Merge remote-tracking branch 'upstream/main' into detectCharset

* upstream/main:
  Bump checkstyle from 10.1 to 10.3.1 (#8950)
  Bump mariadb-java-client from 2.7.5 to 2.7.6 (#8953)
  Add notification when adding previous entries to new group configuration (#8919)
  Remember Sidepane width after restart (#8936)
  move "Warn about duplicates on import" preferences option (#8937)
  Fix theme switching exception (#8939)

Author: Siedlerchr

CHANGELOG.md

@@ -34,10 +34,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We improved group expansion arrow that prevent it from activating group when expanding or collapsing. [#7982](https://github.com/JabRef/jabref/issues/7982), [#3176](https://github.com/JabRef/jabref/issues/3176)
 - When configured SSL certificates changed, JabRef warns the user to restart to apply the configuration.
 - We improved the appearances and logic of the "Manage field names & content" dialog, and renamed it to "Automatic field editor". [#6536](https://github.com/JabRef/jabref/issues/6536)
-- We fixed an issue that caused JabRef to sometimes open multiple instances when "Remote Operation" is enabled. [#8653](https://github.com/JabRef/jabref/issues/8653)
+- We improved the message explaining the options when modifying an automatic keyword group [#8911](https://github.com/JabRef/jabref/issues/8911)
+- We moved the preferences option "Warn about duplicates on import" option from the tab "File" to the tab "Import and Export". [kopper#570](https://github.com/koppor/jabref/issues/570)
 
 ### Fixed
 
+- We fixed an issue that caused JabRef to sometimes open multiple instances when "Remote Operation" is enabled. [#8653](https://github.com/JabRef/jabref/issues/8653)
 - We fixed an issue where linked files with the filetype "application/pdf" in an entry were not shown with the correct PDF-Icon in the main table [8930](https://github.com/JabRef/jabref/issues/8930)
 - We fixed an issue where "open folder" for linked files did not open the folder and did not select the file unter certain Linux desktop environments [#8679](https://github.com/JabRef/jabref/issues/8679), [#8849](https://github.com/JabRef/jabref/issues/8849)
 - We fixed an issue where the content of a big shared database library is not shown [#8788](https://github.com/JabRef/jabref/issues/8788)
@@ -50,6 +52,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the exception that there are invalid characters in filename. [#8786](https://github.com/JabRef/jabref/issues/8786)
 - When the proxy configuration removed the proxy user/password, this change is applied immediately.
 - We fixed an issue where removing several groups deletes only one of them. [#8390](https://github.com/JabRef/jabref/issues/8390)
+- We fixed an issue where the Sidepane (groups, web search and open office) width is not remembered after restarting JabRef. [#8907](https://github.com/JabRef/jabref/issues/8907)
+- We fixed a bug where switching between themes will cause an error/exception. [#8939](https://github.com/JabRef/jabref/pull/8939)
 
 ### Removed
 

build.gradle

@@ -151,7 +151,7 @@ dependencies {
     implementation group: 'com.fasterxml.jackson.dataformat', name: 'jackson-dataformat-yaml', version: '2.13.3'
     implementation group: 'com.fasterxml.jackson.datatype', name: 'jackson-datatype-jsr310', version: '2.13.3'
 
-    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.5'
+    implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.6'
 
     implementation 'org.postgresql:postgresql:42.4.0'
 
@@ -221,7 +221,7 @@ dependencies {
     testImplementation "org.testfx:testfx-junit5:4.0.16-alpha"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:10.1'
+    checkstyle 'com.puppycrawl.tools:checkstyle:10.3.1'
     // xjc needs the runtime as well for the ant task, otherwise it fails
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'

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

@@ -80,7 +80,6 @@ public JabRefDialogService(Window mainWindow, Pane mainPane, ThemeManager themeM
 
     private FXDialog createDialog(AlertType type, String title, String content) {
         FXDialog alert = new FXDialog(type, title, true);
-        themeManager.installCss(alert.getDialogPane().getScene());
         alert.setHeaderText(null);
         alert.setContentText(content);
         alert.getDialogPane().setMinHeight(Region.USE_PREF_SIZE);
@@ -113,7 +112,6 @@ protected Node createDetailsButton() {
 
         // Reset the dialog graphic using the default style
         alert.getDialogPane().setGraphic(graphic);
-        themeManager.installCss(alert.getDialogPane().getScene());
         alert.setHeaderText(null);
         alert.setContentText(content);
         alert.getDialogPane().setMinHeight(Region.USE_PREF_SIZE);
@@ -138,7 +136,6 @@ public <T> Optional<T> showChoiceDialogAndWait(String title, String content, Str
         choiceDialog.setTitle(title);
         choiceDialog.setContentText(content);
         choiceDialog.initOwner(mainWindow);
-        themeManager.installCss(choiceDialog.getDialogPane().getScene());
         return choiceDialog.showAndWait();
     }
 
