Properly Copy Associated PDFs Between .bib Files

CHANGELOG.md

@@ -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
 

src/main/java/org/jabref/gui/LibraryTab.java

@@ -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;
@@ -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.
  */
@@ -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()}.
@@ -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));
@@ -933,6 +941,7 @@ private int doCopyEntry(List<BibEntry> selectedEntries) {
     }
 
     public void pasteEntry() {
+
         List<BibEntry> entriesToAdd;
         String content = ClipBoardManager.getContents();
         entriesToAdd = importHandler.handleBibTeXData(content);
@@ -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());
+                    }
+                }
+            }
+        }
         importHandler.importEntriesWithDuplicateCheck(bibDatabaseContext, entriesToAdd);
     }
 

src/main/java/org/jabref/gui/copyfiles/CopyFilesAction.java

@@ -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;
@@ -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 {
 
@@ -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();
 
@@ -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()));
         });
     }

src/main/java/org/jabref/gui/copyfiles/CopyFilesDialogView.java

@@ -59,3 +59,4 @@ private void setupTable() {
         tvResult.setColumnResizePolicy(param -> true);
     }
 }
+

src/main/java/org/jabref/gui/copyfiles/CopyFilesTask.java

@@ -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 {
@@ -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);

src/main/java/org/jabref/logic/util/io/FileUtil.java

@@ -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);