Process CLI arguments before starting gui

.devcontainer/devcontainer.json

@@ -23,6 +23,9 @@
 
     "onCreateCommand": "gradle assemble",
 
+    // Forward the noVNC port (desktop-lite: https://github.com/devcontainers/features/tree/main/src/desktop-lite)  
+    "forwardPorts": [6080],
+
     // Need to connect as root otherwise we run into issues with gradle.
     // default option is "vscode". More info: https://aka.ms/vscode-remote/containers/non-root.
     "remoteUser": "root",

build.gradle

@@ -49,7 +49,7 @@ java {
 }
 
 application {
-    mainClass.set('org.jabref.gui.JabRefLauncher')
+    mainClass.set('org.jabref.cli.Launcher')
     mainModule.set('org.jabref')
 }
 

src/main/java/org/jabref/gui/JabRefMain.java → src/main/java/org/jabref/cli/Launcher.java

@@ -1,4 +1,4 @@
-package org.jabref.gui;
+package org.jabref.cli;
 
 import java.io.File;
 import java.io.IOException;
@@ -9,13 +9,8 @@
 import java.util.Comparator;
 import java.util.Map;
 
-import javafx.application.Application;
-import javafx.application.Platform;
-import javafx.stage.Stage;
-
-import org.jabref.cli.ArgumentProcessor;
-import org.jabref.cli.JabRefCLI;
-import org.jabref.gui.openoffice.OOBibBaseConnect;
+import org.jabref.gui.Globals;
+import org.jabref.gui.MainApplication;
 import org.jabref.gui.remote.JabRefMessageHandler;
 import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
@@ -42,99 +37,84 @@
 import org.tinylog.configuration.Configuration;
 
 /**
- * JabRef's main class to process command line options and to start the UI
+ * The main entry point for the JabRef application.
+ * <p>
+ * It has two main functions:
+ * - Handle the command line arguments
+ * - Start the JavaFX application (if not in cli mode)
  */
-public class JabRefMain extends Application {
+public class Launcher {
     private static Logger LOGGER;
 
-    private static String[] arguments;
-
     public static void main(String[] args) {
         addLogToDisk();
-        arguments = args;
-        launch(arguments);
-    }
-
-    private static void initializeLogger() {
-         LOGGER = LoggerFactory.getLogger(JabRefMain.class);
-    }
-
-    /**
-     * This needs to be called as early as possible. After the first log write, it is not possible to alter
-     * the log configuration programmatically anymore.
-     */
-    private static void addLogToDisk() {
-        Path directory = Path.of(AppDirsFactory.getInstance().getUserLogDir(
-                                     "jabref",
-                                     new BuildInfo().version.toString(),
-                                     "org.jabref"));
-        try {
-            Files.createDirectories(directory);
-        } catch (IOException e) {
-            initializeLogger();
-            LOGGER.error("Could not create log directory {}", directory, e);
-            return;
-        }
-        // The "Shared File Writer" is explained at https://tinylog.org/v2/configuration/#shared-file-writer
-        Map<String, String> configuration = Map.of(
-                "writerFile", "shared file",
-                "writerFile.level", "info",
-                "writerFile.file", directory.resolve("log.txt").toString(),
-                "writerFile.charset", "UTF-8");
-
-        configuration.entrySet().forEach(config -> Configuration.set(config.getKey(), config.getValue()));
-        initializeLogger();
-    }
-
-    @Override
-    public void start(Stage mainStage) {
         try {
-            FallbackExceptionHandler.installExceptionHandler();
-
             // Init preferences
             final JabRefPreferences preferences = JabRefPreferences.getInstance();
             Globals.prefs = preferences;
-            // Perform migrations
             PreferencesMigrations.runMigrations();
 
-            configureProxy(preferences.getProxyPreferences());
+            // Early exit in case another instance is already running
+            if (!handleMultipleAppInstances(args, preferences)) {
+                return;
+            }
 
+            // Init rest of preferences
+            configureProxy(preferences.getProxyPreferences());
             configureSSL(preferences.getSSLPreferences());
-
-            Globals.startBackgroundTasks();
-
             applyPreferences(preferences);
-
             clearOldSearchIndices();
 
             try {
                 // Process arguments
-                ArgumentProcessor argumentProcessor = new ArgumentProcessor(arguments, ArgumentProcessor.Mode.INITIAL_START, preferences);
-                // Check for running JabRef
-                if (!handleMultipleAppInstances(arguments, preferences) || argumentProcessor.shouldShutDown()) {
-                    Platform.exit();
+                ArgumentProcessor argumentProcessor = new ArgumentProcessor(args, ArgumentProcessor.Mode.INITIAL_START,
+                        preferences);
+                if (argumentProcessor.shouldShutDown()) {
+                    LOGGER.debug("JabRef shut down after processing command line arguments");
                     return;
                 }
 
