Merge remote-tracking branch 'upstream/master' into writebackupToTemp

* upstream/master:
  Fix icon issue (#6858)
  No sync of specialfields to keywords as default (#6846)
  Don't show entry editor on startup (#6861)
  Sort-in root classes into packages (#6853)
  Add "Fetchers" to DevDocs

CHANGELOG.md

@@ -21,9 +21,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We restructured the 'File' tab and extracted some parts into the 'Linked files' tab [#6779](https://github.com/JabRef/jabref/pull/6779)
 - JabRef now offers journal lists from <https://abbrv.jabref.org>. JabRef the lists which use a dot inside the abbreviations. [#5749](https://github.com/JabRef/jabref/pull/5749)
 - We removed two useless preferences in the groups preferences dialog. [#6836](https://github.com/JabRef/jabref/pull/6836)
+- Synchronization of SpecialFields to keywords is now disabled by default. [#6621](https://github.com/JabRef/jabref/issues/6621)
+- JabRef no longer opens the entry editor with the first entry on startup [6855](https://github.com/JabRef/jabref/issues/6855)
 
 ### Fixed
 
+- We fixed an issue changing the icon link_variation_off that is not meaningful. [#6834][https://github.com/JabRef/jabref/issues/6834]
 - We fixed an issue where the `.sav` file was not deleted upon exiting JabRef. [#6109](https://github.com/JabRef/jabref/issues/6109)
 - We fixed a linked identifier icon inconsistency. [#6705](https://github.com/JabRef/jabref/issues/6705)
 - We fixed the wrong behavior that font size changes are not reflected in dialogs. [#6039](https://github.com/JabRef/jabref/issues/6039)

build.gradle

@@ -46,7 +46,7 @@ java {
 }
 
 application {
-    mainClassName = "$moduleName/org.jabref.JabRefLauncher"
+    mainClassName = "$moduleName/org.jabref.gui.JabRefLauncher"
 }
 
 // TODO: Ugly workaround to temporarily ignore build errors to dependencies of latex2unicode

buildres/linux/JabRef.desktop

@@ -9,4 +9,4 @@ Type=Application
 DESKTOP_MIMES
 Categories=DEPLOY_BUNDLE_CATEGORY
 Keywords=bibtex;biblatex;latex;bibliography
-StartupWMClass=org.jabref.JabRefMain
+StartupWMClass=org.jabref.gui.JabRefMain

docs/SUMMARY.md

@@ -13,6 +13,7 @@
   * [Code Quality](advanced-reading/code-quality.md)
   * [Recommendations for UI design](advanced-reading/ui-recommendations.md)
   * [Custom SVG icons](advanced-reading/custom-svg-icons.md)
+  * [Working on fetchers](advanced-reading/fetchers.md)
   * [Creating a binary and debug it](advanced-reading/jpackage.md)
 * [JabRef and Software Engineering](teaching.md)
 * [Readings on Coding](readings-on-coding/README.md)

docs/advanced-reading/jpackage.md

@@ -28,7 +28,7 @@ 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
 
    ```text
-   pushd %DIR% & %JAVA_EXEC% -Xdebug -Xrunjdwp:server=y,transport=dt_socket,address=8000,suspend=n -p "%~dp0/../app" -m org.jabref/org.jabref.JabRefLauncher  %* & popd
+   pushd %DIR% & %JAVA_EXEC% -Xdebug -Xrunjdwp:server=y,transport=dt_socket,address=8000,suspend=n -p "%~dp0/../app" -m org.jabref/org.jabref.gui.JabRefLauncher  %* & popd
    ```
 
 4. Open your IDE and add a "Remote Debugging Configuration" for `localhost:8000`

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

@@ -197,7 +197,7 @@ Make sure your Eclipse installation us up to date, Eclipse JEE 2020-03 or newer
 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.JabRefLauncher` and/or for `org.jabref.JabRefMain` \(both can be used equivalently\)
+4. Create a run/debug configuration for the main class `org.jabref.gui.JabRefLauncher` 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 \(e.g. JabRefLauncher or JabRefMain\) otherwise it will not work.
 
