Add Markdown rendering to AI Chat by Yubo-Cao · Pull Request #13194 · JabRef/jabref

Yubo-Cao · 2025-05-30T18:14:58Z

Closes #12234 (partially)

See this: https://drive.google.com/file/d/1VOvWBLP5E9I_sLXd7RpShfXoP0ttg0JZ/view?usp=sharing for a quick demo. Ctrl+C is supported as a part of this PR as well.

Before:

After:

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) (not 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.

… markdown-ai

subhramit

Code reads really good.
Did not try out, but demo is attached to the description, so green from me.
Thanks @Yubo-Cao!

koppor · 2025-05-31T07:38:02Z

See this: drive.google.com/file/d/1VOvWBLP5E9I_sLXd7RpShfXoP0ttg0JZ/view?usp=sharing for a quick demo.

Looks very nice.

Side track: "Summary" is a very different AI function, therefore @InAnYan put another tab for "Summary". -- For instance, for large PDFs, JabRef splits into chuncks and summarizes chunks.

koppor

Only a small comment.

Are spaces correctly handled for the getTextFlowContent()?

I assume, adding test cases is too hard here?

InAnYan · 2025-05-31T18:58:04Z

This is wonderful, Yubo!

I can copy text! And you also solved a very very naughty problem, when you could click on past messages and chat scrolled down! That problem make me feel desperate about JavaFX.

I could approve this PR without reviewing code 😄

Though, I remembered I have one small addition

InAnYan

Unfortunately, I had to request one small change

InAnYan · 2025-05-31T19:04:58Z

+/**
+ * A TextFlow that allows text selection and copying.
+ */
+public class SelectableTextFlow extends TextFlow {


OMG, Yubo, is it possible to submit this code to some library? GemsFX maybe? This is a very useful piece of code

+1 for GemsFX. If the maintainer Dirk doesn't want it, then ControlsFX

Yubo-Cao · 2025-06-01T02:02:23Z

Only a small comment.

Are spaces correctly handled for the getTextFlowContent()?

I assume, adding test cases is too hard here?

So after actually switch to Arch Linux and run testcases over there (of course that was not needed at all to come up with this conclusion looking at how I butchered the Markdown AST), is that we currently don't handle whitespace perfectly, if at all.

White space inside a single markdown node is always preserved, so *italic with space* that kind of thing is OK
White space between nodes is always not preserved.
Bulleted indentation always get destroyed (if you nest).
Original markdown style marker would always disappear (think * and all those special characters)

I think my new attempt would be trying to keep track a bit more metadata in MarkdownTextflow and basically override getTextFlowContent.

subhramit · 2025-06-01T11:45:54Z

@Yubo-Cao Please resolve conversations after you push the commits resolving them, not before

subhramit · 2025-06-02T22:35:05Z

If things get too convoluted, git merge upstream/main, git reset upstream/main and then make a fresh commit. you may have to force push.

Note: gitk --all to have the commit ids ready in gitk in case something goes wrong. Your local changes should not be lost, but it is always a good idea to have a trace/backup.

subhramit · 2025-06-02T22:37:26Z

If things get too convoluted, git merge upstream/main, git reset upstream/main and then make a fresh commit. you may have to force push.

Note: gitk --all to have the commit ids ready in gitk in case something goes wrong. Your local changes should not be lost, but it is always a good idea to have a trace/backup.

Another handy resource: https://ohshitgit.com/

koppor · 2025-06-02T22:41:19Z

If things get too convoluted, git merge upstream/main, git reset upstream/main and then make a fresh commit. you may have to force push.

However, JabRef mainatinaers don't like force pushes - only in rare emergency cases ^^

I always direct to https://lostechies.com/joshuaflanagan/2010/09/03/use-gitk-to-understand-git/ -- then, the git commands should be more understandable.

koppor · 2025-06-29T14:05:19Z

The IOB looks like it's coming from Flexmark.
Debug and see what token(s) produce this and then file an issue at their repo

Maybe MWE using a JUnit test...

subhramit

Green from me.
To summarize, TODOs:

Submission of useful jfx snippet to GemsFX/ControlsFX
MWE reproduction and reporting to Flexmark
File known issues in JabRef

Current:
Address Ruslan's comment on the changelog entry.

Rest seems good to go, thank you for such wonderful work, Yubo.

Yubo-Cao · 2025-06-29T14:24:40Z

I cannot reproduce the errors that Ruslan encountered. However, I added a check for string boundaries to ensure that this won't happen. Regarding the color contrast, I simply derived -jr-theme up a bit, and I think that would be sufficient.

InAnYan · 2025-06-29T15:10:40Z

OMG, maybe it is something wrong with my machine, if Yubo cannot reproduce my issues 🤣

Nice color change

calixtus · 2025-06-29T16:50:47Z

Can you do a screenshot with dark theme too please?

