Refactor of DOI import failure dialog, import format reader and clipboard manager

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

@@ -5,10 +5,7 @@
 import java.awt.datatransfer.StringSelection;
 import java.awt.datatransfer.Transferable;
 import java.awt.datatransfer.UnsupportedFlavorException;
-import java.io.ByteArrayInputStream;
 import java.io.IOException;
-import java.nio.charset.StandardCharsets;
-import java.util.Collections;
 import java.util.List;
 import java.util.Optional;
 
@@ -22,19 +19,8 @@
 import org.jabref.architecture.AllowedToUseAwt;
 import org.jabref.logic.bibtex.BibEntryWriter;
 import org.jabref.logic.bibtex.FieldWriter;
-import org.jabref.logic.importer.FetcherException;
-import org.jabref.logic.importer.ImportException;
-import org.jabref.logic.importer.ImportFormatReader;
-import org.jabref.logic.importer.ImportFormatReader.UnknownFormatImport;
-import org.jabref.logic.importer.ParseException;
-import org.jabref.logic.importer.fetcher.ArXiv;
-import org.jabref.logic.importer.fetcher.DoiFetcher;
-import org.jabref.logic.importer.fileformat.BibtexParser;
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
-import org.jabref.model.entry.identifier.ArXivIdentifier;
-import org.jabref.model.entry.identifier.DOI;
-import org.jabref.model.util.OptionalUtil;
 import org.jabref.preferences.PreferencesService;
 
 import org.slf4j.Logger;
@@ -49,18 +35,16 @@ public class ClipBoardManager {
 
     private static Clipboard clipboard;
     private static java.awt.datatransfer.Clipboard primary;
-    private static ImportFormatReader importFormatReader;
+
     private final PreferencesService preferencesService;
 
     public ClipBoardManager(PreferencesService preferencesService) {
-        this(Clipboard.getSystemClipboard(), Toolkit.getDefaultToolkit().getSystemSelection(), Globals.IMPORT_FORMAT_READER, preferencesService);
+        this(Clipboard.getSystemClipboard(), Toolkit.getDefaultToolkit().getSystemSelection(), preferencesService);
     }
 
-    public ClipBoardManager(Clipboard clipboard, java.awt.datatransfer.Clipboard primary, ImportFormatReader importFormatReader, PreferencesService preferencesService) {
+    public ClipBoardManager(Clipboard clipboard, java.awt.datatransfer.Clipboard primary, PreferencesService preferencesService) {
         ClipBoardManager.clipboard = clipboard;
         ClipBoardManager.primary = primary;
-        ClipBoardManager.importFormatReader = importFormatReader;
-
         this.preferencesService = preferencesService;
     }
 
@@ -103,6 +87,10 @@ public static String getContents() {
         return result;
     }
 
+    public Optional<String> getBibTeXEntriesFromClipbaord() {
+        return Optional.ofNullable(clipboard.getContent(DragAndDropDataFormats.ENTRIES)).map(String.class::cast);
+    }
+
     /**
      * Get the String residing on the primary clipboard (if it exists).
      *
@@ -167,71 +155,4 @@ public void setContent(List<BibEntry> entries) throws IOException {
         clipboard.setContent(content);
         setPrimaryClipboardContent(content);
     }
-
-    public List<BibEntry> extractData() {
-        Object entries = clipboard.getContent(DragAndDropDataFormats.ENTRIES);
-
-        if (entries == null) {
-            return handleStringData(clipboard.getString());
-        }
-        return handleBibTeXData((String) entries);
-    }
-
-    private List<BibEntry> handleBibTeXData(String entries) {
-        BibtexParser parser = new BibtexParser(preferencesService.getImportFormatPreferences(), Globals.getFileUpdateMonitor());
-        try {
-            return parser.parseEntries(new ByteArrayInputStream(entries.getBytes(StandardCharsets.UTF_8)));
-        } catch (ParseException ex) {
-            LOGGER.error("Could not paste", ex);
-            return Collections.emptyList();
-        }
-    }
-
-    private List<BibEntry> handleStringData(String data) {
-        if ((data == null) || data.isEmpty()) {
-            return Collections.emptyList();
-        }
-
-        Optional<DOI> doi = DOI.parse(data);
-        if (doi.isPresent()) {
-            return fetchByDOI(doi.get());
-        }
-        Optional<ArXivIdentifier> arXiv = ArXivIdentifier.parse(data);
-        if (arXiv.isPresent()) {
-            return fetchByArXiv(arXiv.get());
-        }
-
-        return tryImportFormats(data);
-    }
-
-    private List<BibEntry> tryImportFormats(String data) {
-        try {
-            UnknownFormatImport unknownFormatImport = importFormatReader.importUnknownFormat(data);
-            return unknownFormatImport.parserResult.getDatabase().getEntries();
-        } catch (ImportException ignored) {
-            return Collections.emptyList();
-        }
-    }
-
-    private List<BibEntry> fetchByDOI(DOI doi) {
-        LOGGER.info("Found DOI in clipboard");
-        try {
-            Optional<BibEntry> entry = new DoiFetcher(preferencesService.getImportFormatPreferences()).performSearchById(doi.getDOI());
-            return OptionalUtil.toList(entry);
-        } catch (FetcherException ex) {
-            LOGGER.error("Error while fetching", ex);
-            return Collections.emptyList();
-        }
-    }
-
-    private List<BibEntry> fetchByArXiv(ArXivIdentifier arXivIdentifier) {
-        LOGGER.info("Found arxiv identifier in clipboard");
-        try {
-            Optional<BibEntry> entry = new ArXiv(preferencesService.getImportFormatPreferences()).performSearchById(arXivIdentifier.getNormalizedWithoutVersion());
-            return OptionalUtil.toList(entry);
-        } catch (FetcherException ex) {
-            LOGGER.error("Error while fetching", ex);
-            return Collections.emptyList();
-        }
-    }
 }

