Merge remote-tracking branch 'upstream/main' into fix-for-issue-348

* upstream/main:
  Fix CHANGELOG.md
  Bump commons-cli:commons-cli from 1.5.0 to 1.6.0 (JabRef#10607)
  Fix issue JabRef#9306: Move "Open only one instance of JabRef" preference option to somewhere else (JabRef#10602)
  Update README.md (JabRef#10604)
  Bump me.champeau.jmh from 0.7.1 to 0.7.2
  Bump org.beryx.jlink from 3.0.0 to 3.0.1
  Bump com.dlsc.gemsfx:gemsfx from 1.82.0 to 1.84.0
  Bump org.apache.logging.log4j:log4j-to-slf4j from 2.21.0 to 2.21.1

# Conflicts:
#	src/main/resources/l10n/JabRef_en.properties

CHANGELOG.md

@@ -17,13 +17,14 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 
 ### Changed
 
-- The two previews in the change resolver dialog now have their scrollbars synchronized [#9576](https://github.com/JabRef/jabref/issues/9576).
+- We moved the location of the 'Open only one instance of JabRef' preference option from "Network" to "General". [#9306](https://github.com/JabRef/jabref/issues/9306)
+- The two previews in the change resolver dialog now have their scrollbars synchronized. [#9576](https://github.com/JabRef/jabref/issues/9576).
 - We changed the setting of the keyword separator to accept a single character only. [#177](https://github.com/koppor/jabref/issues/177)
 
 ### Fixed
 
-- We fixed an issue where the added protected term has unwanted leading and trailing whitespaces, where the formatted text has unwanted empty brackets and where the word at the cursor in the textbox can be added to the list [#10415](https://github.com/JabRef/jabref/issues/10415).
-- We fixed an issue where in the merge dialog the file field of entries was not correctly merged when the first and second entry both contained values inside the file field [#10572](https://github.com/JabRef/jabref/issues/10572)
+- We fixed an issue where the added protected term has unwanted leading and trailing whitespaces, where the formatted text has unwanted empty brackets and where the word at the cursor in the textbox can be added to the list. [#10415](https://github.com/JabRef/jabref/issues/10415).
+- We fixed an issue where in the merge dialog the file field of entries was not correctly merged when the first and second entry both contained values inside the file field. [#10572](https://github.com/JabRef/jabref/issues/10572)
 
 ### Removed
 

README.md

@@ -18,13 +18,13 @@ It supports you in every step of your research work.
 - Easily retrieve and link full-text articles
 - Fetch complete bibliographic information based on ISBN, DOI, PubMed-ID and arXiv-ID
 - Extract metadata from PDFs
-- Import new references directly from the browser with one click using the [official browser extension](https://github.com/JabRef/JabRef-Browser-Extension) for [Firefox](https://addons.mozilla.org/en-US/firefox/addon/jabref/?src=external-github),  [Chrome](https://chrome.google.com/webstore/detail/jabref-browser-extension/bifehkofibaamoeaopjglfkddgkijdlh), [Edge](https://microsoftedge.microsoft.com/addons/detail/pgkajmkfgbehiomipedjhoddkejohfna) and [Vivaldi](https://chrome.google.com/webstore/detail/jabref-browser-extension/bifehkofibaamoeaopjglfkddgkijdlh)
+- Import new references directly from the browser with one click using the [official browser extension](https://github.com/JabRef/JabRef-Browser-Extension) for [Firefox](https://addons.mozilla.org/en-US/firefox/addon/jabref/?src=external-github),  [Chrome](https://chrome.google.com/webstore/detail/jabref-browser-extension/bifehkofibaamoeaopjglfkddgkijdlh), [Edge](https://microsoftedge.microsoft.com/addons/detail/pgkajmkfgbehiomipedjhoddkejohfna), and [Vivaldi](https://chrome.google.com/webstore/detail/jabref-browser-extension/bifehkofibaamoeaopjglfkddgkijdlh)
 
