Merge branch 'main' into fix-10558

.github/workflows/check-links.yml

@@ -4,6 +4,8 @@ on:
   push:
     paths:
       - '.github/workflows/check-links.yml'
+      - '.lycheeignore'
+      - 'lychee.toml'
       - '**/*.md'
   schedule:
     # Run on the first of each month at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07)
@@ -32,4 +34,4 @@ jobs:
         uses: lycheeverse/lychee-action@v1.9.3
         with:
           fail: true
-          args: --accept '200,201,202,203,204,429,500' --max-concurrency 1 --cache --no-progress --exclude-all-private './**/*.md'
+          args: --accept '200,201,202,203,204,403,429,500' --max-concurrency 1 --cache --no-progress --exclude-all-private './**/*.md'

.github/workflows/deployment-arm64.yml

@@ -104,7 +104,7 @@ jobs:
         shell: bash
         run: |
           jpackage \
-          --module org.jabref/org.jabref.cli.Launcher \
+          --module org.jabref/org.jabref.Launcher \
           --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
           --add-modules org.jabref,org.jabref.merged.module  \
           --dest build/distribution \
@@ -129,7 +129,7 @@ jobs:
         shell: bash
         run: |
           jpackage \
-          --module org.jabref/org.jabref.cli.Launcher \
+          --module org.jabref/org.jabref.Launcher \
           --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
           --add-modules org.jabref,org.jabref.merged.module  \
           --dest build/distribution \

.github/workflows/deployment.yml

@@ -116,7 +116,7 @@ jobs:
         shell: bash
         run: |
           jpackage \
-          --module org.jabref/org.jabref.cli.Launcher \
+          --module org.jabref/org.jabref.Launcher \
           --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
           --add-modules org.jabref,org.jabref.merged.module  \
           --dest build/distribution \
@@ -141,7 +141,7 @@ jobs:
         shell: bash
         run: |
           jpackage \
-          --module org.jabref/org.jabref.cli.Launcher \
+          --module org.jabref/org.jabref.Launcher \
           --module-path ${{env.JAVA_HOME}}/jmods/:build/jlinkbase/jlinkjars \
           --add-modules org.jabref,org.jabref.merged.module  \
           --dest build/distribution \

.lycheeignore

@@ -1,4 +1,5 @@
 https://arxiv.org/
+https://chrome.google.com/
 https://contribute.jabref.org/
 https://donations.jabref.org/
 https://pubs.acs.org/

CHANGELOG.md

@@ -19,6 +19,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added a new boolean to the style files for Openoffice/Libreoffice integration to switch between ZERO_WIDTH_SPACE (default) and no space. [#10843](https://github.com/JabRef/jabref/pull/10843)
 - When pasting HTML into the abstract or a comment field, the hypertext is automatically converted to Markdown. [#10558](https://github.com/JabRef/jabref/issues/10558)
 - We added the possibility to redownload files that had been present but are no longer in the specified location. [#10848](https://github.com/JabRef/jabref/issues/10848)
+- We added the citation key pattern `[camelN]`. Equivalent to the first N words of the `[camel]` pattern.
 
 ### Changed
 

build.gradle

@@ -56,7 +56,7 @@ java {
 }
 
 application {
-    mainClass.set('org.jabref.cli.Launcher')
+    mainClass.set('org.jabref.Launcher')
     mainModule.set('org.jabref')
 }
 

docs/code-howtos/jpackage.md

@@ -31,7 +31,7 @@ Sometimes issues with modularity only arise in the installed version and do not
 3. Modify the `build\image\JabRef\runtime\bin\Jabref.bat` file, replace the last line with
 
     ```shell
-    pushd %DIR% & %JAVA_EXEC% -Xdebug -Xrunjdwp:server=y,transport=dt_socket,address=8000,suspend=n -p "%~dp0/../app" -m org.jabref/org.jabref.cli.Launcher  %* & popd
+    pushd %DIR% & %JAVA_EXEC% -Xdebug -Xrunjdwp:server=y,transport=dt_socket,address=8000,suspend=n -p "%~dp0/../app" -m org.jabref/org.jabref.Launcher  %* & popd
     ```
 
 4. Open your IDE and add a "Remote Debugging Configuration" for `localhost:8000`

docs/code-howtos/tools.md

@@ -10,7 +10,7 @@ This page lists some software we consider useful.
 * [Refined GitHub](https://github.com/sindresorhus/refined-github) - GitHub on steroids
 * [GitHub Issue Link Status](https://github.com/fregante/github-issue-link-status) - proper coloring of linked issues and PRs.
 * [Codecov Browser Extension](https://github.com/codecov/browser-extension) - displaying code coverage directly when browsing GitHub
-* [Sourcegraph Browser Extension](https://docs.sourcegraph.com/integration/browser\_extension) - Navigate through source on GitHub
+* [Sourcegraph Browser Extension](https://sourcegraph.com/docs/integration/browser_extension) - Navigate through source on GitHub
 
