Merge branch 'main' into jackson3

Author: Siedlerchr

.jbang/JabLsLauncher.java

@@ -49,7 +49,7 @@
 //DEPS org.tinylog:slf4j-tinylog:2.7.0
 //DEPS org.tinylog:tinylog-impl:2.7.0
 //DEPS com.github.ben-manes.caffeine:caffeine:3.2.3
-//DEPS org.apache.commons:commons-lang3:3.19.0
+//DEPS org.apache.commons:commons-lang3:3.20.0
 
 /// This class is required for [jbang](https://www.jbang.dev/)
 public class JabLsLauncher {

.jbang/JabSrvLauncher.java

@@ -79,11 +79,11 @@
 //DEPS org.jabref:afterburner.fx:2.0.0
 //DEPS net.harawata:appdirs:1.5.0
 //DEPS de.undercouch:citeproc-java:3.4.0
-//DEPS com.github.ben-manes.caffeine:caffeine:3.2.3
+//DEPS com.github.ben-manes.caffeine:caffeine:3.2.3 
 //DEPS tools.jackson.core:jackson-core:3.0.2
 //DEPS tools.jackson.core:jackson-databind:3.0.2
 //DEPS tools.jackson.dataformat:jackson-dataformat-yaml:3.0.2
-//DEPS org.apache.commons:commons-lang3:3.19.0
+//DEPS org.apache.commons:commons-lang3:3.20.0
 
 /// This class is required for [jbang](https://www.jbang.dev/)
 public class JabSrvLauncher {

CHANGELOG.md

@@ -14,6 +14,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added "IEEE" as another option for parsing plain text citations. [#14233](github.com/JabRef/jabref/pull/14233)
 - We added automatic date-based groups that create year/month/day subgroups from an entry’s date fields. [#10822](https://github.com/JabRef/jabref/issues/10822)
 - We added `doi-to-bibtex` to `JabKit`. [#14244](https://github.com/JabRef/jabref/pull/14244)
+- We added a "Regenerate" button for the AI chat allowing the user to make the language model reformulate its response to the previous prompt. [#12191](https://github.com/JabRef/jabref/issues/12191)
 - We added support for transliteration of fields to English and automatic transliteration of generated citation key. [#11377](https://github.com/JabRef/jabref/issues/11377)
 
 ### Changed

build.gradle.kts

@@ -3,7 +3,7 @@ plugins {
     id("org.jabref.gradle.feature.compile") // for openrewrite
     id("org.openrewrite.rewrite") version "7.20.0"
     id("org.itsallcode.openfasttrace") version "3.1.0"
-    id("org.cyclonedx.bom") version "3.0.1"
+    id("org.cyclonedx.bom") version "3.0.2"
 }
 
 // OpenRewrite should rewrite all sources

jabgui/src/main/java/org/jabref/gui/ai/components/aichat/AiChatComponent.java

@@ -3,6 +3,7 @@
 import java.nio.file.Path;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Optional;
 import java.util.stream.Stream;
 
 import javafx.beans.Observable;
@@ -43,6 +44,7 @@
 import com.google.common.annotations.VisibleForTesting;
 import dev.langchain4j.data.message.AiMessage;
 import dev.langchain4j.data.message.ChatMessage;
+import dev.langchain4j.data.message.ChatMessageType;
 import dev.langchain4j.data.message.UserMessage;
 import org.controlsfx.control.PopOver;
 import org.slf4j.Logger;
@@ -191,6 +193,22 @@ private void initializeChatPrompt() {
             onSendMessage(userMessage);
         });
 
