AI Refactoring by InAnYan · Pull Request #726 · JabRef/jabref-koppor

InAnYan · 2026-04-24T20:10:50Z

Related issues and pull requests

Closes https://github.com/JabRef/jabref-issue-melting-pot/issues/698

Relevant documentation change: JabRef/user-documentation#625

PR Description

A big refactoring PR of the AI features. Also has new features.

Main changes:

Refactored UI to use the MVVM pattern.
Added regenerate button to chat messages.
Added the "AI Chat Status" window to show the state of an AI chat, ingested files, chatted entries and miscalleneus actions.
Added an abstraction layer for document splitter algorithms.
Added an abstraction layer for summarization algorithms.
Added a "full-document" summarization algorithm which just sends the full paper to the user message.
Added an abstraction layer for token estimation algorithms.
Added an abstraction layer for "answer engines" (it controls how RAG is performed).
Added a "full text" document engine: the full paper is sent to the AI instead of embeddings (customizable).
Added some starting code to allow to customize AI parameters per session (for default values for summarization algorithm and answer engine is stored in AI preferences, but they can be customized in place).
Added abilities to cancel AI requests (summarization, chatting).
Added AI requirements (yes, it's a bit extra and low-priority, but I liked the idea of requirements tracking and wanted to see how it would work and look in practice).
Made the task and storage logic more clear (TrackedBackgroundTask, *TaskAggregator, InMemoryChache).
Added unit tests for many clases.
Migrated to other schema of storage for summaries, chat history, and embeddings. As a result wrote a migration.
(Controversial) added an AI library ID that is a part of database metadata. I admit I should've discussed this with the maintainers team, but it solves some architectural problems of storing AI artifacts.
Ocasinally added some helpers for JavaFX observables.
Chat messages now have a timestamp.
Added comments for some classes whose purpose is not understood on the first sight.

Preferences:

Summarization:

AI chat:

Steps to test

Test summarization:

Click on an entry with a linked file.
Go to "AI Summary" tab.
Wait for summary generation.
Observe the summary.
Try clicking on "Regenerate (custom)" and choose other summarization algorithm.

Test chatting:

Click on an entry with a linked file.
Go to "AI Chat" tab.
Click on info button to open the chat status window.
See that you have the current chat model, selected answer engine, look at the entries used in chat (more interesting in the group chat), check the status of ingestion.
Close and chat with AI.
Hover on an AI message and find the "rotation" button. Click on it to regenerate the response.
Go to the AI chat status window and change the answer engine.
Chat and compare the results.
Close JabRef.
Open again JabRef, the same library and entry.
See that the chat history is preserved.

Test chat/summary migration:

Run this PR.
Open a library with entries you have chatted before.
Open logs and see that there should be a log about "Successfully migrated chat messages/summaries".
Open entries and see that you have the same chats and summaries.

Checklist

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 added a screenshot in the PR description showing a library with a single entry with me as author and as title the issue number
I described the change in CHANGELOG.md in a way that can be understood by the average user (if change is visible to the user)
I checked the user documentation for up to dateness and submitted a pull request to our user documentation repository

AI Usage Disclosure

While refactoring and adding new features I have used the AI tools like GitHub Copilot, IntelliJ Junie a lot. All AI generated code was carefully reviewed, edited and tested by me, and I take the full responsibility of the AI results.

…gic.ai.preferences`; update package structure and adjust imports across the codebase.

…ic package structure; update imports and restructure hierarchy accordingly.

…ion components into dedicated classes and interfaces.

Maran23 · 2026-05-04T19:22:14Z

+    }
+
+    private void setupItemReferenceListener() {
+        if (itemsProperty.get() != null) {


Can't be null ever since this is only called in the constructor, right?

