Revert "Process CLI arguments before starting gui"

.devcontainer/devcontainer.json

@@ -23,9 +23,6 @@
 
     "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.cli.Launcher')
+    mainClass.set('org.jabref.gui.JabRefLauncher')
     mainModule.set('org.jabref')
 }
 

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

@@ -0,0 +1,10 @@
+package org.jabref.gui;
+
+/**
+ * JabRef launcher: This just starts JabRefMain. It is there because to have the name consistent to other Java applications.
+ */
+public class JabRefLauncher {
+    public static void main(String[] args) {
+        JabRefMain.main(args);
+    }
+}

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

@@ -1,4 +1,4 @@
-package org.jabref.cli;
+package org.jabref.gui;
 
 import java.io.File;
 import java.io.IOException;
@@ -9,8 +9,13 @@
 import java.util.Comparator;
 import java.util.Map;
 
-import org.jabref.gui.Globals;
-import org.jabref.gui.MainApplication;
+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.remote.JabRefMessageHandler;
 import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
@@ -37,72 +42,40 @@
 import org.tinylog.configuration.Configuration;
 
 /**
- * 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)
+ * JabRef's main class to process command line options and to start the UI
  */
-public class Launcher {
+public class JabRefMain extends Application {
     private static Logger LOGGER;
 
+    private static String[] arguments;
+
     public static void main(String[] args) {
         addLogToDisk();
-        try {
-            // Init preferences
-            final JabRefPreferences preferences = JabRefPreferences.getInstance();
-            Globals.prefs = preferences;
-            PreferencesMigrations.runMigrations();
-
-            // Early exit in case another instance is already running
-            if (!handleMultipleAppInstances(args, preferences)) {
-                return;
-            }
-
-            // Init rest of preferences
-            configureProxy(preferences.getProxyPreferences());
-            configureSSL(preferences.getSSLPreferences());
-            applyPreferences(preferences);
-            clearOldSearchIndices();
-
-            try {
-                // Process arguments
-                ArgumentProcessor argumentProcessor = new ArgumentProcessor(args, ArgumentProcessor.Mode.INITIAL_START,
-                        preferences);
-                if (argumentProcessor.shouldShutDown()) {
-                    LOGGER.debug("JabRef shut down after processing command line arguments");
-                    return;
-                }
+        arguments = args;
+        launch(arguments);
+    }
 
-                MainApplication.create(argumentProcessor.getParserResults(), argumentProcessor.isBlank(), preferences);
-            } catch (ParseException e) {
-                LOGGER.error("Problem parsing arguments", e);
-                JabRefCLI.printUsage();
-            }
-        } catch (Exception ex) {
-            LOGGER.error("Unexpected exception", ex);
-        }
+    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
+     * 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"));
+                                     "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
+        // 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",
@@ -113,8 +86,55 @@ private static void addLogToDisk() {
         initializeLogger();
     }
 
-    private static void initializeLogger() {
-        LOGGER = LoggerFactory.getLogger(MainApplication.class);
+    @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());
+
+            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();
+                    return;
+                }
+
+                // If not, start GUI
+                new JabRefGUI(mainStage, 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();
     }
 
     private static boolean handleMultipleAppInstances(String[] args, PreferencesService preferences) {
@@ -123,8 +143,7 @@ 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."));
@@ -134,17 +153,15 @@ 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(
@@ -191,13 +208,12 @@ 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/errorconsole/ErrorConsoleViewModel.java

@@ -14,7 +14,6 @@
 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;
@@ -26,7 +25,6 @@
 import org.slf4j.LoggerFactory;
 
 public class ErrorConsoleViewModel extends AbstractViewModel {
-
     private static final Logger LOGGER = LoggerFactory.getLogger(ErrorConsoleViewModel.class);
 
     private final DialogService dialogService;
@@ -38,7 +36,7 @@ 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(BindingsHelper.forUI(LogMessages.getInstance().getMessages()), LogEventViewModel::new);
+        ObservableList<LogEventViewModel> eventViewModels = EasyBind.map(LogMessages.getInstance().getMessages(), LogEventViewModel::new);
         allMessagesData = new ReadOnlyListWrapper<>(eventViewModels);
     }
 

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

@@ -5,6 +5,7 @@
 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;
@@ -28,7 +29,7 @@ public Collection<LogEntryValue> getRequiredLogEntryValues() {
 
     @Override
     public void write(LogEntry logEntry) throws Exception {
-        LogMessages.getInstance().add(logEntry);
+        DefaultTaskExecutor.runInJavaFXThread(() -> 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.debug("Trust store path: {}", storePath.toAbsolutePath());
+            LOGGER.info("Trust store path: {}", storePath.toAbsolutePath());
             Path storeResourcePath = Path.of(TrustStoreManager.class.getResource("/ssl/truststore.jks").toURI());
             Files.createDirectories(storePath.getParent());
             if (Files.notExists(storePath)) {

src/test/java/org/jabref/testutils/TestUtils.java

@@ -0,0 +1,28 @@
+package org.jabref.testutils;
+
+import org.jabref.gui.JabRefGUI;
+import org.jabref.gui.JabRefMain;
+
+public class TestUtils {
+
+    private static final String PATH_TO_TEST_BIBTEX = "src/test/resources/org/jabref/bibtexFiles/test.bib";
+
+    /**
+     * Initialize JabRef. Can be cleaned up with {@link TestUtils#closeJabRef()}
+     *
+     * @see TestUtils#closeJabRef()
+     */
+    public static void initJabRef() {
+        String[] args = {"-p", " ", TestUtils.PATH_TO_TEST_BIBTEX};
+        JabRefMain.main(args);
+    }
+
+    /**
+     * Closes the current instance of JabRef.
+     */
+    public static void closeJabRef() {
+        if (JabRefGUI.getMainFrame() != null) {
+            // TODO
+        }
+    }
+}