update findAssociatedFiles to find all instead of the first one by LangInteger · Pull Request #14700 · JabRef/jabref

LangInteger · 2025-12-23T13:13:59Z

User description

Closes #14697

reformated code with better naming
eliminated one performance issue by avoiding a loop in another loop
updated the find associated files by broken linked file name logic to return all files instead of only the first one
added a unit test

Steps to test

Preparation

Ensure [Options/Preferences/Linked files/Automatically search and show unlinked files] is checked.
Open any database with a file directory set (e.g., set to ".").
Attach a PDF minimal.pdf under the same directory to an entry via the “General” tab.
Close the entry editor.

Simulate a file move

Outside JabRef, move the file from ./minimal.pdf to ./sub1/minimal.pdf.

Create a second copy of the file

Outside JabRef, copy the file from ./sub1/minimal.pdf to ./sub2/minimal.pdf.

Check the auto-searched associated but unlinked files result

Reopen the entry editor.
The original linked file turns orange and shows “Could not find file minimal.pdf” when hovering on it
Two associated files are shown below the orange one for the user to check and link

Screenshot of my manual test

Before this PR, only one of the two associated files are displayed

After fixing in this PR, the two associated files are displayed

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.

PR Type

Enhancement, Tests

Description

Modified findAssociatedFilesByBrokenLinkedFile to return all matching files instead of just the first one
Refactored variable naming for clarity and improved code readability
Eliminated nested loop performance issue by pre-computing linked files list
Added comprehensive unit test for finding multiple associated files

Diagram Walkthrough

flowchart LR
  A["Broken Linked File"] -->|Search by name| B["Find Associated Files"]
  B -->|Old: findFirst| C["Return First Match Only"]
  B -->|New: toList| D["Return All Matches"]
  D --> E["Display Multiple Options to User"]

File Walkthrough

Relevant files

Enhancement

AutoSetFileLinksUtil.java `Find all associated files instead of first one` jabgui/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java Renamed variables for better clarity: `linkedFiles` → `associatedNotLinkedFiles`, `linkedFile` → `associateNotLinkedFile` Refactored `findByBrokenLinkName` method to `findAssociatedFilesByBrokenLinkedFile` with improved logic Changed `.findFirst()` to `.toList()` to collect all matching files instead of only the first one Optimized nested loop by pre-computing `linkedFiles` list outside the loop to avoid redundant stream operations Improved variable naming in the broken link search logic for better readability	+35/-32

Tests

AutoSetFileLinksUtilTest.java `Add test for multiple associated files discovery` jabgui/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java Added new test method `findAllAssociatedNotLinkedFilesInsteadOfTheFirstOne` to verify multiple file discovery Test simulates file move and creates duplicate copies to validate all matches are returned Added assertion import for `assertTrue` to support new test validations Test verifies both files are found and correctly identified by their relative paths	+42/-0

Documentation

CHANGELOG.md `Document unlinked files feature improvement` CHANGELOG.md Added entry documenting improvement to "search and show unlinked files" feature References issue All the associated files should be displayed for broken linked files instead of only the first one #14697 and highlights that all associated files are now shown instead of just the first one	+1/-0

LangInteger · 2025-12-23T13:26:09Z


        for (BibEntry entry : entries) {
-            List<LinkedFile> linkedFiles = new ArrayList<>();
+            List<LinkedFile> associatedNotLinkedFiles = new ArrayList<>();


reformatted code with better naming

LangInteger · 2025-12-23T13:26:40Z

+        List<Path> linkedFiles = entry.getFiles().stream()
+                                      .map(file -> file.findIn(directories))
+                                      .filter(Optional::isPresent)
+                                      .map(Optional::get)
+                                      .toList();
        for (Path foundFile : result) {
-            boolean fileAlreadyLinked = entry.getFiles().stream()
-                                             .map(file -> file.findIn(directories))
-                                             .anyMatch(linked -> linked.filter(path -> {
-                                                 try {
-                                                     return Files.isSameFile(path, foundFile);
-                                                 } catch (IOException e) {
-                                                     LOGGER.debug("Unable to check file identity, assuming no identity", e);
-                                                     return false;
-                                                 }
-                                             }).isPresent());
+            boolean fileAlreadyLinked = linkedFiles.stream()
+                                                   .anyMatch(linked -> {
+                                                       try {
+                                                           return Files.isSameFile(linked, foundFile);
+                                                       } catch (IOException e) {
+                                                           LOGGER.debug("Unable to check file identity, assuming no identity", e);
+                                                           return false;
+                                                       }
+                                                   });


eliminated one performance issue here by avoiding a loop in another loop

LangInteger · 2025-12-23T13:27:41Z

+    private List<Path> findAssociatedFilesByBrokenLinkedFile(BibEntry entry) throws IOException {
        List<Path> matches = new ArrayList<>();

