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

* upstream/master:
  fix checsktyle
  Fix for application dialogs opening in wrong displays (#7273)
  Only disable  move to file dir when path equals (#7269)
  Improved detection of long DOI's within text (#7260)
  Add missing author and fix name
  Fix style of highlighted checkboxes while searching in preferences (#7258)
  Updates to institution citation keys (#7210)
  Bump xmlunit-core from 2.8.1 to 2.8.2 (#7251)
  Bump classgraph from 4.8.97 to 4.8.98 (#7250)
  Bump bcprov-jdk15on from 1.67 to 1.68 (#7249)
  Bump xmlunit-matchers from 2.8.1 to 2.8.2 (#7252)
  Bump unirest-java from 3.11.06 to 3.11.09 (#7254)
  Bump org.beryx.jlink from 2.23.0 to 2.23.1 (#7253)
  Bump pascalgn/automerge-action from v0.12.0 to v0.13.0 (#7255)

# Conflicts:
#	src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java

.github/workflows/automerge.yml

@@ -16,7 +16,7 @@ jobs:
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.12.0
+        uses: pascalgn/automerge-action@v0.13.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "squash"

.github/workflows/tests.yml

@@ -261,6 +261,6 @@ jobs:
           echo
           echo "In case you want to use a different one, please comment here and adjust your name in your git configuration for future commits"
           echo
-          echo "Just adding yourself into the AUHTORS file does not help as it is overwritten by our script ./scripts/generate-authors."
+          echo "Just adding yourself into the AUTHORS file does not help as it is overwritten by our script ./scripts/generate-authors."
           echo "Read more on the AUTHORS file at found at https://github.com/JabRef/jabref/blob/master/CONTRIBUTING.md#author-credits"
           exit 1

AUTHORS

@@ -133,6 +133,7 @@ Felix Luthman
 Felix Wilke
 Fernando Santagata
 ffffatgoose
+Fiyinfolu Eludire
 Florian Beetz
 Florian Straßer
 Foivos Christoulakis

CHANGELOG.md

@@ -17,6 +17,10 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Fixed
 
+- We fixed an issue with the style of highlighted check boxes while searching in preferences. [#7226](https://github.com/JabRef/jabref/issues/7226)
+- We fixed an issue where the option "Move file to file directory" was disabled in the entry editor for all files [#7194](https://github.com/JabRef/jabref/issues/7194)
+- We fixed an issue where application dialogs were opening in the wrong display when using multiple screens [#7273](https://github.com/JabRef/jabref/pull/7273)
+
 ### Removed
 
 ## [5.2] – 2020-12-24
@@ -90,6 +94,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the password for a shared SQL database was not remembered [#6869](https://github.com/JabRef/jabref/issues/6869)
 - We fixed an issue where newly added entires were not synced to a shared SQL database [#7176](https://github.com/JabRef/jabref/issues/7176)
 - We fixed an issue where the PDF-Content importer threw an exception when no DOI number is present at the first page of the PDF document [#7203](https://github.com/JabRef/jabref/issues/7203)
+- We fixed an issue where authors that only have last names were incorrectly identified as institutes when generating citation keys [#7199](https://github.com/JabRef/jabref/issues/7199)
+- We fixed an issue where institutes were incorrectly identified as universities when generating citation keys [#6942](https://github.com/JabRef/jabref/issues/6942)
 
 ### Removed
 

build.gradle

@@ -14,7 +14,7 @@ plugins {
     id 'com.github.ben-manes.versions' version '0.36.0'
     id 'org.javamodularity.moduleplugin' version '1.7.0'
     id 'org.openjfx.javafxplugin' version '0.0.9'
-    id 'org.beryx.jlink' version '2.23.0'
+    id 'org.beryx.jlink' version '2.23.1'
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
     id 'com.adarshr.test-logger' version '2.1.1'
@@ -106,7 +106,7 @@ dependencies {
     implementation group: 'org.apache.tika', name: 'tika-core', version: '1.25'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    implementation 'org.bouncycastle:bcprov-jdk15on:1.67'
+    implementation 'org.bouncycastle:bcprov-jdk15on:1.68'
 
     implementation 'commons-cli:commons-cli:1.4'
 
