Merge branch 'main' into version6

CHANGELOG.md

@@ -26,6 +26,8 @@ From the user perspective, the combination of the pull request needs to be teste
 - We integrated a new three-way merge UI for merging entries in the Entries Merger Dialog, the Duplicate Resolver Dialog, the Entry Importer Dialog, and the External Changes Resolver Dialog. [#8945](https://github.com/JabRef/jabref/pull/8945)
 - We added the ability to merge groups, keywords, comments and files when merging entries. [#9022](https://github.com/JabRef/jabref/pull/9022)
 - We added a warning message next to the authors field in the merge dialog to warn users when the authors are the same but formatted differently. [#8745](https://github.com/JabRef/jabref/issues/8745)
+- The properties of an existing systematic literature review can be edited. [koppor#604](https://github.com/koppor/jabref/issues/604)
+- An SLR can now be started from the SLR itself. [#9131](https://github.com/JabRef/jabref/pull/9131), [koppor#601](https://github.com/koppor/jabref/issues/601)
 
 ### Changed
 
@@ -41,6 +43,7 @@ From the user perspective, the combination of the pull request needs to be teste
 - The global default directory for storing PDFs is now the subdirectory "JabRef" in the user's home.
 - We reworked the Define study parameters dialog. [#9123](https://github.com/JabRef/jabref/pull/9123)
 
+
 ### Fixed
 
 - We fixed an issue where author names with tilde accents (for example ñ) were marked as "Names are not in the standard BibTex format" [#8071](https://github.com/JabRef/jabref/issues/8071)

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

@@ -109,6 +109,7 @@
 import org.jabref.gui.shared.PullChangesFromSharedAction;
 import org.jabref.gui.sidepane.SidePane;
 import org.jabref.gui.sidepane.SidePaneType;
+import org.jabref.gui.slr.EditExistingStudyAction;
 import org.jabref.gui.slr.ExistingStudySearchAction;
 import org.jabref.gui.slr.StartNewStudyAction;
 import org.jabref.gui.specialfields.SpecialFieldMenuItemFactory;
@@ -541,7 +542,6 @@ private Node createToolbar() {
         // Setup Toolbar
 
         ToolBar toolBar = new ToolBar(
-
                 new HBox(
                         factory.createIconButton(StandardActions.NEW_LIBRARY, new NewDatabaseAction(this, prefs)),
                         factory.createIconButton(StandardActions.OPEN_LIBRARY, new OpenDatabaseAction(this, prefs, dialogService, stateManager, themeManager)),
@@ -874,9 +874,13 @@ private MenuBar createMenu() {
 
                 factory.createMenuItem(StandardActions.SEND_AS_EMAIL, new SendAsEMailAction(dialogService, this.prefs, stateManager)),
                 pushToApplicationMenuItem,
+
                 new SeparatorMenuItem(),
+
+                // Systematic Literature Review (SLR)
                 factory.createMenuItem(StandardActions.START_NEW_STUDY, new StartNewStudyAction(this, Globals.getFileUpdateMonitor(), Globals.TASK_EXECUTOR, prefs, stateManager, themeManager)),
-                factory.createMenuItem(StandardActions.SEARCH_FOR_EXISTING_STUDY, new ExistingStudySearchAction(this, Globals.getFileUpdateMonitor(), Globals.TASK_EXECUTOR, prefs, stateManager, themeManager)),
+                factory.createMenuItem(StandardActions.EDIT_EXISTING_STUDY, new EditExistingStudyAction(this.dialogService, this.stateManager)),
+                factory.createMenuItem(StandardActions.UPDATE_SEARCH_RESULTS_OF_STUDY, new ExistingStudySearchAction(this, this.getOpenDatabaseAction(), this.getDialogService(), Globals.getFileUpdateMonitor(), Globals.TASK_EXECUTOR, prefs, stateManager, themeManager)),
 