-        for (LinkedFile brokenLink : entry.getFiles()) {
-            if (brokenLink.findIn(directories).isPresent()) {
-                continue;
-            }
-
-            String wantedBase = FileUtil.getBaseName(brokenLink.getLink());
-
-            for (Path directory : directories) {
-                try (Stream<Path> walk = Files.walk(directory)) {
-                    walk.filter(path -> !Files.isDirectory(path))
-                        .filter(path -> FileUtil.getBaseName(path).equalsIgnoreCase(wantedBase))
-                        .findFirst()
-                        .ifPresent(matches::add);
+        for (LinkedFile linkedFile : entry.getFiles()) {
+            boolean isLinkedFileBroken = linkedFile.findIn(directories).isEmpty();
+            if (isLinkedFileBroken) {
+                String linkedFileBaseName = FileUtil.getBaseName(linkedFile.getLink());
+
+                for (Path directory : directories) {
+                    try (Stream<Path> walk = Files.walk(directory)) {
+                        List<Path> found = walk.filter(path -> !Files.isDirectory(path))
+                                               .filter(path -> FileUtil.getBaseName(path).equalsIgnoreCase(linkedFileBaseName))
+                                               .toList();
+                        matches.addAll(found);
+                    }


updated the find associated files by broken linked file name logic to return all files instead of only the first one

qodo-free-for-open-source-projects · 2025-12-23T13:29:07Z

PR Compliance Guide 🔍

Below is a summary of compliance checks for this PR:

Security Compliance

⚪

Unbounded directory traversal

Description: Unbounded directory traversal using Files.walk(directory) without depth limit could cause
performance issues or resource exhaustion if directories contain deeply nested structures
or symbolic link loops. AutoSetFileLinksUtil.java [152-157]

Referred Code

try (Stream<Path> walk = Files.walk(directory)) {
    List<Path> found = walk.filter(path -> !Files.isDirectory(path))
                           .filter(path -> FileUtil.getBaseName(path).equalsIgnoreCase(linkedFileBaseName))
                           .toList();
    matches.addAll(found);
}

Ticket Compliance

🟡

🎫 #13109

🔴	Add pseudonymization functionality to the CLI
	Make `org.jabref.logic.pseudonymization.Pseudonymization` available on the CLI
	Provide a similar CLI experience to the consistency check
	Follow the implementation pattern of `org.jabref.cli.CheckConsistency` class

Codebase Duplication Compliance

⚪

Codebase context is not defined

Follow the guide to enable codebase context checks.

Custom Compliance

🟢

Generic: Comprehensive Audit Trails

Objective: To create a detailed and reliable record of critical system actions for security analysis
and compliance.

Status: Passed

Learn more about managing compliance generic rules or creating your own custom rules

Generic: Meaningful Naming and Self-Documenting Code

Objective: Ensure all identifiers clearly express their purpose and intent, making code
self-documenting

Status: Passed

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Generic: Robust Error Handling and Edge Case Management

Objective: Ensure comprehensive error handling that provides meaningful context and graceful
degradation

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Generic: Secure Error Handling

Objective: To prevent the leakage of sensitive system information through error messages while
providing sufficient detail for internal debugging.

Status: Passed

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Generic: Secure Logging Practices

Objective: To ensure logs are useful for debugging and auditing without exposing sensitive
information like PII, PHI, or cardholder data.

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Generic: Security-First Input Validation and Data Handling

Objective: Ensure all data inputs are validated, sanitized, and handled securely to prevent
vulnerabilities

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Update

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⚪ - Requires Further Human Verification
🏷️ - Compliance label

qodo-free-for-open-source-projects · 2025-12-23T13:29:56Z

PR Code Suggestions ✨

Explore these optional code suggestions:

Category Suggestion Impact

General

✅ ~~Optimize file search by reducing traversals~~

Suggestion Impact:

The commit directly implements the suggested optimization. It collects broken link base names upfront in a Set, adds an early return for empty sets, and restructures the nested loops to traverse each directory only once while checking against all broken link base names using a Set.contains() operation.