@@ -157,7 +157,7 @@ dependencies {
     implementation 'org.controlsfx:controlsfx:11.0.3'
 
     implementation 'org.jsoup:jsoup:1.13.1'
-    implementation 'com.konghq:unirest-java:3.11.06'
+    implementation 'com.konghq:unirest-java:3.11.09'
 
     implementation 'org.slf4j:slf4j-api:2.0.0-alpha1'
     implementation group: 'org.apache.logging.log4j', name: 'log4j-jcl', version: '3.0.0-SNAPSHOT'
@@ -186,7 +186,7 @@ dependencies {
     implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.62.2'
     implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.62.2'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.97'
+    testImplementation 'io.github.classgraph:classgraph:4.8.98'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.7.0'
     testRuntimeOnly 'org.junit.vintage:junit-vintage-engine:5.7.0'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.7.0'
@@ -195,8 +195,8 @@ dependencies {
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntime group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
     testImplementation 'org.mockito:mockito-core:3.6.28'
-    testImplementation 'org.xmlunit:xmlunit-core:2.8.1'
-    testImplementation 'org.xmlunit:xmlunit-matchers:2.8.1'
+    testImplementation 'org.xmlunit:xmlunit-core:2.8.2'
+    testImplementation 'org.xmlunit:xmlunit-matchers:2.8.2'
     testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.15.0'
     testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.15.0'
     testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"

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 \(see `JabRefException`\).
@@ -57,7 +58,7 @@ Many times there is a need to provide an object on many locations simultaneously
 
 ### Main principle
 
-`EventBus` represents a communication line between multiple components. Objects can be passed through the bus and reach the listening method of another object which is registered on that `EventBus` instance. Hence the passed object is available as a parameter in the listening method.
+`EventBus` represents a communication line between multiple components. Objects can be passed through the bus and reach the listening method of another object which is registered on that `EventBus` instance. Hence, the passed object is available as a parameter in the listening method.
 
