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

* upstream/master:
  Add docbook 5 support (#4319)
  Bump java-diff-utils from 2.2.0 to 4.0 (#4507)
  3189 fix group renaming (#4470)
  Create test (#4505)
  Bump archunit-junit5-engine from 0.9.2 to 0.9.3 (#4503)
  Bump archunit-junit5-api from 0.9.2 to 0.9.3 (#4504)
  Bump mockito-core from 2.23.0 to 2.23.4 (#4502)
  Bump guava from 27.0-jre to 27.0.1-jre (#4499)
  Improve page checker (#4498)
  Add color picker to groups dialog (#4492)
  Fix kbd XML closing tag

CHANGELOG.md

@@ -43,7 +43,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We removed the redundant new lines of markings and wrapped the summary in the File annotation tab. [#3823](https://github.com/JabRef/jabref/issues/3823)
 - We add auto url formatting when user paste link to URL field in entry editor. [koppor#254](https://github.com/koppor/jabref/issues/254)
 - We added a minimal height for the entry editor so that it can no longer be hidden by accident. [#4279](https://github.com/JabRef/jabref/issues/4279)
-- We added a new keyboard shortcut so that the entry editor could be closed by <kbd>Ctrl<kbd> + <kbd>E<kbd>. [#4222] (https://github.com/JabRef/jabref/issues/4222)
+- We added a new keyboard shortcut so that the entry editor could be closed by <kbd>Ctrl</kbd> + <kbd>E</kbd>. [#4222] (https://github.com/JabRef/jabref/issues/4222)
 - We added an option in the preference dialog box, that allows user to pick the dark or light theme option. [#4130] (https://github.com/JabRef/jabref/issues/4130)
 - We updated updated the Related Articles tab to accept JSON from the new version of the Mr. DLib service
 - We added an option in the preference dialog box that allows user to choose behavior after dragging and dropping files in Entry Editor. [#4356](https://github.com/JabRef/jabref/issues/4356)
@@ -68,6 +68,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the custom file column were sorted incorrectly. https://github.com/JabRef/jabref/issues/3119
 - We fixed an issues where the entry losses focus when a field is edited and at the same time used for sorting. https://github.com/JabRef/jabref/issues/3373
 - We fixed an issue where the menu on Mac OS was not displayed in the usual Mac-specific way. https://github.com/JabRef/jabref/issues/3146
+- We improved the integrity check for page numbers. [#4113](https://github.com/JabRef/jabref/issues/4113) and [feature request in the forum](http://discourse.jabref.org/t/pages-field-allow-use-of-en-dash/1199)
 - We fixed an issue where the order of fields in customized entry types was not saved correctly. [#4033](http://github.com/JabRef/jabref/issues/4033)
 - We fixed an issue where the groups tree of the last database was still shown even after the database was already closed.
 - We fixed an issue where the "Open file dialog" may disappear behind other windows. https://github.com/JabRef/jabref/issues/3410

build.gradle

@@ -110,7 +110,7 @@ dependencies {
     compile "org.libreoffice:ridl:5.4.2"
     compile "org.libreoffice:unoil:5.4.2"
 
-    compile 'io.github.java-diff-utils:java-diff-utils:2.2.0'
+    compile 'io.github.java-diff-utils:java-diff-utils:4.0'
     compile 'info.debatty:java-string-similarity:1.1.0'
 
     antlr3 'org.antlr:antlr:3.5.2'
@@ -125,7 +125,7 @@ dependencies {
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
-    compile 'com.google.guava:guava:27.0-jre'
+    compile 'com.google.guava:guava:27.0.1-jre'
 
     // JavaFX stuff
     compile 'de.jensd:fontawesomefx-materialdesignfont:1.7.22-4'
@@ -168,14 +168,14 @@ dependencies {
     testCompile 'org.junit-pioneer:junit-pioneer:0.3.0'
     testRuntime 'org.apache.logging.log4j:log4j-core:2.11.1'
     testRuntime 'org.apache.logging.log4j:log4j-jul:2.11.1'
-    testCompile 'org.mockito:mockito-core:2.23.0'
+    testCompile 'org.mockito:mockito-core:2.23.4'
     testCompile 'com.github.tomakehurst:wiremock:2.19.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
     testCompile 'org.xmlunit:xmlunit-core:2.6.2'
     testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
-    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.9.2'
-    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.2'
+    testRuntime 'com.tngtech.archunit:archunit-junit5-engine:0.9.3'
+    testCompile 'com.tngtech.archunit:archunit-junit5-api:0.9.3'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 

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

@@ -291,7 +291,6 @@
 .check-box > .box,
 .menu-button,
 .choice-box,
-.color-picker.split-button > .color-picker-label,
 .combo-box-base,
 .combo-box-base:editable > .arrow-button {
     -fx-background-color: transparent;
@@ -956,3 +955,23 @@ We want to have a look that matches our icons in the tool-bar */
 .progress-bar > .track {
     -fx-background-color: -jr-accent;
 }
+
+.jfx-color-picker:armed,
+.jfx-color-picker:hover,
+.jfx-color-picker:focused,
+.jfx-color-picker {
+    -fx-background-color: transparent, transparent, transparent, transparent;
+    -fx-background-radius: 0px;
+    -fx-background-insets: 0px;
+    -fx-effect: null;
+}
+
+.color-palette {
+    -fx-background-color: -fx-background;
+    -fx-background-radius: 0px;
+    -fx-background-insets: 0px;
+}
+
+.color-palette-region .button {
+    -fx-border-width: 0px;
+}