      ![Creating the run/debug configuration by right clicking on the class](../.gitbook/assets/eclipse-create-run-config%20%281%29.png)

snap/local/JabRef-launcher

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

src/jmh/java/org/jabref/benchmarks/Benchmarks.java

@@ -7,7 +7,7 @@
 import java.util.Random;
 import java.util.stream.Collectors;
 
-import org.jabref.Globals;
+import org.jabref.gui.Globals;
 import org.jabref.logic.exporter.BibtexDatabaseWriter;
 import org.jabref.logic.exporter.SavePreferences;
 import org.jabref.logic.formatter.bibtexfields.HtmlToLatexFormatter;

src/main/java/org/jabref/architecture/AllowedToUseAwt.java

@@ -0,0 +1,10 @@
+package org.jabref.architecture;
+
+/**
+ * Annotation to indicate that this logic class can access AWT
+ */
+public @interface AllowedToUseAwt {
+
+    // The rationale
+    String value();
+}

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

@@ -11,11 +11,11 @@
 import java.util.Set;
 import java.util.prefs.BackingStoreException;
 
-import org.jabref.Globals;
-import org.jabref.JabRefException;
+import org.jabref.gui.Globals;
 import org.jabref.gui.externalfiles.AutoSetFileLinksUtil;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;
 import org.jabref.gui.undo.NamedCompound;
+import org.jabref.logic.JabRefException;
 import org.jabref.logic.citationkeypattern.CitationKeyGenerator;
 import org.jabref.logic.exporter.AtomicFileWriter;
 import org.jabref.logic.exporter.BibDatabaseWriter;
@@ -48,6 +48,7 @@
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.strings.StringUtil;
+import org.jabref.model.util.DummyFileUpdateMonitor;
 import org.jabref.preferences.SearchPreferences;
 
 import com.google.common.base.Throwables;
@@ -83,7 +84,7 @@ private static Optional<ParserResult> importToOpenBase(String argument) {
     }
 
     private static Optional<ParserResult> importBibtexToOpenBase(String argument) {
-        BibtexParser parser = new BibtexParser(Globals.prefs.getImportFormatPreferences(), Globals.getFileUpdateMonitor());
+        BibtexParser parser = new BibtexParser(Globals.prefs.getImportFormatPreferences(), new DummyFileUpdateMonitor());
         try {
             List<BibEntry> entries = parser.parseEntries(argument);
             ParserResult result = new ParserResult(entries);
@@ -143,7 +144,7 @@ private static Optional<ParserResult> importFile(Path file, String importFormat)
                 // * means "guess the format":
                 System.out.println(Localization.lang("Importing in unknown format") + ": " + file);
 
-                ImportFormatReader.UnknownFormatImport importResult = Globals.IMPORT_FORMAT_READER.importUnknownFormat(file, Globals.getFileUpdateMonitor());
+                ImportFormatReader.UnknownFormatImport importResult = Globals.IMPORT_FORMAT_READER.importUnknownFormat(file, new DummyFileUpdateMonitor());
 
                 System.out.println(Localization.lang("Format used") + ": " + importResult.format);
                 return Optional.of(importResult.parserResult);

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

@@ -9,7 +9,7 @@
 import java.util.concurrent.Executors;
 import java.util.concurrent.atomic.AtomicInteger;
 
-import org.jabref.Globals;
+import org.jabref.gui.Globals;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.fetcher.CrossRef;

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

@@ -2,7 +2,7 @@
 
 import java.util.List;
 
-import org.jabref.Globals;
+import org.jabref.gui.Globals;
 import org.jabref.logic.l10n.Localization;
 
 import org.apache.commons.cli.CommandLine;

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

@@ -12,7 +12,6 @@
 import javafx.scene.control.SplitPane;
 import javafx.scene.layout.StackPane;
 
-import org.jabref.Globals;
 import org.jabref.gui.autocompleter.AutoCompletePreferences;
 import org.jabref.gui.autocompleter.PersonNameSuggestionProvider;
 import org.jabref.gui.autocompleter.SuggestionProviders;
@@ -120,8 +119,6 @@ public BasePanel(JabRefFrame frame, BasePanelPreferences preferences, BibDatabas
         this.getDatabase().registerListener(new UpdateTimestampListener(Globals.prefs));
 
         this.entryEditor = new EntryEditor(this, externalFileTypes);
-        // Open entry editor for first entry on start up.
-        Platform.runLater(this::clearAndSelectFirst);
     }
 
     @Subscribe

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

@@ -3,7 +3,6 @@
 import javafx.beans.property.DoubleProperty;
 import javafx.beans.property.SimpleDoubleProperty;
 
-import org.jabref.Globals;
 import org.jabref.gui.autocompleter.AutoCompletePreferences;
 import org.jabref.gui.entryeditor.EntryEditorPreferences;
 import org.jabref.gui.keyboard.KeyBindingRepository;

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

@@ -19,7 +19,7 @@
 import javafx.scene.input.DataFormat;
 import javafx.scene.input.MouseButton;
 