 ### Register to the `EventBus`
 
@@ -398,3 +399,20 @@ All radio buttons that should be grouped together need to have a ToggleGroup def
 </VBox>
 ```
 
+### JavaFX Dialogs
+
+All dialogs should be displayed to the user via `DialogService` interface methods.
+`DialogService` provides methods to display various dialogs (including custom ones) to the user.
+It also ensures the displayed dialog opens on the correct window via `initOwner()` (for cases where the user has multiple screens).
+The following code snippet demonstrates how a custom dialog is displayed to the user:
+
+```java
+dialogService.showCustomDialog(new DocumentViewerView());
+```
+
+If an instance of `DialogService` is unavailable within current class/scope in which the dialog needs to be displayed,
+`DialogService` can be instantiated via the code snippet shown as follows:
+
+```java
+DialogService dialogService = Injector.instantiateModelOrService(DialogService.class);
+```

src/main/java/module-info.java

@@ -57,6 +57,7 @@
     requires reactfx;
     requires commons.cli;
     requires com.github.tomtung.latex2unicode;
+    requires fastparse;
     requires jbibtex;
     requires citeproc.java;
     requires antlr.runtime;

src/main/java/org/jabref/gui/Base.css

@@ -427,8 +427,11 @@
 }
 
 .check-box > .box > .mark {
-    -fx-background-color: -fx-control-inner-background;
     -fx-padding: 0.2em 0.2em 0.2em 0.2em;
+}
+
+.check-box:selected > .box > .mark {
+    -fx-background-color: -fx-control-inner-background;
     -fx-shape: "M6.61 11.89L3.5 8.78 2.44 9.84 6.61 14l8.95-8.95L14.5 4z";
     -fx-stroke-width: 5;
 }

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

@@ -15,6 +15,7 @@
 import javafx.scene.control.DialogPane;
 import javafx.scene.control.TextInputDialog;
 
+import org.jabref.gui.util.BaseDialog;
 import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.logic.l10n.Localization;
@@ -160,6 +161,13 @@ boolean showConfirmationDialogWithOptOutAndWait(String title, String content,
                                                     String okButtonLabel, String cancelButtonLabel,
                                                     String optOutMessage, Consumer<Boolean> optOutAction);
 
+    /**
+     * Shows a custom dialog without returning any results.
+     *
+     * @param dialog dialog to show
+     */
+    void showCustomDialog(BaseDialog<?> dialog);
+
     /**
      * This will create and display a new dialog of the specified
      * {@link Alert.AlertType} but with user defined buttons as optional
@@ -184,7 +192,7 @@ Optional<ButtonType> showCustomButtonDialogAndWait(Alert.AlertType type, String
      * @param dialog dialog to show
      * @param <R>    type of result
      */
-    <R> Optional<R> showCustomDialogAndWait(Dialog<R> dialog);
+    <R> Optional<R> showCustomDialogAndWait(javafx.scene.control.Dialog<R> dialog);
 
     /**
      * Constructs and shows a canceable {@link ProgressDialog}. Clicking cancel will cancel the underlying service and close the dialog

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

@@ -155,7 +155,7 @@ public void runFetcherWorker() {
                 Optional<BibEntry> duplicate = new DuplicateCheck(Globals.entryTypesManager).containsDuplicate(libraryTab.getDatabase(), entry, libraryTab.getBibDatabaseContext().getMode());
                 if ((duplicate.isPresent())) {
                     DuplicateResolverDialog dialog = new DuplicateResolverDialog(entry, duplicate.get(), DuplicateResolverDialog.DuplicateResolverType.IMPORT_CHECK, libraryTab.getBibDatabaseContext(), stateManager);
-                    switch (dialog.showAndWait().orElse(DuplicateResolverDialog.DuplicateResolverResult.BREAK)) {
+                    switch (dialogService.showCustomDialogAndWait(dialog).orElse(DuplicateResolverDialog.DuplicateResolverResult.BREAK)) {
                         case KEEP_LEFT:
                             libraryTab.getDatabase().removeEntry(duplicate.get());
                             libraryTab.getDatabase().insertEntry(entry);

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

@@ -36,6 +36,7 @@
 
 import org.jabref.gui.icon.IconTheme;
 import org.jabref.gui.util.BackgroundTask;
+import org.jabref.gui.util.BaseDialog;
 import org.jabref.gui.util.DirectoryDialogConfiguration;
 import org.jabref.gui.util.FileDialogConfiguration;
 import org.jabref.gui.util.ZipFileChooser;
@@ -78,17 +79,18 @@ public JabRefDialogService(Window mainWindow, Pane mainPane, PreferencesService
