Persist selection of databases in SLR (JabRef#11635)

* Attempt: Persist selection of databases

* Use ObservableSet

* ObservableList

* set fetchers

* Revise architecture

* Revise test

* Fix indent

* Fix indent 2

* Add changelog entry

* Fix indent

* Update CHANGELOG.md

* Chris' update

Co-authored-by: Christoph <siedlerkiller@gmail.com>

* Update src/main/java/org/jabref/preferences/WorkspacePreferences.java

Co-authored-by: Christoph <siedlerkiller@gmail.com>

* Update src/main/java/org/jabref/preferences/JabRefPreferences.java

Co-authored-by: Christoph <siedlerkiller@gmail.com>

* !Remove duplicated line

* Return ObservableList

* Remove unused import

* Rename foreach loop variable

* Rename foreach loop variable

* Rename fetcher->catalog

* Fix overwriting of existing study catalogs

* Merge upstream/main

* Fix merge issue

* Persist for edits on existing studies

* Save preferences only on a "new run" or "save".

---------

Co-authored-by: Christoph <siedlerkiller@gmail.com>
Co-authored-by: Oliver Kopp <kopp.dev@gmail.com>

Author: 3 people

CHANGELOG.md

@@ -23,6 +23,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We enabled creating a new file link manually. [#11017](https://github.com/JabRef/jabref/issues/11017)
 - We added a toggle button to invert the selected groups. [#9073](https://github.com/JabRef/jabref/issues/9073)
 - We reintroduced the floating search in the main table. [#4237](https://github.com/JabRef/jabref/issues/4237)
+- When starting a new SLR, the selected catalogs now persist within and across JabRef sessions. [koppor#614](https://github.com/koppor/jabref/issues/614)
 - We added a different background color to the search bar to indicate when the search syntax is wrong. [#11658](https://github.com/JabRef/jabref/pull/11658)
 
 ### Changed

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

@@ -111,7 +111,7 @@ public ManageStudyDefinitionView(Path pathToStudyDataDirectory) {
     /**
      * This is used to edit an existing study.
      *
-     * @param study          the study to edit
+     * @param study the study to edit
      * @param studyDirectory the directory of the study
      */
     public ManageStudyDefinitionView(Study study, Path studyDirectory) {
@@ -145,6 +145,7 @@ private void setupSaveSurveyButton(boolean isEdit) {
 
         setResultConverter(button -> {
             if (button == saveSurveyButtonType) {
+                viewModel.updateSelectedCatalogs();
                 return viewModel.saveStudy();
             }
             // Cancel button will return null
@@ -158,14 +159,16 @@ private void initialize() {
             viewModel = new ManageStudyDefinitionViewModel(
                     prefs.getImportFormatPreferences(),
                     prefs.getImporterPreferences(),
-                    dialogService);
+                    dialogService,
+                    prefs);
         } else {
             viewModel = new ManageStudyDefinitionViewModel(
                     study.get(),
                     pathToStudyDataDirectory,
                     prefs.getImportFormatPreferences(),
                     prefs.getImporterPreferences(),
-                    dialogService);
+                    dialogService,
+                    prefs);
 
             // The directory of the study cannot be changed
             studyDirectory.setEditable(false);
@@ -237,6 +240,10 @@ private void initCatalogsTab() {
                 })
                 .install(catalogTable);
 
+        if (study.isEmpty()) {
+            viewModel.initializeSelectedCatalogs();
+        }
+
         catalogColumn.setReorderable(false);
         catalogColumn.setCellFactory(TextFieldTableCell.forTableColumn());
 

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

@@ -32,6 +32,7 @@
 import org.jabref.model.study.Study;
 import org.jabref.model.study.StudyDatabase;
 import org.jabref.model.study.StudyQuery;
+import org.jabref.preferences.PreferencesService;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -60,12 +61,15 @@ public class ManageStudyDefinitionViewModel {
 
     private final DialogService dialogService;
 
+    private final PreferencesService preferencesService;
+
     /**
      * Constructor for a new study
      */
     public ManageStudyDefinitionViewModel(ImportFormatPreferences importFormatPreferences,
                                           ImporterPreferences importerPreferences,
-                                          DialogService dialogService) {
+                                          DialogService dialogService,
+                                          PreferencesService preferencesService) {
         databases.addAll(WebFetchers.getSearchBasedFetchers(importFormatPreferences, importerPreferences)
                                     .stream()
                                     .map(SearchBasedFetcher::getName)
@@ -78,6 +82,7 @@ public ManageStudyDefinitionViewModel(ImportFormatPreferences importFormatPrefer
                                     })
                                     .toList());
         this.dialogService = Objects.requireNonNull(dialogService);
+        this.preferencesService = Objects.requireNonNull(preferencesService);
     }
 
