Preferences for Grobid

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

@@ -124,7 +124,7 @@ private static void applyPreferences(PreferencesService preferences) {
         Globals.journalAbbreviationRepository = JournalAbbreviationLoader.loadRepository(preferences.getJournalAbbreviationPreferences());
 
         // Build list of Import and Export formats
-        Globals.IMPORT_FORMAT_READER.resetImportFormats(preferences.getImportFormatPreferences(),
+        Globals.IMPORT_FORMAT_READER.resetImportFormats(preferences.getImportSettingsPreferences(), preferences.getImportFormatPreferences(),
                 preferences.getXmpPreferences(), Globals.getFileUpdateMonitor());
         Globals.entryTypesManager.addCustomOrModifiedTypes(preferences.getBibEntryTypes(BibDatabaseMode.BIBTEX),
                 preferences.getBibEntryTypes(BibDatabaseMode.BIBLATEX));

src/main/java/org/jabref/gui/bibtexextractor/BibtexExtractorViewModel.java

@@ -1,6 +1,7 @@
 package org.jabref.gui.bibtexextractor;
 
 import java.util.HashMap;
+import java.util.List;
 import java.util.Map;
 
 import javax.swing.undo.UndoManager;
@@ -32,7 +33,7 @@ public class BibtexExtractorViewModel {
 
     private final StringProperty inputTextProperty = new SimpleStringProperty("");
     private final DialogService dialogService;
-    private final GrobidCitationFetcher currentCitationfetcher;
+    private final PreferencesService preferencesService;
     private final TaskExecutor taskExecutor;
     private final ImportHandler importHandler;
 
@@ -45,7 +46,7 @@ public BibtexExtractorViewModel(BibDatabaseContext bibdatabaseContext,
                                     StateManager stateManager) {
 
         this.dialogService = dialogService;
-        currentCitationfetcher = new GrobidCitationFetcher(preferencesService.getImportFormatPreferences());
+        this.preferencesService = preferencesService;
         this.taskExecutor = taskExecutor;
         this.importHandler = new ImportHandler(
                 bibdatabaseContext,
@@ -61,7 +62,22 @@ public StringProperty inputTextProperty() {
     }
 
     public void startParsing() {
-        BackgroundTask.wrap(() -> currentCitationfetcher.performSearch(inputTextProperty.getValue()))
+        if (preferencesService.getImportSettingsPreferences().isGrobidEnabled()) {
+            parseUsingGrobid();
+        } else {
+            parseUsingBibtexExtractor();
+        }
+    }
+
+    private void parseUsingBibtexExtractor() {
+        BibEntry parsedEntry = new BibtexExtractor().extract(inputTextProperty.getValue());
+        importHandler.importEntries(List.of(parsedEntry));
+        trackNewEntry(parsedEntry, "ParseWithBibTeXExtractor");
+    }
+
+    private void parseUsingGrobid() {
+        GrobidCitationFetcher grobidCitationFetcher = new GrobidCitationFetcher(preferencesService.getImportSettingsPreferences(), preferencesService.getImportFormatPreferences());
+        BackgroundTask.wrap(() -> grobidCitationFetcher.performSearch(inputTextProperty.getValue()))
                       .onRunning(() -> dialogService.notify(Localization.lang("Your text is being parsed...")))
                       .onFailure((e) -> {
                           if (e instanceof FetcherException) {
@@ -76,14 +92,14 @@ public void startParsing() {
                           dialogService.notify(Localization.lang("%0 entries were parsed from your query.", String.valueOf(parsedEntries.size())));
                           importHandler.importEntries(parsedEntries);
                           for (BibEntry bibEntry : parsedEntries) {
-                              trackNewEntry(bibEntry);
+                              trackNewEntry(bibEntry, "ParseWithGrobid");
                           }
                       }).executeWith(taskExecutor);
     }
 
