Fix import entry by id does not generate citation key

CHANGELOG.md

@@ -41,6 +41,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where opening the changelog from withing JabRef led to a 404 error [#8563](https://github.com/JabRef/jabref/issues/8563)
 - We fixed an issue where not all found unlinked local files were imported correctly due to some race condition. [#8444](https://github.com/JabRef/jabref/issues/8444)
 - We fixed an issue where Merge entries dialog exceeds screen boundaries.
+- We fixed an issue where no citationkey was generated on import, pasting a doi or an entry on the main table [8406](https://github.com/JabRef/jabref/issues/8406), [koppor#553](https://github.com/koppor/jabref/issues/553)
 
 ### Removed
 

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

@@ -14,13 +14,11 @@
 import javafx.concurrent.Task;
 import javafx.concurrent.Worker;
 
-import org.jabref.gui.duplicationFinder.DuplicateResolverDialog;
+import org.jabref.gui.externalfiles.ImportHandler;
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.importer.NewEntryAction;
-import org.jabref.logic.citationkeypattern.CitationKeyGenerator;
-import org.jabref.logic.database.DuplicateCheck;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.IdBasedFetcher;
-import org.jabref.logic.importer.ImportCleanup;
 import org.jabref.logic.importer.WebFetchers;
 import org.jabref.logic.importer.fetcher.DoiFetcher;
 import org.jabref.logic.l10n.Localization;
@@ -153,28 +151,10 @@ public void runFetcherWorker() {
             Optional<BibEntry> result = fetcherWorker.getValue();
             if (result.isPresent()) {
                 final BibEntry entry = result.get();
-                ImportCleanup cleanup = new ImportCleanup(libraryTab.getBibDatabaseContext().getMode());
-                cleanup.doPostCleanup(entry);
-                Optional<BibEntry> duplicate = new DuplicateCheck(Globals.entryTypesManager).containsDuplicate(libraryTab.getDatabase(), entry, libraryTab.getBibDatabaseContext().getMode());
-                if (duplicate.isPresent()) {
-                    DuplicateResolverDialog dialog = new DuplicateResolverDialog(entry, duplicate.get(), DuplicateResolverDialog.DuplicateResolverType.IMPORT_CHECK, libraryTab.getBibDatabaseContext(), stateManager);
-                    switch (dialogService.showCustomDialogAndWait(dialog)
-                                         .orElse(DuplicateResolverDialog.DuplicateResolverResult.BREAK)) {
-                        case KEEP_LEFT -> {
-                            libraryTab.getDatabase().removeEntry(duplicate.get());
-                            libraryTab.getDatabase().insertEntry(entry);
-                        }
-                        case KEEP_BOTH -> libraryTab.getDatabase().insertEntry(entry);
-                        case KEEP_MERGE -> {
-                            libraryTab.getDatabase().removeEntry(duplicate.get());
-                            libraryTab.getDatabase().insertEntry(dialog.getMergedEntry());
-                        }
-                    }
-                } else {
-                    // Regenerate CiteKey of imported BibEntry
-                    new CitationKeyGenerator(libraryTab.getBibDatabaseContext(), preferencesService.getCitationKeyPatternPreferences()).generateAndSetKey(entry);
-                    libraryTab.insertEntry(entry);
-                }
+
+                ImportHandler handler = new ImportHandler(libraryTab.getBibDatabaseContext(), ExternalFileTypes.getInstance(), preferencesService, Globals.getFileUpdateMonitor(), libraryTab.getUndoManager(), stateManager, dialogService);
+                handler.importEntryWithDuplicateCheck(libraryTab.getBibDatabaseContext(), entry);
+
                 searchSuccesfulProperty.set(true);
             } else if (StringUtil.isBlank(idText.getValue())) {
                 dialogService.showWarningDialogAndWait(Localization.lang("Empty search ID"), Localization.lang("The given search ID was empty."));

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

@@ -757,7 +757,7 @@ public void copy() {
     }
 
     public void paste() {
-        mainTable.paste(this.bibDatabaseContext.getMode());
+        mainTable.paste();
     }
 
     public void cut() {

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

@@ -54,7 +54,8 @@ public BibtexExtractorViewModel(BibDatabaseContext bibdatabaseContext,
                 preferencesService,
                 fileUpdateMonitor,
                 undoManager,
-                stateManager);
+                stateManager,
+                dialogService);
     }
 
     public StringProperty inputTextProperty() {

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

@@ -6,16 +6,21 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
+import java.util.Optional;
 
 import javax.swing.undo.CompoundEdit;
 import javax.swing.undo.UndoManager;
 
