Merge remote-tracking branch 'upstream/floating-mode' into floating-mode

# Conflicts:
#	src/main/java/org/jabref/gui/util/FilteredListProxy.java

Author: calixtus

CHANGELOG.md

@@ -14,6 +14,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added support for selecting and using CSL Styles in JabRef's OpenOffice/LibreOffice integration for inserting bibliographic and in-text citations into a document. [#2146](https://github.com/JabRef/jabref/issues/2146), [#8893](https://github.com/JabRef/jabref/issues/8893)
 - We added Tools > New library based on references in PDF file... to create a new library based on the references section in a PDF file. [#11522](https://github.com/JabRef/jabref/pull/11522)
 - When converting the references section of a paper (PDF file), more than the last page is treated. [#11522](https://github.com/JabRef/jabref/pull/11522)
+- Added the functionality to invoke offline reference parsing explicitly. [#11565](https://github.com/JabRef/jabref/pull/11565)
+- The dialog for [adding an entry using reference text](https://docs.jabref.org/collect/newentryfromplaintext) is now filled with the clipboard contents as default. [#11565](https://github.com/JabRef/jabref/pull/11565)
 - Added minimal support for [biblatex data annotation](https://mirrors.ctan.org/macros/latex/contrib/biblatex/doc/biblatex.pdf#subsection.3.7) fields in `.layout` files. [#11505](https://github.com/JabRef/jabref/issues/11505)
 - Added saving of selected options in the [Lookup -> Search for unlinked local files dialog](https://docs.jabref.org/collect/findunlinkedfiles#link-the-pdfs-to-your-bib-library). [#11439](https://github.com/JabRef/jabref/issues/11439)
 - We added a toggle button to invert the selected groups. [#9073](https://github.com/JabRef/jabref/issues/9073)
@@ -24,12 +26,14 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - The Pubmed/Medline Plain importer now imports the PMID field as well [#11488](https://github.com/JabRef/jabref/issues/11488)
 - The 'Check for updates' menu bar button is now always enabled. [#11485](https://github.com/JabRef/jabref/pull/11485)
 - JabRef respects the [configuration for storing files relative to the .bib file](https://docs.jabref.org/finding-sorting-and-cleaning-entries/filelinks#directories-for-files) in more cases. [#11492](https://github.com/JabRef/jabref/pull/11492)
+- JabRef does not show finished background tasks in the status bar popup. [#11574](https://github.com/JabRef/jabref/pull/11574)
 - We enhanced the indexing speed. [#11502](https://github.com/JabRef/jabref/pull/11502)
 
 ### Fixed
 
 - We fixed an issue where the "Check for updates" preference was not saved. [#11485](https://github.com/JabRef/jabref/pull/11485)
 - We fixed an issue where an exception was thrown after changing "show preview as a tab" in the preferences. [#11515](https://github.com/JabRef/jabref/pull/11515)
+- We fixed an issue that online and offline mode for new library creation were handled incorrectly. [#11565](https://github.com/JabRef/jabref/pull/11565)
 - We fixed an issue with colors in the search bar when dark theme is enabled. [#11569](https://github.com/JabRef/jabref/issues/11569)
 - We fixed an issue where a new unsaved library was not marked with an asterisk. [#11519](https://github.com/JabRef/jabref/pull/11519)
 - We fixed an issue where JabRef starts without window decorations. [#11440](https://github.com/JabRef/jabref/pull/11440)

src/main/java/module-info.java

@@ -6,18 +6,28 @@
     requires java.sql;
     requires java.sql.rowset;
 
-    // JavaFX
+    // region JavaFX
     requires javafx.base;
     requires javafx.graphics;
     requires javafx.controls;
     requires javafx.web;
     requires javafx.fxml;
+
     requires afterburner.fx;
+    provides com.airhacks.afterburner.views.ResourceLocator
+            with org.jabref.gui.util.JabRefResourceLocator;
+
     requires com.dlsc.gemsfx;
     uses com.dlsc.gemsfx.TagsField;
+
+    requires com.tobiasdiez.easybind;
+
     requires de.saxsys.mvvmfx;
-    requires reactfx;
+    requires de.saxsys.mvvmfx.validation;
+
+    requires org.controlsfx.controls;
     requires org.fxmisc.flowless;
+    requires org.fxmisc.richtext;
 
     requires org.kordamp.ikonli.core;
     requires org.kordamp.ikonli.javafx;
@@ -30,20 +40,17 @@
     provides org.kordamp.ikonli.IkonProvider
             with org.jabref.gui.icon.JabrefIconProvider;
 
-    requires org.controlsfx.controls;
-    requires org.fxmisc.richtext;
-    requires com.tobiasdiez.easybind;
-
-    provides com.airhacks.afterburner.views.ResourceLocator
-            with org.jabref.gui.util.JabRefResourceLocator;
+    requires reactfx;
+    // endregion
 