 ### Organize
 
-- Group your research into hierarchical collections and organize research items based on keywords/tags, search terms or your manual assignments
+- Group your research into hierarchical collections and organize research items based on keywords/tags, search terms, or your manual assignments
 - Advanced search and filter features
-- Complete and fix bibliographic data by comparing with curated online catalogs such as Google Scholar, Springer or MathSciNet
+- Complete and fix bibliographic data by comparing with curated online catalogs such as Google Scholar, Springer, or MathSciNet
 - Customizable citation key generator
 - Customize and add new metadata fields or reference types
 - Find and merge duplicates

build.gradle

@@ -7,13 +7,13 @@ plugins {
 
     id 'com.github.andygoossens.modernizer' version '1.9.0'
 
-    id 'me.champeau.jmh' version '0.7.1'
+    id 'me.champeau.jmh' version '0.7.2'
 
     id 'org.javamodularity.moduleplugin' version '1.8.12'
 
     id 'org.openjfx.javafxplugin' version '0.1.0'
 
-    id 'org.beryx.jlink' version '3.0.0'
+    id 'org.beryx.jlink' version '3.0.1'
 
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
@@ -130,7 +130,7 @@ dependencies {
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
     implementation 'org.bouncycastle:bcprov-jdk18on:1.76'
 
-    implementation 'commons-cli:commons-cli:1.5.0'
+    implementation 'commons-cli:commons-cli:1.6.0'
 
     implementation 'org.libreoffice:unoloader:7.6.1'
     implementation 'org.libreoffice:libreoffice:7.6.1'
@@ -174,7 +174,7 @@ dependencies {
     implementation('com.tobiasdiez:easybind:2.2.1-SNAPSHOT')
     implementation 'org.fxmisc.flowless:flowless:0.7.1'
     implementation 'org.fxmisc.richtext:richtextfx:0.11.1'
-    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '1.82.0') {
+    implementation (group: 'com.dlsc.gemsfx', name: 'gemsfx', version: '1.84.0') {
         exclude module: 'javax.inject' // Split package, use only jakarta.inject
         exclude group: 'org.apache.logging.log4j'
     }
@@ -192,7 +192,7 @@ dependencies {
     // route all requests to java.util.logging to SLF4J (which in turn routes to tinylog)
     implementation 'org.slf4j:jul-to-slf4j:2.0.9'
     // route all requests to log4j to SLF4J
-    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.21.0'
+    implementation 'org.apache.logging.log4j:log4j-to-slf4j:2.21.1'
 
     implementation('de.undercouch:citeproc-java:3.0.0-beta.2') {
         exclude group: 'org.antlr'

src/main/java/module-info.java

@@ -88,7 +88,7 @@
     uses org.mariadb.jdbc.credential.CredentialPlugin;
 
     // Apache Commons and other (similar) helper libraries
-    requires commons.cli;
+    requires org.apache.commons.cli;
     requires org.apache.commons.csv;
     requires org.apache.commons.lang3;
     requires com.google.common;

src/main/java/org/jabref/gui/preferences/general/GeneralTab.fxml

@@ -4,6 +4,7 @@
 <?import javafx.scene.control.Button?>
 <?import javafx.scene.control.CheckBox?>
 <?import javafx.scene.control.ComboBox?>
+<?import javafx.scene.control.Hyperlink?>
 <?import javafx.scene.control.Label?>
 <?import javafx.scene.control.Spinner?>
 <?import javafx.scene.control.TextField?>
@@ -13,7 +14,6 @@
 <?import javafx.scene.layout.HBox?>
 <?import javafx.scene.layout.VBox?>
 <?import org.jabref.gui.icon.JabRefIconView?>
-<?import javafx.scene.control.Hyperlink?>
 <fx:root spacing="10.0" type="VBox"
          xmlns="http://javafx.com/javafx" xmlns:fx="http://javafx.com/fxml"
          fx:controller="org.jabref.gui.preferences.general.GeneralTab">
@@ -70,6 +70,13 @@
     <CheckBox fx:id="confirmDelete" text="%Show confirmation dialog when deleting entries"/>
     <CheckBox fx:id="collectTelemetry" text="%Collect and share telemetry data to help improve JabRef"/>
 