-                // If not, start GUI
-                new JabRefGUI(mainStage, argumentProcessor.getParserResults(), argumentProcessor.isBlank(), preferences);
+                MainApplication.create(argumentProcessor.getParserResults(), argumentProcessor.isBlank(), preferences);
             } catch (ParseException e) {
                 LOGGER.error("Problem parsing arguments", e);
-
                 JabRefCLI.printUsage();
-                Platform.exit();
             }
         } catch (Exception ex) {
             LOGGER.error("Unexpected exception", ex);
-            Platform.exit();
         }
     }
 
-    @Override
-    public void stop() {
-        OOBibBaseConnect.closeOfficeConnection();
-        Globals.stopBackgroundTasks();
-        Globals.shutdownThreadPools();
+    /**
+     * This needs to be called as early as possible. After the first log write, it
+     * is not possible to alter
+     * the log configuration programmatically anymore.
+     */
+    private static void addLogToDisk() {
+        Path directory = Path.of(AppDirsFactory.getInstance().getUserLogDir(
+                "jabref",
+                new BuildInfo().version.toString(),
+                "org.jabref"));
+        try {
+            Files.createDirectories(directory);
+        } catch (IOException e) {
+            initializeLogger();
+            LOGGER.error("Could not create log directory {}", directory, e);
+            return;
+        }
+        // The "Shared File Writer" is explained at
+        // https://tinylog.org/v2/configuration/#shared-file-writer
+        Map<String, String> configuration = Map.of(
+                "writerFile", "shared file",
+                "writerFile.level", "info",
+                "writerFile.file", directory.resolve("log.txt").toString(),
+                "writerFile.charset", "UTF-8");
+
+        configuration.entrySet().forEach(config -> Configuration.set(config.getKey(), config.getValue()));
+        initializeLogger();
+    }
+
+    private static void initializeLogger() {
+        LOGGER = LoggerFactory.getLogger(MainApplication.class);
     }
 
     private static boolean handleMultipleAppInstances(String[] args, PreferencesService preferences) {
@@ -143,7 +123,8 @@ private static boolean handleMultipleAppInstances(String[] args, PreferencesServ
             // Try to contact already running JabRef
             RemoteClient remoteClient = new RemoteClient(remotePreferences.getPort());
             if (remoteClient.ping()) {
-                // We are not alone, there is already a server out there, send command line arguments to other instance
+                // We are not alone, there is already a server out there, send command line
+                // arguments to other instance
                 if (remoteClient.sendCommandLineArguments(args)) {
                     // So we assume it's all taken care of, and quit.
                     LOGGER.info(Localization.lang("Arguments passed on to running JabRef instance. Shutting down."));
@@ -153,15 +134,17 @@ private static boolean handleMultipleAppInstances(String[] args, PreferencesServ
                 }
             } else {
                 // We are alone, so we start the server
-                Globals.REMOTE_LISTENER.openAndStart(new JabRefMessageHandler(), remotePreferences.getPort(), preferences);
+                Globals.REMOTE_LISTENER.openAndStart(new JabRefMessageHandler(), remotePreferences.getPort(),
+                        preferences);
             }
         }
         return true;
     }
 
     private static void applyPreferences(PreferencesService preferences) {
         // Read list(s) of journal names and abbreviations
-        Globals.journalAbbreviationRepository = JournalAbbreviationLoader.loadRepository(preferences.getJournalAbbreviationPreferences());
+        Globals.journalAbbreviationRepository = JournalAbbreviationLoader
+                .loadRepository(preferences.getJournalAbbreviationPreferences());
 
