Implement an interface to import PDF metadata from multiple sources (XMP, Grobid, ...)

CHANGELOG.md

@@ -15,6 +15,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We added a fulltext search feature. [#2838](https://github.com/JabRef/jabref/pull/2838)
 - We improved the deduction of bib-entries from imported fulltext pdfs. [#7947](https://github.com/JabRef/jabref/pull/7947)
 - We added unprotect_terms to the list of bracketed pattern modifiers [#7826](https://github.com/JabRef/jabref/pull/7960)
+- We added a dialog that allows to parse metadata from linked pdfs. [#7929](https://github.com/JabRef/jabref/pull/7929)
 - We added an icon picker in group edit dialog. [#6142](https://github.com/JabRef/jabref/issues/6142)
 - We added a preference to Opt-In to JabRef's online metadata extraction service (Grobid) usage. [8002](https://github.com/JabRef/jabref/pull/8002)
 

src/main/java/org/jabref/gui/externalfiles/DownloadFullTextAction.java

@@ -144,8 +144,7 @@ private void addLinkedFileFromURL(BibDatabaseContext databaseContext, URL url, B
                     databaseContext,
                     Globals.TASK_EXECUTOR,
                     dialogService,
-                    preferences.getXmpPreferences(),
-                    preferences.getFilePreferences(),
+                    preferences,
                     ExternalFileTypes.getInstance());
 
             onlineFile.download();

src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java

@@ -9,6 +9,7 @@
 import java.util.List;
 import java.util.Optional;
 import java.util.function.BiPredicate;
+import java.util.function.Supplier;
 
 import javax.net.ssl.HostnameVerifier;
 import javax.net.ssl.HttpsURLConnection;
@@ -35,23 +36,30 @@
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.icon.JabRefIcon;
 import org.jabref.gui.linkedfile.LinkedFileEditDialogView;
+import org.jabref.gui.mergeentries.MultiMergeEntriesView;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.ControlHelper;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.externalfiles.LinkedFileHandler;
+import org.jabref.logic.importer.Importer;
+import org.jabref.logic.importer.ParserResult;
+import org.jabref.logic.importer.fileformat.PdfContentImporter;
+import org.jabref.logic.importer.fileformat.PdfEmbeddedBibFileImporter;
+import org.jabref.logic.importer.fileformat.PdfGrobidImporter;
+import org.jabref.logic.importer.fileformat.PdfVerbatimBibTextImporter;
+import org.jabref.logic.importer.fileformat.PdfXmpImporter;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.URLDownload;
 import org.jabref.logic.util.io.FileNameUniqueness;
 import org.jabref.logic.util.io.FileUtil;
-import org.jabref.logic.xmp.XmpPreferences;
 import org.jabref.logic.xmp.XmpUtilWriter;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.FileHelper;
 import org.jabref.model.util.OptionalUtil;
-import org.jabref.preferences.FilePreferences;
+import org.jabref.preferences.PreferencesService;
 
 import de.saxsys.mvvmfx.utils.validation.FunctionBasedValidator;
 import de.saxsys.mvvmfx.utils.validation.ValidationMessage;
@@ -69,12 +77,11 @@ public class LinkedFileViewModel extends AbstractViewModel {
     private final DoubleProperty downloadProgress = new SimpleDoubleProperty(-1);
     private final BooleanProperty downloadOngoing = new SimpleBooleanProperty(false);
     private final BooleanProperty isAutomaticallyFound = new SimpleBooleanProperty(false);
-    private final BooleanProperty canWriteXMPMetadata = new SimpleBooleanProperty(false);
+    private final BooleanProperty isOfflinePdf = new SimpleBooleanProperty(false);
     private final DialogService dialogService;
     private final BibEntry entry;
     private final TaskExecutor taskExecutor;
-    private final FilePreferences filePreferences;
-    private final XmpPreferences xmpPreferences;
+    private final PreferencesService preferences;
     private final LinkedFileHandler linkedFileHandler;
     private final ExternalFileTypes externalFileTypes;
 