-import org.jabref.Globals;
+import org.jabref.architecture.AllowedToUseAwt;
 import org.jabref.logic.bibtex.BibEntryWriter;
 import org.jabref.logic.bibtex.FieldWriter;
 import org.jabref.logic.importer.FetcherException;
@@ -37,6 +37,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+@AllowedToUseAwt("Requires ava.awt.datatransfer.Clipboard")
 public class ClipBoardManager {
 
     public static final DataFormat XML = new DataFormat("application/xml");

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

@@ -4,8 +4,6 @@
 
 import javax.swing.undo.UndoManager;
 
-import org.jabref.Globals;
-import org.jabref.JabRefGUI;
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.journals.JournalAbbreviationRepository;

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

@@ -18,7 +18,6 @@
 import javafx.scene.layout.FlowPane;
 import javafx.stage.Screen;
 
-import org.jabref.Globals;
 import org.jabref.gui.util.BaseDialog;
 import org.jabref.gui.util.ControlHelper;
 import org.jabref.gui.util.IconValidationDecorator;

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

@@ -14,7 +14,6 @@
 import javafx.concurrent.Task;
 import javafx.concurrent.Worker;
 
-import org.jabref.Globals;
 import org.jabref.gui.duplicationFinder.DuplicateResolverDialog;
 import org.jabref.logic.citationkeypattern.CitationKeyGenerator;
 import org.jabref.logic.database.DuplicateCheck;

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

@@ -8,7 +8,6 @@
 import javafx.stage.Modality;
 import javafx.stage.Stage;
 
-import org.jabref.Globals;
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.keyboard.KeyBinding;
 import org.jabref.gui.keyboard.KeyBindingRepository;

src/main/java/org/jabref/FallbackExceptionHandler.java → src/main/java/org/jabref/gui/FallbackExceptionHandler.java

@@ -1,4 +1,4 @@
-package org.jabref;
+package org.jabref.gui;
 
 import org.jabref.gui.util.DefaultTaskExecutor;
 

src/main/java/org/jabref/Globals.java → src/main/java/org/jabref/gui/Globals.java

@@ -1,13 +1,12 @@
-package org.jabref;
+package org.jabref.gui;
 
 import java.awt.GraphicsEnvironment;
 import java.util.Optional;
 import java.util.UUID;
 
 import javafx.stage.Screen;
 
-import org.jabref.gui.ClipBoardManager;
-import org.jabref.gui.StateManager;
+import org.jabref.architecture.AllowedToUseAwt;
 import org.jabref.gui.keyboard.KeyBindingRepository;
 import org.jabref.gui.undo.CountingUndoManager;
 import org.jabref.gui.util.DefaultFileUpdateMonitor;
@@ -33,6 +32,7 @@
  * @deprecated try to use {@link StateManager} and {@link org.jabref.preferences.PreferencesService}
  */
 @Deprecated
+@AllowedToUseAwt("Requires AWT for headless check")
 public class Globals {
 
     /**

src/main/java/org/jabref/JabRefExecutorService.java → src/main/java/org/jabref/gui/JabRefExecutorService.java

@@ -1,4 +1,4 @@
-package org.jabref;
+package org.jabref.gui;
 
 import java.util.Collection;
 import java.util.Collections;

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

@@ -46,8 +46,6 @@
 import javafx.scene.shape.Rectangle;
 import javafx.stage.Stage;
 
-import org.jabref.Globals;
-import org.jabref.JabRefExecutorService;
 import org.jabref.gui.actions.ActionFactory;
 import org.jabref.gui.actions.ActionHelper;
 import org.jabref.gui.actions.SimpleCommand;
@@ -219,9 +217,7 @@ private void initDragAndDrop() {
                 }
             });
 
-            this.getScene().setOnDragExited(event -> {
-                tabbedPane.getTabs().remove(dndIndicator);
-            });
+            this.getScene().setOnDragExited(event -> tabbedPane.getTabs().remove(dndIndicator));
 
             this.getScene().setOnDragDropped(event -> {
                 tabbedPane.getTabs().remove(dndIndicator);
@@ -793,7 +789,7 @@ private MenuBar createMenu() {
                 factory.createMenuItem(StandardActions.MASS_SET_FIELDS, new MassSetFieldsAction(stateManager, dialogService, undoManager))
         );
 