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

@@ -7,6 +7,7 @@
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.theme.ThemeManager;
 import org.jabref.gui.util.TaskExecutor;
+import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.journals.JournalAbbreviationRepository;
 import org.jabref.logic.protectedterms.ProtectedTermsLoader;
 import org.jabref.model.entry.BibEntryTypesManager;
@@ -52,6 +53,8 @@ private static Object createDependency(Class<?> clazz) {
             return Globals.undoManager;
         } else if (clazz == BibEntryTypesManager.class) {
             return Globals.entryTypesManager;
+        } else if (clazz == ImportFormatReader.class) {
+            return Globals.IMPORT_FORMAT_READER;
         } else {
             try {
                 return clazz.newInstance();

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

@@ -24,6 +24,7 @@
 import org.jabref.gui.util.IconValidationDecorator;
 import org.jabref.gui.util.ViewModelListCellFactory;
 import org.jabref.logic.importer.IdBasedFetcher;
+import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.importer.WebFetcher;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseMode;
@@ -47,6 +48,7 @@
 public class EntryTypeView extends BaseDialog<EntryType> {
 
     @Inject StateManager stateManager;
+    @Inject ImportFormatReader importFormatReader;
 
     @FXML private ButtonType generateButton;
     @FXML private TextField idTextField;
@@ -118,7 +120,7 @@ private void addEntriesToPane(FlowPane pane, Collection<? extends BibEntryType>
     @FXML
     public void initialize() {
         visualizer.setDecoration(new IconValidationDecorator());
-        viewModel = new EntryTypeViewModel(preferencesService, libraryTab, dialogService, stateManager);
+        viewModel = new EntryTypeViewModel(preferencesService, libraryTab, dialogService, stateManager, importFormatReader);
 
         idBasedFetchers.itemsProperty().bind(viewModel.fetcherItemsProperty());
         idTextField.textProperty().bindBidirectional(viewModel.idTextProperty());

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

@@ -19,6 +19,7 @@
 import org.jabref.gui.importer.NewEntryAction;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.IdBasedFetcher;
+import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.importer.WebFetchers;
 import org.jabref.logic.importer.fetcher.DoiFetcher;
 import org.jabref.logic.l10n.Localization;
@@ -50,15 +51,19 @@ public class EntryTypeViewModel {
     private final DialogService dialogService;
     private final Validator idFieldValidator;
     private final StateManager stateManager;
+    private final ImportFormatReader importFormatReader;
 
     public EntryTypeViewModel(PreferencesService preferences,
                               LibraryTab libraryTab,
                               DialogService dialogService,
-                              StateManager stateManager) {
+                              StateManager stateManager,
+                              ImportFormatReader importFormatReader) {
         this.libraryTab = libraryTab;
         this.preferencesService = preferences;
         this.dialogService = dialogService;
         this.stateManager = stateManager;
+        this.importFormatReader = importFormatReader;
+
         fetchers.addAll(WebFetchers.getIdBasedFetchers(
                 preferences.getImportFormatPreferences(),
                 preferences.getImporterPreferences()));
@@ -164,7 +169,8 @@ public void runFetcherWorker() {
                         Globals.getFileUpdateMonitor(),
                         libraryTab.getUndoManager(),
                         stateManager,
-                        dialogService);
+                        dialogService,
+                        importFormatReader);
                 handler.importEntryWithDuplicateCheck(libraryTab.getBibDatabaseContext(), entry);
 
                 searchSuccesfulProperty.set(true);