     /**
@@ -90,7 +95,8 @@ public ManageStudyDefinitionViewModel(Study study,
                                           Path studyDirectory,
                                           ImportFormatPreferences importFormatPreferences,
                                           ImporterPreferences importerPreferences,
-                                          DialogService dialogService) {
+                                          DialogService dialogService,
+                                          PreferencesService preferencesService) {
         // copy the content of the study object into the UI fields
         authors.addAll(Objects.requireNonNull(study).getAuthors());
         title.setValue(study.getTitle());
@@ -111,6 +117,7 @@ public ManageStudyDefinitionViewModel(Study study,
 
         this.directory.set(Objects.requireNonNull(studyDirectory).toString());
         this.dialogService = Objects.requireNonNull(dialogService);
+        this.preferencesService = Objects.requireNonNull(preferencesService);
     }
 
     public StringProperty getTitle() {
@@ -217,4 +224,20 @@ public void deleteQuestion(String item) {
     public void deleteQuery(String item) {
         queries.remove(item);
     }
+
+    public void initializeSelectedCatalogs() {
+        List<String> selectedCatalogs = preferencesService.getWorkspacePreferences().getSelectedSlrCatalogs();
+        for (StudyCatalogItem catalog : databases) {
+            catalog.setEnabled(selectedCatalogs.contains(catalog.getName()));
+        }
+    }
+
+    public void updateSelectedCatalogs() {
+        List<String> selectedCatalogsList = databases.stream()
+                                                     .filter(StudyCatalogItem::isEnabled)
+                                                     .map(StudyCatalogItem::getName)
+                                                     .collect(Collectors.toList());
+
+        preferencesService.getWorkspacePreferences().setSelectedSlrCatalogs(selectedCatalogsList);
+    }
 }

src/main/java/org/jabref/preferences/JabRefPreferences.java

@@ -493,6 +493,9 @@ public class JabRefPreferences implements PreferencesService, AiApiKeyProvider {
     private static final Logger LOGGER = LoggerFactory.getLogger(JabRefPreferences.class);
     private static final Preferences PREFS_NODE = Preferences.userRoot().node("/org/jabref");
 
+    // SLR
+    private static final String SELECTED_SLR_CATALOGS = "selectedSlrCatalogs";
+
     // The only instance of this class:
     private static JabRefPreferences singleton;
     /**
@@ -2182,7 +2185,8 @@ public WorkspacePreferences getWorkspacePreferences() {
                 getBoolean(OPEN_LAST_EDITED),
                 getBoolean(SHOW_ADVANCED_HINTS),
                 getBoolean(WARN_ABOUT_DUPLICATES_IN_INSPECTION),
-                getBoolean(CONFIRM_DELETE));
+                getBoolean(CONFIRM_DELETE),
+                getStringList(SELECTED_SLR_CATALOGS));
 
         EasyBind.listen(workspacePreferences.languageProperty(), (obs, oldValue, newValue) -> {
             put(LANGUAGE, newValue.getId());
@@ -2200,6 +2204,8 @@ public WorkspacePreferences getWorkspacePreferences() {
         EasyBind.listen(workspacePreferences.showAdvancedHintsProperty(), (obs, oldValue, newValue) -> putBoolean(SHOW_ADVANCED_HINTS, newValue));
         EasyBind.listen(workspacePreferences.warnAboutDuplicatesInInspectionProperty(), (obs, oldValue, newValue) -> putBoolean(WARN_ABOUT_DUPLICATES_IN_INSPECTION, newValue));
         EasyBind.listen(workspacePreferences.confirmDeleteProperty(), (obs, oldValue, newValue) -> putBoolean(CONFIRM_DELETE, newValue));
+        workspacePreferences.getSelectedSlrCatalogs().addListener((ListChangeListener<String>) change ->
+                putStringList(SELECTED_SLR_CATALOGS, workspacePreferences.getSelectedSlrCatalogs()));
         return workspacePreferences;
     }
 

src/main/java/org/jabref/preferences/WorkspacePreferences.java

@@ -1,11 +1,15 @@
 package org.jabref.preferences;
 