 ## git hints
 

docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/eclipse.md

@@ -29,7 +29,7 @@ Always make sure your Eclipse installation us up to date.
 3. Open or import the existing project in Eclipse as Java project.
    * Remark: Importing it as gradle project will not work correctly.
    * Refresh the project in Eclipse
-4. Create a run/debug configuration for the main class `org.jabref.cli.Launcher` and/or for `org.jabref.gui.JabRefMain` (both can be used equivalently)
+4. Create a run/debug configuration for the main class `org.jabref.Launcher` and/or for `org.jabref.gui.JabRefMain` (both can be used equivalently)
    * Remark: The run/debug configuration needs to be added by right-clicking the class (e.g. `Launcher` or JabRefMain) otherwise it will not work.
 
        ![Creating the run/debug configuration by right-clicking on the class](../../images/eclipse-create-run-config.png)

docs/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.md

@@ -158,7 +158,7 @@ Now, `BibEntryTest` should appear first:
 
 Press <kbd>Enter</kbd> to jump to that class.
 
-Hover on the green play button on `testDefaultConstructor`:
+Hover on the green play button on `defaultConstructor`:
 
 {% figure caption:"However on green play button" %}
 ![However on green play button](guidelines-intellij-run-single-test.png)

snap/local/JabRef-launcher

@@ -1,3 +1,3 @@
 #! /bin/sh
 DIR="$SNAP/lib/runtime/bin"
-"$DIR/java"  -p "$DIR/../app" -m org.jabref/org.jabref.cli.Launcher  "$@"
+"$DIR/java"  -p "$DIR/../app" -m org.jabref/org.jabref.Launcher  "$@"

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

@@ -1,4 +1,4 @@
-package org.jabref.cli;
+package org.jabref;
 
 import java.io.File;
 import java.io.IOException;
@@ -11,8 +11,11 @@
 import java.util.List;
 import java.util.Map;
 
+import org.jabref.architecture.AllowedToUseStandardStreams;
+import org.jabref.cli.ArgumentProcessor;
+import org.jabref.cli.JabRefCLI;
 import org.jabref.gui.Globals;
-import org.jabref.gui.MainApplication;
+import org.jabref.gui.JabRefGUI;
 import org.jabref.logic.UiCommand;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.journals.predatory.PredatoryJournalListLoader;
@@ -45,20 +48,19 @@
  * - Handle the command line arguments
  * - Start the JavaFX application (if not in cli mode)
  */
+@AllowedToUseStandardStreams("Direct output to the user")
 public class Launcher {
     private static Logger LOGGER;
-    private static String[] ARGUMENTS;
     private static boolean isDebugEnabled;
 
     public static void main(String[] args) {
         routeLoggingToSlf4J();
-        ARGUMENTS = args;
 
         // We must configure logging as soon as possible, which is why we cannot wait for the usual
         // argument parsing workflow to parse logging options .e.g. --debug
         JabRefCLI jabRefCLI;
         try {
-            jabRefCLI = new JabRefCLI(ARGUMENTS);
+            jabRefCLI = new JabRefCLI(args);
             isDebugEnabled = jabRefCLI.isDebugLogging();
         } catch (ParseException e) {
             isDebugEnabled = false;
@@ -73,7 +75,7 @@ public static void main(String[] args) {
             final JabRefPreferences preferences = JabRefPreferences.getInstance();
 
             // Early exit in case another instance is already running
-            if (!handleMultipleAppInstances(ARGUMENTS, preferences.getRemotePreferences())) {
+            if (!handleMultipleAppInstances(args, preferences.getRemotePreferences())) {
                 return;
             }
 
@@ -91,7 +93,7 @@ public static void main(String[] args) {
 
                 // Process arguments
                 ArgumentProcessor argumentProcessor = new ArgumentProcessor(
-                        ARGUMENTS,
+                        args,
                         ArgumentProcessor.Mode.INITIAL_START,
                         preferences,
                         fileUpdateMonitor,
@@ -105,7 +107,8 @@ public static void main(String[] args) {
                 }
 
                 List<UiCommand> uiCommands = new ArrayList<>(argumentProcessor.getUiCommands());
-                MainApplication.main(uiCommands, preferences, fileUpdateMonitor, ARGUMENTS);
+                JabRefGUI.setup(uiCommands, preferences, fileUpdateMonitor);
+                JabRefGUI.launch(JabRefGUI.class, args);
             } catch (ParseException e) {
                 LOGGER.error("Problem parsing arguments", e);
                 JabRefCLI.printUsage(preferences);
@@ -148,7 +151,7 @@ private static void addLogToDisk() {
     }
 
     private static void initializeLogger() {
-        LOGGER = LoggerFactory.getLogger(MainApplication.class);
+        LOGGER = LoggerFactory.getLogger(Launcher.class);
     }
 