…abRef#15672) Bumps [com.github.javaparser:javaparser-core](https://github.com/javaparser/javaparser) from 3.28.0 to 3.28.1. - [Release notes](https://github.com/javaparser/javaparser/releases) - [Changelog](https://github.com/javaparser/javaparser/blob/master/changelog.md) - [Commits](javaparser/javaparser@javaparser-parent-3.28.0...javaparser-parent-3.28.1) --- updated-dependencies: - dependency-name: com.github.javaparser:javaparser-core dependency-version: 3.28.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…JabRef#15674) Bumps [com.github.javaparser:javaparser-symbol-solver-core](https://github.com/javaparser/javaparser) from 3.28.0 to 3.28.1. - [Release notes](https://github.com/javaparser/javaparser/releases) - [Changelog](https://github.com/javaparser/javaparser/blob/master/changelog.md) - [Commits](javaparser/javaparser@javaparser-parent-3.28.0...javaparser-parent-3.28.1) --- updated-dependencies: - dependency-name: com.github.javaparser:javaparser-symbol-solver-core dependency-version: 3.28.1 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…#15663) * Mark bst package as nonnull by default * Enhance comment and fix abbreviation * Replace apache commons * Remove trivial comment * Ease error level for clear log info * Empty citation key * Enhance null safety for BstVMContext * Revert "Ease error level for clear log info" This reverts commit f4fcf7a. * Cleanups and fix test * Fix comment * Reintroduced null checks to harden --------- Co-authored-by: Carl Christian Snethlage <calixtus@users.noreply.github.com> Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>

…JabRef#15673) Bumps [com.github.ben-manes.caffeine:caffeine](https://github.com/ben-manes/caffeine) from 3.2.3 to 3.2.4. - [Release notes](https://github.com/ben-manes/caffeine/releases) - [Commits](ben-manes/caffeine@v3.2.3...v3.2.4) --- updated-dependencies: - dependency-name: com.github.ben-manes.caffeine:caffeine dependency-version: 3.2.4 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

calixtus

On @koppor vouching approved

koppor · 2026-05-04T20:45:12Z

@jjohannes - we get

[0](https://github.com/JabRef/jabref-koppor/actions/runs/25341431051/job/74299395885?pr=726#step:4:1181)
Execution failed for task ':jabgui:checkModuleDirectivesScope' (registered by plugin class 'org.gradlex.javamodule.dependencies.JavaModuleDependenciesPlugin').
> /home/runner/work/jabref-koppor/jabref-koppor/jabgui/src/main/java/module-info.java
  
  Please add the following requires directives:
      requires org.jspecify;

but we have requires transitive org.jspecify; - am I overlooking somethinghere?

* New translations jabref_en.properties (French) [ci skip] * New translations jabref_en.properties (Italian) [ci skip] * New translations jabref_en.properties (Portuguese, Brazilian) [ci skip]

…odel#parse() (JabRef#15576) * Fix empty column name causing WARN in MainTableColumnModel#parse() fixes JabRef#15571 * Update CHANGELOG for JabRef#15571 * Fix null check and filter null columns in MainTableColumnFactory * Remove filter and annotate createColumn() with @nullable * Move @nullable annotation to createColumn() instead of createColumns() --------- Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>

* Fix requirements * Fix requirements tracing defects Resolve duplicate req~ui.dialogs.confirmation.naming~1 by linking ui-recommendations.md to the canonical definition in ux.md. Drop unmet "Needs: impl" from the two aspirational search requirements and add an impl marker for req~ux.disabled-vs-hidden~1 in OpenUrlAction (the exact example from the requirement). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com> Co-authored-by: Christoph <siedlerkiller@gmail.com>