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

@@ -127,6 +127,7 @@
 import org.jabref.logic.help.HelpFile;
 import org.jabref.logic.importer.IdFetcher;
 import org.jabref.logic.importer.ImportCleanup;
+import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.WebFetchers;
 import org.jabref.logic.l10n.Localization;
@@ -183,6 +184,7 @@ public class JabRefFrame extends BorderPane {
     private Subscription dividerSubscription;
 
     private final TaskExecutor taskExecutor;
+    private final ImportFormatReader importFormatReader;
 
     public JabRefFrame(Stage mainStage) {
         this.mainStage = mainStage;
@@ -194,6 +196,7 @@ public JabRefFrame(Stage mainStage) {
         this.globalSearchBar = new GlobalSearchBar(this, stateManager, prefs, undoManager);
         this.fileHistory = new FileHistoryMenu(prefs, dialogService, getOpenDatabaseAction());
         this.taskExecutor = Globals.TASK_EXECUTOR;
+        this.importFormatReader = Globals.IMPORT_FORMAT_READER;
         this.setOnKeyTyped(key -> {
             if (this.fileHistory.isShowing()) {
                 if (this.fileHistory.openFileByKey(key)) {
@@ -1092,7 +1095,7 @@ private void trackOpenNewDatabase(LibraryTab libraryTab) {
     public LibraryTab addTab(BibDatabaseContext databaseContext, boolean raisePanel) {
         Objects.requireNonNull(databaseContext);
 
-        LibraryTab libraryTab = new LibraryTab(this, prefs, stateManager, themeManager, databaseContext, ExternalFileTypes.getInstance());
+        LibraryTab libraryTab = new LibraryTab(this, prefs, stateManager, themeManager, databaseContext, ExternalFileTypes.getInstance(), importFormatReader);
         addTab(libraryTab, raisePanel);
         return libraryTab;
     }

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

@@ -163,7 +163,7 @@ private static void applyPreferences(PreferencesService preferences) {
 
         // Build list of Import and Export formats
         Globals.IMPORT_FORMAT_READER.resetImportFormats(preferences.getImporterPreferences(),
-                preferences.getGeneralPreferences(), preferences.getImportFormatPreferences(),
+                preferences.getImportFormatPreferences(),
                 preferences.getXmpPreferences(), Globals.getFileUpdateMonitor());
         Globals.entryTypesManager.addCustomOrModifiedTypes(preferences.getBibEntryTypes(BibDatabaseMode.BIBTEX),
                 preferences.getBibEntryTypes(BibDatabaseMode.BIBLATEX));

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

@@ -43,6 +43,7 @@
 import org.jabref.logic.autosaveandbackup.AutosaveManager;
 import org.jabref.logic.autosaveandbackup.BackupManager;
 import org.jabref.logic.citationstyle.CitationStyleCache;
+import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.util.FileFieldParser;
 import org.jabref.logic.l10n.Localization;
@@ -113,13 +114,15 @@ public class LibraryTab extends Tab {
     private BackgroundTask<ParserResult> dataLoadingTask = BackgroundTask.wrap(() -> null);
 
     private final IndexingTaskManager indexingTaskManager = new IndexingTaskManager(Globals.TASK_EXECUTOR);
+    private final ImportFormatReader importFormatReader;
 
     public LibraryTab(JabRefFrame frame,
                       PreferencesService preferencesService,
                       StateManager stateManager,
                       ThemeManager themeManager,
                       BibDatabaseContext bibDatabaseContext,
-                      ExternalFileTypes externalFileTypes) {
+                      ExternalFileTypes externalFileTypes,
+                      ImportFormatReader importFormatReader) {
         this.frame = Objects.requireNonNull(frame);
         this.bibDatabaseContext = Objects.requireNonNull(bibDatabaseContext);
         this.externalFileTypes = Objects.requireNonNull(externalFileTypes);
@@ -128,6 +131,7 @@ public LibraryTab(JabRefFrame frame,
         this.preferencesService = Objects.requireNonNull(preferencesService);
         this.stateManager = Objects.requireNonNull(stateManager);
         this.themeManager = Objects.requireNonNull(themeManager);
+        this.importFormatReader = importFormatReader;
 
         bibDatabaseContext.getDatabase().registerListener(this);
         bibDatabaseContext.getMetaData().registerListener(this);
@@ -480,7 +484,9 @@ private void createMainTable() {
                 dialogService,
                 stateManager,
                 externalFileTypes,
-                Globals.getKeyPrefs());
+                Globals.getKeyPrefs(),
+                Globals.getClipboardManager(),
+                Globals.IMPORT_FORMAT_READER);
 