+import java.util.List;
+
 import javafx.beans.property.BooleanProperty;
 import javafx.beans.property.IntegerProperty;
 import javafx.beans.property.ObjectProperty;
 import javafx.beans.property.SimpleBooleanProperty;
 import javafx.beans.property.SimpleIntegerProperty;
 import javafx.beans.property.SimpleObjectProperty;
+import javafx.collections.FXCollections;
+import javafx.collections.ObservableList;
 
 import org.jabref.gui.theme.Theme;
 import org.jabref.logic.l10n.Language;
@@ -21,6 +25,7 @@ public class WorkspacePreferences {
     private final BooleanProperty showAdvancedHints;
     private final BooleanProperty warnAboutDuplicatesInInspection;
     private final BooleanProperty confirmDelete;
+    private final ObservableList<String> selectedSlrCatalogs;
 
     public WorkspacePreferences(Language language,
                                 boolean shouldOverrideDefaultFontSize,
@@ -31,7 +36,8 @@ public WorkspacePreferences(Language language,
                                 boolean shouldOpenLastEdited,
                                 boolean showAdvancedHints,
                                 boolean warnAboutDuplicatesInInspection,
-                                boolean confirmDelete) {
+                                boolean confirmDelete,
+                                List<String> selectedSlrCatalogs) {
         this.language = new SimpleObjectProperty<>(language);
         this.shouldOverrideDefaultFontSize = new SimpleBooleanProperty(shouldOverrideDefaultFontSize);
         this.mainFontSize = new SimpleIntegerProperty(mainFontSize);
@@ -42,6 +48,7 @@ public WorkspacePreferences(Language language,
         this.showAdvancedHints = new SimpleBooleanProperty(showAdvancedHints);
         this.warnAboutDuplicatesInInspection = new SimpleBooleanProperty(warnAboutDuplicatesInInspection);
         this.confirmDelete = new SimpleBooleanProperty(confirmDelete);
+        this.selectedSlrCatalogs = FXCollections.observableArrayList(selectedSlrCatalogs);
     }
 
     public Language getLanguage() {
@@ -155,4 +162,12 @@ public BooleanProperty confirmDeleteProperty() {
     public void setConfirmDelete(boolean confirmDelete) {
         this.confirmDelete.set(confirmDelete);
     }
+
+    public ObservableList<String> getSelectedSlrCatalogs() {
+        return selectedSlrCatalogs;
+    }
+
+    public void setSelectedSlrCatalogs(List<String> catalogs) {
+        selectedSlrCatalogs.setAll(catalogs);
+    }
 }

src/test/java/org/jabref/gui/slr/ManageStudyDefinitionViewModelTest.java

@@ -8,6 +8,7 @@
 import org.jabref.logic.importer.ImporterPreferences;
 import org.jabref.model.study.Study;
 import org.jabref.model.study.StudyDatabase;
+import org.jabref.preferences.PreferencesService;
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -21,18 +22,20 @@ class ManageStudyDefinitionViewModelTest {
     private ImportFormatPreferences importFormatPreferences;
     private ImporterPreferences importerPreferences;
     private DialogService dialogService;
+    private PreferencesService preferencesService;
 
     @BeforeEach
     void setUp() {
         // code taken from org.jabref.logic.importer.WebFetchersTest.setUp
         importFormatPreferences = mock(ImportFormatPreferences.class, Answers.RETURNS_DEEP_STUBS);
         importerPreferences = mock(ImporterPreferences.class, Answers.RETURNS_DEEP_STUBS);
         dialogService = mock(DialogService.class);
+        preferencesService = mock(PreferencesService.class);
     }
 
     @Test
     void emptyStudyConstructorFillsDatabasesCorrectly() {
-        ManageStudyDefinitionViewModel manageStudyDefinitionViewModel = new ManageStudyDefinitionViewModel(importFormatPreferences, importerPreferences, dialogService);
+        ManageStudyDefinitionViewModel manageStudyDefinitionViewModel = new ManageStudyDefinitionViewModel(importFormatPreferences, importerPreferences, dialogService, preferencesService);
         assertEquals(List.of(
                 new StudyCatalogItem("ACM Portal", true),
                 new StudyCatalogItem("ArXiv", false),
@@ -103,6 +106,7 @@ private ManageStudyDefinitionViewModel getManageStudyDefinitionViewModel(Path te
                 tempDir,
                 importFormatPreferences,
                 importerPreferences,
-                dialogService);
+                dialogService,
+                preferencesService);
     }
 }