         JabRefDialogService.preferences = preferences;
     }
 
-    private static FXDialog createDialog(AlertType type, String title, String content) {
+    private FXDialog createDialog(AlertType type, String title, String content) {
         FXDialog alert = new FXDialog(type, title, true);
         preferences.getTheme().installCss(alert.getDialogPane().getScene());
         alert.setHeaderText(null);
         alert.setContentText(content);
         alert.getDialogPane().setMinHeight(Region.USE_PREF_SIZE);
+        alert.initOwner(mainWindow);
         return alert;
     }
 
-    private static FXDialog createDialogWithOptOut(AlertType type, String title, String content,
-                                                   String optOutMessage, Consumer<Boolean> optOutAction) {
+    private FXDialog createDialogWithOptOut(AlertType type, String title, String content,
+                                            String optOutMessage, Consumer<Boolean> optOutAction) {
         FXDialog alert = new FXDialog(type, title, true);
         // Need to force the alert to layout in order to grab the graphic as we are replacing the dialog pane with a custom pane
         alert.getDialogPane().applyCss();
@@ -117,6 +119,7 @@ protected Node createDetailsButton() {
         alert.setHeaderText(null);
         alert.setContentText(content);
         alert.getDialogPane().setMinHeight(Region.USE_PREF_SIZE);
+        alert.initOwner(mainWindow);
         return alert;
     }
 
@@ -136,6 +139,7 @@ public <T> Optional<T> showChoiceDialogAndWait(String title, String content, Str
         choiceDialog.setHeaderText(title);
         choiceDialog.setTitle(title);
         choiceDialog.setContentText(content);
+        choiceDialog.initOwner(mainWindow);
         preferences.getTheme().installCss(choiceDialog.getDialogPane().getScene());
         return choiceDialog.showAndWait();
     }
@@ -145,6 +149,7 @@ public Optional<String> showInputDialogAndWait(String title, String content) {
         TextInputDialog inputDialog = new TextInputDialog();
         inputDialog.setHeaderText(title);
         inputDialog.setContentText(content);
+        inputDialog.initOwner(mainWindow);
         preferences.getTheme().installCss(inputDialog.getDialogPane().getScene());
         return inputDialog.showAndWait();
     }
@@ -154,6 +159,7 @@ public Optional<String> showInputDialogWithDefaultAndWait(String title, String c
         TextInputDialog inputDialog = new TextInputDialog(defaultValue);
         inputDialog.setHeaderText(title);
         inputDialog.setContentText(content);
+        inputDialog.initOwner(mainWindow);
         preferences.getTheme().installCss(inputDialog.getDialogPane().getScene());
         return inputDialog.showAndWait();
     }
@@ -181,6 +187,7 @@ public void showErrorDialogAndWait(String message, Throwable exception) {
         ExceptionDialog exceptionDialog = new ExceptionDialog(exception);
         exceptionDialog.getDialogPane().setMaxWidth(mainWindow.getWidth() / 2);
         exceptionDialog.setHeaderText(message);
+        exceptionDialog.initOwner(mainWindow);
         preferences.getTheme().installCss(exceptionDialog.getDialogPane().getScene());
         exceptionDialog.showAndWait();
     }
@@ -190,6 +197,7 @@ public void showErrorDialogAndWait(String title, String content, Throwable excep
         ExceptionDialog exceptionDialog = new ExceptionDialog(exception);
         exceptionDialog.setHeaderText(title);
         exceptionDialog.setContentText(content);
+        exceptionDialog.initOwner(mainWindow);
         preferences.getTheme().installCss(exceptionDialog.getDialogPane().getScene());
         exceptionDialog.showAndWait();
     }
@@ -259,12 +267,14 @@ public Optional<ButtonType> showCustomDialogAndWait(String title, DialogPane con
         alert.getButtonTypes().setAll(buttonTypes);
         alert.getDialogPane().setMinHeight(Region.USE_PREF_SIZE);
         alert.setResizable(true);
+        alert.initOwner(mainWindow);
         preferences.getTheme().installCss(alert.getDialogPane().getScene());
         return alert.showAndWait();
     }
 
     @Override
-    public <R> Optional<R> showCustomDialogAndWait(Dialog<R> dialog) {
+    public <R> Optional<R> showCustomDialogAndWait(javafx.scene.control.Dialog<R> dialog) {
+        dialog.initOwner(mainWindow);
         return dialog.showAndWait();
     }
 
