Updates to colored group indicator for cited entries

CHANGELOG.md

@@ -94,6 +94,7 @@ 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 groups created from aux files did not update on file changes [#6394](https://github.com/JabRef/jabref/issues/6394)
 - 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)
 

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

@@ -24,21 +24,22 @@ public GroupChangeViewModel(GroupDiff diff) {
 
     @Override
     public void makeChange(BibDatabaseContext database, NamedCompound undoEdit) {
-        GroupTreeNode root = database.getMetaData().getGroups().orElse(null);
-        if (root == null) {
-            root = new GroupTreeNode(DefaultGroupsFactory.getAllEntriesGroup());
-            database.getMetaData().setGroups(root);
-        }
+        GroupTreeNode root = database.getMetaData().getGroups().orElseGet(() -> {
+            GroupTreeNode groupTreeNode = new GroupTreeNode(DefaultGroupsFactory.getAllEntriesGroup());
+            database.getMetaData().setGroups(groupTreeNode);
+            return groupTreeNode;
+        });
+
         final UndoableModifySubtree undo = new UndoableModifySubtree(
                 new GroupTreeNodeViewModel(database.getMetaData().getGroups().orElse(null)),
                 new GroupTreeNodeViewModel(root), Localization.lang("Modified groups"));
         root.removeAllChildren();
         if (changedGroups == null) {
             // I think setting root to null is not possible
-            root.setGroup(DefaultGroupsFactory.getAllEntriesGroup());
+            root.setGroup(DefaultGroupsFactory.getAllEntriesGroup(), false, false, null);
         } else {
             // change root group, even though it'll be AllEntries anyway
-            root.setGroup(changedGroups.getGroup());
+            root.setGroup(changedGroups.getGroup(), false, false, null);
             for (GroupTreeNode child : changedGroups.getChildren()) {
                 child.copySubtree().moveTo(root);
             }

src/main/java/org/jabref/gui/groups/GroupNodeViewModel.java

@@ -6,6 +6,8 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import javafx.beans.InvalidationListener;
+import javafx.beans.WeakInvalidationListener;
 import javafx.beans.binding.Bindings;
 import javafx.beans.binding.BooleanBinding;
 import javafx.beans.binding.IntegerBinding;
@@ -23,6 +25,7 @@
 import org.jabref.gui.icon.JabRefIcon;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.CustomLocalDragboard;
+import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.DroppingMouseLocation;
 import org.jabref.gui.util.TaskExecutor;
 import org.jabref.logic.groups.DefaultGroupsFactory;
@@ -34,6 +37,7 @@
 import org.jabref.model.groups.AutomaticGroup;
 import org.jabref.model.groups.GroupEntryChanger;
 import org.jabref.model.groups.GroupTreeNode;
+import org.jabref.model.groups.TexGroup;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.preferences.PreferencesService;
 
@@ -59,6 +63,7 @@ public class GroupNodeViewModel {
     private final CustomLocalDragboard localDragBoard;
     private final ObservableList<BibEntry> entriesList;
     private final PreferencesService preferencesService;
+    private final InvalidationListener onInvalidatedGroup = (listener) -> refreshGroup();
 
     public GroupNodeViewModel(BibDatabaseContext databaseContext, StateManager stateManager, TaskExecutor taskExecutor, GroupTreeNode groupNode, CustomLocalDragboard localDragBoard, PreferencesService preferencesService) {
         this.databaseContext = Objects.requireNonNull(databaseContext);
@@ -81,6 +86,9 @@ public GroupNodeViewModel(BibDatabaseContext databaseContext, StateManager state
         } else {
             children = EasyBind.mapBacked(groupNode.getChildren(), this::toViewModel);
         }
+        if (groupNode.getGroup() instanceof TexGroup) {
+            databaseContext.getMetaData().groupsBinding().addListener(new WeakInvalidationListener(onInvalidatedGroup));
+        }
         hasChildren = new SimpleBooleanProperty();
         hasChildren.bind(Bindings.isNotEmpty(children));
         updateMatchedEntries();
@@ -250,6 +258,17 @@ private void onDatabaseChanged(ListChangeListener.Change<? extends BibEntry> cha
         }
     }
 