@@ -148,7 +145,6 @@ public Optional<String> showInputDialogAndWait(String title, String content) {
         inputDialog.setHeaderText(title);
         inputDialog.setContentText(content);
         inputDialog.initOwner(mainWindow);
-        themeManager.installCss(inputDialog.getDialogPane().getScene());
         return inputDialog.showAndWait();
     }
 
@@ -158,7 +154,6 @@ public Optional<String> showInputDialogWithDefaultAndWait(String title, String c
         inputDialog.setHeaderText(title);
         inputDialog.setContentText(content);
         inputDialog.initOwner(mainWindow);
-        themeManager.installCss(inputDialog.getDialogPane().getScene());
         return inputDialog.showAndWait();
     }
 
@@ -186,7 +181,6 @@ public void showErrorDialogAndWait(String message, Throwable exception) {
         exceptionDialog.getDialogPane().setMaxWidth(mainWindow.getWidth() / 2);
         exceptionDialog.setHeaderText(message);
         exceptionDialog.initOwner(mainWindow);
-        themeManager.installCss(exceptionDialog.getDialogPane().getScene());
         exceptionDialog.showAndWait();
     }
 
@@ -196,7 +190,6 @@ public void showErrorDialogAndWait(String title, String content, Throwable excep
         exceptionDialog.setHeaderText(title);
         exceptionDialog.setContentText(content);
         exceptionDialog.initOwner(mainWindow);
-        themeManager.installCss(exceptionDialog.getDialogPane().getScene());
         exceptionDialog.showAndWait();
     }
 
@@ -266,7 +259,6 @@ public Optional<ButtonType> showCustomDialogAndWait(String title, DialogPane con
         alert.getDialogPane().setMinHeight(Region.USE_PREF_SIZE);
         alert.setResizable(true);
         alert.initOwner(mainWindow);
-        themeManager.installCss(alert.getDialogPane().getScene());
         return alert.showAndWait();
     }
 
@@ -294,7 +286,6 @@ public <V> void showProgressDialog(String title, String content, Task<V> task) {
             task.cancel();
             progressDialog.close();
         });
-        themeManager.installCss(progressDialog.getDialogPane().getScene());
         progressDialog.initOwner(mainWindow);
         progressDialog.show();
     }
@@ -319,7 +310,6 @@ public <V> Optional<ButtonType> showBackgroundProgressDialogAndWait(String title
         alert.getDialogPane().setMinHeight(Region.USE_PREF_SIZE);
         alert.setResizable(true);
         alert.initOwner(mainWindow);
-        themeManager.installCss(alert.getDialogPane().getScene());
 
         stateManager.getAnyTasksThatWillNotBeRecoveredRunning().addListener((observable, oldValue, newValue) -> {
             if (!newValue) {

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

@@ -448,8 +448,10 @@ private void initLayout() {
             @Override
             public void invalidated(Observable observable) {
                 if (mainStage.isShowing()) {
-                    setDividerPosition();
-                    observable.removeListener(this);
+                    Platform.runLater(() -> {
+                        setDividerPosition();
+                        observable.removeListener(this);
+                    });
                 }
             }
         });
@@ -472,10 +474,9 @@ private void updateSidePane() {
     }
 
     private void setDividerPosition() {
-        splitPane.setDividerPositions(prefs.getGuiPreferences().getSidePaneWidth());
         if (mainStage.isShowing() && !sidePane.getChildren().isEmpty()) {
-            dividerSubscription = EasyBind.subscribe(splitPane.getDividers().get(0).positionProperty(),
-                    position -> prefs.getGuiPreferences().setSidePaneWidth(position.doubleValue()));
+            splitPane.setDividerPositions(prefs.getGuiPreferences().getSidePaneWidth() / splitPane.getWidth());
+            dividerSubscription = EasyBind.subscribe(sidePane.widthProperty(), width -> prefs.getGuiPreferences().setSidePaneWidth(width.doubleValue()));
         }
     }
 

src/main/java/org/jabref/gui/groups/GroupTreeViewModel.java

@@ -17,6 +17,9 @@
 import javafx.beans.property.StringProperty;
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
+import javafx.scene.control.Alert;
+import javafx.scene.control.ButtonBar;
+import javafx.scene.control.ButtonType;
 
 import org.jabref.gui.AbstractViewModel;
 import org.jabref.gui.DialogService;
@@ -29,6 +32,7 @@
 import org.jabref.model.groups.AbstractGroup;
 import org.jabref.model.groups.ExplicitGroup;
 import org.jabref.model.groups.GroupTreeNode;
+import org.jabref.model.groups.WordKeywordGroup;
 import org.jabref.model.metadata.MetaData;
 import org.jabref.preferences.PreferencesService;
 
