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

* upstream/master:
  Fix error when path is no valid directory (#2527)
  French localization: translation of a string
  French menu: localization
  Highlight groups that match any/all of the entries selected in the main table. (#2515)
  Fix % sign cleanup (#2521)
  Revert "Fix repeated escaping of % sign" (#2520)
  Fix repeated escaping of % sign (#2519)
  fix for #2482 deadlock on PDF import (#2517)

CHANGELOG.md

@@ -15,6 +15,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - Add tab which shows the MathSciNet review website if the `MRNumber` field is present.
 - Partly switched to new UI technology (JavaFX).
     - Redesigned group panel.
+      - Number of matched entries is always shown.
+      - The background color of the hit counter signals whether the group contains all/any of the entries selected in the main table. 
     - Redesigned about dialog.
     - Redesigned key bindings dialog.
     - Redesigned journal abbreviations dialog.
@@ -27,6 +29,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
  - Fix import of journal title in ris format. [#2506](https://github.com/JabRef/jabref/issues/2506)
  - We fixed the export of the `number` field in MS-Office XML export. [#2509](https://github.com/JabRef/jabref/issues/2509)
  - The field `issue` is now always exported to the corresponding `issue` field in MS-Office XML.
+ - We fixed an issue with repeated escaping of the %-sign when running the LaTeXCleanup more than once. [#2451](https://github.com/JabRef/jabref/issues/2451)
 ### Removed
 
 

src/main/java/net/sf/jabref/gui/FileDialog.java

@@ -2,6 +2,7 @@
 
 import java.awt.Component;
 import java.io.File;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.Collection;
@@ -59,7 +60,10 @@ public FileDialog(Component parent, String dir) {
 
     public FileDialog(Component parent, Path dir) {
         Objects.requireNonNull(dir, "Directory must not be null");
-
+        //Dir must be a folder, not a file
+        if (!Files.isDirectory(dir)) {
+            dir = dir.getParent();
+        }
         fileChooser = new FileChooser();
         configurationBuilder = new FileDialogConfiguration.Builder();
         configurationBuilder = configurationBuilder.withInitialDirectory(dir);
@@ -137,6 +141,7 @@ public Optional<Path> showDialogAndGetSelectedDirectory() {
 
         return runInJavaFXThread(() -> Optional.ofNullable(directoryChooser.showDialog(null)).map(File::toPath));
     }
+
     /**
      * Shows an {@link JFileChooser#OPEN_DIALOG} and allows to select multiple files
      * @return List containing the paths of all files or an empty list if dialog is canceled

src/main/java/net/sf/jabref/gui/StateManager.java

@@ -1,11 +1,15 @@
 package net.sf.jabref.gui;
 
+import java.util.List;
 import java.util.Optional;
 
 import javafx.beans.property.ObjectProperty;
 import javafx.beans.property.SimpleObjectProperty;
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
 
 import net.sf.jabref.model.database.BibDatabaseContext;
+import net.sf.jabref.model.entry.BibEntry;
 import net.sf.jabref.model.groups.GroupTreeNode;
 
 /**
@@ -20,6 +24,7 @@ public class StateManager {
 
     private final ObjectProperty<Optional<BibDatabaseContext>> activeDatabase = new SimpleObjectProperty<>(Optional.empty());
     private final ObjectProperty<Optional<GroupTreeNode>> activeGroup = new SimpleObjectProperty<>(Optional.empty());
+    private final ObservableList<BibEntry> selectedEntries = FXCollections.observableArrayList();
 
     public ObjectProperty<Optional<BibDatabaseContext>> activeDatabaseProperty() {
         return activeDatabase;
@@ -28,4 +33,13 @@ public ObjectProperty<Optional<BibDatabaseContext>> activeDatabaseProperty() {
     public ObjectProperty<Optional<GroupTreeNode>> activeGroupProperty() {
         return activeGroup;
     }
+
+    public ObservableList<BibEntry> getSelectedEntries() {
+        return FXCollections.unmodifiableObservableList(selectedEntries);
+    }
+
+    public void setSelectedEntries(List<BibEntry> newSelectedEntries) {
+        selectedEntries.clear();
+        selectedEntries.addAll(newSelectedEntries);
+    }
 }

src/main/java/net/sf/jabref/gui/actions/Actions.java

@@ -60,9 +60,6 @@ public class Actions {
     public static final String GLOBAL_SEARCH = "globalSearch";
     public static final String SELECT_ALL = "selectAll";
     public static final String SEND_AS_EMAIL = "sendAsEmail";
-    public static final String TOGGLE_HIGHLIGHTS_GROUPS_MATCHING_ALL = "toggleHighlightGroupsMatchingAll";
-    public static final String TOGGLE_HIGHLIGHTS_GROUPS_MATCHING_ANY = "toggleHighlightGroupsMatchingAny";
-    public static final String TOGGLE_HIGHLIGHTS_GROUPS_MATCHING_DISABLE = "toggleHighlightGroupsMatchingDisable";
     public static final String TOGGLE_GROUPS = "toggleGroups";
     public static final String TOGGLE_PREVIEW = "togglePreview";
     public static final String UNABBREVIATE = "unabbreviate";

