recomment linked files handler

[Siedlerchr]

Related issues and pull requests

Fixes #15104

PR Description

Steps to test

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

[qodo-free-for-open-source-projects]

Review Summary by Qodo

Uncomment disabled linked files handler test case

🧪 Tests

Walkthroughs

Description

• Uncommented previously disabled test case in LinkedFileTransferHelperTest
• Restored test for relative file linking to main file directory

Diagram

flowchart LR
  A["Commented Test Case"] -- "Uncommented" --> B["Active Test Case"]
  B -- "Tests" --> C["LinkedFileTransferHelper"]

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File Changes

1. jablib/src/test/java/org/jabref/logic/externalfiles/LinkedFileTransferHelperTest.java 🧪 Tests +1/-2

Uncomment disabled test case for file linking

• Removed multi-line comment markers that disabled a test case
• Test case validates file linking relative to main file directory
• Test now executes as part of the parameterized test suite

jablib/src/test/java/org/jabref/logic/externalfiles/LinkedFileTransferHelperTest.java

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[testlens-app]

✅ All tests passed ✅

🏷️ Commit: 8e1ffa1
▶️ Tests: 11187 executed
⚪️ Checks: 52/52 completed

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[qodo-free-for-open-source-projects]

Code Review by Qodo

🐞 Bugs (1) 📘 Rule violations (0) 📎 Requirement gaps (0)

✅ 1. Flaky test re-enabled 🐞 Bug ⛯ Reliability

Description

The uncommented parameter set can fail nondeterministically because the helper searches by filename
under the main file directory tree and picks the first match, while the test setup creates multiple
test.pdf candidates under that tree. This can make CI unreliable or fail depending on filesystem
traversal order.

Code

jablib/src/test/java/org/jabref/logic/externalfiles/LinkedFileTransferHelperTest.java[R122-124]

               Arguments.of(
                       "File in main file directory linked as is",
                       FileTestConfigurationBuilder

Evidence

The re-enabled test config creates test.pdf in two different locations under the *same* main file
dir tree: source uses pdfFileDir("main-file-dir") (so main-file-dir/test.pdf) while target uses
pdfFileDir("main-file-dir/sub-dir") (so main-file-dir/sub-dir/test.pdf). When the linked path
has no parent (e.g., test.pdf), adjustLinkedFilesForTarget skips the deterministic
linkedFile.findIn(targetContext, ...) check and instead walks the target directories recursively
and returns the *first* path whose filename matches, which is ambiguous if multiple matches exist.
Also, for shouldStoreFilesRelativeToBibFile=false, the target directory list is just the global
mainFileDirectory (not the sub-dir), so this recursive walk is exactly over the shared
main-file-dir tree where both candidates exist.

jablib/src/test/java/org/jabref/logic/externalfiles/LinkedFileTransferHelperTest.java[122-139]
jablib/src/test/java/org/jabref/logic/externalfiles/BibTestConfiguration.java[39-47]
jablib/src/test/java/org/jabref/logic/externalfiles/BibTestConfiguration.java[78-86]
jablib/src/main/java/org/jabref/model/database/BibDatabaseContext.java[180-194]
jablib/src/main/java/org/jabref/logic/externalfiles/LinkedFileTransferHelper.java[90-112]
jablib/src/main/java/org/jabref/logic/externalfiles/LinkedFileTransferHelper.java[155-162]

Agent prompt

The issue below was found during a code review. Follow the provided context and guidance below and implement a solution

## Issue description
A previously disabled parameterized test case was re-enabled. With the current setup, it can be flaky because the test creates multiple `test.pdf` files under the same main-file-dir tree, while `LinkedFileTransferHelper` may select an arbitrary match via `Files.walk(...).findFirst()`.
### Issue Context
- Source test setup creates `main-file-dir/test.pdf`.
- Target test setup creates `main-file-dir/sub-dir/test.pdf`.
- For non-bib-relative storage, the file directory list comes from `FilePreferences.getMainFileDirectory()`, i.e., the shared `main-file-dir` root.
- The helper’s recursive search matches by filename only and takes the first hit.
### Fix Focus Areas
- jablib/src/test/java/org/jabref/logic/externalfiles/LinkedFileTransferHelperTest.java[122-139]
- jablib/src/main/java/org/jabref/logic/externalfiles/LinkedFileTransferHelper.java[90-112]
- jablib/src/main/java/org/jabref/logic/externalfiles/LinkedFileTransferHelper.java[155-162]

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[Siedlerchr]

added a commebt

[koppor]

Very strange that the test worked before...