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

@@ -272,7 +272,7 @@ public void output(String s) {
     }
 
     private void setupActions() {
-        SaveDatabaseAction saveAction = new SaveDatabaseAction(this);
+        SaveDatabaseAction saveAction = new SaveDatabaseAction(this, Globals.prefs);
         CleanupAction cleanUpAction = new CleanupAction(this, Globals.prefs);
 
         actions.put(Actions.UNDO, undoAction);

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

@@ -1335,7 +1335,7 @@ private boolean confirmClose(BasePanel panel) {
         if (response.isPresent() && response.get().equals(saveChanges)) {
             // The user wants to save.
             try {
-                SaveDatabaseAction saveAction = new SaveDatabaseAction(panel);
+                SaveDatabaseAction saveAction = new SaveDatabaseAction(panel, Globals.prefs);
                 if (!saveAction.save()) {
                     // The action was either canceled or unsuccessful.
                     output(Localization.lang("Unable to save library"));

src/main/java/org/jabref/gui/dialogs/AutosaveUIManager.java

@@ -1,5 +1,6 @@
 package org.jabref.gui.dialogs;
 
+import org.jabref.Globals;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.exporter.SaveDatabaseAction;
 import org.jabref.model.database.event.AutosaveEvent;
@@ -25,7 +26,7 @@ public AutosaveUIManager(BasePanel panel) {
     @Subscribe
     public void listen(@SuppressWarnings("unused") AutosaveEvent event) {
         try {
-            new SaveDatabaseAction(panel).save();
+            new SaveDatabaseAction(panel, Globals.prefs).save();
         } catch (Throwable e) {
             LOGGER.error("Problem occured while saving.", e);
         }

src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java

@@ -14,7 +14,6 @@
 import javafx.scene.layout.VBox;
 import javafx.scene.text.Text;
 
-import org.jabref.Globals;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.DialogService;
 import org.jabref.gui.JabRefFrame;
@@ -53,16 +52,18 @@ public class SaveDatabaseAction {
     private final BasePanel panel;
     private final JabRefFrame frame;
     private final DialogService dialogService;
+    private final JabRefPreferences prefs;
 
-    public SaveDatabaseAction(BasePanel panel) {
+    public SaveDatabaseAction(BasePanel panel, JabRefPreferences prefs) {
         this.panel = panel;
         this.frame = panel.frame();
         this.dialogService = frame.getDialogService();
+        this.prefs = prefs;
     }
 
     private boolean saveDatabase(Path file, boolean selectedOnly, Charset encoding, SavePreferences.DatabaseSaveType saveType) throws SaveException {
         try {
-            SavePreferences preferences = Globals.prefs.loadForSaveFromPreferences()
+            SavePreferences preferences = prefs.loadForSaveFromPreferences()
                                                        .withEncoding(encoding)
                                                        .withSaveType(saveType);
 
@@ -124,7 +125,7 @@ private boolean doSave() {
                     panel.getBibDatabaseContext()
                          .getMetaData()
                          .getEncoding()
-                         .orElse(Globals.prefs.getDefaultEncoding()),
+                         .orElse(prefs.getDefaultEncoding()),
                     SavePreferences.DatabaseSaveType.ALL);
 
             if (success) {
@@ -182,10 +183,10 @@ private Optional<Path> getSavePath() {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
                 .addExtensionFilter(StandardFileType.BIBTEX_DB)
                 .withDefaultExtension(StandardFileType.BIBTEX_DB)
-                .withInitialDirectory(Globals.prefs.get(JabRefPreferences.WORKING_DIRECTORY))
+                .withInitialDirectory(prefs.get(JabRefPreferences.WORKING_DIRECTORY))
                 .build();
         Optional<Path> selectedPath = dialogService.showFileSaveDialog(fileDialogConfiguration);
-        selectedPath.ifPresent(path -> Globals.prefs.setWorkingDir(path.getParent()));
+        selectedPath.ifPresent(path -> prefs.setWorkingDir(path.getParent()));
         return selectedPath;
     }
 
@@ -228,7 +229,7 @@ public void saveAs(Path file) {
     private boolean readyForAutosave(BibDatabaseContext context) {
         return ((context.getLocation() == DatabaseLocation.SHARED) ||
                 ((context.getLocation() == DatabaseLocation.LOCAL)
-                        && Globals.prefs.getBoolean(JabRefPreferences.LOCAL_AUTO_SAVE)))
+                        && prefs.getBoolean(JabRefPreferences.LOCAL_AUTO_SAVE)))
                 &&
                 context.getDatabasePath().isPresent();
     }
@@ -240,7 +241,7 @@ private boolean readyForBackup(BibDatabaseContext context) {
     public void saveSelectedAsPlain() {
         getSavePath().ifPresent(path -> {
             try {
-                saveDatabase(path, true, Globals.prefs.getDefaultEncoding(), SavePreferences.DatabaseSaveType.PLAIN_BIBTEX);
+                saveDatabase(path, true, prefs.getDefaultEncoding(), SavePreferences.DatabaseSaveType.PLAIN_BIBTEX);
                 frame.getFileHistory().newFile(path);
                 frame.output(Localization.lang("Saved selected to '%0'.", path.toString()));
             } catch (SaveException ex) {