                 new SeparatorMenuItem(),
 

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

@@ -89,6 +89,7 @@ public class LibraryTab extends Tab {
     private final ThemeManager themeManager;
     private final BooleanProperty changedProperty = new SimpleBooleanProperty(false);
     private final BooleanProperty nonUndoableChangeProperty = new SimpleBooleanProperty(false);
+
     private BibDatabaseContext bibDatabaseContext;
     private MainTableDataModel tableModel;
     private CitationStyleCache citationStyleCache;
@@ -98,17 +99,22 @@ public class LibraryTab extends Tab {
     private BasePanelMode mode = BasePanelMode.SHOWING_NOTHING;
     private SplitPane splitPane;
     private DatabaseNotification databaseNotificationPane;
-
     private boolean saving;
     private PersonNameSuggestionProvider searchAutoCompleter;
+
     // Used to track whether the base has changed since last save.
     private BibEntry showing;
+
     private SuggestionProviders suggestionProviders;
+
     @SuppressWarnings({"FieldCanBeLocal"})
     private Subscription dividerPositionSubscription;
+
     // the query the user searches when this BasePanel is active
     private Optional<SearchQuery> currentSearchQuery = Optional.empty();
+
     private Optional<DatabaseChangeMonitor> changeMonitor = Optional.empty();
+
     // initializing it so we prevent NullPointerException
     private BackgroundTask<ParserResult> dataLoadingTask = BackgroundTask.wrap(() -> null);
 
@@ -213,6 +219,14 @@ public void onDatabaseLoadingSucceed(ParserResult result) {
 
         feedData(context);
 
+        if (preferencesService.getFilePreferences().shouldFulltextIndexLinkedFiles()) {
+            try {
+                indexingTaskManager.updateIndex(PdfIndexer.of(bibDatabaseContext, preferencesService.getFilePreferences()), bibDatabaseContext);
+            } catch (IOException e) {
+                LOGGER.error("Cannot access lucene index", e);
+            }
+        }
+
         // a temporary workaround to update groups pane
         stateManager.activeDatabaseProperty().bind(
                 EasyBind.map(frame.getTabbedPane().getSelectionModel().selectedItemProperty(),

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

@@ -13,6 +13,7 @@
 
 import org.jabref.gui.StateManager;
 import org.jabref.logic.shared.DatabaseLocation;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.entry.field.Field;
@@ -33,6 +34,11 @@ public static BooleanExpression needsSharedDatabase(StateManager stateManager) {
         return BooleanExpression.booleanExpression(binding);
     }
 
+    public static BooleanExpression needsStudyDatabase(StateManager stateManager) {
+        EasyBinding<Boolean> binding = EasyBind.map(stateManager.activeDatabaseProperty(), context -> context.filter(BibDatabaseContext::isStudy).isPresent());
+        return BooleanExpression.booleanExpression(binding);
+    }
+
     public static BooleanExpression needsEntriesSelected(StateManager stateManager) {
         return Bindings.isNotEmpty(stateManager.getSelectedEntries());
     }

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

@@ -87,8 +87,11 @@ 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),
     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),
+
     START_NEW_STUDY(Localization.lang("Start new systematic literature review")),
-    SEARCH_FOR_EXISTING_STUDY(Localization.lang("Perform search for existing systematic literature review")),
+    UPDATE_SEARCH_RESULTS_OF_STUDY(Localization.lang("Update study search results")),
+    EDIT_EXISTING_STUDY(Localization.lang("Manage study definition")),
+
     OPEN_DATABASE_FOLDER(Localization.lang("Reveal in file explorer")),
     OPEN_FOLDER(Localization.lang("Open folder"), Localization.lang("Open folder"), IconTheme.JabRefIcons.FOLDER, KeyBinding.OPEN_FOLDER),
     OPEN_FILE(Localization.lang("Open file"), Localization.lang("Open file"), IconTheme.JabRefIcons.FILE, KeyBinding.OPEN_FILE),