code diff:

     private List<Path> findAssociatedFilesByBrokenLinkedFile(BibEntry entry) throws IOException {
+
+        Set<String> brokenLinkBaseNames = entry.getFiles().stream()
+                                               .filter(linkedFile -> linkedFile.findIn(directories).isEmpty())
+                                               .map(linkedFile -> FileUtil.getBaseName(linkedFile.getLink()).toLowerCase())
+                                               .collect(Collectors.toSet());
+
+        if (brokenLinkBaseNames.isEmpty()) {
+            return List.of();
+        }
+
         List<Path> matches = new ArrayList<>();
-
-        for (LinkedFile linkedFile : entry.getFiles()) {
-            boolean isLinkedFileBroken = linkedFile.findIn(directories).isEmpty();
-            if (isLinkedFileBroken) {
-                String linkedFileBaseName = FileUtil.getBaseName(linkedFile.getLink());
-
-                for (Path directory : directories) {
-                    try (Stream<Path> walk = Files.walk(directory)) {
-                        List<Path> found = walk.filter(path -> !Files.isDirectory(path))
-                                               .filter(path -> FileUtil.getBaseName(path).equalsIgnoreCase(linkedFileBaseName))
-                                               .toList();
-                        matches.addAll(found);
-                    }
-                }
+        for (Path directory : directories) {
+            try (Stream<Path> walk = Files.walk(directory)) {
+                List<Path> found = walk.filter(path -> !Files.isDirectory(path))
+                                       .filter(path -> brokenLinkBaseNames.contains(FileUtil.getBaseName(path).toLowerCase()))
+                                       .toList();
+                matches.addAll(found);
             }
         }
-
         return matches;
     }

Optimize the findAssociatedFilesByBrokenLinkedFile method to improve performance
by reducing redundant file system traversals. First, collect all unique base
names of broken links, then iterate through each directory only once to find all
matching files.

jabgui/src/main/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtil.java [143-163]

 private List<Path> findAssociatedFilesByBrokenLinkedFile(BibEntry entry) throws IOException {
+    Set<String> brokenLinkBaseNames = entry.getFiles().stream()
+                                           .filter(linkedFile -> linkedFile.findIn(directories).isEmpty())
+                                           .map(linkedFile -> FileUtil.getBaseName(linkedFile.getLink()).toLowerCase())
+                                           .collect(Collectors.toSet());
+
+    if (brokenLinkBaseNames.isEmpty()) {
+        return List.of();
+    }
+
     List<Path> matches = new ArrayList<>();
-
-    for (LinkedFile linkedFile : entry.getFiles()) {
-        boolean isLinkedFileBroken = linkedFile.findIn(directories).isEmpty();
-        if (isLinkedFileBroken) {
-            String linkedFileBaseName = FileUtil.getBaseName(linkedFile.getLink());
-
-            for (Path directory : directories) {
-                try (Stream<Path> walk = Files.walk(directory)) {
-                    List<Path> found = walk.filter(path -> !Files.isDirectory(path))
-                                           .filter(path -> FileUtil.getBaseName(path).equalsIgnoreCase(linkedFileBaseName))
-                                           .toList();
-                    matches.addAll(found);
-                }
-            }
+    for (Path directory : directories) {
+        try (Stream<Path> walk = Files.walk(directory)) {
+            List<Path> found = walk.filter(path -> !Files.isDirectory(path))
+                                   .filter(path -> brokenLinkBaseNames.contains(FileUtil.getBaseName(path).toLowerCase()))
+                                   .toList();
+            matches.addAll(found);
         }
     }
 
     return matches;
 }

[Suggestion processed]

Suggestion importance[1-10]: 7

__

Why: The suggestion correctly identifies a performance bottleneck where the file system is traversed multiple times and proposes an effective optimization to walk each directory only once, which can significantly improve performance.

Medium

Update

LangInteger · 2025-12-23T13:45:15Z

@koppor Hi, I finished this PR. Feel free to review the changes here. I will avoid main branch next time.

koppor · 2025-12-23T14:12:56Z

+        assertEquals(2, matches.size());
+        assertTrue(matches.stream().anyMatch(file -> {
+            return FileUtil.relativize(newPath1, List.of(directory)).equals(Path.of(file.getLink()));
+        }));
+        assertTrue(matches.stream().anyMatch(file -> {
+            return FileUtil.relativize(newPath2, List.of(directory)).equals(Path.of(file.getLink()));
+        }));


I think, FileUtil is used, but not scope of the test

Just test matches with a List.of(...) w/o calling FileUtil. I think, it should be easy to hard code the expected result?

That makes sense. Now the FileUtil is avoided.

koppor

Thank you for the comments in the PR. This makes reviewing easier.

