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Properly Copy Associated PDFs Between .bib Files #700

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Properly Copy Associated PDFs Between .bib Files #700

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76acb3c
pdf successfully paste into new folder
rioxddd Oct 25, 2024
dbe498a
pdf successfully paste into new folder
rioxddd Oct 25, 2024
0758a4c
update CHANGELOG.md
rioxddd Oct 25, 2024
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -139,6 +139,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
- We added an exporter and improved the importer for Endnote XML format. [#11137](https://github.com/JabRef/jabref/issues/11137)
- We added support for using BibTeX Style files (BST) in the Preview. [#11102](https://github.com/JabRef/jabref/issues/11102)
- We added support for automatically update LaTeX citations when a LaTeX file is created, removed, or modified. [#10585](https://github.com/JabRef/jabref/issues/10585)
- We Added functionality to copy associated PDF files when moving entries between `.bib` files, ensuring linked PDFs are also transferred to the destination's designated file directory. [#520](https://github.com/koppor/jabref/issues/520)


### Changed

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37 changes: 37 additions & 0 deletions src/main/java/org/jabref/gui/LibraryTab.java
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@@ -1,7 +1,10 @@
package org.jabref.gui;

import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.nio.file.StandardCopyOption;
import java.util.Collections;
import java.util.List;
import java.util.Objects;
Expand Down Expand Up @@ -109,6 +112,8 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import static com.ibm.icu.text.PluralRules.Operand.e;

/**
* Represents the ui area where the notifier pane, the library table and the entry editor are shown.
*/
Expand Down Expand Up @@ -172,6 +177,8 @@ private enum PanelMode { MAIN_TABLE, MAIN_TABLE_AND_ENTRY_EDITOR }

private final AiService aiService;

private static BibDatabaseContext copiedBibDatabaseContext;

/**
* @param isDummyContext Indicates whether the database context is a dummy. A dummy context is used to display a progress indicator while parsing the database.
* If the context is a dummy, the Lucene index should not be created, as both the dummy context and the actual context share the same index path {@link BibDatabaseContext#getFulltextIndexPath()}.
Expand Down Expand Up @@ -905,6 +912,7 @@ public void insertEntries(final List<BibEntry> entries) {
}

public void copyEntry() {
copiedBibDatabaseContext = this.bibDatabaseContext;
int entriesCopied = doCopyEntry(getSelectedEntries());
if (entriesCopied >= 0) {
dialogService.notify(Localization.lang("Copied %0 entry(ies)", entriesCopied));
Expand Down Expand Up @@ -933,6 +941,7 @@ private int doCopyEntry(List<BibEntry> selectedEntries) {
}

public void pasteEntry() {

List<BibEntry> entriesToAdd;
String content = ClipBoardManager.getContents();
entriesToAdd = importHandler.handleBibTeXData(content);
Expand All @@ -943,6 +952,34 @@ public void pasteEntry() {
return;
}

Optional<String> optionalBibFolderPath = copiedBibDatabaseContext.getMetaData().getDefaultFileDirectory();
if(optionalBibFolderPath.isEmpty()){
LOGGER.warn("can not find the file path");
return;
}

Path sourceBibFolder = Paths.get(optionalBibFolderPath.get());

for(BibEntry entry:entriesToAdd){
List<LinkedFile> linkedFiles = entry.getFiles();
for(LinkedFile linkedFile: linkedFiles){
if("pdf".equalsIgnoreCase(linkedFile.getFileType())){
List<Path> folderList = List.of(sourceBibFolder);
Optional<Path> sourcePath = linkedFile.findIn(folderList);
if(sourcePath.isPresent() && Files.exists(sourcePath.get())){
Path targetFolder = bibDatabaseContext.getMetaData().getDefaultFileDirectory().map(Paths::get).orElseThrow();
Path targetPath = targetFolder.resolve(sourcePath.get().getFileName());
try{
Files.copy(sourcePath.get(), targetPath, StandardCopyOption.REPLACE_EXISTING);
} catch (IOException e) {
LOGGER.error("failed to copy PDF file: {}", sourcePath.get(),e);
}
}else{
LOGGER.warn("did not find PDF: {}", linkedFile.getLink());
}
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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());
            });

}
}
}
importHandler.importEntriesWithDuplicateCheck(bibDatabaseContext, entriesToAdd);
}