-    // Logging
+    // region: Logging
     requires org.slf4j;
     requires jul.to.slf4j;
     requires org.apache.logging.log4j.to.slf4j;
     requires org.tinylog.api;
     requires org.tinylog.api.slf4j;
     requires org.tinylog.impl;
+    // endregion
 
     provides org.tinylog.writers.Writer
     with org.jabref.gui.logging.GuiWriter;
@@ -55,16 +62,18 @@
     // YAML
     requires org.yaml.snakeyaml;
 
-    // Annotations (@PostConstruct)
+    // region: Annotations (@PostConstruct)
     requires jakarta.annotation;
     requires jakarta.inject;
+    // endregion
 
-    // http server and client exchange
+    // region: http server and client exchange
     requires java.net.http;
     requires jakarta.ws.rs;
     requires org.glassfish.grizzly;
+    // endregion
 
-    // data mapping
+    // region: data mapping
     requires jakarta.xml.bind;
     requires jdk.xml.dom;
     requires com.google.gson;
@@ -73,22 +82,26 @@
     requires com.fasterxml.jackson.datatype.jsr310;
     // needs to be loaded here as it's otherwise not found at runtime
     requires org.glassfish.jaxb.runtime;
+    // endregion
 
     // dependency injection using HK2
     requires org.glassfish.hk2.api;
 
-    // http clients
+    // region: http clients
     requires unirest.java.core;
     requires unirest.modules.gson;
+    requires org.apache.httpcomponents.core5.httpcore5;
     requires org.jsoup;
+    // endregion
 
-    // SQL databases
+    // region: SQL databases
     requires ojdbc10;
     requires org.postgresql.jdbc;
     requires org.mariadb.jdbc;
     uses org.mariadb.jdbc.credential.CredentialPlugin;
+    // endregion
 
-    // Apache Commons and other (similar) helper libraries
+    // region: Apache Commons and other (similar) helper libraries
     requires com.google.common;
     requires io.github.javadiffutils;
     requires java.string.similarity;
@@ -98,9 +111,13 @@
     requires org.apache.commons.lang3;
     requires org.apache.commons.text;
     requires org.apache.commons.logging;
+    // endregion
 
+    // region: latex2unicode
     requires com.github.tomtung.latex2unicode;
     requires fastparse;
+    requires scala.library;
+    // endregion
 
     requires jbibtex;
     requires citeproc.java;
@@ -123,15 +140,15 @@
 
     requires org.jooq.jool;
 
-    // fulltext search
+    // region: fulltext search
     requires org.apache.lucene.core;
     // In case the version is updated, please also adapt SearchFieldConstants#VERSION to the newly used version
     uses org.apache.lucene.codecs.lucene99.Lucene99Codec;
-
     requires org.apache.lucene.queryparser;
     uses org.apache.lucene.queryparser.classic.MultiFieldQueryParser;
     requires org.apache.lucene.analysis.common;
     requires org.apache.lucene.highlighter;
+    // endregion
 
     requires net.harawata.appdirs;
     requires com.sun.jna;
@@ -143,11 +160,10 @@
 
     requires transitive org.jspecify;
 
-    // other libraries
-    requires org.antlr.antlr4.runtime;
-    requires org.libreoffice.uno;
-    requires de.saxsys.mvvmfx.validation;
+    // region: other libraries (alphabetically)
     requires dd.plist;
     requires mslinks;
-    requires org.apache.httpcomponents.core5.httpcore5;
+    requires org.antlr.antlr4.runtime;
+    requires org.libreoffice.uno;
+    // endregion
 }

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

@@ -348,7 +348,7 @@ public <V> void showProgressDialogAndWait(String title, String content, Task<V>
     @Override
     public <V> Optional<ButtonType> showBackgroundProgressDialogAndWait(String title, String content, StateManager stateManager) {
         TaskProgressView<Task<?>> taskProgressView = new TaskProgressView<>();
-        EasyBind.bindContent(taskProgressView.getTasks(), stateManager.getBackgroundTasks());
+        EasyBind.bindContent(taskProgressView.getTasks(), stateManager.getRunningBackgroundTasks());
         taskProgressView.setRetainTasks(false);
         taskProgressView.setGraphicFactory(BackgroundTask::getIcon);
 

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

@@ -13,6 +13,7 @@
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
 import javafx.collections.ObservableMap;
+import javafx.collections.transformation.FilteredList;
 import javafx.concurrent.Task;
 import javafx.scene.Node;
 import javafx.util.Pair;
@@ -139,8 +140,9 @@ public Optional<Node> getFocusOwner() {
         return focusOwner.get();
     }
 
