SLR data is now editable

CHANGELOG.md

@@ -16,6 +16,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - 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.
 
 ### Changed
 

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)),
@@ -878,9 +878,13 @@ 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);
 

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("Perform search for existing systematic literature review")),
+    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/slr/EditExistingStudyAction.java

@@ -0,0 +1,64 @@
+package org.jabref.gui.slr;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.util.Objects;
+
+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("Database 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));
+    }
+}

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

@@ -8,6 +8,7 @@
 import org.jabref.gui.DialogService;
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.StateManager;
+import org.jabref.gui.actions.ActionHelper;
 import org.jabref.gui.actions.SimpleCommand;
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
 import org.jabref.gui.theme.ThemeManager;
@@ -22,6 +23,7 @@
 import org.jabref.logic.importer.ParseException;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.io.FileUtil;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntryTypesManager;
 import org.jabref.model.util.FileUpdateMonitor;
 import org.jabref.preferences.GeneralPreferences;
@@ -35,30 +37,50 @@ public class ExistingStudySearchAction extends SimpleCommand {
     private static final Logger LOGGER = LoggerFactory.getLogger(ExistingStudySearchAction.class);
 
     protected final DialogService dialogService;
-    protected final Path workingDirectory;
 
-    Path studyDirectory;
+    protected Path studyDirectory;
+    protected final PreferencesService preferencesService;
+    protected final StateManager stateManager;
 
-    private final JabRefFrame frame;
     private final FileUpdateMonitor fileUpdateMonitor;
     private final TaskExecutor taskExecutor;
-    private final PreferencesService preferencesService;
-    private final StateManager stateManager;
     private final ThemeManager themeManager;
     private final GeneralPreferences generalPreferences;
     private final ImportFormatPreferences importFormatPreferences;
     private final ImporterPreferences importerPreferences;
     private final SavePreferences savePreferences;
-    // This can be either populated before crawl is called or is populated in the call using the directory dialog. This is helpful if the directory is selected in a previous dialog/UI element
-
-    public ExistingStudySearchAction(JabRefFrame frame,
-                                     FileUpdateMonitor fileUpdateMonitor,
-                                     TaskExecutor taskExecutor,
-                                     PreferencesService preferencesService,
-                                     StateManager stateManager,
-                                     ThemeManager themeManager) {
+    private final JabRefFrame frame;
+    private final OpenDatabaseAction openDatabaseAction;
+
+    /**
+     * @param frame Required to close the tab before the study is updated
+     * @param openDatabaseAction Required to open the tab after the study is exectued
+     */
+    public ExistingStudySearchAction(
+            JabRefFrame frame,
+            OpenDatabaseAction openDatabaseAction,
+            DialogService dialogService,
+            FileUpdateMonitor fileUpdateMonitor,
+            TaskExecutor taskExecutor,
+            PreferencesService preferencesService,
+            StateManager stateManager,
+            ThemeManager themeManager) {
+        this(frame, openDatabaseAction, dialogService, fileUpdateMonitor, taskExecutor, preferencesService, stateManager, themeManager, false);
+    }
+
+    protected ExistingStudySearchAction(
+            JabRefFrame frame,
+            OpenDatabaseAction openDatabaseAction,
+            DialogService dialogService,
+            FileUpdateMonitor fileUpdateMonitor,
+            TaskExecutor taskExecutor,
+            PreferencesService preferencesService,
+            StateManager stateManager,
+            ThemeManager themeManager,
+            boolean isNew) {
         this.frame = frame;
-        this.dialogService = frame.getDialogService();
+        this.openDatabaseAction = openDatabaseAction;
+        this.dialogService = dialogService;
         this.fileUpdateMonitor = fileUpdateMonitor;
         this.taskExecutor = taskExecutor;
         this.preferencesService = preferencesService;
@@ -69,46 +91,45 @@ public ExistingStudySearchAction(JabRefFrame frame,
         this.importerPreferences = preferencesService.getImporterPreferences();
         this.savePreferences = preferencesService.getSavePreferences();
 
-        this.workingDirectory = stateManager.getActiveDatabase()
-                                            .map(database -> FileUtil.getInitialDirectory(
-                                                    database,
-                                                    preferencesService.getFilePreferences().getWorkingDirectory()))
-                                            .orElse(preferencesService.getFilePreferences().getWorkingDirectory());
+        if (!isNew) {
+            this.executable.bind(ActionHelper.needsStudyDatabase(stateManager));
+        }
     }
 
     @Override
     public void execute() {
-        // Reset before each execution
-        studyDirectory = null;
-        crawl();
-    }
+        if (stateManager.getActiveDatabase().isEmpty()) {
+            LOGGER.error("Database is not present, even if it should");
+            return;
+        }
+        BibDatabaseContext bibDatabaseContext = stateManager.getActiveDatabase().get();
 
-    public void crawl() {
-        if (Objects.isNull(studyDirectory)) {
-            DirectoryDialogConfiguration directoryDialogConfiguration = new DirectoryDialogConfiguration.Builder()
-                    .withInitialDirectory(workingDirectory)
-                    .build();
+        if (bibDatabaseContext.getDatabasePath().isEmpty()) {
+            LOGGER.error("Database path is not present, even if it should");
+            return;
+        }
+        this.studyDirectory = bibDatabaseContext.getDatabasePath().get().getParent();
 
-            Optional<Path> studyRepositoryRoot = dialogService.showDirectorySelectionDialog(directoryDialogConfiguration);
+        crawl();
+    }
 
-            if (studyRepositoryRoot.isEmpty()) {
-                // Do nothing if selection was canceled
-                return;
-            }
-            studyDirectory = studyRepositoryRoot.get();
-        }
+    protected void crawl() {
+        // We hard close the tab
+        // Future work: Properly close the tab (with saving, ...)
+        frame.closeCurrentTab();
 
         try {
-            setupRepository(studyDirectory);
+            setupRepository(this.studyDirectory);
         } catch (IOException | GitAPIException e) {
             dialogService.showErrorDialogAndWait(Localization.lang("Study repository could not be created"), e);
             return;
         }
+
         final Crawler crawler;
         try {
             crawler = new Crawler(
-                    studyDirectory,
-                    new SlrGitHandler(studyDirectory),
+                    this.studyDirectory,
+                    new SlrGitHandler(this.studyDirectory),
                     generalPreferences,
                     importFormatPreferences,
                     importerPreferences,
@@ -120,7 +141,8 @@ public void crawl() {
             dialogService.showErrorDialogAndWait(Localization.lang("Error during reading of study definition file."), e);
             return;
         }
-        dialogService.notify(Localization.lang("Searching"));
+
+        dialogService.notify(Localization.lang("Searching..."));
         BackgroundTask.wrap(() -> {
                           crawler.performCrawl();
                           return 0; // Return any value to make this a callable instead of a runnable. This allows throwing exceptions.
@@ -130,9 +152,8 @@ public void crawl() {
                           dialogService.showErrorDialogAndWait(Localization.lang("Error during persistence of crawling results."), e);
                       })
                       .onSuccess(unused -> {
-                          new OpenDatabaseAction(frame, preferencesService, dialogService, stateManager, themeManager).openFile(Path.of(studyDirectory.toString(), "studyResult.bib"));
-                          // If  finished reset command object for next use
-                          studyDirectory = null;
+                          dialogService.notify(Localization.lang("Finished Searching"));
+                          openDatabaseAction.openFile(Path.of(this.studyDirectory.toString(), Crawler.FILENAME_STUDY_RESULT_BIB));
                       })
                       .executeWith(taskExecutor);
     }