@@ -285,6 +295,7 @@ public <V> void showProgressDialog(String title, String content, Task<V> task) {
             progressDialog.close();
         });
         preferences.getTheme().installCss(progressDialog.getDialogPane().getScene());
+        progressDialog.initOwner(mainWindow);
         progressDialog.show();
     }
 
@@ -307,6 +318,7 @@ public <V> Optional<ButtonType> showBackgroundProgressDialogAndWait(String title
         alert.getButtonTypes().setAll(ButtonType.YES, ButtonType.CANCEL);
         alert.getDialogPane().setMinHeight(Region.USE_PREF_SIZE);
         alert.setResizable(true);
+        alert.initOwner(mainWindow);
         preferences.getTheme().installCss(alert.getDialogPane().getScene());
 
         stateManager.getAnyTaskRunning().addListener((observable, oldValue, newValue) -> {
@@ -316,9 +328,7 @@ public <V> Optional<ButtonType> showBackgroundProgressDialogAndWait(String title
             }
         });
 
-        Dialog<ButtonType> dialog = alert::showAndWait;
-
-        return showCustomDialogAndWait(dialog);
+        return alert.showAndWait();
     }
 
     @Override
@@ -385,4 +395,10 @@ public Optional<Path> showFileOpenFromArchiveDialog(Path archivePath) throws IOE
             throw new IOException("Could not instantiate ZIP-archive reader.", exc);
         }
     }
+
+    @Override
+    public void showCustomDialog(BaseDialog<?> aboutDialogView) {
+        aboutDialogView.initOwner(mainWindow);
+        aboutDialogView.show();
+    }
 }

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

@@ -1089,7 +1089,7 @@ private void addImportedEntries(final LibraryTab panel, final ParserResult parse
         cleanup.doPostCleanup(parserResult.getDatabase().getEntries());
         ImportEntriesDialog dialog = new ImportEntriesDialog(panel.getBibDatabaseContext(), task);
         dialog.setTitle(Localization.lang("Import"));
-        dialog.showAndWait();
+        dialogService.showCustomDialogAndWait(dialog);
     }
 
     public FileHistoryMenu getFileHistory() {

src/main/java/org/jabref/gui/auximport/NewSubLibraryAction.java

@@ -1,9 +1,12 @@
 package org.jabref.gui.auximport;
 
+import org.jabref.gui.DialogService;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.actions.SimpleCommand;
 
+import com.airhacks.afterburner.injection.Injector;
+
 import static org.jabref.gui.actions.ActionHelper.needsDatabase;
 
 /**
@@ -21,7 +24,7 @@ public NewSubLibraryAction(JabRefFrame jabRefFrame, StateManager stateManager) {
 
     @Override
     public void execute() {
-        FromAuxDialog dialog = new FromAuxDialog(jabRefFrame);
-        dialog.showAndWait();
+        DialogService dialogService = Injector.instantiateModelOrService(DialogService.class);
+        dialogService.showCustomDialogAndWait(new FromAuxDialog(jabRefFrame));
     }
 }

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

@@ -1,8 +1,11 @@
 package org.jabref.gui.bibtexextractor;
 
+import org.jabref.gui.DialogService;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.actions.SimpleCommand;
 
+import com.airhacks.afterburner.injection.Injector;
+
 import static org.jabref.gui.actions.ActionHelper.needsDatabase;
 
 public class ExtractBibtexAction extends SimpleCommand {
@@ -13,7 +16,7 @@ public ExtractBibtexAction(StateManager stateManager) {
 
     @Override
     public void execute() {
-        ExtractBibtexDialog dlg = new ExtractBibtexDialog();
-        dlg.showAndWait();
+        DialogService dialogService = Injector.instantiateModelOrService(DialogService.class);
+        dialogService.showCustomDialogAndWait(new ExtractBibtexDialog());
     }
 }

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

@@ -1,9 +1,12 @@
 package org.jabref.gui.citationkeypattern;
 
+import org.jabref.gui.DialogService;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.StateManager;
 import org.jabref.gui.actions.SimpleCommand;
 
+import com.airhacks.afterburner.injection.Injector;
+
 import static org.jabref.gui.actions.ActionHelper.needsDatabase;
 
 public class CitationKeyPatternAction extends SimpleCommand {
@@ -18,6 +21,7 @@ public CitationKeyPatternAction(JabRefFrame frame, StateManager stateManager) {
 
     @Override
     public void execute() {
-        new CitationKeyPatternDialog(frame.getCurrentLibraryTab()).showAndWait();
+        DialogService dialogService = Injector.instantiateModelOrService(DialogService.class);
+        dialogService.showCustomDialogAndWait(new CitationKeyPatternDialog(frame.getCurrentLibraryTab()));
     }
 }