@@ -85,38 +92,36 @@ public LinkedFileViewModel(LinkedFile linkedFile,
                                BibDatabaseContext databaseContext,
                                TaskExecutor taskExecutor,
                                DialogService dialogService,
-                               XmpPreferences xmpPreferences,
-                               FilePreferences filePreferences,
+                               PreferencesService preferences,
                                ExternalFileTypes externalFileTypes) {
 
         this.linkedFile = linkedFile;
-        this.filePreferences = filePreferences;
-        this.linkedFileHandler = new LinkedFileHandler(linkedFile, entry, databaseContext, filePreferences);
+        this.preferences = preferences;
+        this.linkedFileHandler = new LinkedFileHandler(linkedFile, entry, databaseContext, preferences.getFilePreferences());
         this.databaseContext = databaseContext;
         this.entry = entry;
         this.dialogService = dialogService;
         this.taskExecutor = taskExecutor;
         this.externalFileTypes = externalFileTypes;
-        this.xmpPreferences = xmpPreferences;
 
         fileExistsValidator = new FunctionBasedValidator<>(
                 linkedFile.linkProperty(),
                 link -> {
                     if (linkedFile.isOnlineLink()) {
                         return true;
                     } else {
-                        Optional<Path> path = FileHelper.find(databaseContext, link, filePreferences);
+                        Optional<Path> path = FileHelper.find(databaseContext, link, preferences.getFilePreferences());
                         return path.isPresent() && Files.exists(path.get());
                     }
                 },
                 ValidationMessage.warning(Localization.lang("Could not find file '%0'.", linkedFile.getLink())));
 
         downloadOngoing.bind(downloadProgress.greaterThanOrEqualTo(0).and(downloadProgress.lessThan(1)));
-        canWriteXMPMetadata.setValue(!linkedFile.isOnlineLink() && linkedFile.getFileType().equalsIgnoreCase("pdf"));
+        isOfflinePdf.setValue(!linkedFile.isOnlineLink() && linkedFile.getFileType().equalsIgnoreCase("pdf"));
     }
 
-    public BooleanProperty canWriteXMPMetadataProperty() {
-        return canWriteXMPMetadata;
+    public BooleanProperty isOfflinePdfProperty() {
+        return isOfflinePdf;
     }
 
     public boolean isAutomaticallyFound() {
@@ -211,7 +216,7 @@ public void openFolder() {
                 Optional<Path> resolvedPath = FileHelper.find(
                         databaseContext,
                         linkedFile.getLink(),
-                        filePreferences);
+                        preferences.getFilePreferences());
 
                 if (resolvedPath.isPresent()) {
                     JabRefDesktop.openFolderAndSelectFile(resolvedPath.get());
@@ -246,7 +251,7 @@ public void renameFileToName(String targetFileName) {
             return;
         }
 
-        Optional<Path> file = linkedFile.findIn(databaseContext, filePreferences);
+        Optional<Path> file = linkedFile.findIn(databaseContext, preferences.getFilePreferences());
         if (file.isPresent()) {
             performRenameWithConflictCheck(targetFileName);
         } else {
@@ -283,13 +288,13 @@ public void moveToDefaultDirectory() {
         }
 
         // Get target folder
-        Optional<Path> fileDir = databaseContext.getFirstExistingFileDir(filePreferences);
+        Optional<Path> fileDir = databaseContext.getFirstExistingFileDir(preferences.getFilePreferences());
         if (fileDir.isEmpty()) {
             dialogService.showErrorDialogAndWait(Localization.lang("Move file"), Localization.lang("File directory is not set or does not exist!"));
             return;
         }
 
-        Optional<Path> file = linkedFile.findIn(databaseContext, filePreferences);
+        Optional<Path> file = linkedFile.findIn(databaseContext, preferences.getFilePreferences());
         if ((file.isPresent())) {
             // Found the linked file, so move it
             try {
@@ -325,9 +330,9 @@ public boolean isGeneratedNameSameAsOriginal() {
      * @return true if suggested filepath is same as existing filepath.
      */
     public boolean isGeneratedPathSameAsOriginal() {
-        Optional<Path> newDir = databaseContext.getFirstExistingFileDir(filePreferences);
+        Optional<Path> newDir = databaseContext.getFirstExistingFileDir(preferences.getFilePreferences());
 
