Import & Add PDF Upload Endpoint by sonthien22501 · Pull Request #14907 · JabRef/jabref

sonthien22501 · 2026-01-23T17:05:08Z

PR Description

Sumary

This PR fixes critical UnsatisfiedDependencyException errors preventing the HTTP Import API from working (as introduced in #14855) and implements the missing PDF Upload endpoint (POST .../files) required for the Researcher Cockpit extension.

Fix Dependency Injection (Server.java)
- Problem: The server crashed with HTTP 500 because UiMessageHandler and CliPreferences were bound using Named Bindings ("uimessagehandler"), but Resources injected them without names. Additionally, addOneConstant(obj) bound concrete classes (e.g., JabRefFrame) instead of Interfaces (UiMessageHandler), causing HK2 resolution failures.
- Fix: Switched to AbstractBinder to explicitly bind instances to their Interface contracts (bind(instance).to(Interface.class)).
Fix CLI Server Crash (EntriesResource.java)
- Problem: EntriesResource requires UiMessageHandler. When running in CLI mode (headless), this handler is null. This caused the CLI server to crash on startup during dependency resolution because of the mandatory field injection.
- Fix: Implemented Lazy Injection using ServiceLocator. The resource now retrieves the handler only when addBibtex is called, allowing the server to start safely in CLI mode (throwing a graceful 500 if invoked without UI).

Implement PDF Upload (EntryResource.java)
- Feature: Added POST /libraries/{id}/entries/{entryId}/files endpoint.
- Implementation:
  - Accepts application/pdf InputStream.
  - Uses LinkedFileHandler logic to generate standard filenames (e.g., Author - Title.pdf).
  - Includes robust fallback logic to save files to the .bib directory if no specific "Linked Files" directory is configured in preferences.

Steps to test

 * Run ./gradlew clean :jabsrv:assemble              
 * Run ./gradlew :jabgui:run 
 * Enable HTTP in Jabref Preference
 * Create test file "test.bib" (@article{test_entry_2026, title={Test Entry from Curl}, author={Tester}, year={2026}}) and "test.pdf"  
 * Run curl -v -X POST -H "Content-Type: application/x-bibtex" --data-binary {dir}/test.bib http://localhost:23119/libraries/current/entries to test Import        
 * Run curl -v -X POST -H "Content-Type: application/pdf" --data-binary {dir}/test.pdf http://localhost:23119/libraries/current/entries/Tester2026/files to test PDF Upload

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.

github-actions · 2026-01-24T03:36:07Z

Your pull request conflicts with the target branch.

Please merge with your code. For a step-by-step guide to resolve merge conflicts, see https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/addressing-merge-conflicts/resolving-a-merge-conflict-using-the-command-line.

koppor

The issue causing the 500 was different - see #14930

I found out by using the debugger, breakpoints, and following the call hierarchy. The main cause was that the wrong http server constructor was called - without uiMessageHandler.

Please submit Implement PDF Upload (EntryResource.java) as separate PR (based on upstreammain`)

Reason: For each use case a different PR

In case you want to have all updates integrated in your IDE, use GitButler - and maybe magic-merge-commit

koppor · 2026-01-26T11:50:11Z

CHANGELOG.md

+- REST-API: Added more commands (`selectentries`, `open`, `focus`).
+- REST-API: Added the possibility to trigger the import dialog


Something is wrong with this PR - maybe not a clean base on upstream/main?

Maybe try:

Ensure everything is committed

gitk --all& (to start gitk to have the commit IDs ready if something goes wrong)

git merge upstream/main (to merge the latest upstream changes)

git reset upstream/main (to discard all commits and start a fresh commit)

git gui (to craft a new commit. Do NOT commit the changes in the submodule. Try to revert these changes using "Commit" -> "Revert Changes")

Create a new commit using git gui (maybe other git tooling you use)

git push -f (to overwrite the changes also in this PR)

koppor

(see above)

koppor · 2026-01-27T07:16:52Z

jabsrv/src/main/java/org/jabref/http/server/resources/EntryResource.java

+        // Fallback: Use the directory where the bib file is located
+        if (targetDirOpt.isEmpty()) {
+            targetDirOpt = databaseContext.getDatabasePath().map(java.nio.file.Path::getParent);
+        }
+
+        if (targetDirOpt.isEmpty()) {
+            throw new BadRequestException("Library must be saved or have a file directory configured to attach files.");
+        }


No fallback - return bad request if there is no dir.