+    <Label styleClass="sectionHeader" text="%Single instance" />
+    <HBox alignment="CENTER_LEFT" spacing="10.0">
+        <CheckBox fx:id="remoteServer" text="%Enforce single JabRef instance (and allow remote operations) using port" />
+        <TextField fx:id="remotePort" maxWidth="100.0" HBox.hgrow="ALWAYS" />
+        <Button fx:id="remoteHelp" prefWidth="20.0" />
+    </HBox>
+
     <Label styleClass="sectionHeader" text="%Libraries"/>
     <GridPane hgap="10.0" vgap="4.0">
         <columnConstraints>

src/main/java/org/jabref/gui/preferences/general/GeneralTab.java

@@ -25,10 +25,13 @@
 import org.jabref.logic.l10n.Language;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseMode;
+import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.util.FileUpdateMonitor;
 
 import com.airhacks.afterburner.views.ViewLoader;
 import com.tobiasdiez.easybind.EasyBind;
 import de.saxsys.mvvmfx.utils.validation.visualization.ControlsFxVisualizer;
+import jakarta.inject.Inject;
 
 public class GeneralTab extends AbstractPreferenceTabView<GeneralTabViewModel> implements PreferencesTab {
 
@@ -49,6 +52,11 @@ public class GeneralTab extends AbstractPreferenceTabView<GeneralTabViewModel> i
     @FXML private Button autosaveLocalLibrariesHelp;
     @FXML private CheckBox createBackup;
     @FXML private TextField backupDirectory;
+    @FXML private CheckBox remoteServer;
+    @FXML private TextField remotePort;
+    @FXML private Button remoteHelp;
+    @Inject private FileUpdateMonitor fileUpdateMonitor;
+    @Inject private BibEntryTypesManager entryTypesManager;
 
     private final ControlsFxVisualizer validationVisualizer = new ControlsFxVisualizer();
 
@@ -74,7 +82,7 @@ public String getTabName() {
     }
 
     public void initialize() {
-        this.viewModel = new GeneralTabViewModel(dialogService, preferencesService);
+        this.viewModel = new GeneralTabViewModel(dialogService, preferencesService, fileUpdateMonitor, entryTypesManager);
 
         new ViewModelListCellFactory<Language>()
                 .withText(Language::getDisplayName)
@@ -122,15 +130,21 @@ public void initialize() {
         autosaveLocalLibraries.selectedProperty().bindBidirectional(viewModel.autosaveLocalLibrariesProperty());
         ActionFactory actionFactory = new ActionFactory(preferencesService.getKeyBindingRepository());
         actionFactory.configureIconButton(StandardActions.HELP, new HelpAction(HelpFile.AUTOSAVE, dialogService, preferencesService.getFilePreferences()), autosaveLocalLibrariesHelp);
+        actionFactory.configureIconButton(StandardActions.HELP, new HelpAction(HelpFile.REMOTE, dialogService, preferencesService.getFilePreferences()), remoteHelp);
 
         createBackup.selectedProperty().bindBidirectional(viewModel.createBackupProperty());
         backupDirectory.textProperty().bindBidirectional(viewModel.backupDirectoryProperty());
         backupDirectory.disableProperty().bind(viewModel.createBackupProperty().not());
 
         Platform.runLater(() -> {
+            validationVisualizer.initVisualization(viewModel.remotePortValidationStatus(), remotePort);
             validationVisualizer.initVisualization(viewModel.fontSizeValidationStatus(), fontSize);
             validationVisualizer.initVisualization(viewModel.customPathToThemeValidationStatus(), customThemePath);
         });
+
+        remoteServer.selectedProperty().bindBidirectional(viewModel.remoteServerProperty());
+        remotePort.textProperty().bindBidirectional(viewModel.remotePortProperty());
+        remotePort.disableProperty().bind(remoteServer.selectedProperty().not());
     }
 