+import org.jabref.gui.DialogService;
+import org.jabref.gui.Globals;
 import org.jabref.gui.StateManager;
+import org.jabref.gui.duplicationFinder.DuplicateResolverDialog;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.undo.UndoableInsertEntries;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.citationkeypattern.CitationKeyGenerator;
+import org.jabref.logic.database.DuplicateCheck;
 import org.jabref.logic.externalfiles.ExternalFilesContentImporter;
 import org.jabref.logic.importer.ImportCleanup;
 import org.jabref.logic.l10n.Localization;
@@ -36,25 +41,28 @@
 public class ImportHandler {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(ImportHandler.class);
-    private final BibDatabaseContext bibdatabase;
+    private final BibDatabaseContext bibDatabaseContext;
     private final PreferencesService preferencesService;
     private final FileUpdateMonitor fileUpdateMonitor;
     private final ExternalFilesEntryLinker linker;
     private final ExternalFilesContentImporter contentImporter;
     private final UndoManager undoManager;
     private final StateManager stateManager;
+    private final DialogService dialogService;
 
     public ImportHandler(BibDatabaseContext database,
                          ExternalFileTypes externalFileTypes,
                          PreferencesService preferencesService,
                          FileUpdateMonitor fileupdateMonitor,
                          UndoManager undoManager,
-                         StateManager stateManager) {
+                         StateManager stateManager,
+                         DialogService dialogService) {
 
-        this.bibdatabase = database;
+        this.bibDatabaseContext = database;
         this.preferencesService = preferencesService;
         this.fileUpdateMonitor = fileupdateMonitor;
         this.stateManager = stateManager;
+        this.dialogService = dialogService;
 
         this.linker = new ExternalFilesEntryLinker(externalFileTypes, preferencesService.getFilePreferences(), database);
         this.contentImporter = new ExternalFilesContentImporter(
@@ -127,7 +135,7 @@ protected List<ImportFilesResultItemViewModel> call() {
                     // We need to run the actual import on the FX Thread, otherwise we will get some deadlocks with the UIThreadList
                     DefaultTaskExecutor.runInJavaFXThread(() -> importEntries(entriesToAdd));
 
-                    ce.addEdit(new UndoableInsertEntries(bibdatabase.getDatabase(), entriesToAdd));
+                    ce.addEdit(new UndoableInsertEntries(bibDatabaseContext.getDatabase(), entriesToAdd));
                     ce.end();
                     undoManager.addEdit(ce);
 
@@ -151,9 +159,9 @@ private BibEntry createEmptyEntryWithLink(Path file) {
     }
 
     public void importEntries(List<BibEntry> entries) {
-        ImportCleanup cleanup = new ImportCleanup(bibdatabase.getMode());
+        ImportCleanup cleanup = new ImportCleanup(bibDatabaseContext.getMode());
         cleanup.doPostCleanup(entries);
-        bibdatabase.getDatabase().insertEntries(entries);
+        bibDatabaseContext.getDatabase().insertEntries(entries);
 
         // Set owner/timestamp
         UpdateField.setAutomaticFields(entries,
@@ -166,7 +174,43 @@ public void importEntries(List<BibEntry> entries) {
         }
 
         // Add to group
-        addToGroups(entries, stateManager.getSelectedGroup(bibdatabase));
+        addToGroups(entries, stateManager.getSelectedGroup(bibDatabaseContext));
+    }
+
+    public void importEntryWithDuplicateCheck(BibDatabaseContext bibDatabaseContext, BibEntry entry) {
+        ImportCleanup cleanup = new ImportCleanup(bibDatabaseContext.getMode());
+        BibEntry cleanedEntry = cleanup.doPostCleanup(entry);
+        BibEntry entryToInsert = cleanedEntry;
+
+        Optional<BibEntry> existingDuplicateInLibrary = new DuplicateCheck(Globals.entryTypesManager).containsDuplicate(bibDatabaseContext.getDatabase(), entryToInsert, bibDatabaseContext.getMode());
+        if (existingDuplicateInLibrary.isPresent()) {
+            DuplicateResolverDialog dialog = new DuplicateResolverDialog(existingDuplicateInLibrary.get(), entryToInsert, DuplicateResolverDialog.DuplicateResolverType.IMPORT_CHECK, bibDatabaseContext, stateManager);
+            switch (dialogService.showCustomDialogAndWait(dialog).orElse(DuplicateResolverDialog.DuplicateResolverResult.BREAK)) {
+                case KEEP_LEFT:
+                    bibDatabaseContext.getDatabase().removeEntry(existingDuplicateInLibrary.get());
+                    break;
+                case KEEP_BOTH:
+                    break;
+                case KEEP_MERGE:
+                    bibDatabaseContext.getDatabase().removeEntry(existingDuplicateInLibrary.get());
+                    entryToInsert = dialog.getMergedEntry();
+                    break;
+                default:
+                   return;
+            }
+        }
+        // Regenerate CiteKey of imported BibEntry
+        if (preferencesService.getImporterPreferences().isGenerateNewKeyOnImport()) {
+            generateKeys(List.of(entryToInsert));
+        }
+        bibDatabaseContext.getDatabase().insertEntry(entryToInsert);
+
+        // Set owner/timestamp
+        UpdateField.setAutomaticFields(List.of(entryToInsert),
+                                       preferencesService.getOwnerPreferences(),
+                                       preferencesService.getTimestampPreferences());
+
+        addToGroups(List.of(entry), stateManager.getSelectedGroup(this.bibDatabaseContext));
     }
 