src/main/java/net/sf/jabref/gui/groups/GroupNodeViewModel.java

@@ -4,10 +4,13 @@
 
 import javafx.application.Platform;
 import javafx.beans.binding.Bindings;
+import javafx.beans.binding.BooleanBinding;
 import javafx.beans.property.SimpleBooleanProperty;
 import javafx.beans.property.SimpleIntegerProperty;
 import javafx.collections.ObservableList;
 
+import net.sf.jabref.gui.StateManager;
+import net.sf.jabref.gui.util.BindingsHelper;
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.model.database.BibDatabaseContext;
 import net.sf.jabref.model.entry.event.EntryEvent;
@@ -28,31 +31,44 @@ public class GroupNodeViewModel {
     private final GroupTreeNode groupNode;
     private final SimpleIntegerProperty hits;
     private final SimpleBooleanProperty hasChildren;
+    private final BooleanBinding anySelectedEntriesMatched;
+    private final BooleanBinding allSelectedEntriesMatched;
 
-    public GroupNodeViewModel(BibDatabaseContext databaseContext, GroupTreeNode groupNode) {
+    public GroupNodeViewModel(BibDatabaseContext databaseContext, StateManager stateManager, GroupTreeNode groupNode) {
         this.databaseContext = Objects.requireNonNull(databaseContext);
         this.groupNode = Objects.requireNonNull(groupNode);
 
         name = groupNode.getName();
         isRoot = groupNode.isRoot();
         iconCode = "";
-        children = EasyBind.map(groupNode.getChildren(), child -> new GroupNodeViewModel(databaseContext, child));
+        children = EasyBind.map(groupNode.getChildren(), child -> new GroupNodeViewModel(databaseContext, stateManager, child));
         hasChildren = new SimpleBooleanProperty();
         hasChildren.bind(Bindings.isNotEmpty(children));
         hits = new SimpleIntegerProperty(0);
         calculateNumberOfMatches();
 
         // Register listener
         databaseContext.getDatabase().registerListener(this);
+
+        ObservableList<Boolean> selectedEntriesMatchStatus = EasyBind.map(stateManager.getSelectedEntries(), groupNode::matches);
+        anySelectedEntriesMatched = BindingsHelper.any(selectedEntriesMatchStatus, matched -> matched);
+        allSelectedEntriesMatched = BindingsHelper.all(selectedEntriesMatchStatus, matched -> matched);
+    }
+
+    public GroupNodeViewModel(BibDatabaseContext databaseContext, StateManager stateManager, AbstractGroup group) {
+        this(databaseContext, stateManager, new GroupTreeNode(group));
     }
 
+    static GroupNodeViewModel getAllEntriesGroup(BibDatabaseContext newDatabase, StateManager stateManager) {
+        return new GroupNodeViewModel(newDatabase, stateManager, new AllEntriesGroup(Localization.lang("All entries")));
+    }
 
-    public GroupNodeViewModel(BibDatabaseContext databaseContext, AbstractGroup group) {
-        this(databaseContext, new GroupTreeNode(group));
+    public BooleanBinding anySelectedEntriesMatchedProperty() {
+        return anySelectedEntriesMatched;
     }
 
-    static GroupNodeViewModel getAllEntriesGroup(BibDatabaseContext newDatabase) {
-        return new GroupNodeViewModel(newDatabase, new AllEntriesGroup(Localization.lang("All entries")));
+    public BooleanBinding allSelectedEntriesMatchedProperty() {
+        return allSelectedEntriesMatched;
     }
 
     public SimpleBooleanProperty hasChildrenProperty() {

src/main/java/net/sf/jabref/gui/groups/GroupTree.css

@@ -21,6 +21,14 @@
     -fx-background-radius: 10px;
 }
 
+.numberColumn > .hits:any-selected {
+    -fx-background-color: #c6c44f;
+}
+
+.numberColumn > .hits:all-selected {
+    -fx-background-color: #4dc64f;
+}
+
 .disclosureNodeColumn {
     -fx-alignment: top-right;
     -fx-font-size: 12px;

src/main/java/net/sf/jabref/gui/groups/GroupTreeController.java

@@ -19,6 +19,7 @@
 import net.sf.jabref.gui.AbstractController;
 import net.sf.jabref.gui.DialogService;
 import net.sf.jabref.gui.StateManager;
+import net.sf.jabref.gui.util.BindingsHelper;
 import net.sf.jabref.gui.util.RecursiveTreeItem;
 import net.sf.jabref.gui.util.ViewModelTreeTableCellFactory;
 import net.sf.jabref.logic.l10n.Localization;
@@ -59,10 +60,16 @@ public void initialize() {
         );
 