Yubo-Cao · 2025-07-01T11:16:43Z

Can you do a screenshot with dark theme too please?

Thank you so much for the catch! I honestly forget about the dark theme users ...

subhramit

Failing tests are related to CSL, ~~so I am queuing this.~~ Nvm there's conflicts and failing build tests too.

koppor · 2025-07-04T17:38:08Z

Failing tests are related to CSL, ~~so I am queuing this.~~ Nvm there's conflicts and failing build tests too.

I reverted CSL so that the assigned contributor has time to work on it.

trag-bot · 2025-07-04T18:39:51Z

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

Yubo-Cao and others added 3 commits May 30, 2025 14:07

feat: markdown in AI messages

e04f0de

docs: update CHANGELOG

ebcd900

Merge branch 'JabRef:main' into markdown-ai

ae2e2fa

trag-bot Bot reviewed May 30, 2025

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Comment thread jabgui/src/main/java/org/jabref/gui/util/MarkdownTextFlow.java Outdated

Yubo-Cao added 2 commits May 30, 2025 14:21

fix: note that Markdown is always valid, it never throw.

2b2fa66

Merge branch 'markdown-ai' of https://github.com/Yubo-Cao/jabref into…

be60b42

… markdown-ai

subhramit previously approved these changes May 30, 2025

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koppor reviewed May 31, 2025

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Comment thread jabgui/src/main/java/module-info.java Outdated

Comment thread jabgui/src/main/java/org/jabref/gui/ai/components/aichat/chatmessage/ChatMessageComponent.java Outdated

Comment thread jabgui/src/main/java/org/jabref/gui/util/SelectableTextFlow.java Outdated

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Yubo-Cao added 3 commits May 31, 2025 12:23

chore: move Flexmark dependency up

3336504

fix: remove null check for scnee

17becfb

docs: remove trivial documentation

abd52c0

Yubo-Cao dismissed subhramit’s stale review via abd52c0 May 31, 2025 16:26

trag-bot Bot reviewed May 31, 2025

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Comment thread jabgui/src/main/java/org/jabref/gui/util/MarkdownTextFlow.java Outdated

InAnYan requested changes May 31, 2025

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koppor reviewed May 31, 2025

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Comment thread jabgui/src/main/java/module-info.java Outdated

Improve whitespace and MarkdownTextflow's coping experience

99a6c3d

Yubo-Cao requested a review from InAnYan June 2, 2025 22:10

Yubo-Cao force-pushed the markdown-ai branch from 4e5b8c2 to 99a6c3d Compare June 2, 2025 22:55

Merge remote-tracking branch 'upstream/main' into markdown-ai

9e4ccfc

trag-bot Bot reviewed Jun 2, 2025

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Comment thread jabgui/src/main/java/org/jabref/gui/util/SelectableTextFlow.java Outdated

Use Deque and StringJoiner per code review.

9c31517

trag-bot Bot reviewed Jun 2, 2025

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Comment thread jabgui/src/main/java/org/jabref/gui/util/MarkdownTextFlow.java Outdated

subhramit previously approved these changes Jun 29, 2025

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Fix according to Ruslan

e3fa14f

Yubo-Cao dismissed stale reviews from subhramit and InAnYan via e3fa14f June 29, 2025 14:22

trag-bot Bot reviewed Jun 29, 2025

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Comment thread jabgui/src/main/java/org/jabref/gui/util/MarkdownTextFlow.java Outdated

Fix according to Trag

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Comment thread jabgui/src/main/java/org/jabref/gui/util/MarkdownTextFlow.java

subhramit previously approved these changes Jun 29, 2025

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subhramit added status: awaiting-second-review For non-trivial changes and removed status: ready-for-review Pull Requests that are ready to be reviewed by the maintainers labels Jun 29, 2025

Merge remote-tracking branch 'upstream/main' into markdown-ai

8547591

Improve dark theme for Markdown AI rendering

c402958

Yubo-Cao dismissed subhramit’s stale review via c402958 July 1, 2025 11:17

subhramit previously approved these changes Jul 4, 2025

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Merge remote-tracking branch 'upstream/main' into markdown-ai

6c8440d

Yubo-Cao dismissed subhramit’s stale review via 6c8440d July 4, 2025 18:34

subhramit approved these changes Jul 4, 2025

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subhramit added this pull request to the merge queue Jul 4, 2025

subhramit removed the status: awaiting-second-review For non-trivial changes label Jul 4, 2025

Merged via the queue into JabRef:main with commit f41f8ab Jul 4, 2025
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github-actions Bot mentioned this pull request Jul 4, 2025

Use Markdown in AI chat messages #12234

Closed

InAnYan mentioned this pull request Sep 12, 2025

When message in AI chat is clicked, it scrolls down #12232

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