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

* upstream/master:
  Throw BibEntryNotFound exception in case entry is no longer present  (#4935)
  Improve author parsing (#4931)
  Ui preferences global modifications (#4926)
  Bump checkstyle from 8.19 to 8.20 (#4928)
  Bump mysql-connector-java from 8.0.15 to 8.0.16 (#4924)
  UI Preferences->advanced tab optimization : separators and text modification (#4922)

# Conflicts:
#	src/main/java/org/jabref/gui/search/SearchWorker.java

CHANGELOG.md

@@ -82,6 +82,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where a non-existing aux file in a group made it impossible to open the library. [#4735](https://github.com/JabRef/jabref/issues/4735)
 - We fixed an issue where some journal names were wrongly marked as abbreviated. [#4115](https://github.com/JabRef/jabref/issues/4115)
 - We fixed an issue where the custom file column were sorted incorrectly. https://github.com/JabRef/jabref/issues/3119
+- We improved the parsing of author names whose infix is abbreviated without a dot. [#4864](https://github.com/JabRef/jabref/issues/4864)
 - 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)
@@ -112,6 +113,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where ranking an entry would generate an IllegalArgumentException. [#4754](https://github.com/JabRef/jabref/issues/4754)
 - We fixed an issue where special characters where removed from non label key generation pattern parts [#4767](https://github.com/JabRef/jabref/issues/4767)
 - We fixed an issue where the RIS import would overwite the article date with the value of the acessed date [#4816](https://github.com/JabRef/jabref/issues/4816)
+- We fixed an issue where an NullPointer exception was thrown when a referenced entry in an Open/Libre Office document was no longer present in the library. Now an error message with the reference marker of the missing entry is shown. [#4932](https://github.com/JabRef/jabref/issues/4932)
 
 
 

build.gradle

@@ -115,7 +115,7 @@ dependencies {
     antlr4 'org.antlr:antlr4:4.7.2'
     compile 'org.antlr:antlr4-runtime:4.7.2'
 
-    compile 'mysql:mysql-connector-java:8.0.15'
+    compile 'mysql:mysql-connector-java:8.0.16'
 
     compile 'org.postgresql:postgresql:42.2.5'
 
@@ -173,7 +173,7 @@ dependencies {
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
 
-    checkstyle 'com.puppycrawl.tools:checkstyle:8.19'
+    checkstyle 'com.puppycrawl.tools:checkstyle:8.20'
 }
 
 jacoco {

src/main/java/org/jabref/gui/autocompleter/SuggestionProvider.java

@@ -29,7 +29,6 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
-import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashSet;
 import java.util.List;
@@ -55,7 +54,6 @@ public abstract class SuggestionProvider<T> implements Callback<ISuggestionReque
     /**
      * Create a default suggestion provider based on the toString() method of the generic objects
      * @param possibleSuggestions All possible suggestions
-     * @return
      */
     public static <T> SuggestionProvider<T> create(Collection<T> possibleSuggestions) {
         return create(null, possibleSuggestions);
@@ -67,7 +65,6 @@ public static <T> SuggestionProvider<T> create(Collection<T> possibleSuggestions
      *
      * @param stringConverter A stringConverter which converts generic T into a string
      * @param possibleSuggestions All possible suggestions
-     * @return
      */
     public static <T> SuggestionProvider<T> create(Callback<T, String> stringConverter, Collection<T> possibleSuggestions) {
         SuggestionProviderString<T> suggestionProvider = new SuggestionProviderString<>(stringConverter);
@@ -77,15 +74,13 @@ public static <T> SuggestionProvider<T> create(Callback<T, String> stringConvert
 
     /**
      * Add the given new possible suggestions to this  SuggestionProvider
-     * @param newPossible
      */
     public void addPossibleSuggestions(@SuppressWarnings("unchecked") T... newPossible) {
         addPossibleSuggestions(Arrays.asList(newPossible));
     }
 