@see

* including SearchRxiv integration for SLR and enhancements to citation fetching and PDF downloads. * Add share functionality for SearchRxiv * introduce buildStudy method for creating Study instances and enhance share functionality for SearchRxiv * adding a button for exporting search queries to SearchRxiv and improving layout for validation messages. * Implement SearchRxivExporter for exporting study search queries in JSON format, adhering to the search-query library's specifications. * adding export options for search queries in JSON format * Add unit tests for SearchRxivExporter, verifying file creation and JSON structure for study exports * Revert unrelated changes, keep only SearchRxiv integration files * Sync remaining unrelated files with upstream main * Fix localization * Fix localization: match tooltip key with FXML * Fix localization: add missing key and match tooltip with FXML * Fix CHANGELOG, restore some missing * Extract noCatalogEnabled to ActionHelper * Address review comment * Use FileUtil.getValidFileName for SearchRxiv export filenames Replace ad-hoc regex-based filename cleaning and arbitrary 20-char truncation with the existing FileUtil.getValidFileName helper, so the SearchRxiv exporter follows the same illegal-character handling and filesystem length limit as the rest of JabRef. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * Clean filename components and add parameterized test FileUtil.getValidFileName only cleans illegal characters when it also truncates (length > 255), so short filenames like "IEEE-a/b:c*d-0.json" slipped through unchanged and broke Path.resolve. Apply FileNameCleaner.cleanFileName per component, then keep FileUtil.getValidFileName as a length safeguard. Add a parameterized test covering illegal chars, blank query fallback, and a regular query. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * Compare exported JSON as a tree in a single assertion Replace the field-by-field assertions with a single JsonNode tree equality check against an inline expected document. Tree equality is order- and whitespace-independent, and any unexpected extra field (such as "title") fails naturally. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * Use Markdown link in buildJson Javadoc description Convert the inline HTML link in the buildJson description to Markdown syntax. The @see tags are kept as HTML since the codebase uniformly uses HTML there and JEP 467 only guarantees reference-link form for @see, not inline links. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * Link to SearchRxiv in CHANGELOG entry Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * Use @CsvSource textBlock for filename parameterized test Replace the @MethodSource Stream<Arguments> with @CsvSource using a text block. Single-quoted values preserve whitespace and special characters; surrounding spaces are trimmed by the CSV parser, so the columns can be padded for visual alignment. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> * Drop redundant BooleanExpression wrap in noCatalogEnabled Bindings.createBooleanBinding already returns a BooleanBinding (which extends BooleanExpression), so wrapping it in BooleanExpression.booleanExpression is a no-op. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com> --------- Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com> Co-authored-by: Oliver Kopp <kopp.dev@gmail.com> Co-authored-by: Claude Opus 4.7 <noreply@anthropic.com>

jjohannes · 2026-05-05T05:49:06Z

@koppor I am afraid you are running into this: gradlex-org/java-module-dependencies#46

If a project is only an application, and not a java-library, Gradle does not offer an api (== requires transitive) scope. The rational is that a pure application is not something anything else depends on. Because of the linked issue, a requires transitive entry is ignored in such cases and that's why the advice from the check task is incomplete.

Fix is to replace requires transitive org.jspecify; with requires org.jspecify;.

In any case, the plugin should behave better - see linked issue.

…5679)

…f#15681) Bumps org.glassfish.jaxb:jaxb-runtime from 4.0.7 to 4.0.8. --- updated-dependencies: - dependency-name: org.glassfish.jaxb:jaxb-runtime dependency-version: 4.0.8 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…f#15682) Bumps [com.konghq:unirest-modules-gson](https://github.com/Kong/unirest-java) from 4.8.1 to 4.9.0. - [Release notes](https://github.com/Kong/unirest-java/releases) - [Changelog](https://github.com/Kong/unirest-java/blob/main/CHANGELOG.md) - [Commits](Kong/unirest-java@v4.8.1...v4.9.0) --- updated-dependencies: - dependency-name: com.konghq:unirest-modules-gson dependency-version: 4.9.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [com.dlsc.gemsfx:gemsfx](https://github.com/dlsc-software-consulting-gmbh/GemsFX) from 4.0.3 to 4.0.4. - [Release notes](https://github.com/dlsc-software-consulting-gmbh/GemsFX/releases) - [Commits](dlsc-software-consulting-gmbh/GemsFX@v4.0.3...v4.0.4) --- updated-dependencies: - dependency-name: com.dlsc.gemsfx:gemsfx dependency-version: 4.0.4 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…5683) Bumps com.konghq:unirest-java-core from 4.8.1 to 4.9.0. --- updated-dependencies: - dependency-name: com.konghq:unirest-java-core dependency-version: 4.9.0 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* New translations jabref_en.properties (French) [ci skip] * New translations jabref_en.properties (Arabic) [ci skip] * New translations jabref_en.properties (Italian) [ci skip]