-    public ObservableList<Task<?>> getBackgroundTasks() {
-        return EasyBind.map(backgroundTasks, Pair::getValue);
+    public ObservableList<Task<?>> getRunningBackgroundTasks() {
+        FilteredList<Pair<BackgroundTask<?>, Task<?>>> pairs = new FilteredList<>(backgroundTasks, task -> task.getValue().isRunning());
+        return EasyBind.map(pairs, Pair::getValue);
     }
 
     public void addBackgroundTask(BackgroundTask<?> backgroundTask, Task<?> task) {

src/main/java/org/jabref/gui/actions/ActionFactory.java

@@ -146,7 +146,9 @@ public Button createIconButton(Action action, Command command) {
         button.graphicProperty().unbind();
         action.getIcon().ifPresent(icon -> button.setGraphic(icon.getGraphicNode()));
 
-        button.setFocusTraversable(false); // Prevent the buttons from stealing the focus
+        // Prevent the buttons from stealing the focus
+        button.setFocusTraversable(false);
+
         return button;
     }
 

src/main/java/org/jabref/gui/actions/StandardActions.java

@@ -93,7 +93,7 @@ public enum StandardActions implements Action {
 
     PARSE_LATEX(Localization.lang("Search for citations in LaTeX files..."), IconTheme.JabRefIcons.LATEX_CITATIONS),
     NEW_SUB_LIBRARY_FROM_AUX(Localization.lang("New sublibrary based on AUX file") + "...", Localization.lang("New BibTeX sublibrary") + Localization.lang("This feature generates a new library based on which entries are needed in an existing LaTeX document."), IconTheme.JabRefIcons.NEW),
-    NEW_LIBRARY_FROM_PDF_ONLINE(Localization.lang("New library based on references in PDF file... (online)"), Localization.lang("This feature generates a new library based on the list of references in a PDF file. Thereby, it uses GROBID's functionality."), IconTheme.JabRefIcons.NEW),
+    NEW_LIBRARY_FROM_PDF_ONLINE(Localization.lang("New library based on references in PDF file... (online)"), Localization.lang("This feature generates a new library based on the list of references in a PDF file. Thereby, it uses Grobid's functionality."), IconTheme.JabRefIcons.NEW),
     NEW_LIBRARY_FROM_PDF_OFFLINE(Localization.lang("New library based on references in PDF file... (offline)"), Localization.lang("This feature generates a new library based on the list of references in a PDF file. Thereby, it uses JabRef's built-in functionality."), IconTheme.JabRefIcons.NEW),
     WRITE_METADATA_TO_PDF(Localization.lang("Write metadata to PDF files"), Localization.lang("Will write metadata to the PDFs linked from selected entries."), KeyBinding.WRITE_METADATA_TO_PDF),
 
@@ -135,7 +135,9 @@ public enum StandardActions implements Action {
 
     NEW_ENTRY(Localization.lang("New entry"), IconTheme.JabRefIcons.ADD_ENTRY, KeyBinding.NEW_ENTRY),
     NEW_ARTICLE(Localization.lang("New article"), IconTheme.JabRefIcons.ADD_ARTICLE),
-    NEW_ENTRY_FROM_PLAIN_TEXT(Localization.lang("New entry from plain text"), IconTheme.JabRefIcons.NEW_ENTRY_FROM_PLAIN_TEXT, KeyBinding.NEW_ENTRY_FROM_PLAIN_TEXT),
+    NEW_ENTRY_FROM_PLAIN_TEXT(Localization.lang("New entry from plain text"), IconTheme.JabRefIcons.NEW_ENTRY_FROM_PLAIN_TEXT),
+    NEW_ENTRY_FROM_PLAIN_TEXT_ONLINE(Localization.lang("New entry from plain text (online)"), IconTheme.JabRefIcons.NEW_ENTRY_FROM_PLAIN_TEXT, KeyBinding.NEW_ENTRY_FROM_PLAIN_TEXT_ONLINE),
+    NEW_ENTRY_FROM_PLAIN_TEXT_OFFLINE(Localization.lang("New entry from plain text (offline)"), IconTheme.JabRefIcons.NEW_ENTRY_FROM_PLAIN_TEXT),
     LIBRARY_PROPERTIES(Localization.lang("Library properties")),
     FIND_DUPLICATES(Localization.lang("Find duplicates"), IconTheme.JabRefIcons.FIND_DUPLICATES),
     MERGE_ENTRIES(Localization.lang("Merge entries"), IconTheme.JabRefIcons.MERGE_ENTRIES, KeyBinding.MERGE_ENTRIES),

src/main/java/org/jabref/gui/bibtexextractor/BibtexExtractorViewModel.java

@@ -1,8 +1,6 @@
 package org.jabref.gui.bibtexextractor;
 