+    private void refreshGroup() {
+        DefaultTaskExecutor.runInJavaFXThread(() -> {
+            updateMatchedEntries(); // Update the entries matched by the group
+            // "Re-add" to the selected groups if it were selected, this refreshes the entries the user views
+            ObservableList<GroupTreeNode> selectedGroups = this.stateManager.getSelectedGroup(this.databaseContext);
+            if (selectedGroups.remove(this.groupNode)) {
+                selectedGroups.add(this.groupNode);
+            }
+        });
+    }
+
     private void updateMatchedEntries() {
         // We calculate the new hit value
         // We could be more intelligent and try to figure out the new number of hits based on the entry change
@@ -290,10 +309,11 @@ public Optional<GroupNodeViewModel> getChildByPath(String pathToSource) {
     }
 
     /**
-     * Decides if the content stored in the given {@link Dragboard} can be droped on the given target row.
-     * Currently, the following sources are allowed:
-     *  - another group (will be added as subgroup on drop)
-     *  - entries if the group implements {@link GroupEntryChanger} (will be assigned to group on drop)
+     * Decides if the content stored in the given {@link Dragboard} can be dropped on the given target row. Currently, the following sources are allowed:
+     * <ul>
+     *     <li>another group (will be added as subgroup on drop)</li>
+     *     <li>entries if the group implements {@link GroupEntryChanger} (will be assigned to group on drop)</li>
+     * </ul>
      */
     public boolean acceptableDrop(Dragboard dragboard) {
         // TODO: we should also check isNodeDescendant
@@ -343,15 +363,9 @@ public void draggedOn(GroupNodeViewModel target, DroppingMouseLocation mouseLoca
             // Bottom + top -> insert source row before / after this row
             // Center -> add as child
             switch (mouseLocation) {
-                case BOTTOM:
-                    this.moveTo(targetParent.get(), targetIndex + 1);
-                    break;
-                case CENTER:
-                    this.moveTo(target);
-                    break;
-                case TOP:
-                    this.moveTo(targetParent.get(), targetIndex);
-                    break;
+                case BOTTOM -> this.moveTo(targetParent.get(), targetIndex + 1);
+                case CENTER -> this.moveTo(target);
+                case TOP -> this.moveTo(targetParent.get(), targetIndex);
             }
         } else {
             // No parent = root -> just add

src/main/java/org/jabref/gui/maintable/BibEntryTableViewModel.java

@@ -6,14 +6,16 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
+import java.util.function.Predicate;
 import java.util.stream.Collectors;
 
 import javafx.beans.Observable;
+import javafx.beans.binding.Binding;
 import javafx.beans.binding.Bindings;
-import javafx.beans.property.SimpleObjectProperty;
 import javafx.beans.value.ObservableValue;
 
 import org.jabref.gui.specialfields.SpecialFieldValueViewModel;
+import org.jabref.gui.util.uithreadaware.UiThreadBinding;
 import org.jabref.logic.importer.util.FileFieldParser;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -36,7 +38,7 @@ public class BibEntryTableViewModel {
     private final Map<SpecialField, OptionalBinding<SpecialFieldValueViewModel>> specialFieldValues = new HashMap<>();
     private final EasyBinding<List<LinkedFile>> linkedFiles;
     private final EasyBinding<Map<Field, String>> linkedIdentifiers;
-    private final ObservableValue<List<AbstractGroup>> matchedGroups;
+    private final Binding<List<AbstractGroup>> matchedGroups;
 
     public BibEntryTableViewModel(BibEntry entry, BibDatabaseContext bibDatabaseContext, ObservableValue<MainTableFieldValueFormatter> fieldValueFormatter) {
         this.entry = entry;
@@ -67,19 +69,15 @@ public BibEntry getEntry() {
         return entry;
     }
 
-    private static ObservableValue<List<AbstractGroup>> createMatchedGroupsBinding(BibDatabaseContext database, BibEntry entry) {
-        Optional<GroupTreeNode> root = database.getMetaData().getGroups();
-        if (root.isPresent()) {
-            return EasyBind.map(entry.getFieldBinding(StandardField.GROUPS), field -> {
-                List<AbstractGroup> groups = root.get().getMatchingGroups(entry)
-                                                 .stream()
-                                                 .map(GroupTreeNode::getGroup)
-                                                 .collect(Collectors.toList());
-                groups.remove(root.get().getGroup());
-                return groups;
-            });
-        }
-        return new SimpleObjectProperty<>(Collections.emptyList());
+    private static Binding<List<AbstractGroup>> createMatchedGroupsBinding(BibDatabaseContext database, BibEntry entry) {
+        return new UiThreadBinding<>(EasyBind.combine(entry.getFieldBinding(StandardField.GROUPS), database.getMetaData().groupsBinding(),
+                (a, b) ->
+                        database.getMetaData().getGroups().map(groupTreeNode ->
+                                groupTreeNode.getMatchingGroups(entry).stream()
+                                             .map(GroupTreeNode::getGroup)
+                                             .filter(Predicate.not(Predicate.isEqual(groupTreeNode.getGroup())))
+                                             .collect(Collectors.toList()))
+                                .orElse(Collections.emptyList())));
     }
 