-        if (Globals.prefs.getBoolean(JabRefPreferences.SPECIALFIELDSENABLED)) {
+        if (Globals.prefs.getSpecialFieldsPreferences().isSpecialFieldsEnabled()) {
             edit.getItems().addAll(
                     new SeparatorMenuItem(),
                     // ToDo: SpecialField needs the active BasePanel to mark it as changed.
@@ -1034,7 +1030,7 @@ public void addParserResult(ParserResult parserResult, boolean focusPanel) {
         } else {
             // only add tab if DB is not already open
             Optional<BasePanel> panel = getBasePanelList().stream()
-                                                          .filter(p -> p.getBibDatabaseContext().getDatabasePath().equals(parserResult.getFile()))
+                                                          .filter(p -> p.getBibDatabaseContext().getDatabasePath().equals(parserResult.getPath()))
                                                           .findFirst();
 
             if (panel.isPresent()) {

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

@@ -1,4 +1,4 @@
-package org.jabref;
+package org.jabref.gui;
 
 import java.io.File;
 import java.sql.SQLException;
@@ -11,8 +11,6 @@
 import javafx.stage.Screen;
 import javafx.stage.Stage;
 
-import org.jabref.gui.BasePanel;
-import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.dialogs.BackupUIManager;
 import org.jabref.gui.help.VersionWorker;
 import org.jabref.gui.icon.IconTheme;

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

@@ -1,4 +1,4 @@
-package org.jabref;
+package org.jabref.gui;
 
 /**
  * JabRef launcher: This just starts JabRefMain. It is there because to have the name consistent to other Java applications.

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

@@ -1,4 +1,4 @@
-package org.jabref;
+package org.jabref.gui;
 
 import java.net.Authenticator;
 
@@ -9,7 +9,6 @@
 
 import org.jabref.cli.ArgumentProcessor;
 import org.jabref.cli.JabRefCLI;
-import org.jabref.gui.FXDialog;
 import org.jabref.gui.remote.JabRefMessageHandler;
 import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.journals.JournalAbbreviationLoader;

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

@@ -8,7 +8,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import org.jabref.Globals;
+import org.jabref.architecture.AllowedToUseAwt;
 import org.jabref.gui.actions.ActionHelper;
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.desktop.JabRefDesktop;
@@ -34,6 +34,7 @@
  * are opened. This feature is disabled by default and can be switched on at
  * preferences/external programs
  */
+@AllowedToUseAwt("Requires AWT to send an email")
 public class SendAsEMailAction extends SimpleCommand {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(SendAsEMailAction.class);

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

@@ -7,7 +7,6 @@
 import java.util.Map;
 import java.util.stream.Stream;
 
-import org.jabref.Globals;
 import org.jabref.gui.groups.GroupSidePane;
 import org.jabref.gui.importer.fetcher.WebSearchPane;
 import org.jabref.gui.openoffice.OpenOfficeSidePanel;

src/main/java/org/jabref/gui/actions/JabRefAction.java

@@ -5,7 +5,7 @@
 
 import javafx.beans.binding.Bindings;
 
-import org.jabref.Globals;
+import org.jabref.gui.Globals;
 import org.jabref.gui.keyboard.KeyBindingRepository;
 
 import de.saxsys.mvvmfx.utils.commands.Command;

src/main/java/org/jabref/gui/bibtexextractor/BibtexExtractorViewModel.java

@@ -8,8 +8,8 @@
 import javafx.beans.property.SimpleStringProperty;
 import javafx.beans.property.StringProperty;
 
-import org.jabref.Globals;
 import org.jabref.gui.DialogService;
+import org.jabref.gui.Globals;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.externalfiles.ImportHandler;
 import org.jabref.gui.externalfiletype.ExternalFileTypes;

src/main/java/org/jabref/gui/citationkeypattern/CitationKeyPatternDialog.java

@@ -2,8 +2,8 @@
 
 import javafx.scene.control.ButtonType;
 
-import org.jabref.Globals;
 import org.jabref.gui.BasePanel;
+import org.jabref.gui.Globals;
 import org.jabref.gui.util.BaseDialog;
 import org.jabref.logic.citationkeypattern.AbstractCitationKeyPattern;
 import org.jabref.logic.l10n.Localization;

src/main/java/org/jabref/gui/citationkeypattern/CitationKeyPatternPanel.java

@@ -10,8 +10,8 @@
 import javafx.scene.layout.GridPane;
 import javafx.scene.layout.Pane;
 
-import org.jabref.Globals;
 import org.jabref.gui.BasePanel;
+import org.jabref.gui.Globals;
 import org.jabref.gui.actions.ActionFactory;
 import org.jabref.gui.actions.StandardActions;
 import org.jabref.gui.help.HelpAction;