     private void addToGroups(List<BibEntry> entries, Collection<GroupTreeNode> groups) {
@@ -189,9 +233,9 @@ private void addToGroups(List<BibEntry> entries, Collection<GroupTreeNode> group
      */
     private void generateKeys(List<BibEntry> entries) {
         CitationKeyGenerator keyGenerator = new CitationKeyGenerator(
-                bibdatabase.getMetaData().getCiteKeyPattern(preferencesService.getCitationKeyPatternPreferences()
-                                                                              .getKeyPattern()),
-                bibdatabase.getDatabase(),
+                bibDatabaseContext.getMetaData().getCiteKeyPattern(preferencesService.getCitationKeyPatternPreferences()
+                                                                                     .getKeyPattern()),
+                bibDatabaseContext.getDatabase(),
                 preferencesService.getCitationKeyPatternPreferences());
 
         for (BibEntry entry : entries) {

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

@@ -97,7 +97,8 @@ public UnlinkedFilesDialogViewModel(DialogService dialogService,
                 preferences,
                 fileUpdateMonitor,
                 undoManager,
-                stateManager);
+                stateManager,
+                dialogService);
 
         this.fileFilterList = FXCollections.observableArrayList(
                 new FileExtensionViewModel(StandardFileType.ANY_FILE, externalFileTypes),

src/main/java/org/jabref/gui/importer/GenerateEntryFromIdAction.java

@@ -7,13 +7,13 @@
 import org.jabref.gui.LibraryTab;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.gui.externalfiles.ImportHandler;
+import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.JabRefException;
-import org.jabref.logic.database.DuplicateCheck;
 import org.jabref.logic.importer.CompositeIdFetcher;
 import org.jabref.logic.importer.FetcherException;
-import org.jabref.logic.importer.ImportCleanup;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.types.StandardEntryType;
@@ -50,26 +50,32 @@ public void execute() {
         backgroundTask.onFailure((e) -> {
             // When unable to import by ID, present the user options to cancel or add entry manually
             boolean addEntryFlag = dialogService.showConfirmationDialogAndWait(Localization.lang("Failed to import by ID"),
-                                    e.getMessage(),
-                                   Localization.lang("Add entry manually"));
+                                                                               e.getMessage(),
+                                                                               Localization.lang("Add entry manually"));
             if (addEntryFlag) {
                 // add entry manually
                 new NewEntryAction(libraryTab.frame(), StandardEntryType.Article, dialogService,
-                                    preferencesService, stateManager).execute();
+                                   preferencesService, stateManager).execute();
             }
         });
-        backgroundTask.onSuccess((bibEntry) -> bibEntry.ifPresentOrElse((entry) -> {
-                libraryTab.insertEntry(entry);
-                entryFromIdPopOver.hide();
-                dialogService.notify(Localization.lang("Imported one entry"));
-                },
-                () -> dialogService.notify(Localization.lang("Import canceled"))
-        ));
+        backgroundTask.onSuccess((bibEntry) -> {
+            Optional<BibEntry> result = bibEntry;
+            if (result.isPresent()) {
+                final BibEntry entry = result.get();
+                ImportHandler handler = new ImportHandler(libraryTab.getBibDatabaseContext(), ExternalFileTypes.getInstance(), preferencesService, Globals.getFileUpdateMonitor(), libraryTab.getUndoManager(), stateManager, dialogService);
+                handler.importEntryWithDuplicateCheck(libraryTab.getBibDatabaseContext(), entry);
+            } else {
+                dialogService.notify("No entry found or import canceled");
+            }
+
+            entryFromIdPopOver.hide();
+        });
         backgroundTask.executeWith(taskExecutor);
     }
 