     public OptionalBinding<String> getField(Field field) {
@@ -119,7 +117,7 @@ public ObservableValue<String> getFields(OrFields fields) {
         observables.add(fieldValueFormatter);
 
         value = Bindings.createStringBinding(() ->
-                fieldValueFormatter.getValue().formatFieldsValues(fields, entry),
+                        fieldValueFormatter.getValue().formatFieldsValues(fields, entry),
                 observables.toArray(Observable[]::new));
         fieldValues.put(fields, value);
         return value;

src/main/java/org/jabref/gui/preview/CopyCitationAction.java

@@ -31,8 +31,7 @@
 import org.slf4j.LoggerFactory;
 
 /**
- * Copies the selected entries and formats them with the selected citation style (or preview), then it is copied to the clipboard.
- * This worker cannot be reused.
+ * Copies the selected entries and formats them with the selected citation style (or preview), then it is copied to the clipboard. This worker cannot be reused.
  */
 public class CopyCitationAction extends SimpleCommand {
 
@@ -93,8 +92,7 @@ private List<String> generateCitations() throws IOException {
     }
 
     /**
-     * Generates a plain text string out of the preview and copies it additionally to the html to the clipboard
-     * (WYSIWYG Editors use the HTML, plain text editors the text)
+     * Generates a plain text string out of the preview and copies it additionally to the html to the clipboard (WYSIWYG Editors use the HTML, plain text editors the text)
      */
     protected static ClipboardContent processPreview(List<String> citations) {
         ClipboardContent content = new ClipboardContent();
@@ -182,23 +180,14 @@ private void setClipBoardContent(List<String> citations) {
             // if it's generated by a citation style take care of each output format
             ClipboardContent content;
             switch (outputFormat) {
-                case HTML:
-                    content = processHtml(citations);
-                    break;
-                case RTF:
-                    content = processRtf(citations);
-                    break;
-                case XSL_FO:
-                    content = processXslFo(citations);
-                    break;
-                case ASCII_DOC:
-                case TEXT:
-                    content = processText(citations);
-                    break;
-                default:
+                case HTML -> content = processHtml(citations);
+                case RTF -> content = processRtf(citations);
+                case XSL_FO -> content = processXslFo(citations);
+                case ASCII_DOC, TEXT -> content = processText(citations);
+                default -> {
                     LOGGER.warn("unknown output format: '" + outputFormat + "', processing it via the default.");
                     content = processText(citations);
-                    break;
+                }
             }
             clipBoardManager.setContent(content);
         }

src/main/java/org/jabref/gui/util/BindingsHelper.java

@@ -25,8 +25,7 @@
 import com.tobiasdiez.easybind.Subscription;
 
 /**
- * Helper methods for javafx binding.
- * Some methods are taken from https://bugs.openjdk.java.net/browse/JDK-8134679
+ * Helper methods for javafx binding. Some methods are taken from https://bugs.openjdk.java.net/browse/JDK-8134679
  */
 public class BindingsHelper {
 
@@ -43,7 +42,7 @@ public static Subscription includePseudoClassWhen(Node node, PseudoClass pseudoC
     }
 
     public static <T, U> ObservableList<U> map(ObservableValue<T> source, Function<T, List<U>> mapper) {
-        PreboundBinding<List<U>> binding = new PreboundBinding<List<U>>(source) {
+        PreboundBinding<List<U>> binding = new PreboundBinding<>(source) {
 
             @Override
             protected List<U> computeValue() {
@@ -57,7 +56,7 @@ protected List<U> computeValue() {
     }
 
     /**
-     * Binds propertA bidirectional to propertyB using the provided map functions to convert between them.
+     * Binds propertyA bidirectional to propertyB using the provided map functions to convert between them.
      */
     public static <A, B> void bindBidirectional(Property<A> propertyA, Property<B> propertyB, Function<A, B> mapAtoB, Function<B, A> mapBtoA) {
         Consumer<B> updateA = newValueB -> propertyA.setValue(mapBtoA.apply(newValueB));
@@ -66,15 +65,14 @@ public static <A, B> void bindBidirectional(Property<A> propertyA, Property<B> p
     }
 