-    private void trackNewEntry(BibEntry bibEntry) {
+    private void trackNewEntry(BibEntry bibEntry, String eventMessage) {
         Map<String, String> properties = new HashMap<>();
         properties.put("EntryType", bibEntry.typeProperty().getValue().getName());
-        Globals.getTelemetryClient().ifPresent(client -> client.trackEvent("ParseWithGrobid", properties, new HashMap<>()));
+        Globals.getTelemetryClient().ifPresent(client -> client.trackEvent(eventMessage, properties, new HashMap<>()));
     }
 }

src/main/java/org/jabref/gui/bibtexextractor/ExtractBibtexDialog.java

@@ -46,7 +46,18 @@ public ExtractBibtexDialog() {
 
         buttonParse = (Button) getDialogPane().lookupButton(parseButtonType);
         buttonParse.setTooltip(new Tooltip((Localization.lang("Starts the extraction and adds the resulting entries to the currently opened database"))));
-        buttonParse.setOnAction(event -> viewModel.startParsing());
+        buttonParse.setOnAction(event -> {
+            if (!preferencesService.getImportSettingsPreferences().isGrobidEnabled() && !preferencesService.getImportSettingsPreferences().isGrobidOptOut()) {
+                boolean confirmGrobidUsage = dialogService.showConfirmationDialogWithOptOutAndWait(
+                        "Remote services",
+                        "Allow sending PDF files and raw citation strings to a JabRef online service (Grobid) to determine Metadata",
+                        "Use BibTeX parser instead",
+                        this::optOutOfGrobid
+                );
+                preferencesService.storeImportSettingsPreferences(preferencesService.getImportSettingsPreferences().withGrobidEnabled(confirmGrobidUsage));
+            }
+            viewModel.startParsing();
+        });
         buttonParse.disableProperty().bind(viewModel.inputTextProperty().isEmpty());
     }
 
@@ -56,4 +67,8 @@ private void initialize() {
         this.viewModel = new BibtexExtractorViewModel(database, dialogService, preferencesService, fileUpdateMonitor, taskExecutor, undoManager, stateManager);
         input.textProperty().bindBidirectional(viewModel.inputTextProperty());
     }
+
+    private void optOutOfGrobid(boolean optOut) {
+        preferencesService.storeImportSettingsPreferences(preferencesService.getImportSettingsPreferences().withGrobidOptOut(optOut));
+    }
 }

src/main/java/org/jabref/gui/entryeditor/EntryEditor.java

@@ -45,6 +45,7 @@
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.importer.EntryBasedFetcher;
 import org.jabref.logic.importer.WebFetchers;
+import org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.field.Field;
@@ -355,11 +356,27 @@ private void setupToolBar() {
 
         // Add menu for fetching bibliographic information
         ContextMenu fetcherMenu = new ContextMenu();
-        for (EntryBasedFetcher fetcher : WebFetchers.getEntryBasedFetchers(preferencesService.getImportFormatPreferences(), preferencesService.getFilePreferences(), databaseContext, preferencesService.getDefaultEncoding())) {
+        for (EntryBasedFetcher fetcher : WebFetchers.getEntryBasedFetchers(preferencesService.getImportSettingsPreferences(), preferencesService.getImportFormatPreferences(), preferencesService.getFilePreferences(), databaseContext, preferencesService.getDefaultEncoding())) {
             MenuItem fetcherMenuItem = new MenuItem(fetcher.getName());
             fetcherMenuItem.setOnAction(event -> fetchAndMerge(fetcher));
             fetcherMenu.getItems().add(fetcherMenuItem);
         }
+        // Treat the PdfMergeMetadataImporter separately since if the use never accepted or disabled grobid, we ask to enable it
+        MenuItem pdfMergeMetadataImporterMenuItem = new MenuItem("PDFmergemetadata");
+        pdfMergeMetadataImporterMenuItem.setOnAction(event -> {
+            if (!preferencesService.getImportSettingsPreferences().isGrobidEnabled() && !preferencesService.getImportSettingsPreferences().isGrobidOptOut()) {
+                boolean confirmGrobidUsage = dialogService.showConfirmationDialogWithOptOutAndWait(
+                        "Remote services",
+                        "Allow sending PDF files and raw citation strings to a JabRef online service (Grobid) to determine Metadata",
+                        "Use other importers instead",
+                        (optOut) -> preferencesService.storeImportSettingsPreferences(preferencesService.getImportSettingsPreferences().withGrobidOptOut(optOut))
+                );
+                preferencesService.storeImportSettingsPreferences(preferencesService.getImportSettingsPreferences().withGrobidEnabled(confirmGrobidUsage));
+            }
+            PdfMergeMetadataImporter.EntryBasedFetcherWrapper pdfMergeMetadataImporter= new PdfMergeMetadataImporter.EntryBasedFetcherWrapper(preferencesService.getImportSettingsPreferences(), preferencesService.getImportFormatPreferences(), preferencesService.getFilePreferences(), databaseContext, preferencesService.getDefaultEncoding());
+            fetchAndMerge(pdfMergeMetadataImporter);
+        });
+        fetcherMenu.getItems().add(pdfMergeMetadataImporterMenuItem);
         fetcherButton.setOnMouseClicked(event -> fetcherMenu.show(fetcherButton, Side.RIGHT, 0, 0));
     }
 