         // Build list of Import and Export formats
         Globals.IMPORT_FORMAT_READER.resetImportFormats(
@@ -208,12 +191,13 @@ private static void clearOldSearchIndices() {
 
         try (DirectoryStream<Path> stream = Files.newDirectoryStream(appData)) {
             for (Path path : stream) {
-                if (Files.isDirectory(path) && !path.toString().endsWith("ssl") && path.toString().contains("lucene") && !path.equals(currentIndexPath)) {
+                if (Files.isDirectory(path) && !path.toString().endsWith("ssl") && path.toString().contains("lucene")
+                        && !path.equals(currentIndexPath)) {
                     LOGGER.info("Deleting out-of-date fulltext search index at {}.", path);
                     Files.walk(path)
-                         .sorted(Comparator.reverseOrder())
-                         .map(Path::toFile)
-                         .forEach(File::delete);
+                            .sorted(Comparator.reverseOrder())
+                            .map(Path::toFile)
+                            .forEach(File::delete);
                 }
             }
         } catch (IOException e) {

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

@@ -0,0 +1,41 @@
+package org.jabref.gui;
+
+import java.util.List;
+
+import javafx.application.Application;
+import javafx.stage.Stage;
+
+import org.jabref.gui.openoffice.OOBibBaseConnect;
+import org.jabref.logic.importer.ParserResult;
+import org.jabref.preferences.JabRefPreferences;
+
+/**
+ * JabRef's main class to process command line options and to start the UI
+ */
+public class MainApplication extends Application {
+    private static List<ParserResult> parserResults;
+    private static boolean isBlank;
+    private static JabRefPreferences preferences;
+
+    public static void create(List<ParserResult> parserResults, boolean blank, JabRefPreferences preferences) {
+        MainApplication.parserResults = parserResults;
+        MainApplication.isBlank = blank;
+        MainApplication.preferences = preferences;
+        launch();
+    }
+
+    @Override
+    public void start(Stage mainStage) {
+        FallbackExceptionHandler.installExceptionHandler();
+
+        Globals.startBackgroundTasks();
+        new JabRefGUI(mainStage, parserResults, isBlank, preferences);
+    }
+
+    @Override
+    public void stop() {
+        OOBibBaseConnect.closeOfficeConnection();
+        Globals.stopBackgroundTasks();
+        Globals.shutdownThreadPools();
+    }
+}

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

@@ -14,6 +14,7 @@
 import org.jabref.gui.ClipBoardManager;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.desktop.JabRefDesktop;
+import org.jabref.gui.util.BindingsHelper;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.logging.LogMessages;
 import org.jabref.logic.util.BuildInfo;
@@ -25,6 +26,7 @@
 import org.slf4j.LoggerFactory;
 
 public class ErrorConsoleViewModel extends AbstractViewModel {
+
     private static final Logger LOGGER = LoggerFactory.getLogger(ErrorConsoleViewModel.class);
 
     private final DialogService dialogService;
@@ -36,7 +38,7 @@ public ErrorConsoleViewModel(DialogService dialogService, ClipBoardManager clipB
         this.dialogService = Objects.requireNonNull(dialogService);
         this.clipBoardManager = Objects.requireNonNull(clipBoardManager);
         this.buildInfo = Objects.requireNonNull(buildInfo);
-        ObservableList<LogEventViewModel> eventViewModels = EasyBind.map(LogMessages.getInstance().getMessages(), LogEventViewModel::new);
+        ObservableList<LogEventViewModel> eventViewModels = EasyBind.map(BindingsHelper.forUI(LogMessages.getInstance().getMessages()), LogEventViewModel::new);
         allMessagesData = new ReadOnlyListWrapper<>(eventViewModels);
     }
 

src/main/java/org/jabref/gui/logging/GuiWriter.java

@@ -5,7 +5,6 @@
 import java.util.EnumSet;
 import java.util.Map;
 
-import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.logging.LogMessages;
 
 import org.tinylog.core.LogEntry;
@@ -29,7 +28,7 @@ public Collection<LogEntryValue> getRequiredLogEntryValues() {
 
     @Override
     public void write(LogEntry logEntry) throws Exception {
-        DefaultTaskExecutor.runInJavaFXThread(() -> LogMessages.getInstance().add(logEntry));
+        LogMessages.getInstance().add(logEntry);
     }
 
     @Override

src/main/java/org/jabref/logic/net/ssl/TrustStoreManager.java

@@ -138,7 +138,7 @@ public X509Certificate getCertificate(String alias) {
      */
     public static void createTruststoreFileIfNotExist(Path storePath) {
         try {
-            LOGGER.info("Trust store path: {}", storePath.toAbsolutePath());
+            LOGGER.debug("Trust store path: {}", storePath.toAbsolutePath());
             Path storeResourcePath = Path.of(TrustStoreManager.class.getResource("/ssl/truststore.jks").toURI());
             Files.createDirectories(storePath.getParent());
             if (Files.notExists(storePath)) {