     @FXML

src/main/java/org/jabref/gui/preferences/general/GeneralTabViewModel.java

@@ -4,6 +4,7 @@
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Optional;
 
 import javafx.beans.property.BooleanProperty;
 import javafx.beans.property.ListProperty;
@@ -19,18 +20,26 @@
 import javafx.scene.control.SpinnerValueFactory;
 
 import org.jabref.gui.DialogService;
+import org.jabref.gui.Globals;
 import org.jabref.gui.desktop.JabRefDesktop;
 import org.jabref.gui.preferences.PreferenceTabViewModel;
+import org.jabref.gui.remote.CLIMessageHandler;
 import org.jabref.gui.theme.Theme;
 import org.jabref.gui.theme.ThemeTypes;
 import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.l10n.Language;
 import org.jabref.logic.l10n.Localization;
+import org.jabref.logic.net.ssl.TrustStoreManager;
+import org.jabref.logic.remote.RemotePreferences;
+import org.jabref.logic.remote.RemoteUtil;
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.database.BibDatabaseMode;
+import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.strings.StringUtil;
+import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.FilePreferences;
+import org.jabref.preferences.InternalPreferences;
 import org.jabref.preferences.LibraryPreferences;
 import org.jabref.preferences.PreferencesService;
 import org.jabref.preferences.TelemetryPreferences;
@@ -81,19 +90,33 @@ public class GeneralTabViewModel implements PreferenceTabViewModel {
     private final TelemetryPreferences telemetryPreferences;
     private final LibraryPreferences libraryPreferences;
     private final FilePreferences filePreferences;
+    private final RemotePreferences remotePreferences;
 
     private final Validator fontSizeValidator;
     private final Validator customPathToThemeValidator;
 
     private final List<String> restartWarning = new ArrayList<>();
-
-    public GeneralTabViewModel(DialogService dialogService, PreferencesService preferences) {
+    private final BooleanProperty remoteServerProperty = new SimpleBooleanProperty();
+    private final StringProperty remotePortProperty = new SimpleStringProperty("");
+    private final Validator remotePortValidator;
+    private final InternalPreferences internalPreferences;
+    private final BooleanProperty versionCheckProperty = new SimpleBooleanProperty();
+    private final FileUpdateMonitor fileUpdateMonitor;
+    private final BibEntryTypesManager entryTypesManager;
+    private TrustStoreManager trustStoreManager;
+
+    public GeneralTabViewModel(DialogService dialogService, PreferencesService preferences, FileUpdateMonitor fileUpdateMonitor, BibEntryTypesManager entryTypesManager) {
         this.dialogService = dialogService;
         this.preferences = preferences;
         this.workspacePreferences = preferences.getWorkspacePreferences();
         this.telemetryPreferences = preferences.getTelemetryPreferences();
         this.libraryPreferences = preferences.getLibraryPreferences();
         this.filePreferences = preferences.getFilePreferences();
+        this.remotePreferences = preferences.getRemotePreferences();
+        this.internalPreferences = preferences.getInternalPreferences();
+        this.fileUpdateMonitor = fileUpdateMonitor;
+        this.entryTypesManager = entryTypesManager;
+        this.trustStoreManager = trustStoreManager;
 
         fontSizeValidator = new FunctionBasedValidator<>(
                 fontSizeProperty,
@@ -116,6 +139,27 @@ public GeneralTabViewModel(DialogService dialogService, PreferencesService prefe
                         Localization.lang("General"),
                         Localization.lang("Visual theme"),
                         Localization.lang("Please specify a css theme file."))));
+
+        remotePortValidator = new FunctionBasedValidator<>(
+                remotePortProperty,
+                input -> {
+                    try {
+                        int portNumber = Integer.parseInt(remotePortProperty().getValue());
+                        return RemoteUtil.isUserPort(portNumber);
+                    } catch (NumberFormatException ex) {
+                        return false;
+                    }
+                },
+                ValidationMessage.error(String.format("%s > %s %n %n %s",
+                        Localization.lang("Network"),
+                        Localization.lang("Remote operation"),
+                        Localization.lang("You must enter an integer value in the interval 1025-65535"))));
+
+        this.trustStoreManager = new TrustStoreManager(Path.of(preferences.getSSLPreferences().getTruststorePath()));
+    }
+
+    public ValidationStatus remotePortValidationStatus() {
+        return remotePortValidator.getValidationStatus();
     }
 