I am not able to fully test and review; therefore a small comment on the test setup. (I think, the PR is fine otherwise; need to check later)

koppor · 2025-12-23T19:07:15Z

+        assertEquals(2, matches.size());
+        assertTrue(matches.stream().anyMatch(file ->
+                Path.of(newPath1String).equals(Path.of(file.getLink()))));
+        assertTrue(matches.stream().anyMatch(file ->
+                Path.of(newPath2String).equals(Path.of(file.getLink()))));


Have

List<LinkedFile> expected = List.of(new LinkedFile(...), ...)

koppor · 2025-12-23T19:38:59Z

-        assertTrue(matches.stream().anyMatch(file ->
-                Path.of(newPath2String).equals(Path.of(file.getLink()))));
+        List<String> expected = List.of(newPath1String, newPath2String);
+        // findAssociatedNotLinkedFiles does not guarantee how the returned files are ordered


Then we found a flaw, don't we?

Stabilize findAssociatedNotLinkedFiles to return the files in the order they appear in the BibEntry

Use Collection as return value

I prefer the former.

I was about to comment

The function that accumulates associated files says nothing about how the returned file is ordered, so I used the HashSet trick to check.

Since multiple files (with the same name) might be found here for one broken linked file in a BibEntry, it seems there is no way to arrange the found files according to their order in BibEntry.

Then I should go with option 2. How do you think?

OK for me - one can sort "later"

(I haven't checked all the code, just my gut feeling)

koppor · 2025-12-23T19:39:11Z

-        List<LinkedFile> matches = util.findAssociatedNotLinkedFiles(entry);
+        List<String> matchedFiles = util.findAssociatedNotLinkedFiles(entry)
+                                        .stream().map(LinkedFile::getLink).toList();
+        assertEquals(2, matchedFiles.size());


No need, will be done with assertEquals below

LangInteger · 2025-12-23T20:08:52Z

-        );
+        assertEquals(newFile,
+                matches.stream().findFirst().map(LinkedFile::getLink).orElse(""));
    }


fix previous test to avoid FIleUtil here

koppor · 2025-12-23T20:10:07Z


        for (BibEntry entry : entries) {
-            List<LinkedFile> linkedFiles = new ArrayList<>();
+            Collection<LinkedFile> associatedNotLinkedFiles = new ArrayList<>();


Suggested change

Collection<LinkedFile> associatedNotLinkedFiles = new ArrayList<>();

Collection<LinkedFile> associatedNotLinkedFiles = Set.of();

Because you overwrite?

Maybe even move the assignment to the catch block?

Both fixed.

koppor · 2025-12-23T20:10:28Z

+    /// 1. This method does not check if the file is already linked to another entry.
+    /// 2. This method does not guarantee how the returned files are ordered.
+    ///    Order by how they appear in BibEntry does not work since findAssociatedFilesByBrokenLinkedFile may return
+    ///      multiple files (with the same name) for one broken linked file in the entry.


Indent...

(Otherwise nice)

fixed. Let me know if the fix is still not standard

koppor · 2025-12-23T20:11:39Z

+
+        Collection<String> matchedFiles = util.findAssociatedNotLinkedFiles(entry)
+                                              .stream().map(LinkedFile::getLink).toList();
+        List<String> expected = List.of(newPath1String, newPath2String);


Why List? Shouldn't Set be OK?

koppor · 2025-12-23T20:39:35Z

+        Set<String> expected = Set.of(newPath1String, newPath2String);
+        // findAssociatedNotLinkedFiles does not guarantee how the returned files are ordered
+        // so here we compare equality without considering order
+        assertEquals(new HashSet<>(matchedFiles), expected);


Still not OK

I cannot push my updates to your main

To github.com:LangInteger/jabref.git ! [remote rejected] LangInteger/main -> LangInteger/main (permission denied) error: failed to push some refs to 'github.com:LangInteger/jabref.git'

Please, in future, allow updates from maintainers!

