Merge remote-tracking branch 'upstream/main' into dependabot/gradle/c…

…om.github.tomtung-latex2unicode_2.12-0.3.0 * upstream/main: Remove obsolete comments Improve key generation (#8641) Refine search code (#8636) Fix import entry by id does not generate citation key (#8361) Update Gradle Wrapper from 7.4.1 to 7.4.2. (#8637) Bump hmarr/auto-approve-action from 2.1.0 to 2.2.0 (#8638)
JabRef · Apr 5, 2022 · cce5a92 · cce5a92
2 parents d7fbd59 + dbf921e
commit cce5a92
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diff --git a/.github/workflows/automerge.yml b/.github/workflows/automerge.yml
@@ -16,7 +16,7 @@ jobs:
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Auto approve
-        uses: hmarr/auto-approve-action@v2.1.0
+        uses: hmarr/auto-approve-action@v2.2.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -42,6 +42,7 @@ 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
 

diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties
@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionSha256Sum=e5444a57cda4a95f90b0c9446a9e1b47d3d7f69057765bfb54bd4f482542d548
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.1-bin.zip
+distributionSha256Sum=29e49b10984e585d8118b7d0bc452f944e386458df27371b49b4ac1dec4b7fda
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.2-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
diff --git a/src/main/java/org/jabref/gui/EntryTypeViewModel.java b/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."));

diff --git a/src/main/java/org/jabref/gui/LibraryTab.java b/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() {

diff --git a/src/main/java/org/jabref/gui/bibtexextractor/BibtexExtractorViewModel.java b/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() {

diff --git a/src/main/java/org/jabref/gui/collab/EntryChangeViewModel.java b/src/main/java/org/jabref/gui/collab/EntryChangeViewModel.java
@@ -47,7 +47,7 @@ public void setAccepted(boolean accepted) {
     public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
         this.description(); // Init dialog to prevent NPE
         database.getDatabase().removeEntry(oldEntry);
-        BibEntry mergedEntry = mergePanel.getMergeEntry();
+        BibEntry mergedEntry = mergePanel.getMergedEntry();
         mergedEntry.setId(oldEntry.getId()); // Keep ID
         database.getDatabase().insertEntry(mergedEntry);
         undoEdit.addEdit(new UndoableInsertEntries(database.getDatabase(), oldEntry));

diff --git a/src/main/java/org/jabref/gui/duplicationFinder/DuplicateResolverDialog.java b/src/main/java/org/jabref/gui/duplicationFinder/DuplicateResolverDialog.java
@@ -38,7 +38,7 @@ public enum DuplicateResolverResult {
         BREAK
     }
 
-    private MergeEntries me;
+    private MergeEntries mergeEntries;
 
     public DuplicateResolverDialog(BibEntry one, BibEntry two, DuplicateResolverType type, BibDatabaseContext database, StateManager stateManager) {
         this.setTitle(Localization.lang("Possible duplicate entries"));
@@ -48,7 +48,6 @@ public DuplicateResolverDialog(BibEntry one, BibEntry two, DuplicateResolverType
     }
 
     private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
-
         HelpAction helpCommand = new HelpAction(HelpFile.FIND_DUPLICATES);
         ButtonType help = new ButtonType(Localization.lang("Help"), ButtonData.HELP);
 
@@ -67,13 +66,13 @@ private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
                 first = new ButtonType(Localization.lang("Keep left"), ButtonData.APPLY);
                 second = new ButtonType(Localization.lang("Keep right"), ButtonData.APPLY);
                 both = new ButtonType(Localization.lang("Keep both"), ButtonData.APPLY);
-                me = new MergeEntries(one, two);
+                mergeEntries = new MergeEntries(one, two);
                 break;
             case INSPECTION:
                 first = new ButtonType(Localization.lang("Remove old entry"), ButtonData.APPLY);
                 second = new ButtonType(Localization.lang("Remove entry from import"), ButtonData.APPLY);
                 both = new ButtonType(Localization.lang("Keep both"), ButtonData.APPLY);
-                me = new MergeEntries(one, two, Localization.lang("Old entry"),
+                mergeEntries = new MergeEntries(one, two, Localization.lang("Old entry"),
                         Localization.lang("From import"));
                 break;
             case DUPLICATE_SEARCH_WITH_EXACT:
@@ -83,13 +82,13 @@ private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
 
                 removeExactVisible = true;
 
-                me = new MergeEntries(one, two);
+                mergeEntries = new MergeEntries(one, two);
                 break;
             default:
                 first = new ButtonType(Localization.lang("Import and remove old entry"), ButtonData.APPLY);
                 second = new ButtonType(Localization.lang("Do not import entry"), ButtonData.APPLY);
                 both = new ButtonType(Localization.lang("Import and keep old entry"), ButtonData.APPLY);
-                me = new MergeEntries(one, two, Localization.lang("Old entry"),
+                mergeEntries = new MergeEntries(one, two, Localization.lang("Old entry"),
                         Localization.lang("From import"));
                 break;
         }
@@ -107,7 +106,7 @@ private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
             this.setY(state.getY());
         }
 
-        BorderPane borderPane = new BorderPane(me);
+        BorderPane borderPane = new BorderPane(mergeEntries);
         borderPane.setBottom(options);
 
         this.setResultConverter(button -> {
@@ -134,6 +133,6 @@ private void init(BibEntry one, BibEntry two, DuplicateResolverType type) {
     }
 
     public BibEntry getMergedEntry() {
-        return me.getMergeEntry();
+        return mergeEntries.getMergedEntry();
     }
 }
diff --git a/src/main/java/org/jabref/gui/externalfiles/ImportHandler.java b/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 +174,46 @@ 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;
+                case KEEP_RIGHT:
+                case AUTOREMOVE_EXACT:
+                case 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 +236,9 @@ 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) {

diff --git a/src/main/java/org/jabref/gui/externalfiles/UnlinkedFilesDialogViewModel.java b/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),