+        chatPrompt.setRegenerateCallback(() -> {
+            setLoading(true);
+            Optional<UserMessage> lastUserPrompt = Optional.empty();
+            if (!aiChatLogic.getChatHistory().isEmpty()) {
+                lastUserPrompt = getLastUserMessage();
+            }
+            if (lastUserPrompt.isPresent()) {
+                while (aiChatLogic.getChatHistory().getLast().type() != ChatMessageType.USER) {
+                    deleteLastMessage();
+                }
+                deleteLastMessage();
+                chatPrompt.switchToNormalState();
+                onSendMessage(lastUserPrompt.get().singleText());
+            }
+        });
+
         chatPrompt.requestPromptFocus();
 
         updatePromptHistory();
@@ -334,4 +352,16 @@ private void deleteLastMessage() {
             aiChatLogic.getChatHistory().remove(index);
         }
     }
+
+    private Optional<UserMessage> getLastUserMessage() {
+        int messageIndex = aiChatLogic.getChatHistory().size() - 1;
+        while (messageIndex >= 0) {
+            ChatMessage chat = aiChatLogic.getChatHistory().get(messageIndex);
+            if (chat.type() == ChatMessageType.USER) {
+                return Optional.of((UserMessage) chat);
+            }
+            messageIndex--;
+        }
+        return Optional.empty();
+    }
 }

jabgui/src/main/java/org/jabref/gui/ai/components/aichat/chatprompt/ChatPromptComponent.java

@@ -30,6 +30,7 @@ public class ChatPromptComponent extends HBox {
     private final ObjectProperty<Consumer<String>> sendCallback = new SimpleObjectProperty<>();
     private final ObjectProperty<Consumer<String>> retryCallback = new SimpleObjectProperty<>();
     private final ObjectProperty<Runnable> cancelCallback = new SimpleObjectProperty<>();
+    private final ObjectProperty<Runnable> regenerateCallback = new SimpleObjectProperty<>();
 
     private final ListProperty<String> history = new SimpleListProperty<>(FXCollections.observableArrayList());
 
@@ -44,6 +45,7 @@ public class ChatPromptComponent extends HBox {
 
     @FXML private ExpandingTextArea userPromptTextArea;
     @FXML private Button submitButton;
+    @FXML private Button regenerateButton;
 
     public ChatPromptComponent() {
         ViewLoader.view(this)
@@ -68,6 +70,10 @@ public void setCancelCallback(Runnable cancelCallback) {
         this.cancelCallback.set(cancelCallback);
     }
 
+    public void setRegenerateCallback(Runnable regenerateCallback) {
+        this.regenerateCallback.set(regenerateCallback);
+    }
+
     public ListProperty<String> getHistory() {
         return history;
     }
@@ -174,6 +180,7 @@ public void switchToNormalState() {
         this.getChildren().clear();
         this.getChildren().add(userPromptTextArea);
         this.getChildren().add(submitButton);
+        this.getChildren().add(regenerateButton);
         requestPromptFocus();
     }
 
@@ -191,4 +198,11 @@ private void onSendMessage() {
             sendCallback.get().accept(userPrompt);
         }
     }
+
+    @FXML
+    private void onRegenerateMessage() {
+        if (regenerateCallback.get() != null) {
+            regenerateCallback.get().run();
+        }
+    }
 }

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

@@ -272,7 +272,7 @@ private void onDatabaseChanged(ListChangeListener.Change<? extends BibEntry> cha
                 // Nothing to do, as permutation doesn't change matched entries
             } else if (change.wasUpdated()) {
                 for (BibEntry changedEntry : change.getList().subList(change.getFrom(), change.getTo())) {
-                    if (groupNode.matches(changedEntry)) {
+                    if (isMatchEffective(this, changedEntry)) {
                         // ADR-0038
                         matchedEntries.add(changedEntry.getId());
                     } else {
@@ -286,7 +286,7 @@ private void onDatabaseChanged(ListChangeListener.Change<? extends BibEntry> cha
                     matchedEntries.remove(removedEntry.getId());
                 }
                 for (BibEntry addedEntry : change.getAddedSubList()) {
-                    if (groupNode.matches(addedEntry)) {
+                    if (isMatchEffective(this, addedEntry)) {
                         // ADR-0038
                         matchedEntries.add(addedEntry.getId());
                     }
@@ -312,7 +312,9 @@ private void updateMatchedEntries() {
         // for example, a previously matched entry gets removed -> hits = hits - 1
         if (preferences.getGroupsPreferences().shouldDisplayGroupCount()) {
             BackgroundTask
-                    .wrap(() -> groupNode.findMatches(databaseContext.getDatabase()))
+                    .wrap(() -> databaseContext.getDatabase().getEntries().stream()
+                                               .filter(e -> isMatchEffective(this, e))
+                                               .toList())
                     .onSuccess(entries -> {
                         matchedEntries.clear();
                         // ADR-0038
@@ -582,6 +584,49 @@ public boolean isEditable() {
         };
     }
 