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30 changes: 30 additions & 0 deletions src/main/java/org/jabref/gui/copyfiles/CopyFilesAction.java
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@@ -1,9 +1,13 @@
package org.jabref.gui.copyfiles;

import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.StandardCopyOption;
import java.util.List;
import java.util.Optional;

import javafx.application.Platform;
import javafx.concurrent.Task;

import org.jabref.gui.DialogService;
Expand All @@ -15,9 +19,12 @@
import org.jabref.logic.preferences.CliPreferences;
import org.jabref.model.database.BibDatabaseContext;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.LinkedFile;


import static org.jabref.gui.actions.ActionHelper.needsDatabase;
import static org.jabref.gui.actions.ActionHelper.needsEntriesSelected;
import static org.jabref.gui.edit.automaticfiededitor.AbstractAutomaticFieldEditorTabViewModel.LOGGER;

public class CopyFilesAction extends SimpleCommand {

Expand Down Expand Up @@ -48,6 +55,7 @@ private void showDialog(List<CopyFilesResultItemViewModel> data) {

@Override
public void execute() {

BibDatabaseContext database = stateManager.getActiveDatabase().orElseThrow(() -> new NullPointerException("Database null"));
List<BibEntry> entries = stateManager.getSelectedEntries();

Expand All @@ -63,7 +71,29 @@ public void execute() {
Localization.lang("Copy linked files to folder..."),
exportTask);

LOGGER.info("Creating CopyFilesTask with path: " + path);
for (BibEntry entry : entries) {
List<LinkedFile> linkedFiles = entry.getFiles();
for (LinkedFile file : linkedFiles) {
Optional<Path> sourcePath = file.findIn(List.of(path));
if (sourcePath.isPresent()) {
Path targetPath = path.resolve(sourcePath.get().getFileName());
try {
Files.copy(sourcePath.get(), targetPath, StandardCopyOption.REPLACE_EXISTING);
LinkedFile newLinkedFile = new LinkedFile(file.getDescription(), targetPath.toString(), file.getFileType());
entry.addFile(newLinkedFile);
LOGGER.info("Successfully copied file: " + sourcePath.get() + " to " + targetPath);
} catch (IOException e) {
LOGGER.error("Failed to copy file: " + sourcePath.get() + " to " + targetPath, e);
}
}else{
LOGGER.warn("Source file not found or doesn't exist: {}", file.getLink());
}
}
}
uiTaskExecutor.execute(exportTask);

LOGGER.info("CopyFilesTask has been executed.");
exportTask.setOnSucceeded(e -> showDialog(exportTask.getValue()));
});
}
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1 change: 1 addition & 0 deletions src/main/java/org/jabref/gui/copyfiles/CopyFilesDialogView.java
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Expand Up @@ -59,3 +59,4 @@ private void setupTable() {
tvResult.setColumnResizePolicy(param -> true);
}
}

2 changes: 2 additions & 0 deletions src/main/java/org/jabref/gui/copyfiles/CopyFilesTask.java
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Expand Up @@ -85,6 +85,7 @@ protected List<CopyFilesResultItemViewModel> call() throws InterruptedException,

if (newPath.isPresent()) {
Path newFile = newPath.get();
LOGGER.info("Calling copyFile method...");
boolean success = FileUtil.copyFile(fileToExport.get(), newFile, false);
updateProgress(totalFilesCounter++, totalFilesCount);
try {
Expand All @@ -97,6 +98,7 @@ protected List<CopyFilesResultItemViewModel> call() throws InterruptedException,
}
if (success) {
updateMessage(localizedSuccessMessage);
fileName.setLink(newFile.toString());
numberSuccessful++;
writeLogMessage(newFile, bw, localizedSuccessMessage);
addResultToList(newFile, success, localizedSuccessMessage);
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2 changes: 2 additions & 0 deletions src/main/java/org/jabref/logic/util/io/FileUtil.java
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Expand Up @@ -228,7 +228,9 @@ public static boolean copyFile(Path pathToSourceFile, Path pathToDestinationFile
}
try {
// This should also preserve Hard Links
LOGGER.info("Attempting to copy file from " + pathToSourceFile + " to " + pathToDestinationFile);
Files.copy(pathToSourceFile, pathToDestinationFile, StandardCopyOption.REPLACE_EXISTING);
LOGGER.info("File copied successfully.");
return true;
} catch (IOException e) {
LOGGER.error("Copying Files failed.", e);
Expand Down
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