When did you experience this? Mayge at a new, unsaved library.

koppor · 2026-01-27T07:17:22Z

jabsrv/src/main/java/org/jabref/http/server/resources/EntryResource.java

+        if (Files.exists(finalPath)) {
+             String name = com.google.common.io.Files.getNameWithoutExtension(suggestedName);
+             String ext = com.google.common.io.Files.getFileExtension(suggestedName);
+             finalPath = targetDir.resolve(name + "_" + System.currentTimeMillis() + "." + ext);


Can't one write directly to this file?

koppor · 2026-01-27T07:19:22Z

jabsrv/src/main/java/org/jabref/http/server/resources/EntryResource.java

+             String name = com.google.common.io.Files.getNameWithoutExtension(suggestedName);
+             String ext = com.google.common.io.Files.getFileExtension(suggestedName);


Please useorg.jabref.logic.util.io.FileUtil#getFileExtension(java.nio.file.Path) and org.jabref.logic.util.io.FileUtil#getBaseName(java.lang.String)

koppor · 2026-01-27T07:20:00Z

jabsrv/src/main/java/org/jabref/http/server/resources/EntryResource.java

+        FilesToServe filesToServe = serviceLocator.getService(FilesToServe.class);
+        SrvStateManager srvStateManager = serviceLocator.getService(SrvStateManager.class);
+        CliPreferences preferences = serviceLocator.getService(CliPreferences.class);
+
+        if (filesToServe == null || srvStateManager == null || preferences == null) {
+            throw new IOException("Required services not found in ServiceLocator");
+        }


All these changes are not necessary AFAIK.

koppor · 2026-01-27T07:20:32Z

jabsrv/src/main/java/org/jabref/http/server/Server.java

-        // Required for CLI only
-        // GUI uses HttpServerManager


Strong hint that this is AI generated and the resulting code not reviewed.

Yes, this is because I have the issue with the http 500 and I ask AI about it. But I am sure that I have reverted everything, pull the latest code for importing and enabling http in Jabref Application. It worked then I implemented the PDF Uploading Endpoints with the same concept of Import. Maybe i have committed no-needed code in Server.java and I don't remember about it. Sorry

sonthien22501 · 2026-01-27T21:56:05Z

I have checked that the Import function works without error 500
I follow the EntriesResource.java to implement PDF Uploading in EntryResource.java
New PR: #14942

jabref-machine · 2026-01-29T22:35:10Z

Note that your PR will not be reviewed/accepted until you have gone through the mandatory checks in the description and marked each of them them exactly in the format of [x] (done), [ ] (not done yet) or [/] (not applicable). Please adhere to our pull request template.

koppor · 2026-01-29T22:35:51Z

jabsrv/src/main/java/org/jabref/http/server/resources/EntryResource.java

+        if (Files.exists(finalPath)) {
+             String name = com.google.common.io.Files.getNameWithoutExtension(suggestedName);
+             String ext = com.google.common.io.Files.getFileExtension(suggestedName);
+             finalPath = targetDir.resolve(name + "_" + System.currentTimeMillis() + "." + ext);


Please do not use a timestamp for the filename. This is not user friendly. Just keep the original name.

koppor · 2026-01-29T22:36:20Z

In the exchange today, we decided to go on with this PR.

This comment needs to be resolved: https://github.com/JabRef/jabref/pull/14907/changes#r2730600414

This comment needs to be resolved: https://github.com/JabRef/jabref/pull/14907/changes#r2743826996

This one needs more thought and can be skipped for now to move forward: https://github.com/JabRef/jabref/pull/14907/changes#r2730594969

koppor · 2026-01-29T22:36:49Z

I merged upstream/main. Please use git pull to update your branch.

jabref-machine · 2026-01-30T11:48:38Z

Hey, we noticed that you force-pushed your changes. Force pushing is a bad practice when working together on a project (mainly because it is not supported well by GitHub itself). Commits are lost and comments on commits lose their context, thus making it harder to review changes.

When the pull request is getting integrated into main, all commits will be squashed anyway. Thus, your individual commit history will not be visible in main.

In future, please avoid that. For now, you can continue working.

koppor · 2026-02-02T10:21:51Z

Follow-up: #14963

github-actions bot added the status: changes-required Pull requests that are not yet complete label Jan 23, 2026

koppor reviewed Jan 26, 2026

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koppor requested changes Jan 26, 2026

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koppor reviewed Jan 27, 2026

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sonthien22501 force-pushed the pr-14855-latest branch from 0b2941d to 3642482 Compare January 27, 2026 21:47

sonthien22501 closed this Jan 27, 2026

koppor mentioned this pull request Jan 27, 2026

feat: Add PDF Upload endpoint to EntryResource #14942

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koppor reopened this Jan 29, 2026

koppor changed the title ~~Import & Add PDF Upload Endpoint from (PR #14855)~~ Import & Add PDF Upload Endpoint Jan 29, 2026

koppor reviewed Jan 29, 2026

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sonthien22501 force-pushed the pr-14855-latest branch from d785360 to 7875d6f Compare January 30, 2026 11:47

sonthien22501 closed this Jan 30, 2026

sonthien22501 force-pushed the pr-14855-latest branch from 7875d6f to 8ce862d Compare January 30, 2026 12:07

sonthien22501 deleted the pr-14855-latest branch January 30, 2026 12:09

		- REST-API: Added more commands (`selectentries`, `open`, `focus`).
		- REST-API: Added the possibility to trigger the import dialog

		String name = com.google.common.io.Files.getNameWithoutExtension(suggestedName);
		String ext = com.google.common.io.Files.getFileExtension(suggestedName);

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PR Description

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sonthien22501 commented Jan 27, 2026

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sonthien22501 commented Jan 23, 2026 •

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