+    /**
+     * Returns whether the given entry should be considered part of this group
+     * for the purpose of the groups sidebar (hit counter, highlighting, etc.).
+     *
+     * We cannot simply use groupNode.matches(entry) here. That only checks
+     * the rule of this single group and ignores the configured hierarchy type and
+     * any child groups created in the view model (for example automatic subgroups)
+     *
+     * This method applies the hierarchy type:
+     * INDEPENDENT: match this group only,
+     * INCLUDING: match this group or any child group,
+     * REFINING: match this group and all ancestor groups.
+     */
+    private boolean isMatchEffective(GroupNodeViewModel vm, BibEntry entry) {
+        GroupTreeNode node = vm.groupNode;
+        return switch (node.getGroup().getHierarchicalContext()) {
+            case INDEPENDENT ->
+                    node.matches(entry);
+
+            case INCLUDING -> {
+                if (node.matches(entry)) {
+                    yield true;
+                }
+                // recursively check VM-children (including auto-groups)
+                yield vm.children.stream().anyMatch(childVm -> isMatchEffective(childVm, entry));
+            }
+
+            case REFINING -> {
+                if (!node.matches(entry)) {
+                    yield false;
+                }
+                var parent = node.getParent();
+                while (parent.isPresent()) {
+                    if (!parent.get().matches(entry)) {
+                        yield false;
+                    }
+                    parent = parent.get().getParent();
+                }
+                yield true;
+            }
+        };
+    }
+
     class SearchIndexListener {
         @Subscribe
         public void listen(IndexStartedEvent event) {
@@ -603,7 +648,7 @@ public void listen(IndexAddedOrUpdatedEvent event) {
                     }
                 }).onFinished(() -> {
                     for (BibEntry entry : event.entries()) {
-                        if (groupNode.matches(entry)) {
+                        if (GroupNodeViewModel.this.isMatchEffective(GroupNodeViewModel.this, entry)) {
                             matchedEntries.add(entry.getId());
                         } else {
                             matchedEntries.remove(entry.getId());