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

@@ -57,7 +57,7 @@ public ImportHandler(BibDatabaseContext database,
         this.stateManager = stateManager;
 
         this.linker = new ExternalFilesEntryLinker(externalFileTypes, preferencesService.getFilePreferences(), database);
-        this.contentImporter = new ExternalFilesContentImporter(preferencesService.getImportFormatPreferences(), preferencesService.getTimestampPreferences());
+        this.contentImporter = new ExternalFilesContentImporter(preferencesService.getImportSettingsPreferences(), preferencesService.getImportFormatPreferences(), preferencesService.getTimestampPreferences());
         this.undoManager = undoManager;
     }
 

src/main/java/org/jabref/gui/preferences/customimporter/CustomImporterTabViewModel.java

@@ -54,6 +54,7 @@ public void storeSettings() {
                                                       .map(ImporterViewModel::getLogic)
                                                       .collect(Collectors.toSet()));
         Globals.IMPORT_FORMAT_READER.resetImportFormats(
+                preferences.getImportSettingsPreferences(),
                 preferences.getImportFormatPreferences(),
                 preferences.getXmpPreferences(),
                 Globals.getFileUpdateMonitor());

src/main/java/org/jabref/gui/preferences/importexport/ImportExportTab.fxml

@@ -23,4 +23,11 @@
 
     <Label styleClass="sectionHeader" text="%Export sort order"/>
     <SaveOrderConfigPanel fx:id="exportOrderPanel"/>
+
+    <Label styleClass="sectionHeader" text="%Remote services"/>
+    <CheckBox fx:id="grobidEnabled" text="%Allow sending PDF files and raw citation strings to a JabRef online service (Grobid) to determine Metadata"/>
+    <HBox alignment="CENTER_LEFT" spacing="10.0">
+        <Label text="%Grobid URL" />
+        <TextField fx:id="grobidURL" HBox.hgrow="ALWAYS"/>
+    </HBox>
 </fx:root>

src/main/java/org/jabref/gui/preferences/importexport/ImportExportTab.java

@@ -19,6 +19,9 @@ public class ImportExportTab extends AbstractPreferenceTabView<ImportExportTabVi
 
     @FXML private SaveOrderConfigPanel exportOrderPanel;
 
+    @FXML private CheckBox grobidEnabled;
+    @FXML private TextField grobidURL;
+
     public ImportExportTab() {
         ViewLoader.view(this)
                   .root(this)
@@ -45,5 +48,9 @@ public void initialize() {
         exportOrderPanel.sortableFieldsProperty().bind(viewModel.sortableFieldsProperty());
         exportOrderPanel.sortCriteriaProperty().bindBidirectional(viewModel.sortCriteriaProperty());
         exportOrderPanel.setCriteriaLimit(3);
+
+        grobidEnabled.selectedProperty().bindBidirectional(viewModel.grobidEnabledProperty());
+        grobidURL.textProperty().bindBidirectional(viewModel.grobidURLProperty());
+        grobidURL.disableProperty().bind(grobidEnabled.selectedProperty().not());
     }
 }

src/main/java/org/jabref/gui/preferences/importexport/ImportExportTabViewModel.java