         // Add the listener that binds selection to state manager (TODO: should be replaced by proper JavaFX binding as soon as table is implemented in JavaFX)
         mainTable.addSelectionListener(listEvent -> stateManager.setSelectedEntries(mainTable.getSelectedEntries()));
@@ -789,11 +795,11 @@ public void resetChangedProperties() {
     }
 
     public static class Factory {
-        public LibraryTab createLibraryTab(JabRefFrame frame, PreferencesService preferencesService, StateManager stateManager, ThemeManager themeManager, Path file, BackgroundTask<ParserResult> dataLoadingTask) {
+        public LibraryTab createLibraryTab(JabRefFrame frame, PreferencesService preferencesService, StateManager stateManager, ThemeManager themeManager, Path file, BackgroundTask<ParserResult> dataLoadingTask, ImportFormatReader importFormatReader) {
             BibDatabaseContext context = new BibDatabaseContext();
             context.setDatabasePath(file);
 
-            LibraryTab newTab = new LibraryTab(frame, preferencesService, stateManager, themeManager, context, ExternalFileTypes.getInstance());
+            LibraryTab newTab = new LibraryTab(frame, preferencesService, stateManager, themeManager, context, ExternalFileTypes.getInstance(), importFormatReader);
             newTab.setDataLoadingTask(dataLoadingTask);
 
             dataLoadingTask.onRunning(newTab::onDatabaseLoadingStarted)
@@ -929,7 +935,7 @@ public void notify(Node graphic, String text, List<Action> actions, Duration dur
             this.setText(text);
             this.getActions().setAll(actions);
             this.show();
-            if (duration != null && !duration.equals(Duration.ZERO)) {
+            if ((duration != null) && !duration.equals(Duration.ZERO)) {
                 PauseTransition delay = new PauseTransition(duration);
                 delay.setOnFinished(e -> this.hide());
                 delay.play();

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

@@ -17,6 +17,7 @@
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.importer.FetcherException;
+import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.importer.fetcher.GrobidCitationFetcher;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
@@ -43,7 +44,8 @@ public BibtexExtractorViewModel(BibDatabaseContext bibdatabaseContext,
                                     FileUpdateMonitor fileUpdateMonitor,
                                     TaskExecutor taskExecutor,
                                     UndoManager undoManager,
-                                    StateManager stateManager) {
+                                    StateManager stateManager,
+                                    ImportFormatReader importFormatReader) {
 
         this.dialogService = dialogService;
         this.preferencesService = preferencesService;
@@ -55,7 +57,8 @@ public BibtexExtractorViewModel(BibDatabaseContext bibdatabaseContext,
                 fileUpdateMonitor,
                 undoManager,
                 stateManager,
-                dialogService);
+                dialogService,
+                importFormatReader);
     }
 
     public StringProperty inputTextProperty() {

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

@@ -13,6 +13,7 @@
 import org.jabref.gui.StateManager;
 import org.jabref.gui.util.BaseDialog;
 import org.jabref.gui.util.TaskExecutor;
+import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.util.FileUpdateMonitor;
@@ -35,6 +36,7 @@ public class ExtractBibtexDialog extends BaseDialog<Void> {
     @Inject private TaskExecutor taskExecutor;
     @Inject private UndoManager undoManager;
     @Inject private PreferencesService preferencesService;
+    @Inject private ImportFormatReader importFormatReader;
 
     public ExtractBibtexDialog() {
         ViewLoader.view(this)
@@ -53,7 +55,7 @@ public ExtractBibtexDialog() {
     @FXML
     private void initialize() {
         BibDatabaseContext database = stateManager.getActiveDatabase().orElseThrow(() -> new NullPointerException("Database null"));
-        this.viewModel = new BibtexExtractorViewModel(database, dialogService, preferencesService, fileUpdateMonitor, taskExecutor, undoManager, stateManager);
+        this.viewModel = new BibtexExtractorViewModel(database, dialogService, preferencesService, fileUpdateMonitor, taskExecutor, undoManager, stateManager, importFormatReader);
         input.textProperty().bindBidirectional(viewModel.inputTextProperty());
     }
 }

src/main/java/org/jabref/gui/errorconsole/ErrorConsoleViewModel.java

@@ -2,9 +2,6 @@
 
 import java.io.IOException;
 import java.net.URISyntaxException;
-import java.text.DateFormat;
-import java.text.SimpleDateFormat;
-import java.util.Date;
 import java.util.List;
 import java.util.Objects;
 import java.util.stream.Collectors;
@@ -30,8 +27,6 @@
 public class ErrorConsoleViewModel extends AbstractViewModel {
     private static final Logger LOGGER = LoggerFactory.getLogger(ErrorConsoleViewModel.class);
 
-    private final DateFormat dateFormat = new SimpleDateFormat("yyyyMMddHHmmss");
-    private final Date date = new Date();
     private final DialogService dialogService;
     private final ClipBoardManager clipBoardManager;
     private final BuildInfo buildInfo;