Draft:fix:Added copy Markdown to copy citation #12552.~~ Add Copy markdown to copy citation Jun 27, 2025

calixtus added the component: entry-preview label Jun 27, 2025

Merge branch 'main' into fix-for-issue-12552

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Merge branch 'main' into fix-for-issue-12552

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tushar-2320 marked this pull request as ready for review July 19, 2025 04:33

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tushar-panto added 2 commits July 19, 2025 11:57

Merge remote-tracking branch 'origin/fix-for-issue-12552' into fix-fo…

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…r-issue-12552

fix:submodule removal

e805e7e

tushar-panto added 2 commits July 19, 2025 11:58

fix:Added @VisibleForTesting in method processMarkdown JabRef#12552.

7b3fbf7

Revert submodule changes to match main

b3eb93c

tushar-2320 force-pushed the fix-for-issue-12552 branch from 0c2907f to b3eb93c Compare July 19, 2025 06:29

Reset submodule pointers to match main branch

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tushar-2320 requested a review from koppor July 19, 2025 06:52

Siedlerchr reviewed Jul 19, 2025

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Siedlerchr previously approved these changes Jul 19, 2025

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koppor added the status: awaiting-second-review For non-trivial changes label Jul 20, 2025

Merge branch 'main' into fix-for-issue-12552

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subhramit reviewed Jul 21, 2025

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tushar-2320 and others added 2 commits July 21, 2025 14:26

Merge branch 'main' into fix-for-issue-12552

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refactor:removed unecessary debugging statements and whitespace strip…

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…ping.

tushar-2320 dismissed Siedlerchr’s stale review via f6b4131 July 21, 2025 09:04

refactor:used List.of instead of Array.asList

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subhramit previously approved these changes Jul 21, 2025

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subhramit removed the status: awaiting-second-review For non-trivial changes label Jul 21, 2025

tushar-2320 requested a review from Siedlerchr July 21, 2025 09:34

Merge branch 'main' into fix-for-issue-12552

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koppor requested changes Jul 23, 2025

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tushar-2320 commented Jun 21, 2025 •

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