@@ -36,6 +36,9 @@ public class ImportExportTabViewModel implements PreferenceTabViewModel {
     private final ListProperty<Field> sortableFieldsProperty = new SimpleListProperty<>(FXCollections.observableArrayList());
     private final ListProperty<SortCriterionViewModel> sortCriteriaProperty = new SimpleListProperty<>(FXCollections.observableArrayList(new ArrayList<>()));
 
+    private final BooleanProperty grobidEnabledProperty = new SimpleBooleanProperty();
+    private final StringProperty grobidURLProperty = new SimpleStringProperty("");
+
     private final PreferencesService preferencesService;
     private final DOIPreferences initialDOIPreferences;
     private final ImportSettingsPreferences initialImportSettingsPreferences;
@@ -67,12 +70,15 @@ public void setValues() {
         sortCriteriaProperty.addAll(initialExportOrder.getSortCriteria().stream()
                                                       .map(SortCriterionViewModel::new)
                                                       .collect(Collectors.toList()));
+
+        grobidEnabledProperty.setValue(initialImportSettingsPreferences.isGrobidEnabled());
+        grobidURLProperty.setValue(initialImportSettingsPreferences.getGrobidURL());
     }
 
     @Override
     public void storeSettings() {
         preferencesService.storeImportSettingsPreferences(new ImportSettingsPreferences(
-                generateKeyOnImportProperty.getValue()));
+                generateKeyOnImportProperty.getValue(), grobidEnabledProperty.getValue(), preferencesService.getImportSettingsPreferences().isGrobidOptOut(), grobidURLProperty.getValue()));
 
         preferencesService.storeDOIPreferences(new DOIPreferences(
                 useCustomDOIProperty.getValue(),
@@ -118,4 +124,12 @@ public ListProperty<Field> sortableFieldsProperty() {
     public ListProperty<SortCriterionViewModel> sortCriteriaProperty() {
         return sortCriteriaProperty;
     }
+
+    public BooleanProperty grobidEnabledProperty() {
+        return grobidEnabledProperty;
+    }
+
+    public StringProperty grobidURLProperty() {
+        return grobidURLProperty;
+    }
 }

src/main/java/org/jabref/logic/externalfiles/ExternalFilesContentImporter.java

@@ -9,22 +9,25 @@
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter;
 import org.jabref.logic.importer.fileformat.PdfXmpImporter;
+import org.jabref.logic.importer.importsettings.ImportSettingsPreferences;
 import org.jabref.logic.preferences.TimestampPreferences;
 import org.jabref.model.util.FileUpdateMonitor;
 
 public class ExternalFilesContentImporter {
 
+    private final ImportSettingsPreferences importSettingsPreferences;
     private final ImportFormatPreferences importFormatPreferences;
     private final TimestampPreferences timestampPreferences;
 
-    public ExternalFilesContentImporter(ImportFormatPreferences importFormatPreferences, TimestampPreferences timestampPreferences) {
+    public ExternalFilesContentImporter(ImportSettingsPreferences importSettingsPreferences, ImportFormatPreferences importFormatPreferences, TimestampPreferences timestampPreferences) {
+        this.importSettingsPreferences = importSettingsPreferences;
         this.importFormatPreferences = importFormatPreferences;
         this.timestampPreferences = timestampPreferences;
     }
 
     public ParserResult importPDFContent(Path file) {
         try {
-            return new PdfMergeMetadataImporter(importFormatPreferences).importDatabase(file, StandardCharsets.UTF_8);
+            return new PdfMergeMetadataImporter(importSettingsPreferences, importFormatPreferences).importDatabase(file, StandardCharsets.UTF_8);
         } catch (IOException e) {
            return ParserResult.fromError(e);
         }

src/main/java/org/jabref/logic/importer/ImportFormatReader.java

@@ -9,7 +9,6 @@
 import java.util.SortedSet;
 import java.util.TreeSet;
 