-        Optional<Path> currentDir = linkedFile.findIn(databaseContext, filePreferences).map(Path::getParent);
+        Optional<Path> currentDir = linkedFile.findIn(databaseContext, preferences.getFilePreferences()).map(Path::getParent);
 
         BiPredicate<Path, Path> equality = (fileA, fileB) -> {
             try {
@@ -351,7 +356,7 @@ public void moveToDefaultDirectoryAndRename() {
      * successfully, does not exist in the first place or the user choose to remove it)
      */
     public boolean delete() {
-        Optional<Path> file = linkedFile.findIn(databaseContext, filePreferences);
+        Optional<Path> file = linkedFile.findIn(databaseContext, preferences.getFilePreferences());
 
         if (file.isEmpty()) {
             LOGGER.warn("Could not find file " + linkedFile.getLink());
@@ -395,13 +400,13 @@ public void edit() {
     public void writeXMPMetadata() {
         // Localization.lang("Writing XMP metadata...")
         BackgroundTask<Void> writeTask = BackgroundTask.wrap(() -> {
-            Optional<Path> file = linkedFile.findIn(databaseContext, filePreferences);
+            Optional<Path> file = linkedFile.findIn(databaseContext, preferences.getFilePreferences());
             if (file.isEmpty()) {
                 // TODO: Print error message
                 // Localization.lang("PDF does not exist");
             } else {
                 try {
-                    XmpUtilWriter.writeXmp(file.get(), entry, databaseContext.getDatabase(), xmpPreferences);
+                    XmpUtilWriter.writeXmp(file.get(), entry, databaseContext.getDatabase(), preferences.getXmpPreferences());
                 } catch (IOException | TransformerException ex) {
                     // TODO: Print error message
                     // Localization.lang("Error while writing") + " '" + file.toString() + "': " + ex;
@@ -421,7 +426,7 @@ public void download() {
             throw new UnsupportedOperationException("In order to download the file it has to be an online link");
         }
         try {
-            Optional<Path> targetDirectory = databaseContext.getFirstExistingFileDir(filePreferences);
+            Optional<Path> targetDirectory = databaseContext.getFirstExistingFileDir(preferences.getFilePreferences());
             if (targetDirectory.isEmpty()) {
                 dialogService.showErrorDialogAndWait(Localization.lang("Download file"), Localization.lang("File directory is not set or does not exist!"));
                 return;
@@ -443,7 +448,7 @@ public void download() {
                 }
 
                 if (!isDuplicate) {
-                    LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(destination, databaseContext.getFileDirectories(filePreferences), externalFileTypes);
+                    LinkedFile newLinkedFile = LinkedFilesEditorViewModel.fromFile(destination, databaseContext.getFileDirectories(preferences.getFilePreferences()), externalFileTypes);
                     List<LinkedFile> linkedFiles = entry.getFiles();
 