InAnYan · 2026-05-06T07:10:16Z

Moved to: JabRef#15688

InAnYan added 30 commits November 23, 2025 17:36

Refactor AiPreferences and AiDefaultPreferences to `org.jabref.lo…

be13639

…gic.ai.preferences`; update package structure and adjust imports across the codebase.

Refactor AI-related classes in org.jabref.model.ai to a more specif…

add618d

…ic package structure; update imports and restructure hierarchy accordingly.

Introduce modular summarization algorithms and refactor AI summarizat…

b5b8b4e

…ion components into dedicated classes and interfaces.

Finish refactoring GenerateSummaryTask.java

655811e

Rename storages to repositories

77ee8c8

Fix wrong names

b79c223

Introduce FileParser

51a8965

Fix run problems

bfeb1b0

Rename storages package to repository

76dcd79

Move CitationKeyCheck

c0f51ac

Introduce AiIdentifiers

3fb2cd7

Remove AiDefaultPreferences.java

711847c

Refactor constructors

0289b0a

Summarization overhaul

353b6cd

Rename algorithms to logic

17f5ba8

Implement Tokenizers

28af1cf

Remove templates for chatting in AiTemplatesService

7e46164

Refactor LLM citation parsing + get rid of AiTemplatesService.java

6feedc9

Move "Currents" to current package

c25ccce

Introduce AiDefaultExpertSettings

80752c1

Finish previous

e181223

Make summary work again

ff866d7

Fix error

1dac75a

Big renaming

39df01b

Renaming + introduce AnswerEngine

40fb890

Fix errors + finish FullDocumentAnswerEngine

6b2662b

Refactor AiChatLogic.java

e47819d

Refactor a bit chat history

eb525ef

Fix chat history refactoring

6d212be

Refactor chat history

52ce8f1

koppor mentioned this pull request May 4, 2026

ListScrollPane InAnYan/jabref#215

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Maran23 reviewed May 4, 2026

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InAnYan and others added 9 commits May 4, 2026 21:23

reactor(ai): fix new lines at the end

fefce14

reactor(ai): fix from review

a0d172e

reactor(ai): fix do while loop

4f66e5e

reactor(ai): fix new lines

3b4d23b

Fix submodules

8119660

calixtus approved these changes May 4, 2026

View reviewed changes

InAnYan added 2 commits May 4, 2026 22:19

reactor(ai): fix code style

5bc1ab2

reactor(ai): fix annotations

597f0fa

Siedlerchr and others added 5 commits May 4, 2026 22:58

New Crowdin updates (JabRef#15676)

8e155a0

* New translations jabref_en.properties (French) [ci skip] * New translations jabref_en.properties (Italian) [ci skip] * New translations jabref_en.properties (Portuguese, Brazilian) [ci skip]

refactor: less objects during writing (JabRef#15677)

4bc13ca

renovate-bot and others added 7 commits May 5, 2026 13:18

Update dependency com.konghq:unirest-modules-gson to v4.9.0 (JabRef#1…

8b6728d

…5679)

New Crowdin updates (JabRef#15687)

d873447

* New translations jabref_en.properties (French) [ci skip] * New translations jabref_en.properties (Arabic) [ci skip] * New translations jabref_en.properties (Italian) [ci skip]

Merge branch 'main' into refactor/ai-1

2a3a700

InAnYan closed this May 6, 2026

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AI Refactoring#726

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InAnYan commented Apr 24, 2026 •

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