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 import javax.swing.undo.UndoManager;
 
@@ -25,24 +23,33 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+/**
+ * View model for the feature "Extract BibTeX from plain text".
+ * Handles both online and offline case.
+ *
+ * @implNote Instead of using inheritance, we do if/else checks.
+ */
 public class BibtexExtractorViewModel {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(BibtexExtractorViewModel.class);
 
-    private final StringProperty inputTextProperty = new SimpleStringProperty("");
+    private final boolean onlineMode;
     private final DialogService dialogService;
     private final PreferencesService preferencesService;
     private final TaskExecutor taskExecutor;
-    private final ImportHandler importHandler;
 
-    public BibtexExtractorViewModel(BibDatabaseContext bibdatabaseContext,
-                                    DialogService dialogService,
-                                    PreferencesService preferencesService,
-                                    FileUpdateMonitor fileUpdateMonitor,
-                                    TaskExecutor taskExecutor,
-                                    UndoManager undoManager,
-                                    StateManager stateManager) {
+    private final ImportHandler importHandler;
+    private final StringProperty inputTextProperty = new SimpleStringProperty("");
 
+    public BibtexExtractorViewModel(boolean onlineMode,
+                                          BibDatabaseContext bibdatabaseContext,
+                                          DialogService dialogService,
+                                          PreferencesService preferencesService,
+                                          FileUpdateMonitor fileUpdateMonitor,
+                                          TaskExecutor taskExecutor,
+                                          UndoManager undoManager,
+                                          StateManager stateManager) {
+        this.onlineMode = onlineMode;
         this.dialogService = dialogService;
         this.preferencesService = preferencesService;
         this.taskExecutor = taskExecutor;
@@ -56,25 +63,20 @@ public BibtexExtractorViewModel(BibDatabaseContext bibdatabaseContext,
                 taskExecutor);
     }
 
-    public StringProperty inputTextProperty() {
-        return this.inputTextProperty;
-    }
-
     public void startParsing() {
-        if (preferencesService.getGrobidPreferences().isGrobidEnabled()) {
-            parseUsingGrobid();
+        if (onlineMode) {
+            startParsingOnline();
         } else {
-            parseUsingBibtexExtractor();
+            startParsingOffline();
         }
     }
 
-    private void parseUsingBibtexExtractor() {
+    private void startParsingOffline() {
         BibEntry parsedEntry = new BibtexExtractor().extract(inputTextProperty.getValue());
         importHandler.importEntries(List.of(parsedEntry));
-        trackNewEntry(parsedEntry, "ParseWithBibTeXExtractor");
     }
 
-    private void parseUsingGrobid() {
+    private void startParsingOnline() {
         GrobidCitationFetcher grobidCitationFetcher = new GrobidCitationFetcher(preferencesService.getGrobidPreferences(), preferencesService.getImportFormatPreferences());
         BackgroundTask.wrap(() -> grobidCitationFetcher.performSearch(inputTextProperty.getValue()))
                       .onRunning(() -> dialogService.notify(Localization.lang("Your text is being parsed...")))
@@ -90,14 +92,10 @@ private void parseUsingGrobid() {
                       .onSuccess(parsedEntries -> {
                           dialogService.notify(Localization.lang("%0 entries were parsed from your query.", String.valueOf(parsedEntries.size())));
                           importHandler.importEntries(parsedEntries);
-                          for (BibEntry bibEntry : parsedEntries) {
-                              trackNewEntry(bibEntry, "ParseWithGrobid");
-                          }
                       }).executeWith(taskExecutor);
     }
 
-    private void trackNewEntry(BibEntry bibEntry, String eventMessage) {
-        Map<String, String> properties = new HashMap<>();
-        properties.put("EntryType", bibEntry.typeProperty().getValue().getName());
+    public StringProperty inputTextProperty() {
+        return this.inputTextProperty;
     }
 }

src/main/java/org/jabref/gui/bibtexextractor/ExtractBibtexAction.java

@@ -0,0 +1,22 @@
+package org.jabref.gui.bibtexextractor;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.StateManager;
+import org.jabref.gui.actions.SimpleCommand;
+
+import static org.jabref.gui.actions.ActionHelper.needsDatabase;
+
+public class ExtractBibtexActionOffline extends SimpleCommand {
+
+    private final DialogService dialogService;
+
+    public ExtractBibtexActionOffline(DialogService dialogService, StateManager stateManager) {
+        this.dialogService = dialogService;
+        this.executable.bind(needsDatabase(stateManager));
+    }
+
+    @Override
+    public void execute() {
+        dialogService.showCustomDialogAndWait(new ExtractBibtexDialog(false));
+    }
+}