                     entry.addLinkedFile(entry, linkedFile, newLinkedFile, linkedFiles);
@@ -495,7 +500,7 @@ public BackgroundTask<Path> prepareDownloadTask(Path targetDirectory, URLDownloa
                     String suggestedTypeName = externalFileType.getName();
                     linkedFile.setFileType(suggestedTypeName);
                     String suggestedName = linkedFileHandler.getSuggestedFileName(externalFileType.getExtension());
-                    String fulltextDir = FileUtil.createDirNameFromPattern(databaseContext.getDatabase(), entry, filePreferences.getFileDirectoryPattern());
+                    String fulltextDir = FileUtil.createDirNameFromPattern(databaseContext.getDatabase(), entry, preferences.getFilePreferences().getFileDirectoryPattern());
                     suggestedName = FileNameUniqueness.getNonOverWritingFileName(targetDirectory.resolve(fulltextDir), suggestedName);
                     return targetDirectory.resolve(fulltextDir).resolve(suggestedName);
                 })
@@ -538,4 +543,34 @@ public LinkedFile getFile() {
     public ValidationStatus fileExistsValidationStatus() {
         return fileExistsValidator.getValidationStatus();
     }
+
+    public void parsePdfMetadataAndShowMergeDialog() {
+        linkedFile.findIn(databaseContext, preferences.getFilePreferences()).ifPresent(filePath -> {
+            MultiMergeEntriesView dialog = new MultiMergeEntriesView(preferences, taskExecutor);
+            dialog.addSource(Localization.lang("Entry"), entry);
+            dialog.addSource(Localization.lang("Verbatim"), wrapImporterToSupplier(new PdfVerbatimBibTextImporter(preferences.getImportFormatPreferences()), filePath));
+            dialog.addSource(Localization.lang("Embedded"), wrapImporterToSupplier(new PdfEmbeddedBibFileImporter(preferences.getImportFormatPreferences()), filePath));
+            dialog.addSource("Grobid", wrapImporterToSupplier(new PdfGrobidImporter(preferences.getImportSettingsPreferences(), preferences.getImportFormatPreferences()), filePath));
+            dialog.addSource(Localization.lang("XMP metadata"), wrapImporterToSupplier(new PdfXmpImporter(preferences.getXmpPreferences()), filePath));
+            dialog.addSource(Localization.lang("Content"), wrapImporterToSupplier(new PdfContentImporter(preferences.getImportFormatPreferences()), filePath));
+            dialog.showAndWait().ifPresent(newEntry -> {
+                databaseContext.getDatabase().removeEntry(entry);
+                databaseContext.getDatabase().insertEntry(newEntry);
+            });
+        });
+    }
+
+    private Supplier<BibEntry> wrapImporterToSupplier(Importer importer, Path filePath) {
+        return () -> {
+            try {
+                ParserResult parserResult = importer.importDatabase(filePath, preferences.getDefaultEncoding());
+                if (parserResult.isInvalid() || parserResult.isEmpty() || !parserResult.getDatabase().hasEntries()) {
+                    return null;
+                }
+                return parserResult.getDatabase().getEntries().get(0);
+            } catch (IOException e) {
+                return null;
+            }
+        };
+    }
 }

src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditor.java

@@ -23,6 +23,7 @@
 import javafx.scene.input.MouseEvent;
 import javafx.scene.input.TransferMode;
 import javafx.scene.layout.HBox;
+import javafx.scene.layout.Priority;
 import javafx.scene.text.Text;
 
 import org.jabref.gui.DialogService;
@@ -34,6 +35,7 @@
 import org.jabref.gui.autocompleter.SuggestionProvider;
 import org.jabref.gui.copyfiles.CopySingleFileAction;
 import org.jabref.gui.icon.IconTheme;
+import org.jabref.gui.importer.GrobidOptInDialogHelper;
 import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.gui.util.BindingsHelper;
 import org.jabref.gui.util.TaskExecutor;
@@ -81,7 +83,7 @@ public LinkedFilesEditor(Field field,
 
         ViewModelListCellFactory<LinkedFileViewModel> cellFactory = new ViewModelListCellFactory<LinkedFileViewModel>()
                 .withStringTooltip(LinkedFileViewModel::getDescription)
-                .withGraphic(LinkedFilesEditor::createFileDisplay)
+                .withGraphic(this::createFileDisplay)
                 .withContextMenu(this::createContextMenuForFile)
                 .withOnMouseClickedEvent(this::handleItemMouseClick)
                 .setOnDragDetected(this::handleOnDragDetected)
@@ -142,7 +144,7 @@ private void handleOnDragDropped(LinkedFileViewModel originalItem, DragEvent eve
         event.consume();
     }
 
-    private static Node createFileDisplay(LinkedFileViewModel linkedFile) {
+    private Node createFileDisplay(LinkedFileViewModel linkedFile) {
         PseudoClass opacity = PseudoClass.getPseudoClass("opacity");
 