@@ -192,9 +196,21 @@ public void editGroup(GroupNodeViewModel oldGroup) {
 
             newGroup.ifPresent(group -> {
                 // TODO: Keep assignments
-                boolean keepPreviousAssignments = dialogService.showConfirmationDialogAndWait(
+                String content = Localization.lang("Assign the original group's entries to this group?");
+                ButtonType keepAssignments = new ButtonType(Localization.lang("Assign"), ButtonBar.ButtonData.YES);
+                ButtonType removeAssignments = new ButtonType(Localization.lang("Do not assign"), ButtonBar.ButtonData.NO);
+                ButtonType cancel = new ButtonType(Localization.lang("Cancel"), ButtonBar.ButtonData.CANCEL_CLOSE);
+
+                if (newGroup.get().getClass() == WordKeywordGroup.class) {
+                    content = content + "\n\n" +
+                            Localization.lang("(Note: If original entries lack keywords to qualify for the new group configuration, confirming here will add them)");
+                }
+                Optional<ButtonType> previousAssignments = dialogService.showCustomButtonDialogAndWait(Alert.AlertType.WARNING,
                         Localization.lang("Change of Grouping Method"),
-                        Localization.lang("Assign the original group's entries to this group?"));
+                        content,
+                        keepAssignments,
+                        removeAssignments,
+                        cancel);
                 //        WarnAssignmentSideEffects.warnAssignmentSideEffects(newGroup, panel.frame());
                 boolean removePreviousAssignments = (oldGroup.getGroupNode().getGroup() instanceof ExplicitGroup)
                         && (group instanceof ExplicitGroup);
@@ -209,11 +225,22 @@ public void editGroup(GroupNodeViewModel oldGroup) {
                     removePreviousAssignments = false;
                 }
 
-                oldGroup.getGroupNode().setGroup(
-                        group,
-                        keepPreviousAssignments,
-                        removePreviousAssignments,
-                        database.getEntries());
+                if (previousAssignments.isPresent() && (previousAssignments.get().getButtonData() == ButtonBar.ButtonData.YES)) {
+                    oldGroup.getGroupNode().setGroup(
+                            group,
+                            true,
+                            removePreviousAssignments,
+                            database.getEntries());
+                } else if (previousAssignments.isPresent() && (previousAssignments.get().getButtonData() == ButtonBar.ButtonData.NO)) {
+                    oldGroup.getGroupNode().setGroup(
+                            group,
+                            false,
+                            removePreviousAssignments,
+                            database.getEntries());
+                } else if (previousAssignments.isPresent() && (previousAssignments.get().getButtonData() == ButtonBar.ButtonData.CANCEL_CLOSE)) {
+                    return;
+                }
+
                 // stateManager.getEntriesInCurrentDatabase());
 
                 // TODO: Add undo

src/main/java/org/jabref/gui/preferences/file/FileTab.fxml

@@ -42,5 +42,4 @@
     </HBox>
 
     <CheckBox fx:id="alwaysReformatBib" text="%Always reformat BIB file on save and export"/>
-    <CheckBox fx:id="warnAboutDuplicatesOnImport" text="%Warn about duplicates on import"/>
 </fx:root>

src/main/java/org/jabref/gui/preferences/file/FileTab.java

@@ -25,7 +25,6 @@ public class FileTab extends AbstractPreferenceTabView<FileTabViewModel> impleme
     @FXML private RadioButton resolveStrings;
     @FXML private TextField resolveStringsForFields;
     @FXML private CheckBox alwaysReformatBib;
-    @FXML private CheckBox warnAboutDuplicatesOnImport;
 
     @FXML private CheckBox autosaveLocalLibraries;
     @FXML private Button autosaveLocalLibrariesHelp;
@@ -48,7 +47,6 @@ public void initialize() {
         resolveStringsForFields.disableProperty().bind(doNotResolveStrings.selectedProperty());
 
         alwaysReformatBib.selectedProperty().bindBidirectional(viewModel.alwaysReformatBibProperty());
-        warnAboutDuplicatesOnImport.selectedProperty().bindBidirectional(viewModel.warnAboutDuplicatesOnImportProperty());
         autosaveLocalLibraries.selectedProperty().bindBidirectional(viewModel.autosaveLocalLibrariesProperty());
 