     @Override
@@ -125,8 +169,10 @@ public void setValues() {
         // The light theme is in fact the absence of any theme modifying 'base.css'. Another embedded theme like
         // 'dark.css', stored in the classpath, can be introduced in {@link org.jabref.gui.theme.Theme}.
         switch (workspacePreferences.getTheme().getType()) {
-            case DEFAULT -> selectedThemeProperty.setValue(ThemeTypes.LIGHT);
-            case EMBEDDED -> selectedThemeProperty.setValue(ThemeTypes.DARK);
+            case DEFAULT ->
+                    selectedThemeProperty.setValue(ThemeTypes.LIGHT);
+            case EMBEDDED ->
+                    selectedThemeProperty.setValue(ThemeTypes.DARK);
             case CUSTOM -> {
                 selectedThemeProperty.setValue(ThemeTypes.CUSTOM);
                 customPathToThemeProperty.setValue(workspacePreferences.getTheme().getName());
@@ -151,6 +197,9 @@ public void setValues() {
 
         createBackupProperty.setValue(filePreferences.shouldCreateBackup());
         backupDirectoryProperty.setValue(filePreferences.getBackupDirectory().toString());
+
+        remoteServerProperty.setValue(remotePreferences.useRemoteServer());
+        remotePortProperty.setValue(String.valueOf(remotePreferences.getPort()));
     }
 
     @Override
@@ -185,6 +234,38 @@ public void storeSettings() {
 
         filePreferences.createBackupProperty().setValue(createBackupProperty.getValue());
         filePreferences.backupDirectoryProperty().setValue(Path.of(backupDirectoryProperty.getValue()));
+
+        getPortAsInt(remotePortProperty.getValue()).ifPresent(newPort -> {
+            if (remotePreferences.isDifferentPort(newPort)) {
+                remotePreferences.setPort(newPort);
+            }
+        });
+
+        internalPreferences.setVersionCheckEnabled(versionCheckProperty.getValue());
+
+        getPortAsInt(remotePortProperty.getValue()).ifPresent(newPort -> {
+            if (remotePreferences.isDifferentPort(newPort)) {
+                remotePreferences.setPort(newPort);
+            }
+        });
+
+        if (remoteServerProperty.getValue()) {
+            remotePreferences.setUseRemoteServer(true);
+            Globals.REMOTE_LISTENER.openAndStart(new CLIMessageHandler(preferences, fileUpdateMonitor, entryTypesManager), remotePreferences.getPort());
+        } else {
+            remotePreferences.setUseRemoteServer(false);
+            Globals.REMOTE_LISTENER.stop();
+        }
+        trustStoreManager.flush();
+
+        if (remoteServerProperty.getValue()) {
+            remotePreferences.setUseRemoteServer(true);
+            Globals.REMOTE_LISTENER.openAndStart(new CLIMessageHandler(preferences, fileUpdateMonitor, entryTypesManager), remotePreferences.getPort());
+        } else {
+            remotePreferences.setUseRemoteServer(false);
+            Globals.REMOTE_LISTENER.stop();
+        }
+        trustStoreManager.flush();
     }
 
     public ValidationStatus fontSizeValidationStatus() {
@@ -199,6 +280,10 @@ public ValidationStatus customPathToThemeValidationStatus() {
     public boolean validateSettings() {
         CompositeValidator validator = new CompositeValidator();
 
+        if (remoteServerProperty.getValue()) {
+            validator.addValidators(remotePortValidator);
+        }
+
         if (fontOverrideProperty.getValue()) {
             validator.addValidators(fontSizeValidator);
         }
@@ -310,6 +395,14 @@ public void backupFileDirBrowse() {
                      .ifPresent(dir -> backupDirectoryProperty.setValue(dir.toString()));
     }
 
+    public BooleanProperty remoteServerProperty() {
+        return remoteServerProperty;
+    }
+
+    public StringProperty remotePortProperty() {
+        return remotePortProperty;
+    }
+
     public void openBrowser() {
         String url = "https://themes.jabref.org";
         try {
@@ -318,4 +411,12 @@ public void openBrowser() {
             dialogService.showErrorDialogAndWait(Localization.lang("Could not open website."), e);
         }
     }
+
+    private Optional<Integer> getPortAsInt(String value) {
+        try {
+            return Optional.of(Integer.parseInt(value));
+        } catch (NumberFormatException ex) {
+            return Optional.empty();
+        }
+    }
 }