     /**
@@ -167,6 +170,7 @@ private static boolean handleMultipleAppInstances(String[] args, RemotePreferenc
                 if (remoteClient.sendCommandLineArguments(args)) {
                     // So we assume it's all taken care of, and quit.
                     LOGGER.debug("Arguments passed on to running JabRef instance.");
+                    // Used for script-use output etc. to the user
                     System.out.println(Localization.lang("Arguments passed on to running JabRef instance. Shutting down."));
                     return false;
                 } else {

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -33,7 +33,6 @@
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.ImportFormatReader;
 import org.jabref.logic.importer.OpenDatabase;
-import org.jabref.logic.importer.OutputPrinter;
 import org.jabref.logic.importer.ParseException;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.SearchBasedFetcher;
@@ -156,8 +155,7 @@ private Optional<ParserResult> importFile(String argument) {
         Optional<ParserResult> importResult = importFile(file, importFormat);
         importResult.ifPresent(result -> {
             if (result.hasWarnings()) {
-                OutputPrinter printer = new SystemOutputPrinter();
-                printer.showMessage(result.getErrorMessage());
+                System.out.println(result.getErrorMessage());
             }
         });
         return importResult;

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

@@ -3,6 +3,7 @@
 import java.util.List;
 import java.util.Optional;
 
+import javafx.application.Application;
 import javafx.application.Platform;
 import javafx.scene.Scene;
 import javafx.scene.input.KeyEvent;
@@ -13,6 +14,7 @@
 import org.jabref.gui.help.VersionWorker;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.keyboard.TextInputKeyBindings;
+import org.jabref.gui.openoffice.OOBibBaseConnect;
 import org.jabref.gui.theme.ThemeManager;
 import org.jabref.logic.UiCommand;
 import org.jabref.logic.l10n.Localization;
@@ -21,7 +23,7 @@
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.GuiPreferences;
-import org.jabref.preferences.PreferencesService;
+import org.jabref.preferences.JabRefPreferences;
 
 import com.tobiasdiez.easybind.EasyBind;
 import impl.org.controlsfx.skin.DecorationPane;
@@ -31,29 +33,34 @@
 /**
  * Represents the outer stage and the scene of the JabRef window.
  */
-public class JabRefGUI {
+public class JabRefGUI extends Application {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(JabRefGUI.class);
 
+    private static List<UiCommand> uiCommands;
+    private static JabRefPreferences preferencesService;
+    private static FileUpdateMonitor fileUpdateMonitor;
     private static JabRefFrame mainFrame;
     private static DialogService dialogService;
     private static ThemeManager themeManager;
 
-    private final Stage mainStage;
-    private final PreferencesService preferencesService;
+    private boolean correctedWindowPos = false;
+    private Stage mainStage;
 
-    private final List<UiCommand> uiCommands;
-    private boolean correctedWindowPos;
+    public static void setup(List<UiCommand> uiCommands,
+                             JabRefPreferences preferencesService,
+                             FileUpdateMonitor fileUpdateMonitor) {
+        JabRefGUI.uiCommands = uiCommands;
+        JabRefGUI.preferencesService = preferencesService;
+        JabRefGUI.fileUpdateMonitor = fileUpdateMonitor;
+    }
 
-    public JabRefGUI(Stage mainStage,
-                     List<UiCommand> uiCommands,
-                     PreferencesService preferencesService,
-                     FileUpdateMonitor fileUpdateMonitor) {
-        this.mainStage = mainStage;
-        this.uiCommands = uiCommands;
-        this.preferencesService = preferencesService;
+    @Override
+    public void start(Stage stage) {
+        this.mainStage = stage;
 
-        this.correctedWindowPos = false;
+        FallbackExceptionHandler.installExceptionHandler();
+        Globals.startBackgroundTasks();
 
         WebViewStore.init();
 
@@ -90,6 +97,18 @@ public JabRefGUI(Stage mainStage,
         setupProxy();
     }
 
+    @Override
+    public void stop() {
+        OOBibBaseConnect.closeOfficeConnection();
+        Globals.stopBackgroundTasks();
+        Globals.shutdownThreadPools();
+        try {
+            Globals.predatoryJournalRepository.close();
+        } catch (Exception e) {
+            LOGGER.warn("Cloud not shut down predatoryJournalRepository", e);
+        }
+    }
+
     private void setupProxy() {
         if (!preferencesService.getProxyPreferences().shouldUseProxy()
                 || !preferencesService.getProxyPreferences().shouldUseAuthentication()) {

src/main/java/org/jabref/gui/desktop/os/DefaultDesktop.java

@@ -5,8 +5,8 @@
 import java.io.IOException;
 import java.nio.file.Path;
 
+import org.jabref.Launcher;
 import org.jabref.architecture.AllowedToUseAwt;
-import org.jabref.cli.Launcher;
 import org.jabref.gui.DialogService;
 import org.jabref.preferences.FilePreferences;