src/main/java/org/jabref/gui/push/PushToLyx.java

@@ -46,10 +46,10 @@ public JabRefIcon getIcon() {
     public void operationCompleted() {
         if (couldNotConnect) {
             dialogService.showErrorDialogAndWait(Localization.lang("Error pushing entries"),
-                    Localization.lang("verify that LyX is running and that the lyxpipe is valid")
-                            + ". [" + commandPath + "]");
+                    Localization.lang("Verify that LyX is running and that the lyxpipe is valid.")
+                            + "[" + commandPath + "]");
         } else if (couldNotCall) {
-            dialogService.showErrorDialogAndWait(Localization.lang("unable to write to") + " " + commandPath + ".in");
+            dialogService.showErrorDialogAndWait(Localization.lang("Unable to write to %0.", commandPath + ".in"));
         } else {
             super.operationCompleted();
         }

src/main/java/org/jabref/gui/search/rules/describer/GrammarBasedSearchRuleDescriber.java

@@ -41,8 +41,8 @@ public TextFlow getDescription() {
         textFlow.getChildren().addAll(descriptionSearchBaseVisitor.visit(parseTree));
         textFlow.getChildren().add(TooltipTextUtil.createText(". ", TooltipTextUtil.TextType.NORMAL));
         textFlow.getChildren().add(TooltipTextUtil.createText(searchFlags.contains(SearchRules.SearchFlags.CASE_SENSITIVE) ? Localization
-                .lang("The search is case sensitive.") :
-                Localization.lang("The search is case insensitive."), TooltipTextUtil.TextType.NORMAL));
+                .lang("The search is case-sensitive.") :
+                Localization.lang("The search is case-insensitive."), TooltipTextUtil.TextType.NORMAL));
         return textFlow;
     }
 

src/main/java/org/jabref/gui/slr/EditExistingStudyAction.java

@@ -0,0 +1,63 @@
+package org.jabref.gui.slr;
+
+import java.io.IOException;
+import java.nio.file.Path;
+
+import org.jabref.gui.DialogService;
+import org.jabref.gui.StateManager;
+import org.jabref.gui.actions.ActionHelper;
+import org.jabref.gui.actions.SimpleCommand;
+import org.jabref.logic.crawler.StudyRepository;
+import org.jabref.logic.crawler.StudyYamlParser;
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.database.BibDatabaseContext;
+import org.jabref.model.study.Study;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class EditExistingStudyAction extends SimpleCommand {
+    private static final Logger LOGGER = LoggerFactory.getLogger(EditExistingStudyAction.class);
+
+    private final DialogService dialogService;
+    private final StateManager stateManager;
+
+    public EditExistingStudyAction(DialogService dialogService, StateManager stateManager) {
+        this.dialogService = dialogService;
+        this.stateManager = stateManager;
+        this.executable.bind(ActionHelper.needsStudyDatabase(stateManager));
+    }
+
+    @Override
+    public void execute() {
+        // The action works on the current library
+        // This library has to be determined
+        if (stateManager.getActiveDatabase().isEmpty() || !stateManager.getActiveDatabase().get().isStudy()) {
+            return;
+        }
+        BibDatabaseContext bibDatabaseContext = stateManager.getActiveDatabase().get();
+
+        // The action can only be called on an existing AND saved study library
+        // The saving is ensured at creation of a study library
+        // Thus, this check is only existing to check this assumption
+        if (bibDatabaseContext.getDatabasePath().isEmpty()) {
+            LOGGER.error("Library path is not available");
+            return;
+        }
+
+        Path databasePath = bibDatabaseContext.getDatabasePath().get();
+
+        Path studyDirectory = databasePath.getParent();
+
+        Study study;
+        try {
+            study = new StudyYamlParser().parseStudyYamlFile(studyDirectory.resolve(StudyRepository.STUDY_DEFINITION_FILE_NAME));
+        } catch (IOException e) {
+            dialogService.showErrorDialogAndWait(Localization.lang("Error opening file"), e);
+            return;
+        }
+
+        // When the dialog returns, the study.yml file is updated (or kept unmodified at Cancel)
+        dialogService.showCustomDialogAndWait(new ManageStudyDefinitionView(study, studyDirectory));
+    }
+}