     /**
-     * Binds propertA bidirectional to propertyB while using updateB to update propertyB when propertyA changed.
+     * Binds propertyA bidirectional to propertyB while using updateB to update propertyB when propertyA changed.
      */
     public static <A> void bindBidirectional(Property<A> propertyA, ObservableValue<A> propertyB, Consumer<A> updateB) {
         bindBidirectional(propertyA, propertyB, propertyA::setValue, updateB);
     }
 
     /**
-     * Binds propertA bidirectional to propertyB using updateB to update propertyB when propertyA changed and similar
-     * for updateA.
+     * Binds propertyA bidirectional to propertyB using updateB to update propertyB when propertyA changed and similar for updateA.
      */
     public static <A, B> void bindBidirectional(ObservableValue<A> propertyA, ObservableValue<B> propertyB, Consumer<B> updateA, Consumer<A> updateB) {
         final BidirectionalBinding<A, B> binding = new BidirectionalBinding<>(propertyA, propertyB, updateA, updateB);
@@ -135,7 +133,7 @@ public static <A, V, B> void bindContentBidirectional(ObservableMap<A, V> proper
     }
 
     public static <T> ObservableValue<T> constantOf(T value) {
-        return new ObjectBinding<T>() {
+        return new ObjectBinding<>() {
 
             @Override
             protected T computeValue() {

src/main/java/org/jabref/gui/util/uithreadaware/UiThreadBinding.java

@@ -0,0 +1,63 @@
+package org.jabref.gui.util.uithreadaware;
+
+import javafx.beans.InvalidationListener;
+import javafx.beans.binding.Binding;
+import javafx.beans.value.ChangeListener;
+import javafx.collections.ObservableList;
+
+/**
+ * This class can be used to wrap a {@link Binding} inside it. When wrapped, any Listener listening for updates to the wrapped {@link Binding} (for example because of a binding to it) is ensured to be notified on the JavaFX Application Thread. It should be used to implement bindings where updates come in from a background thread but should be reflected in the UI where it is necessary that changes to the UI are performed on the JavaFX Application thread.
+ */
+public class UiThreadBinding<T> implements Binding<T> {
+
+    private final Binding<T> delegate;
+
+    public UiThreadBinding(Binding<T> delegate) {
+        this.delegate = delegate;
+    }
+
+    @Override
+    public void addListener(InvalidationListener listener) {
+        delegate.addListener(new UiThreadInvalidationListener(listener));
+    }
+
+    @Override
+    public void removeListener(InvalidationListener listener) {
+        delegate.removeListener(listener);
+    }
+
+    @Override
+    public void addListener(ChangeListener<? super T> listener) {
+        delegate.addListener(new UiThreadChangeListener<>(listener));
+    }
+
+    @Override
+    public void removeListener(ChangeListener<? super T> listener) {
+        delegate.removeListener(listener);
+    }
+
+    @Override
+    public T getValue() {
+        return delegate.getValue();
+    }
+
+    @Override
+    public boolean isValid() {
+        return delegate.isValid();
+    }
+
+    @Override
+    public void invalidate() {
+        delegate.invalidate();
+    }
+
+    @Override
+    public ObservableList<?> getDependencies() {
+        return delegate.getDependencies();
+    }
+
+    @Override
+    public void dispose() {
+        delegate.dispose();
+    }
+}

src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java

@@ -119,8 +119,7 @@ public Optional<BibEntry> parseSingleEntry(String bibtexString) throws ParseExce
     }
 
     /**
-     * Will parse the BibTex-Data found when reading from reader. Ignores any encoding supplied in the file by
-     * "Encoding: myEncoding".
+     * Will parse the BibTex-Data found when reading from reader. Ignores any encoding supplied in the file by "Encoding: myEncoding".
      * <p>
      * The reader will be consumed.
      * <p>
@@ -311,8 +310,7 @@ private void parseBibtexString() throws IOException {
     }
 
     /**
-     * Puts all text that has been read from the reader, including newlines, etc., since the last call of this method into a string.
-     * Removes the JabRef file header, if it is found
+     * Puts all text that has been read from the reader, including newlines, etc., since the last call of this method into a string. Removes the JabRef file header, if it is found
      *
      * @return the text read so far
      */
@@ -611,8 +609,7 @@ private String parseFieldContent(Field field) throws IOException {
     }
 
     /**
-     * This method is used to parse string labels, field names, entry type and
-     * numbers outside brackets.
+     * This method is used to parse string labels, field names, entry type and numbers outside brackets.
      */
     private String parseTextToken() throws IOException {
         StringBuilder token = new StringBuilder(20);