Merge remote-tracking branch 'upstream/master' into feature/use-unkow…

…n-fields-as-default-fields

.github/workflows/tests.yml

@@ -257,7 +257,7 @@ jobs:
         uses: unsplash/comment-on-pr@master
         if: steps.authors_check.outputs.newauthor == 'true'
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GH_TOKEN_COMMENT_ON_PR }}
         with:
           msg: "${{ steps.authors_check.outputs.message }}"
           check_for_duplicate_msg: true

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/code-howtos.md

@@ -30,6 +30,7 @@ Principles:
                Localization.lang("Something went wrong...", ioe);
        }
     ```
+
 * Never, ever throw and catch `Exception` or `Throwable`
 * Errors should only be logged when they are finally caught \(i.e., logged only once\). See **Logging** for details.
 * If the Exception message is intended to be shown to the User in the UI \(see below\) provide also a localizedMessage \(see `JabRefException`\).
@@ -51,7 +52,7 @@ TODO: Usage of status bar and Swing Dialogs
 
 ## Using the EventSystem
 
-### What the EventSystem is used for?
+### What the EventSystem is used for
 
 Many times there is a need to provide an object on many locations simultaneously. This design pattern is quite similar to Java's Observer, but it is much simplier and readable while having the same functional sense.
 
@@ -368,7 +369,7 @@ The following expressions can be used in FXML attributes, according to the [offi
 
 All radio buttons that should be grouped together need to have a ToggleGroup defined in the FXML code Example:
 
-```markup
+```xml
 <VBox>
             <fx:define>
                 <ToggleGroup fx:id="citeToggleGroup"/>
@@ -383,4 +384,3 @@ All radio buttons that should be grouped together need to have a ToggleGroup def
             </children>
 </VBox>
 ```
-

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)
@@ -222,6 +222,7 @@ Make sure your Eclipse installation us up to date, Eclipse JEE 2020-03 or newer
         --add-exports javafx.web/com.sun.webkit=org.controlsfx.controls
         --add-exports javafx.graphics/com.sun.javafx.css=org.controlsfx.controls
         --add-exports javafx.controls/com.sun.javafx.scene.control.behavior=com.jfoenix
+        --add-exports javafx.graphics/com.sun.javafx.stage=com.jfoenix
         --add-exports com.oracle.truffle.regex/com.oracle.truffle.regex=org.graalvm.truffle
         --patch-module org.jabref=build/resources/main
      ```

scripts/generate-authors.sh

@@ -58,5 +58,5 @@ cd "$(dirname "$(readlink -f "$BASH_SOURCE")")/.."
 
     # co-authors
     coauthors=$(git log -i --grep=co-authored-by  | grep -i "co-authored-by" | sed "s/.*co-authored-by: \(.*\)/\1/I" | sed "s/ <.*//")
-	echo -e "$authors\n$(git log --format='%aN')\n$coauthors" | grep -v "\[bot\]" | grep -v "JabRef" | grep -v "Siedlerchr" | grep -v "^Christoph$" | grep -v "^Mootez$" | grep -v "oscargus" | grep -v "dependabot" | grep -v "github actions" | grep -v "igorsteinmacher" | grep -v "halirutan" | grep -v "matthiasgeiger" | grep -v "Gitter Badger" | grep -v "gdstewart" | LC_ALL=C.UTF-8 sort --unique --ignore-case
+	echo -e "$authors\n$(git log --format='%aN')\n$coauthors" | grep -v "\[bot\]" | grep -v "JabRef" | grep -v "Siedlerchr" | grep -v "^Christoph$" | grep -v "^Mootez$" | grep -v "oscargus" | grep -v "dependabot" | grep -v "github actions" | grep -v "igorsteinmacher" | grep -v "halirutan" | grep -v "matthiasgeiger" | grep -v "Gitter Badger" | grep -v "gdstewart" | grep -v "chenyuheng" | LC_ALL=C.UTF-8 sort --unique --ignore-case
 } > AUTHORS

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;
@@ -614,7 +613,7 @@ public void copy() {
     }
 
     public void paste() {
-        mainTable.paste();
+        mainTable.paste(this.bibDatabaseContext.getMode());
     }
 
     public void cut() {

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

@@ -14,12 +14,12 @@
 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;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.IdBasedFetcher;
+import org.jabref.logic.importer.ImportCleanup;
 import org.jabref.logic.importer.WebFetchers;
 import org.jabref.logic.importer.fetcher.DoiFetcher;
 import org.jabref.logic.l10n.Localization;
@@ -147,6 +147,8 @@ public void runFetcherWorker() {
             Optional<BibEntry> result = fetcherWorker.getValue();
             if (result.isPresent()) {
                 final BibEntry entry = result.get();
+                ImportCleanup cleanup = new ImportCleanup(basePanel.getBibDatabaseContext().getMode());
+                cleanup.doPostCleanup(entry);
                 Optional<BibEntry> duplicate = new DuplicateCheck(Globals.entryTypesManager).containsDuplicate(basePanel.getDatabase(), entry, basePanel.getBibDatabaseContext().getMode());
                 if ((duplicate.isPresent())) {
                     DuplicateResolverDialog dialog = new DuplicateResolverDialog(entry, duplicate.get(), DuplicateResolverDialog.DuplicateResolverType.IMPORT_CHECK, basePanel.getBibDatabaseContext(), stateManager);

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;
@@ -125,6 +123,7 @@
 import org.jabref.logic.autosaveandbackup.BackupManager;
 import org.jabref.logic.citationstyle.CitationStyleOutputFormat;
 import org.jabref.logic.importer.IdFetcher;
+import org.jabref.logic.importer.ImportCleanup;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.WebFetchers;
 import org.jabref.logic.l10n.Localization;
@@ -1191,6 +1190,8 @@ private boolean readyForAutosave(BibDatabaseContext context) {
      */
     private void addImportedEntries(final BasePanel panel, final ParserResult parserResult) {
         BackgroundTask<ParserResult> task = BackgroundTask.wrap(() -> parserResult);
+        ImportCleanup cleanup = new ImportCleanup(panel.getBibDatabaseContext().getMode());
+        cleanup.doPostCleanup(parserResult.getDatabase().getEntries());
         ImportEntriesDialog dialog = new ImportEntriesDialog(panel.getBibDatabaseContext(), task);
         dialog.setTitle(Localization.lang("Import"));
         dialog.showAndWait();

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);