     private BackgroundTask<Optional<BibEntry>> searchAndImportEntryInBackground() {
         return new BackgroundTask<>() {
+
             @Override
             protected Optional<BibEntry> call() throws JabRefException {
                 if (isCanceled()) {
@@ -78,21 +84,8 @@ protected Optional<BibEntry> call() throws JabRefException {
 
                 updateMessage(Localization.lang("Searching..."));
                 try {
-                    Optional<BibEntry> result = new CompositeIdFetcher(preferencesService.getImportFormatPreferences()).performSearchById(identifier);
-                    if (result.isPresent()) {
-                        final BibEntry entry = result.get();
-                        ImportCleanup cleanup = new ImportCleanup(libraryTab.getBibDatabaseContext().getMode());
-                        cleanup.doPostCleanup(entry);
-                        // DuplicateCheck only covers DOI and ISBN at the moment.
-                        Optional<BibEntry> duplicate = new DuplicateCheck(Globals.entryTypesManager).containsDuplicate(libraryTab.getDatabase(), entry, libraryTab.getBibDatabaseContext().getMode());
-                        if (duplicate.isPresent()) {
-                            throw new JabRefException(Localization.lang("Entry already exists"));
-                        }
-                    } else {
-                        throw new JabRefException(Localization.lang("Could not find any bibliographic information."));
-                    }
-                    updateMessage(Localization.lang("Imported one entry"));
-                    return result;
+                    return new CompositeIdFetcher(preferencesService.getImportFormatPreferences()).performSearchById(identifier);
+
                 } catch (FetcherException fetcherException) {
                     throw new JabRefException("Fetcher error: %s".formatted(fetcherException.getMessage()));
                 }

src/main/java/org/jabref/gui/importer/ImportEntriesViewModel.java

@@ -169,7 +169,8 @@ private void buildImportHandlerThenImportEntries(List<BibEntry> entriesToImport)
                 preferences,
                 fileUpdateMonitor,
                 undoManager,
-                stateManager);
+                stateManager,
+                dialogService);
         importHandler.importEntries(entriesToImport);
         dialogService.notify(Localization.lang("Number of entries successfully imported") + ": " + entriesToImport.size());
     }

src/main/java/org/jabref/gui/maintable/MainTable.java

@@ -41,10 +41,8 @@
 import org.jabref.gui.util.CustomLocalDragboard;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.ViewModelTableRowFactory;
-import org.jabref.logic.importer.ImportCleanup;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.database.event.EntriesAddedEvent;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.preferences.PreferencesService;
@@ -92,7 +90,8 @@ public MainTable(MainTableDataModel model,
                 preferencesService,
                 Globals.getFileUpdateMonitor(),
                 undoManager,
-                stateManager);
+                stateManager,
+                dialogService);
 
         localDragboard = stateManager.getLocalDragboard();
 
@@ -303,12 +302,13 @@ private void clearAndSelectLast() {
         scrollTo(getItems().size() - 1);
     }
 
-    public void paste(BibDatabaseMode bibDatabaseMode) {
+    public void paste() {
         // Find entries in clipboard
         List<BibEntry> entriesToAdd = Globals.getClipboardManager().extractData();
-        ImportCleanup cleanup = new ImportCleanup(bibDatabaseMode);
-        cleanup.doPostCleanup(entriesToAdd);
-        libraryTab.insertEntries(entriesToAdd);
+
+        for (BibEntry entry : entriesToAdd) {
+            importHandler.importEntryWithDuplicateCheck(database, entry);
+        }
         if (!entriesToAdd.isEmpty()) {
             this.requestFocus();
         }

src/main/resources/l10n/JabRef_en.properties

@@ -1903,7 +1903,6 @@ New\ entry\ from\ plain\ text=New entry from plain text
 Import\ by\ ID=Import by ID
 Enter\ a\ valid\ ID=Enter a valid ID
 Imported\ one\ entry=Imported one entry
-Entry\ already\ exists=Entry already exists
 New\ sublibrary\ based\ on\ AUX\ file=New sublibrary based on AUX file
 Push\ entries\ to\ external\ application\ (%0)=Push entries to external application (%0)
 Quit=Quit