     /**
      * Add the given new possible suggestions to this  SuggestionProvider
-     * @param newPossible
      */
     public void addPossibleSuggestions(Collection<T> newPossible) {
         synchronized (possibleSuggestionsLock) {
@@ -113,39 +108,21 @@ public final Collection<T> call(final ISuggestionRequest request) {
                     }
                 }
             }
-            Collections.sort(suggestions, getComparator());
+            suggestions.sort(getComparator());
         }
         return suggestions;
     }
 
-
-    /***************************************************************************
-     *                                                                         *
-     * Static methods                                                          *
-     *                                                                         *
-     **************************************************************************/
-
     /**
      * Get the comparator to order the suggestions
-     * @return
      */
     protected abstract Comparator<T> getComparator();
 
     /**
      * Check the given possible suggestion is a match (is a valid suggestion)
-     * @param suggestion
-     * @param request
-     * @return
      */
     protected abstract boolean isMatch(T suggestion, ISuggestionRequest request);
 
-
-    /***************************************************************************
-     *                                                                         *
-     * Default implementations                                                 *
-     *                                                                         *
-     **************************************************************************/
-
     /**
      * This is a simple string based suggestion provider.
      * All generic suggestions T are turned into strings for processing.
@@ -166,18 +143,14 @@ public int compare(T o1, T o2) {
 
         /**
          * Create a new SuggestionProviderString
-         * @param stringConverter
          */
         public SuggestionProviderString(Callback<T, String> stringConverter) {
             this.stringConverter = stringConverter;
 
             // In case no stringConverter was provided, use the default strategy
             if (this.stringConverter == null) {
-                this.stringConverter = new Callback<T, String>() {
-                    @Override
-                    public String call(T obj) {
-                        return obj != null ? obj.toString() : ""; //$NON-NLS-1$
-                    }
+                this.stringConverter = obj -> {
+                    return obj != null ? obj.toString() : ""; //$NON-NLS-1$
                 };
             }
         }

src/main/java/org/jabref/gui/collab/DatabaseChangeViewModel.java

@@ -31,7 +31,6 @@ public void setAccepted(boolean a) {
         accepted = a;
     }
 
-
     /**
      * This method returns a JComponent detailing the nature of the change.
      * @return JComponent

src/main/java/org/jabref/gui/customentrytypes/FieldSetComponent.java

@@ -324,7 +324,6 @@ private void move(int dy) {
         list.setSelectedIndex(newInd);
     }
 
-
     /**
      * FocusListener to select the first entry in the list of fields when they are focused
      */

src/main/java/org/jabref/gui/journals/ManageJournalAbbreviationsView.java

@@ -188,7 +188,6 @@ private void saveAbbreviationsAndCloseDialog() {
         close();
     }
 
-
     /**
      * This class provides a editable text field that is used as table cell.
      * It handles the editing of the name column.

src/main/java/org/jabref/gui/openoffice/OOBibBase.java

@@ -518,7 +518,8 @@ private List<String> refreshCiteMarkersInternal(List<BibDatabase> databases, OOB
                     } else {
                         LOGGER.info("BibTeX key not found: '" + keys[j] + '\'');
                         LOGGER.info("Problem with reference mark: '" + names.get(i) + '\'');
-                        cEntries[j] = new UndefinedBibtexEntry(keys[j]);
+                        throw new BibEntryNotFoundException(names.get(i), Localization
+                                                                                      .lang("Could not resolve BibTeX entry for citation marker '%0'.", names.get(i)));
                     }
                 }
 

src/main/java/org/jabref/gui/preferences/AdvancedTab.java

@@ -2,6 +2,7 @@
 
 import java.util.Optional;
 