         // Number of hits
+        PseudoClass anySelected = PseudoClass.getPseudoClass("any-selected");
+        PseudoClass allSelected = PseudoClass.getPseudoClass("all-selected");
         numberColumn.setCellFactory(new ViewModelTreeTableCellFactory<GroupNodeViewModel, GroupNodeViewModel>()
                 .withGraphic(viewModel -> {
                     final StackPane node = new StackPane();
                     node.getStyleClass().setAll("hits");
+                    if (!viewModel.isRoot()) {
+                        BindingsHelper.includePseudoClassWhen(node, anySelected, viewModel.anySelectedEntriesMatchedProperty());
+                        BindingsHelper.includePseudoClassWhen(node, allSelected, viewModel.allSelectedEntriesMatchedProperty());
+                    }
                     Text text = new Text();
                     text.textProperty().bind(viewModel.getHits().asString());
                     text.getStyleClass().setAll("text");

src/main/java/net/sf/jabref/gui/groups/GroupTreeViewModel.java

@@ -63,8 +63,8 @@ private void onActiveDatabaseChanged(Optional<BibDatabaseContext> newDatabase) {
             GroupNodeViewModel newRoot = newDatabase
                     .map(BibDatabaseContext::getMetaData)
                     .flatMap(MetaData::getGroups)
-                    .map(root -> new GroupNodeViewModel(newDatabase.get(), root))
-                    .orElse(GroupNodeViewModel.getAllEntriesGroup(newDatabase.get()));
+                    .map(root -> new GroupNodeViewModel(newDatabase.get(), stateManager, root))
+                    .orElse(GroupNodeViewModel.getAllEntriesGroup(newDatabase.get(), stateManager));
             rootGroup.setValue(newRoot);
         }
     }

src/main/java/net/sf/jabref/gui/util/BindingsHelper.java

@@ -0,0 +1,47 @@
+package net.sf.jabref.gui.util;
+
+import java.util.function.Predicate;
+
+import javafx.beans.binding.Bindings;
+import javafx.beans.binding.BooleanBinding;
+import javafx.beans.property.BooleanProperty;
+import javafx.beans.property.BooleanPropertyBase;
+import javafx.beans.value.ObservableValue;
+import javafx.collections.ObservableList;
+import javafx.css.PseudoClass;
+import javafx.scene.Node;
+
+/**
+ * Helper methods for javafx binding.
+ * Some methods are taken from https://bugs.openjdk.java.net/browse/JDK-8134679
+ */
+public class BindingsHelper {
+    public static <T> BooleanBinding any(ObservableList<T> source, Predicate<T> predicate) {
+        return Bindings.createBooleanBinding(() -> source.stream().anyMatch(predicate), source);
+    }
+
+    public static <T> BooleanBinding all(ObservableList<T> source, Predicate<T> predicate) {
+        // Stream.allMatch() (in contrast to Stream.anyMatch() returns 'true' for empty streams, so this has to be checked explicitly.
+        return Bindings.createBooleanBinding(() -> !source.isEmpty() && source.stream().allMatch(predicate), source);
+    }
+
+    public static void includePseudoClassWhen(Node node, PseudoClass pseudoClass, ObservableValue<? extends Boolean> condition) {
+        BooleanProperty pseudoClassState = new BooleanPropertyBase(false) {
+            @Override
+            protected void invalidated() {
+                node.pseudoClassStateChanged(pseudoClass, get());
+            }
+
+            @Override
+            public Object getBean() {
+                return node;
+            }
+
+            @Override
+            public String getName() {
+                return pseudoClass.getPseudoClassName();
+            }
+        };
+        pseudoClassState.bind(condition);
+    }
+}

src/main/java/net/sf/jabref/logic/formatter/bibtexfields/LatexCleanupFormatter.java

@@ -1,10 +1,21 @@
 package net.sf.jabref.logic.formatter.bibtexfields;
 
