Properly Copy Associated PDFs Between .bib Files

[rioxddd]

Describe the changes you have made here: what, why, ...
This pull request fixes the issue where associated PDF files were not being copied when entries were moved from one .bib file to another. Now, when copying entries, the linked PDFs are also transferred to the correct folder for the target .bib file.

Changes Made:
Updated copyEntry() to store the source .bib file context.
Modified pasteEntry() to copy linked PDFs to the target .bib file's directory.

Link the issue that will be closed: (#520)

Mandatory checks

• I own the copyright of the code submitted and I licence it under the MIT license
• Change in CHANGELOG.md described in a way that is understandable for the average user (if applicable)
• Tests created for changes (if applicable)
• Manually tested changed features in running JabRef (always required)
• Screenshots added in PR description (for UI changes)
• Checked developer's documentation: Is the information available and up to date? If not, I outlined it in this pull request.
• Checked 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 to the documentation repository.

[koppor]

@rioxddd Do you need a review by a teammate here in this repository? If not, please submit a pull request to https://github.com/JabRef/jabref/pulls - because only PRs there go into the release.

[koppor]

"Unfortunately", JabRef also heads methods for copying files. Please use them. They need to be adapted. I put hints in the code comments.

[koppor]

No manual moving. Try to adapt public boolean copyOrMoveToDefaultDirectory(boolean shouldMove, boolean shouldRenameToFilenamePattern) throws IOException { from LinkedFileHandler.java.

I think, it can be used if user-specific file directory exists.

Proper code for that is to introduce FileDirectoriesInfo. (see below)

org.jabref.model.database.BibDatabaseContext#getFirstExistingFileDir needs to be made for FileDirectoriesInfo.

Then, the result can be checked if it is NOT mainFileDirectory.

Then, before you even start copy, check if the file is reachable from the NEW library (org.jabref.model.entry.LinkedFile#findIn(java.util.List<java.nio.file.Path>)). If yes, do not copy.

Handle all files, not just PDFs.

Introduced following in BibdatabaseContext:

    public record FileDirectoriesInfo(
            Optional<Path> mainFileDirectory,
            Optional<Path> librarySpecificDirectory,
            Optional<Path> userFileDirectory) {
    }

    public FileDirectoriesInfo getFileDirectoriesInfo(FilePreferences preferences) {
        Optional<Path> mainFileDirectory = metaData.getUserFileDirectory(preferences.getUserAndHost()).map(dir -> getFileDirectoryPath(dir));
       if (mainFileDirectory.isEmpty() && preferences.shouldStoreFilesRelativeToBibFile()) {
             // TODO
       }

        Optional<Path> librarySpecificDirectory = metaData.getLibrarySpecificFileDirectory()
                                                          .map(Path::of);

        Optional<Path> userFileDirectory = metaData.getUserFileDirectory(preferences.getUserAndHost())
                                                   .map(Path::of);

        return new FileDirectoriesInfo(mainFileDirectory, librarySpecificDirectory, userFileDirectory);
    }

Replace the TODO part with something like follows - you need to extract that part from org.jabref.model.database.BibDatabaseContext#getFileDirectories into a new method.

            getDatabasePath().ifPresent(dbPath -> {
                Path parentPath = dbPath.getParent();
                if (parentPath == null) {
                    parentPath = Path.of(System.getProperty("user.dir"));
                    LOGGER.warn("Parent path of database file {} is null. Falling back to {}.", dbPath, parentPath);
                }
                Objects.requireNonNull(parentPath, "BibTeX database parent path is null");
                fileDirs.add(parentPath.toAbsolutePath());
            });

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