Have relative paths when creating BibTeX from a PDF

JabRef · Aug 4, 2024 · 17112f1 · 17112f1
1 parent f592819
commit 17112f1
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Showing 7 changed files with 44 additions and 10 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -35,6 +35,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 - We fixed an issue where the "Check for updates" preference was not saved. [#11485](https://github.com/JabRef/jabref/pull/11485)
 - We fixed an issue where an exception was thrown after changing "show preview as a tab" in the preferences. [#11515](https://github.com/JabRef/jabref/pull/11515)
+- We fixed an issue where JabRef put file paths as absolute path when an entry was created using drag and drop of a PDF file. [#11173](https://github.com/JabRef/jabref/issues/11173)
 - We fixed an issue that online and offline mode for new library creation were handled incorrectly. [#11565](https://github.com/JabRef/jabref/pull/11565)
 - We fixed an issue with colors in the search bar when dark theme is enabled. [#11569](https://github.com/JabRef/jabref/issues/11569)
 - We fixed an issue where a new unsaved library was not marked with an asterisk. [#11519](https://github.com/JabRef/jabref/pull/11519)

diff --git a/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java b/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java
@@ -53,6 +53,7 @@
 import org.jabref.model.groups.GroupTreeNode;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.model.util.OptionalUtil;
+import org.jabref.preferences.FilePreferences;
 import org.jabref.preferences.PreferencesService;
 
 import com.airhacks.afterburner.injection.Injector;
@@ -99,7 +100,7 @@ public ExternalFilesEntryLinker getLinker() {
         return linker;
     }
 
-    public BackgroundTask<List<ImportFilesResultItemViewModel>> importFilesInBackground(final List<Path> files) {
+    public BackgroundTask<List<ImportFilesResultItemViewModel>> importFilesInBackground(final List<Path> files, final BibDatabaseContext bibDatabaseContext, final FilePreferences filePreferences) {
         return new BackgroundTask<>() {
             private int counter;
             private final List<ImportFilesResultItemViewModel> results = new ArrayList<>();
@@ -130,7 +131,7 @@ protected List<ImportFilesResultItemViewModel> call() {
                             }
 
                             if (!pdfEntriesInFile.isEmpty()) {
-                                entriesToAdd.addAll(pdfEntriesInFile);
+                                entriesToAdd.addAll(FileUtil.relativize(pdfEntriesInFile, bibDatabaseContext, filePreferences));
                                 addResultToList(file, true, Localization.lang("File was successfully imported as a new entry"));
                             } else {
                                 entriesToAdd.add(createEmptyEntryWithLink(file));

diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java b/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java
@@ -151,7 +151,7 @@ public void startImport() {
         }
         resultList.clear();
 
-        importFilesBackgroundTask = importHandler.importFilesInBackground(fileList)
+        importFilesBackgroundTask = importHandler.importFilesInBackground(fileList, bibDatabase, preferences.getFilePreferences())
                                                  .onRunning(() -> {
                                                      progressValueProperty.bind(importFilesBackgroundTask.workDonePercentageProperty());
                                                      progressTextProperty.bind(importFilesBackgroundTask.messageProperty());

diff --git a/src/main/java/org/jabref/gui/maintable/MainTable.java b/src/main/java/org/jabref/gui/maintable/MainTable.java
@@ -56,6 +56,7 @@
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.entry.BibtexString;
 import org.jabref.model.util.FileUpdateMonitor;
+import org.jabref.preferences.FilePreferences;
 import org.jabref.preferences.PreferencesService;
 
 import com.airhacks.afterburner.injection.Injector;
@@ -84,6 +85,7 @@ public class MainTable extends TableView<BibEntryTableViewModel> {
     private final BibEntryTypesManager entryTypesManager;
     private final TaskExecutor taskExecutor;
     private final UndoManager undoManager;
+    private final FilePreferences filePreferences;
     private long lastKeyPressTime;
     private String columnSearchTerm;
 
@@ -110,6 +112,8 @@ public MainTable(MainTableDataModel model,
         this.entryTypesManager = entryTypesManager;
         this.taskExecutor = taskExecutor;
         this.undoManager = libraryTab.getUndoManager();
+        this.filePreferences = preferencesService.getFilePreferences();
+
         MainTablePreferences mainTablePreferences = preferencesService.getMainTablePreferences();
 