+import java.util.regex.Pattern;
+
 import net.sf.jabref.logic.l10n.Localization;
 import net.sf.jabref.model.cleanup.Formatter;
 
 public class LatexCleanupFormatter implements Formatter {
 
+    private static final Pattern REMOVE_REDUNDANT = Pattern
+            .compile("(?<!\\\\[\\p{Alpha}]{0,100}\\{[^\\}]{0,100})\\}([-/ ]?)\\{");
+
+    private static final Pattern REPLACE_WITH_AT = Pattern.compile("(^|[^\\\\$])\\$");
+    private static final Pattern REPLACE_EVERY_OTHER_AT = Pattern.compile("([^@]*)@@([^@]*)@@");
+    private static final Pattern MOVE_NUMBERS_WITH_OPERATORS = Pattern.compile("([0-9\\(\\.]+[ ]?[-+/]?[ ]?)\\$");
+    private static final Pattern MOVE_NUMBERS_RIGHT_INTO_EQUATION = Pattern.compile("@@([ ]?[-+/]?[ ]?[0-9\\)\\.]+)");
+    private static final Pattern ESCAPE_PERCENT_SIGN_ONCE = Pattern.compile("(^|[^\\\\%])%");
+
     @Override
     public String getName() {
         return Localization.lang("LaTeX cleanup");
@@ -20,19 +31,25 @@ public String format(String oldString) {
         String newValue = oldString;
 
         // Remove redundant $, {, and }, but not if the } is part of a command argument: \mbox{-}{GPS} should not be adjusted
-        newValue = newValue.replace("$$", "").replaceAll("(?<!\\\\[\\p{Alpha}]{0,100}\\{[^\\}]{0,100})\\}([-/ ]?)\\{",
-                "$1");
+        newValue = newValue.replace("$$", "");
+        newValue = REMOVE_REDUNDANT.matcher(newValue).replaceAll("$1");
+
         // Move numbers, +, -, /, and brackets into equations
-        newValue = newValue.replaceAll("(([^$]|\\\\\\$)*)\\$", "$1@@"); // Replace $, but not \$ with @@
-        newValue = newValue.replaceAll("([^@]*)@@([^@]*)@@", "$1\\$$2@@"); // Replace every other @@ with $
+        newValue = REPLACE_WITH_AT.matcher(newValue).replaceAll("$1@@"); // Replace $, but not \$ with @@
+
+        newValue = REPLACE_EVERY_OTHER_AT.matcher(newValue).replaceAll("$1\\$$2@@"); // Replace every other @@ with $
         //newValue = newValue.replaceAll("([0-9\\(\\.]+) \\$","\\$$1\\\\ "); // Move numbers followed by a space left of $ inside the equation, e.g., 0.35 $\mu$m
-        newValue = newValue.replaceAll("([0-9\\(\\.]+[ ]?[-+/]?[ ]?)\\$", "\\$$1"); // Move numbers, possibly with operators +, -, or /,  left of $ into the equation
-        newValue = newValue.replaceAll("@@([ ]?[-+/]?[ ]?[0-9\\)\\.]+)", " $1@@"); // Move numbers right of @@ into the equation
+
+        newValue = MOVE_NUMBERS_WITH_OPERATORS.matcher(newValue).replaceAll("\\$$1"); // Move numbers, possibly with operators +, -, or /,  left of $ into the equation
+        newValue = MOVE_NUMBERS_RIGHT_INTO_EQUATION.matcher(newValue).replaceAll(" $1@@"); // Move numbers right of @@ into the equation
+
         newValue = newValue.replace("@@", "$"); // Replace all @@ with $
         newValue = newValue.replace("  ", " "); // Clean up
         newValue = newValue.replace("$$", "");
         newValue = newValue.replace(" )$", ")$");
-        newValue = newValue.replace("%", "\\%"); // escape % used for comments in TeX
+
+        newValue = ESCAPE_PERCENT_SIGN_ONCE.matcher(newValue).replaceAll("$1\\\\%"); // escape %, but do not escapee \% again,  used for comments in TeX
+
         return newValue;
     }
 

src/main/java/net/sf/jabref/model/groups/GroupTreeNode.java

@@ -216,4 +216,12 @@ public int calculateNumberOfMatches(List<BibEntry> entries) {
     public int calculateNumberOfMatches(BibDatabase database) {
         return calculateNumberOfMatches(database.getEntries());
     }
+
+    /**
+     * Returns whether this group matches the specified {@link BibEntry} while taking the hierarchical information
+     * into account.
+     */
+    public boolean matches(BibEntry entry) {
+        return getSearchMatcher().isMatch(entry);
+    }
 }

src/main/java/net/sf/jabref/pdfimport/PdfImporter.java

@@ -240,7 +240,9 @@ private void doContentImport(String fileName, List<BibEntry> res) {
                 Globals.prefs.getBibtexKeyPatternPreferences());
         DroppedFileHandler dfh = new DroppedFileHandler(frame, panel);
         dfh.linkPdfToEntry(fileName, entry);
-        panel.highlightEntry(entry);
+
+        SwingUtilities.invokeLater(() -> panel.highlightEntry(entry));
+
         if (Globals.prefs.getBoolean(JabRefPreferences.AUTO_OPEN_FORM)) {
             EntryEditor editor = panel.getEntryEditor(entry);
             panel.showEntryEditor(editor);