-import org.jabref.logic.importer.fetcher.GrobidCitationFetcher;
 import org.jabref.logic.importer.fileformat.BibTeXMLImporter;
 import org.jabref.logic.importer.fileformat.BiblioscapeImporter;
 import org.jabref.logic.importer.fileformat.BibtexImporter;
@@ -32,6 +31,7 @@
 import org.jabref.logic.importer.fileformat.RepecNepImporter;
 import org.jabref.logic.importer.fileformat.RisImporter;
 import org.jabref.logic.importer.fileformat.SilverPlatterImporter;
+import org.jabref.logic.importer.importsettings.ImportSettingsPreferences;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.preferences.TimestampPreferences;
 import org.jabref.logic.xmp.XmpPreferences;
@@ -52,7 +52,7 @@ public class ImportFormatReader {
 
     private ImportFormatPreferences importFormatPreferences;
 
-    public void resetImportFormats(ImportFormatPreferences newImportFormatPreferences, XmpPreferences xmpPreferences, FileUpdateMonitor fileMonitor) {
+    public void resetImportFormats(ImportSettingsPreferences importSettingsPreferences, ImportFormatPreferences newImportFormatPreferences, XmpPreferences xmpPreferences, FileUpdateMonitor fileMonitor) {
         this.importFormatPreferences = newImportFormatPreferences;
 
         formats.clear();
@@ -68,11 +68,13 @@ public void resetImportFormats(ImportFormatPreferences newImportFormatPreference
         formats.add(new ModsImporter(importFormatPreferences));
         formats.add(new MsBibImporter());
         formats.add(new OvidImporter());
-        formats.add(new PdfMergeMetadataImporter(importFormatPreferences));
+        formats.add(new PdfMergeMetadataImporter(importSettingsPreferences, importFormatPreferences));
         formats.add(new PdfVerbatimBibTextImporter(importFormatPreferences));
         formats.add(new PdfContentImporter(importFormatPreferences));
         formats.add(new PdfEmbeddedBibFileImporter(importFormatPreferences));
-        formats.add(new PdfGrobidImporter(GrobidCitationFetcher.GROBID_URL, importFormatPreferences));
+        if (importSettingsPreferences.isGrobidEnabled()) {
+            formats.add(new PdfGrobidImporter(importSettingsPreferences, importFormatPreferences));
+        }
         formats.add(new PdfXmpImporter(xmpPreferences));
         formats.add(new RepecNepImporter(importFormatPreferences));
         formats.add(new RisImporter());

src/main/java/org/jabref/logic/importer/WebFetchers.java

@@ -39,6 +39,7 @@
 import org.jabref.logic.importer.fetcher.TitleFetcher;
 import org.jabref.logic.importer.fetcher.ZbMATH;
 import org.jabref.logic.importer.fileformat.PdfMergeMetadataImporter;
+import org.jabref.logic.importer.importsettings.ImportSettingsPreferences;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.StandardField;
@@ -137,15 +138,14 @@ public static SortedSet<IdBasedFetcher> getIdBasedFetchers(ImportFormatPreferenc
     /**
      * @return sorted set containing entry based fetchers
      */
-    public static SortedSet<EntryBasedFetcher> getEntryBasedFetchers(ImportFormatPreferences importFormatPreferences, FilePreferences filePreferences, BibDatabaseContext databaseContext, Charset defaultEncoding) {
+    public static SortedSet<EntryBasedFetcher> getEntryBasedFetchers(ImportSettingsPreferences importSettingsPreferences, ImportFormatPreferences importFormatPreferences, FilePreferences filePreferences, BibDatabaseContext databaseContext, Charset defaultEncoding) {
         SortedSet<EntryBasedFetcher> set = new TreeSet<>(Comparator.comparing(WebFetcher::getName));
         set.add(new AstrophysicsDataSystem(importFormatPreferences));
         set.add(new DoiFetcher(importFormatPreferences));
         set.add(new IsbnFetcher(importFormatPreferences));
         set.add(new MathSciNet(importFormatPreferences));
         set.add(new CrossRef());
         set.add(new ZbMATH(importFormatPreferences));
-        set.add(new PdfMergeMetadataImporter.EntryBasedFetcherWrapper(importFormatPreferences, filePreferences, databaseContext, defaultEncoding));
         return set;
     }