Copy linked files on entry transfer by UmutAkbayin · Pull Request #13535 · JabRef/jabref

UmutAkbayin · 2025-07-13T21:31:46Z

Adds a requirements specification file files.md documenting the linked file transfer logic between BibTeX entries in JabRef.
The document captures three key scenarios for when linked files are reachable or not in the target context and the expected behavior regarding path adjustment and file copying.

This improves traceability by formally specifying requirements that are linked to implementation and tests via OpenFastTrace.

Steps to test

Verify that the new requirements specification file docs/requirements/files.md is present, properly formatted, and follows JabRef conventions.
Run all existing and new unit tests in LinkedFileTransferHelperTest to ensure the linked file transfer logic behaves correctly across all covered scenarios.
Manually verify the business logic in JabRef, especially for the scenario where the linked file is not reachable and a nested directory structure must be created. Reviewers should confirm that the path adjustments and file copying behavior conform to the requirements.
Provide feedback if the handling of the last case (unreachable file with differing paths) aligns with project expectations.

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.

trag-bot · 2025-07-13T22:34:38Z

+    FilePreferences filePreferences
+  ) {
+
+    Set<BibEntry> modifiedEntries = new HashSet<>();


Using constructor for HashSet instead of modern Java collection factory method Set.of(). Modern Java practices recommend using factory methods for cleaner and more maintainable code.

could not find a quick solution. would have to refactor the logic then.

trag-bot · 2025-07-13T22:34:42Z

+
+    for (BibEntry entry : targetContext.getEntries()) {
+      boolean entryChanged = false;
+      List<LinkedFile> linkedFiles = new ArrayList<>();


Using ArrayList constructor instead of modern Java collection factory methods. Should use List.of() for empty list initialization following JabRef's conventions.

could not find a quick solution. would have to refactor the logic then.

TracBot is wrong here 😅

koppor · 2025-07-23T19:18:41Z

@UmutAkbayin Please read the bot comment - one week old

Fix the tests

koppor · 2025-07-23T19:19:05Z

I converted the PR to draft, because a) merge conflicts b) tests failing.

koppor · 2025-07-23T19:19:41Z

"Steps to test" seems to be AI generated. It is not a step-by-step guide. Please refine.

UmutAkbayin · 2025-07-24T06:12:35Z

I noticed that one unit test is affected by the changes in LibraryTab#pasteEntry. I’ll look into it tomorrow or over the weekend. I’ll also review the other things like code style.

Allows tracking the source BibDatabaseContext for later use in pasteEntry()

…er and setter Enables tracking the source database context for use in pasteEntry()

…variable

… CopyTo#copyEntriesWithFeedback and LibraryTab#pasteEntry

Add filePreferences parameter to CopyTo.java to enable LinkedFile#findIn functionality

… transfer

… primary directory

…sferHelperTest#isReachableFromPrimaryDirectory method

Cloning the BibEntry in importEntryWithDuplicateCheck to ensure that any file path adjustments during the copy/paste process do not affect the original entry in the source database. This avoids side effects when imported entries are modified (e.g. file links), especially when the same BibEntry instance is shared between databases.

…ls in LibraryTab and CopyTo to align with new method signature

…pying logic during entry transfer

koppor · 2025-11-19T12:18:45Z

Log output of current version:

2025-11-19 13:16:43 [JavaFX Application Thread] org.jabref.gui.JabRefDialogService.notify()
INFO: Cut 1 entry(s)
2025-11-19 13:16:50 [JavaFX Application Thread] org.jabref.logic.externalfiles.LinkedFileTransferHelper.adjustLinkedFilesForTarget()
DEBUG: Handling LunaOstos2024 - Luna Ostos, Roche, Coroama and Finkbeiner: "Social life cycle assessment in the chocolate industry: A Colombian case study with Luker Chocolate" (2024)
2025-11-19 13:16:50 [JavaFX Application Thread] org.jabref.logic.externalfiles.LinkedFileTransferHelper.adjustLinkedFilesForTarget()
DEBUG: Handling file ParsedFileField{description='', link='LunaOstos_2024 - Social Life Cycle Assessment in the Chocolate Industry - A Colombian Case Study with Luker Chocolate.pdf', fileType='PDF', sourceUrl='https://link.springer.com/content/pdf/10.1007/s11367-023-02261-y.pdf'}
2025-11-19 13:16:50 [JavaFX Application Thread] org.jabref.logic.externalfiles.LinkedFileTransferHelper.adjustLinkedFilesForTarget()
DEBUG: Moving file from C:\git-repositories\jabref-all\jabref-demonstration-libraries\chocolate\pdfs\LunaOstos_2024 - Social Life Cycle Assessment in the Chocolate Industry - A Colombian Case Study with Luker Chocolate.pdf to C:\git-repositories\jabref-all\tmp-test\LunaOstos_2024 - Social Life Cycle Assessment in the Chocolate Industry - A Colombian Case Study with Luker Chocolate.pdf
2025-11-19 13:16:50 [JavaFX Application Thread] org.jabref.gui.JabRefDialogService.notify()
INFO: Pasted 1 entry(s) to tmp-test.bib

koppor · 2025-11-19T12:19:34Z

Settings

koppor · 2025-11-19T12:20:17Z

Default settings BTW

Siedlerchr · 2025-11-25T08:15:51Z

jackson.databind is not visible
import tools.jackson.databind.ObjectMapper;
^
(package tools.jackson.databind is declared in module tools.jackson.databind, but module org.jabref does not read it)
1 error

…-on-entry-transfer

Adressed comments