Please apply following diff:

diff --git a/jabgui/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java b/jabgui/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java index 8db83b9be1..4ac2825da6 100644 --- a/jabgui/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java +++ b/jabgui/src/test/java/org/jabref/gui/externalfiles/AutoSetFileLinksUtilTest.java @@ -4,7 +4,6 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.Collection; -import java.util.HashSet; import java.util.List; import java.util.Set; import java.util.TreeSet; @@ -104,18 +103,15 @@ class AutoSetFileLinksUtilTest { void findAllAssociatedNotLinkedFilesInsteadOfTheFirstOne(@TempDir Path tempDir) throws IOException { Path directory = tempDir.resolve("files"); Path oldPath = directory.resolve("old/minimal.pdf"); - Files.createDirectories(oldPath.getParent()); - Files.createFile(oldPath); - LinkedFile stale = new LinkedFile("", oldPath.toString(), "PDF"); - BibEntry entry = new BibEntry(StandardEntryType.Misc); - entry.addFile(stale); + BibEntry entry = new BibEntry(StandardEntryType.Misc) + .withFiles(List.of(new LinkedFile("", oldPath.toString(), "PDF"))); // Simulate a file move String newPath1String = "new1/minimal.pdf"; Path newPath1 = directory.resolve(newPath1String); Files.createDirectories(newPath1.getParent()); - Files.move(oldPath, newPath1); + Files.createFile(newPath1); // Create a second copy of the file String newPath2String = "new2/minimal.pdf"; @@ -132,11 +128,10 @@ class AutoSetFileLinksUtilTest { filePreferences, autoLinkPrefs); - Collection<String> matchedFiles = util.findAssociatedNotLinkedFiles(entry) - .stream().map(LinkedFile::getLink).toList(); - Set<String> expected = Set.of(newPath1String, newPath2String); - // findAssociatedNotLinkedFiles does not guarantee how the returned files are ordered - // so here we compare equality without considering order - assertEquals(new HashSet<>(matchedFiles), expected); + Collection<LinkedFile> matchedFiles = util.findAssociatedNotLinkedFiles(entry); + Set<LinkedFile> expected = Set.of( + new LinkedFile("", newPath1String, "PDF"), + new LinkedFile("", newPath2String, "PDF")); + assertEquals(expected, Set.copyOf(matchedFiles)); } } ``´

Upate: I filed LangInteger#1

Oh, thx for the PR. I also applied the diff.

jabref-machine · 2025-12-23T20:45:08Z

You committed your code on the main brach of your fork. This is a bad practice. The right way is to branch out from main, work on your patch/feature in that new branch, and then get that branch merged via the pull request (see GitHub flow).

For this pull request, this is OK. For subsequent pull requests, please start with a different branch with a proper branch name. See CONTRIBUTING.md for more details.

github-actions Bot added the status: changes-required Pull requests that are not yet complete label Dec 23, 2025

LangInteger force-pushed the main branch from 4b61ca5 to 0e4a647 Compare December 23, 2025 13:20

LangInteger commented Dec 23, 2025

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LangInteger marked this pull request as ready for review December 23, 2025 13:28

qodo-free-for-open-source-projects Bot added the Review effort 2/5 label Dec 23, 2025

koppor reviewed Dec 23, 2025

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LangInteger requested a review from koppor December 23, 2025 17:56

LangInteger added 5 commits December 23, 2025 11:57

update findAssociatedFiles to find all instead of the first one

d0d4dee

add test findAllAssociatedNotLinkedFilesInsteadOfTheFirstOne

2cfbeae

update Changelog

a80ac43

fix code by AI-suggestion

d3d6766

update test

86f6581

LangInteger force-pushed the main branch from 961a9be to 86f6581 Compare December 23, 2025 17:57

koppor requested changes Dec 23, 2025

View reviewed changes

update test

3b8bb64

koppor requested changes Dec 23, 2025

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LangInteger added 2 commits December 23, 2025 13:45

update test

ac105ef

return collection instead of list

74e2956

LangInteger commented Dec 23, 2025

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koppor requested changes Dec 23, 2025

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LangInteger added 4 commits December 23, 2025 14:13

update test

58aa860

fix indent

9d42516

use set.of

3c72446

move assignment to catch

49f1475

koppor requested changes Dec 23, 2025

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koppor mentioned this pull request Dec 23, 2025

Fix test LangInteger/jabref#1

Closed

update test

8e2c093

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koppor enabled auto-merge December 23, 2025 20:45

koppor added this pull request to the merge queue Dec 23, 2025

Merged via the queue into JabRef:main with commit dd70582 Dec 23, 2025
50 of 51 checks passed

github-actions Bot mentioned this pull request Dec 23, 2025

All the associated files should be displayed for broken linked files instead of only the first one #14697

Closed

LangInteger mentioned this pull request Dec 24, 2025

implement auto-link #14710

Merged

6 tasks

	Collection<LinkedFile> associatedNotLinkedFiles = new ArrayList<>();
	Collection<LinkedFile> associatedNotLinkedFiles = Set.of();

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Steps to test

Screenshot of my manual test

Mandatory checks

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LangInteger commented Dec 23, 2025 •

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