         ActionFactory actionFactory = new ActionFactory(Globals.getKeyPrefs());

src/main/java/org/jabref/gui/preferences/file/FileTabViewModel.java

@@ -16,7 +16,6 @@ public class FileTabViewModel implements PreferenceTabViewModel {
     private final BooleanProperty resolveStringsProperty = new SimpleBooleanProperty();
     private final StringProperty resolveStringsForFieldsProperty = new SimpleStringProperty("");
     private final BooleanProperty alwaysReformatBibProperty = new SimpleBooleanProperty();
-    private final BooleanProperty warnAboutDuplicatesOnImportProperty = new SimpleBooleanProperty();
     private final BooleanProperty autosaveLocalLibraries = new SimpleBooleanProperty();
 
     private final ImportExportPreferences importExportPreferences;
@@ -34,7 +33,6 @@ public void setValues() {
         resolveStringsProperty.setValue(importExportPreferences.resolveStrings());
         resolveStringsForFieldsProperty.setValue(importExportPreferences.getResolvableFields());
         alwaysReformatBibProperty.setValue(importExportPreferences.shouldAlwaysReformatOnSave());
-        warnAboutDuplicatesOnImportProperty.setValue(importExportPreferences.shouldWarnAboutDuplicatesOnImport());
         autosaveLocalLibraries.setValue(importExportPreferences.shouldAutoSave());
     }
 
@@ -45,7 +43,6 @@ public void storeSettings() {
         importExportPreferences.setNonWrappableFields(noWrapFilesProperty.getValue().trim());
         importExportPreferences.setResolvableFields(resolveStringsForFieldsProperty.getValue().trim());
         importExportPreferences.setAlwaysReformatOnSave(alwaysReformatBibProperty.getValue());
-        importExportPreferences.setWarnAboutDuplicatesOnImport(warnAboutDuplicatesOnImportProperty.getValue());
         importExportPreferences.setAutoSave(autosaveLocalLibraries.getValue());
     }
 
@@ -77,10 +74,6 @@ public BooleanProperty alwaysReformatBibProperty() {
         return alwaysReformatBibProperty;
     }
 
-    public BooleanProperty warnAboutDuplicatesOnImportProperty() {
-        return warnAboutDuplicatesOnImportProperty;
-    }
-
     // Autosave
     public BooleanProperty autosaveLocalLibrariesProperty() {
         return autosaveLocalLibraries;

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

@@ -16,6 +16,7 @@
 
     <Label styleClass="sectionHeader" text="%General"/>
     <CheckBox fx:id="generateNewKeyOnImport" text="%Generate a new key for imported entries (overwriting their default)"/>
+    <CheckBox fx:id="warnAboutDuplicatesOnImport" text="%Warn about duplicates on import"/>
 
     <Label styleClass="sectionHeader" text="%Custom DOI URI"/>
     <HBox alignment="CENTER_LEFT" spacing="10.0">

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

@@ -32,6 +32,8 @@ public class ImportExportTab extends AbstractPreferenceTabView<ImportExportTabVi
     @FXML private CheckBox grobidEnabled;
     @FXML private TextField grobidURL;
 
+    @FXML private CheckBox warnAboutDuplicatesOnImport;
+
     public ImportExportTab() {
         ViewLoader.view(this)
                   .root(this)
@@ -44,7 +46,7 @@ public String getTabName() {
     }
 
     public void initialize() {
-        this.viewModel = new ImportExportTabViewModel(preferencesService, preferencesService.getDOIPreferences(), dialogService);
+        this.viewModel = new ImportExportTabViewModel(preferencesService, preferencesService.getDOIPreferences(), dialogService, preferencesService.getImportExportPreferences());
 
         useCustomDOI.selectedProperty().bindBidirectional(viewModel.useCustomDOIProperty());
         useCustomDOIName.textProperty().bindBidirectional(viewModel.useCustomDOINameProperty());
@@ -85,6 +87,8 @@ public void initialize() {
 
         // Content is set later
         viewModel.fetcherApiKeys().addListener((InvalidationListener) change -> apiKeySelector.getSelectionModel().selectFirst());
+
+        warnAboutDuplicatesOnImport.selectedProperty().bindBidirectional(viewModel.warnAboutDuplicatesOnImportProperty());
     }
 
     private void updateFetcherApiKey(FetcherApiKey apiKey) {