         Node icon = linkedFile.getTypeIcon().getGraphicNode();
@@ -162,6 +164,7 @@ private static Node createFileDisplay(LinkedFileViewModel linkedFile) {
         progressIndicator.visibleProperty().bind(linkedFile.downloadOngoingProperty());
 
         HBox info = new HBox(8);
+        HBox.setHgrow(info, Priority.ALWAYS);
         info.setStyle("-fx-padding: 0.5em 0 0.5em 0;"); // To align with buttons below which also have 0.5em padding
         info.getChildren().setAll(icon, link, desc, progressIndicator);
 
@@ -174,14 +177,23 @@ private static Node createFileDisplay(LinkedFileViewModel linkedFile) {
 
         Button writeXMPMetadata = IconTheme.JabRefIcons.IMPORT.asButton();
         writeXMPMetadata.setTooltip(new Tooltip(Localization.lang("Write BibTeXEntry as XMP metadata to PDF.")));
-        writeXMPMetadata.visibleProperty().bind(linkedFile.canWriteXMPMetadataProperty());
+        writeXMPMetadata.visibleProperty().bind(linkedFile.isOfflinePdfProperty());
         writeXMPMetadata.setOnAction(event -> linkedFile.writeXMPMetadata());
         writeXMPMetadata.getStyleClass().setAll("icon-button");
 
+        Button parsePdfMetadata = IconTheme.JabRefIcons.FILE_SEARCH.asButton();
+        parsePdfMetadata.setTooltip(new Tooltip(Localization.lang("Parse Metadata from PDF.")));
+        parsePdfMetadata.visibleProperty().bind(linkedFile.isOfflinePdfProperty());
+        parsePdfMetadata.setOnAction(event -> {
+            GrobidOptInDialogHelper.showAndWaitIfUserIsUndecided(dialogService);
+            linkedFile.parsePdfMetadataAndShowMergeDialog();
+        });
+        parsePdfMetadata.getStyleClass().setAll("icon-button");
+
         HBox container = new HBox(10);
         container.setPrefHeight(Double.NEGATIVE_INFINITY);
 
-        container.getChildren().addAll(acceptAutoLinkedFile, info, writeXMPMetadata);
+        container.getChildren().addAll(acceptAutoLinkedFile, info, writeXMPMetadata, parsePdfMetadata);
 
         return container;
     }

src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java

@@ -106,8 +106,7 @@ public LinkedFileViewModel fromFile(Path file) {
                 databaseContext,
                 taskExecutor,
                 dialogService,
-                preferences.getXmpPreferences(),
-                preferences.getFilePreferences(),
+                preferences,
                 externalFileTypes);
     }
 
@@ -123,8 +122,7 @@ private List<LinkedFileViewModel> parseToFileViewModel(String stringValue) {
                                       databaseContext,
                                       taskExecutor,
                                       dialogService,
-                                      preferences.getXmpPreferences(),
-                                      preferences.getFilePreferences(),
+                                      preferences,
                                       externalFileTypes))
                               .collect(Collectors.toList());
     }
@@ -154,8 +152,7 @@ public void addNewFile() {
                     databaseContext,
                     taskExecutor,
                     dialogService,
-                    preferences.getXmpPreferences(),
-                    preferences.getFilePreferences(),
+                    preferences,
                     externalFileTypes));
         });
     }
@@ -192,8 +189,7 @@ private List<LinkedFileViewModel> findAssociatedNotLinkedFiles(BibEntry entry) {
                         databaseContext,
                         taskExecutor,
                         dialogService,
-                        preferences.getXmpPreferences(),
-                        preferences.getFilePreferences(),
+                        preferences,
                         externalFileTypes);
                 newLinkedFile.markAsAutomaticallyFound();
                 result.add(newLinkedFile);
@@ -243,8 +239,7 @@ private void addFromURL(URL url) {
                 databaseContext,
                 taskExecutor,
                 dialogService,
-                preferences.getXmpPreferences(),
-                preferences.getFilePreferences(),
+                preferences,
                 externalFileTypes);
         files.add(onlineFile);
         onlineFile.download();