jabgui/src/main/java/org/jabref/gui/maintable/MainTable.java

@@ -314,11 +314,12 @@ public void clearAndSelect(BibEntry bibEntry) {
             // keep original entry selected and reset citation merge mode
             this.citationMergeMode = false;
         } else {
-            // select new entry
-            getSelectionModel().clearSelection();
             findEntry(bibEntry).ifPresent(entry -> {
-                getSelectionModel().select(entry);
-                scrollTo(entry);
+                int index = getItems().indexOf(entry);
+                if (index >= 0) {
+                    getSelectionModel().clearAndSelect(index);
+                    scrollTo(index);
+                }
             });
         }
     }
@@ -330,16 +331,24 @@ public void clearAndSelect(List<BibEntry> bibEntries) {
             this.citationMergeMode = false;
         } else {
             // select new entries
-            getSelectionModel().clearSelection();
-            List<BibEntryTableViewModel> entries = bibEntries.stream()
-                                                             .filter(bibEntry -> bibEntry.getCitationKey().isPresent())
-                                                             .map(bibEntry -> findEntryByCitationKey(bibEntry.getCitationKey().get()))
-                                                             .filter(Optional::isPresent)
-                                                             .map(Optional::get)
-                                                             .toList();
-            entries.forEach(entry -> getSelectionModel().select(entry));
-            if (!entries.isEmpty()) {
-                scrollTo(entries.getFirst());
+            List<Integer> indices = bibEntries.stream()
+                                              .filter(bibEntry -> bibEntry.getCitationKey().isPresent())
+                                              .flatMap(bibEntry -> findEntryByCitationKey(bibEntry.getCitationKey().get()).stream())
+                                              .map(entry -> getItems().indexOf(entry))
+                                              .filter(index -> index >= 0)
+                                              .toList();
+
+            if (!indices.isEmpty()) {
+                // For multiple selections, clear once then select all
+                getSelectionModel().clearSelection();
+                indices.forEach(index -> {
+                    if (index < getItems().size()) {
+                        getSelectionModel().select(index);
+                    } else {
+                        LOGGER.debug("Could not select entry at index {} since it is out of bounds", index);
+                    }
+                });
+                scrollTo(indices.getFirst());
             }
         }
     }

jabgui/src/main/resources/org/jabref/gui/ai/components/aichat/chatprompt/ChatPromptComponent.fxml

@@ -18,4 +18,8 @@
             mnemonicParsing="false"
             onAction="#onSendMessage"
             text="%Submit"/>
+    <Button fx:id="regenerateButton"
+            mnemonicParsing="false"
+            onAction="#onRegenerateMessage"
+            text="%Regenerate"/>
 </fx:root>

jabgui/src/test/java/org/jabref/gui/groups/GroupNodeViewModelTest.java

@@ -183,4 +183,44 @@ private GroupNodeViewModel getViewModelForGroup(AbstractGroup group) {
     private GroupNodeViewModel getViewModelForGroup(GroupTreeNode group) {
         return new GroupNodeViewModel(databaseContext, stateManager, taskExecutor, group, new CustomLocalDragboard(), preferences);
     }
+
+    @Test
+    void hitsIncludingAutomaticGroupSumsVmChildren() {
+        // Two entries that will produce VM-only subgroups under the automatic group
+        databaseContext.getDatabase().insertEntry(new BibEntry().withField(StandardField.KEYWORDS, "A > B"));
+        databaseContext.getDatabase().insertEntry(new BibEntry().withField(StandardField.KEYWORDS, "A > C"));
+
+        // Automatic group: its subgroups exist only in the ViewModel
+        AutomaticKeywordGroup autoRoot = new AutomaticKeywordGroup(
+                "Keywords",
+                GroupHierarchyType.INCLUDING,   // UNION behavior expected
+                StandardField.KEYWORDS,
+                ',',
+                '>'
+        );
+
+        GroupNodeViewModel vm = getViewModelForGroup(autoRoot);
+
+        // INCLUDING: automatic root sums direct matches and those of its children -> expect 2.
+        assertEquals(2, vm.getHits().getValue().intValue());
+    }
+
+    @Test
+    void hitsIndependentAutomaticGroupIgnoresVmChildren() {
+        databaseContext.getDatabase().insertEntry(new BibEntry().withField(StandardField.KEYWORDS, "A > B"));
+        databaseContext.getDatabase().insertEntry(new BibEntry().withField(StandardField.KEYWORDS, "A > C"));
+
+        AutomaticKeywordGroup autoRoot = new AutomaticKeywordGroup(
+                "Keywords",
+                GroupHierarchyType.INDEPENDENT, // no hierarchical aggregation
+                StandardField.KEYWORDS,
+                ',',
+                '>'
+        );
+
+        GroupNodeViewModel vm = getViewModelForGroup(autoRoot);
+
+        // INDEPENDENT: automatic root has no direct matches -> expect 0.
+        assertEquals(0, vm.getHits().getValue().intValue());
+    }
 }