         importHandler = new ImportHandler(
@@ -492,8 +496,7 @@ private void handleOnDragDropped(TableRow<BibEntryTableViewModel> row, BibEntryT
             // Center -> link files to entry
             // Depending on the pressed modifier, move/copy/link files to drop target
             switch (ControlHelper.getDroppingMouseLocation(row, event)) {
-                case TOP, BOTTOM ->
-                        importHandler.importFilesInBackground(files).executeWith(taskExecutor);
+                case TOP, BOTTOM -> importHandler.importFilesInBackground(files, database, filePreferences).executeWith(taskExecutor);
                 case CENTER -> {
                     BibEntry entry = target.getEntry();
                     switch (event.getTransferMode()) {
@@ -524,9 +527,8 @@ private void handleOnDragDroppedTableView(DragEvent event) {
         boolean success = false;
 
         if (event.getDragboard().hasFiles()) {
-            List<Path> files = event.getDragboard().getFiles().stream().map(File::toPath).collect(Collectors.toList());
-            importHandler.importFilesInBackground(files).executeWith(taskExecutor);
-
+            List<Path> files = event.getDragboard().getFiles().stream().map(File::toPath).toList();
+            importHandler.importFilesInBackground(files, this.database, filePreferences).executeWith(taskExecutor);
             success = true;
         }
 

diff --git a/src/main/java/org/jabref/logic/importer/ImportFormatReader.java b/src/main/java/org/jabref/logic/importer/ImportFormatReader.java
@@ -55,7 +55,8 @@ public class ImportFormatReader {
 
     public ImportFormatReader(ImporterPreferences importerPreferences,
                               ImportFormatPreferences importFormatPreferences,
-                              CitationKeyPatternPreferences citationKeyPatternPreferences, FileUpdateMonitor fileUpdateMonitor) {
+                              CitationKeyPatternPreferences citationKeyPatternPreferences,
+                              FileUpdateMonitor fileUpdateMonitor) {
         this.importerPreferences = importerPreferences;
         this.importFormatPreferences = importFormatPreferences;
         this.fileUpdateMonitor = fileUpdateMonitor;

diff --git a/src/main/java/org/jabref/logic/importer/fileformat/PdfMergeMetadataImporter.java b/src/main/java/org/jabref/logic/importer/fileformat/PdfMergeMetadataImporter.java
@@ -20,6 +20,7 @@
 import org.jabref.logic.importer.util.FileFieldParser;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.StandardFileType;
+import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
@@ -130,6 +131,8 @@ public ParserResult importDatabase(Path filePath) throws IOException {
             }
         }
 
+        // We use the absolute path here as we do not know the context where this import will be used.
+        // The caller is responsible for making the path relative if necessary.
         entry.addFile(new LinkedFile("", filePath, StandardFileType.PDF.getName()));
         return new ParserResult(List.of(entry));
     }
@@ -169,7 +172,7 @@ public List<BibEntry> performSearch(BibEntry entry) throws FetcherException {
                     try {
                         ParserResult result = importDatabase(filePath.get());
                         if (!result.isEmpty()) {
-                            return result.getDatabase().getEntries();
+                            return FileUtil.relativize(result.getDatabase().getEntries(), databaseContext, filePreferences);
                         }
                     } catch (IOException e) {
                         LOGGER.error("Cannot read {}", filePath.get(), e);

diff --git a/src/main/java/org/jabref/logic/util/io/FileUtil.java b/src/main/java/org/jabref/logic/util/io/FileUtil.java
@@ -27,6 +27,8 @@
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
+import org.jabref.model.entry.LinkedFile;
+import org.jabref.model.entry.field.StandardField;
 import org.jabref.preferences.FilePreferences;
 
 import org.slf4j.Logger;
@@ -268,6 +270,30 @@ public static Path relativize(Path path, BibDatabaseContext databaseContext, Fil
         return relativize(path, fileDirectories);
     }
 
+    /**
+     * Relativizes all BibEntries given to (!) the given database context
+     * <p>
+     * ⚠ Modifies the entries in the list ⚠
+     */
+    public static List<BibEntry> relativize(List<BibEntry> entries, BibDatabaseContext databaseContext, FilePreferences filePreferences) {
+        List<Path> fileDirectories = databaseContext.getFileDirectories(filePreferences);
+
+        return entries.stream()
+                      .map(entry -> {
+                          if (entry.hasField(StandardField.FILE)) {
+                              List<LinkedFile> updatedLinkedFiles = entry.getFiles().stream().map(linkedFile -> {
+                                  if (!linkedFile.isOnlineLink()) {
+                                      String newPath = FileUtil.relativize(Path.of(linkedFile.getLink()), fileDirectories).toString();
+                                      linkedFile.setLink(newPath);
+                                  }
+                                  return linkedFile;
+                              }).toList();
+                              entry.setFiles(updatedLinkedFiles);
+                          }
+                          return entry;
+                      }).toList();
+    }
+
     /**
      * Returns the list of linked files. The files have the absolute filename
      *