+import javafx.geometry.Pos;
 import javafx.scene.Node;
 import javafx.scene.control.Button;
 import javafx.scene.control.CheckBox;
@@ -11,7 +12,7 @@
 import javafx.scene.layout.GridPane;
 import javafx.scene.layout.HBox;
 import javafx.scene.layout.Pane;
-import javafx.scene.shape.Line;
+import javafx.scene.text.Text;
 
 import org.jabref.Globals;
 import org.jabref.gui.DialogService;
@@ -44,6 +45,7 @@ public AdvancedTab(DialogService dialogService, JabRefPreferences prefs) {
         this.dialogService = dialogService;
         preferences = prefs;
         remotePreferences = prefs.getRemotePreferences();
+        builder.setVgap(7);
 
         useRemoteServer = new CheckBox(Localization.lang("Listen for remote operation on port") + ':');
         useIEEEAbrv = new CheckBox(Localization.lang("Use IEEE LaTeX abbreviations"));
@@ -54,56 +56,34 @@ public AdvancedTab(DialogService dialogService, JabRefPreferences prefs) {
         Label remoteOperation = new Label(Localization.lang("Remote operation"));
         remoteOperation.getStyleClass().add("sectionHeader");
         builder.add(remoteOperation, 2, 1);
-        builder.add(new Separator(), 2, 1);
-        builder.add(new Pane(), 1, 2);
-        Label label1 = new Label(Localization.lang("This feature lets new files be opened or imported into an "
-
-                + "already running instance of JabRef<BR>instead of opening a new instance. For instance, this "
-
-                + "is useful when you open a file in JabRef<br>from your web browser."
-
-                + "<BR>Note that this will prevent you from running more than one instance of JabRef at a time."));
-        label1.setVisible(false);
-        builder.add(label1, 2, 22);
-
-        Label textLabel1 = new Label("    This feature lets new files be opened or imported into an already running instance of JabRef instead of opening a new instance. For");
-        builder.add(textLabel1, 2, 3);
-        Label textLabel2 = new Label("instance, this is useful when you open a file in JabRef from your web browser. ");
-        builder.add(textLabel2, 2, 4);
-        Label textLabel3 = new Label("    Note that this will prevent you from running more than one instance of JabRef at a time.");
-        builder.add(textLabel3, 2, 5);
-        builder.add(new Line(), 2, 6);
-        builder.add(new Pane(), 2, 7);
+        Text textRemote = new Text(Localization.lang("This feature lets new files be opened or imported into an already running instance of JabRef " +
+                "instead of opening a new instance. For instance, this is useful when you open a file in JabRef " +
+                "from your web browser. Note that this will prevent you from running more than one instance of JabRef at a time."));
+        textRemote.setWrappingWidth(600);
+        builder.add(textRemote, 2, 4);
 
         HBox p = new HBox();
-        p.getChildren().add(useRemoteServer);
-        p.getChildren().add(remoteServerPort);
-
+        p.setSpacing(8);
+        p.setAlignment(Pos.CENTER_LEFT);
         ActionFactory factory = new ActionFactory(preferences.getKeyBindingRepository());
         Button help = factory.createIconButton(StandardActions.HELP, new HelpAction(HelpFile.REMOTE));
         help.setMaxWidth(Double.MAX_VALUE);
-        p.getChildren().add(help);
-
-        builder.add(p, 2, 9);
-        builder.add(new Label(""), 1, 10);
+        p.getChildren().setAll(useRemoteServer, remoteServerPort, help);
+        builder.add(p, 2, 6);
 
+        builder.add(new Separator(), 2, 11);
         Label explore = new Label(Localization.lang("Search %0", "IEEEXplore"));
         explore.getStyleClass().add("sectionHeader");
-        builder.add(explore, 2, 11);
-        builder.add(new Separator(), 2, 11);
-        builder.add(new Pane(), 2, 12);
-        builder.add(useIEEEAbrv, 2, 13);
-
-        builder.add(new Line(), 2, 16);
-        builder.add(new Label(""), 1, 17);
+        builder.add(explore, 2, 12);
+        builder.add(useIEEEAbrv, 2, 14);
 
+        builder.add(new Separator(), 2, 19);
         Label importConversions = new Label(Localization.lang("Import conversions"));
         importConversions.getStyleClass().add("sectionHeader");
-        builder.add(importConversions, 2, 18);
+        builder.add(importConversions, 2, 20);
 
-        builder.add(useCaseKeeperOnSearch, 2, 19);
-        builder.add(new Pane(), 2, 20);
-        builder.add(useUnitFormatterOnSearch, 2, 21);
+        builder.add(useCaseKeeperOnSearch, 2, 21);
+        builder.add(useUnitFormatterOnSearch, 2, 23);
 
     }
 

src/main/java/org/jabref/gui/preferences/AppearancePrefsTab.java

@@ -1,15 +1,15 @@
 package org.jabref.gui.preferences;
 
-import javafx.geometry.Insets;
+import javafx.geometry.Pos;
 import javafx.scene.Node;
 import javafx.scene.control.CheckBox;
 import javafx.scene.control.Label;
 import javafx.scene.control.RadioButton;
 import javafx.scene.control.TextField;
 import javafx.scene.control.ToggleGroup;
+import javafx.scene.layout.GridPane;
 import javafx.scene.layout.HBox;
 import javafx.scene.layout.Pane;
-import javafx.scene.layout.VBox;
 
 import org.jabref.gui.DialogService;
 import org.jabref.gui.util.ControlHelper;
@@ -24,10 +24,10 @@ class AppearancePrefsTab extends Pane implements PrefsTab {
     private final CheckBox fontTweaksLAF;
     private final TextField fontSize;
     private final CheckBox overrideFonts;
-    private final VBox container = new VBox();
     private final DialogService dialogService;
     private final RadioButton lightTheme;
     private final RadioButton darkTheme;
+    private final GridPane builder = new GridPane();
 
     /**
      * Customization of appearance parameters.
@@ -37,14 +37,12 @@ class AppearancePrefsTab extends Pane implements PrefsTab {
     public AppearancePrefsTab(DialogService dialogService, JabRefPreferences prefs) {
         this.dialogService = dialogService;
         this.prefs = prefs;
+        builder.setVgap(8);
 
         overrideFonts = new CheckBox(Localization.lang("Override default font settings"));
         fontSize = new TextField();
         fontSize.setTextFormatter(ControlHelper.getIntegerTextFormatter());
         Label fontSizeLabel = new Label(Localization.lang("Font size:"));
-        HBox fontSizeContainer = new HBox(fontSizeLabel, fontSize);
-        VBox.setMargin(fontSizeContainer, new Insets(0, 0, 0, 35));
-        fontSizeContainer.disableProperty().bind(overrideFonts.selectedProperty().not());
         fontTweaksLAF = new CheckBox(Localization.lang("Tweak font rendering for entry editor on Linux"));
 
         ToggleGroup themeGroup = new ToggleGroup();
@@ -60,12 +58,24 @@ public AppearancePrefsTab(DialogService dialogService, JabRefPreferences prefs)
             darkTheme.setSelected(true);
         }
 
-        container.getChildren().addAll(overrideFonts, fontSizeContainer, fontTweaksLAF, lightTheme, darkTheme);
+        // Font configuration
+        HBox fontBox = new HBox();
+        fontBox.setSpacing(10);
+        fontBox.setAlignment(Pos.CENTER_LEFT);
+        fontBox.getChildren().setAll(overrideFonts, fontSizeLabel, fontSize);
+        builder.add(fontBox, 1, 2);
+
+        // Theme configuration
+        HBox themeBox = new HBox();
+        themeBox.setSpacing(10);
+        themeBox.setAlignment(Pos.CENTER_LEFT);
+        themeBox.getChildren().setAll(lightTheme, darkTheme);
+        builder.add(themeBox, 1, 4);
     }
 
     @Override
     public Node getBuilder() {
-        return container;
+        return builder;
     }
 
     @Override