Fix save order preferences

CHANGELOG.md

@@ -83,6 +83,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We changed the behavior of group addition/edit, so that sorting by alphabetical order is not performed by default after the modification [#10017](https://github.com/JabRef/jabref/issues/10017)
 - We fixed an issue with spacing in the cleanup dialogue. [#10081](https://github.com/JabRef/jabref/issues/10081)
 - The GVK fetcher now uses the new [K10plus](https://www.bszgbv.de/services/k10plus/) database [#10189](https://github.com/JabRef/jabref/pull/10189)
+- The SLR feature adds new entries sorted into the new bib file (and not at the end).
 
 ### Fixed
 
@@ -134,6 +135,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the ACM Portal search sometimes would not return entries for some search queries when the article author had no given name [#10107](https://github.com/JabRef/jabref/issues/10107)
 - We fixed an issue that caused high CPU usage and a zombie process after quitting JabRef because of author names autocompletion [#10159](https://github.com/JabRef/jabref/pull/10159)
 - We fixed an issue where files with illegal characters in the filename could be added to JabRef. [#10182](https://github.com/JabRef/jabref/issues/10182)
+- We fixed an issue with JabRef respecting the save order. [#9869](https://github.com/JabRef/jabref/issues/9869)
 
 ### Removed
 

build.gradle

@@ -214,6 +214,9 @@ dependencies {
 
     implementation group: 'org.jooq', name: 'jool', version: '0.9.15'
 
+    compileOnly 'org.jspecify:jspecify:0.3.0'
+    testCompileOnly 'org.jspecify:jspecify:0.3.0'
+
     testImplementation 'io.github.classgraph:classgraph:4.8.162'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.10.0'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.10.0'

src/main/java/module-info.java

@@ -123,4 +123,6 @@
     requires org.eclipse.jgit;
     uses org.eclipse.jgit.transport.SshSessionFactory;
     uses org.eclipse.jgit.lib.GpgSigner;
+
+    requires static org.jspecify;
 }

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -601,9 +601,7 @@ private void saveDatabase(BibDatabase newBase, String subName) {
             try (AtomicFileWriter fileWriter = new AtomicFileWriter(Path.of(subName), StandardCharsets.UTF_8)) {
                 BibWriter bibWriter = new BibWriter(fileWriter, OS.NEWLINE);
                 SaveConfiguration saveConfiguration = new SaveConfiguration()
-                        .withMetadataSaveOrder(true)
                         .withReformatOnSave(preferencesService.getLibraryPreferences().shouldAlwaysReformatOnSave());
-
                 BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(
                         bibWriter,
                         saveConfiguration,

src/main/java/org/jabref/gui/auximport/NewSubLibraryAction.java

@@ -11,6 +11,8 @@
 
 /**
  * The action concerned with generate a new (sub-)database from latex AUX file.
+ *
+ * A new library is created by {@link org.jabref.gui.importer.NewDatabaseAction}
  */
 public class NewSubLibraryAction extends SimpleCommand {
 

src/main/java/org/jabref/gui/commonfxcontrols/SaveOrderConfigPanelViewModel.java

@@ -9,7 +9,6 @@
 import javafx.collections.FXCollections;
 
 import org.jabref.model.entry.field.Field;
-import org.jabref.model.metadata.SaveOrder;
 
 public class SaveOrderConfigPanelViewModel {
 
@@ -24,7 +23,7 @@ public SaveOrderConfigPanelViewModel() {
     }
 
     public void addCriterion() {
-        selectedSortCriteriaProperty.add(new SortCriterionViewModel(new SaveOrder.SortCriterion()));
+        selectedSortCriteriaProperty.add(new SortCriterionViewModel());
     }
 
     public void removeCriterion(SortCriterionViewModel sortCriterionViewModel) {

src/main/java/org/jabref/gui/commonfxcontrols/SortCriterionViewModel.java

@@ -6,6 +6,7 @@
 import javafx.beans.property.SimpleObjectProperty;
 
 import org.jabref.model.entry.field.Field;
+import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.metadata.SaveOrder;
 
 public class SortCriterionViewModel {
@@ -18,6 +19,11 @@ public SortCriterionViewModel(SaveOrder.SortCriterion criterion) {
         this.descendingProperty.setValue(criterion.descending);
     }
 
+    public SortCriterionViewModel() {
+        this.fieldProperty.setValue(StandardField.AUTHOR);
+        this.descendingProperty.setValue(false);
+    }
+
     public ObjectProperty<Field> fieldProperty() {
         return fieldProperty;
     }

src/main/java/org/jabref/gui/exporter/CreateModifyExporterDialogViewModel.java

@@ -67,7 +67,7 @@ public ExporterViewModel saveExporter() {
                 layoutFile.get(),
                 extension.get(),
                 preferences.getLayoutFormatterPreferences(),
-                preferences.getExportConfiguration());
+                preferences.getExportConfiguration().getSaveOrder());
         format.setCustomExport(true);
         return new ExporterViewModel(format);
     }

src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java

@@ -37,6 +37,7 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.event.ChangePropagation;
 import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.metadata.SaveOrder;
 import org.jabref.preferences.PreferencesService;
 
 import org.slf4j.Logger;
@@ -79,7 +80,7 @@ public boolean save(SaveDatabaseMode mode) {
     }
 
     /**
-     * Asks the user for the path and saves afterwards
+     * Asks the user for the path and saves afterward
      */
     public void saveAs() {
         askForSavePath().ifPresent(this::saveAs);
@@ -92,7 +93,8 @@ public boolean saveAs(Path file) {
     public void saveSelectedAsPlain() {
         askForSavePath().ifPresent(path -> {
             try {
-                saveDatabase(path, true, StandardCharsets.UTF_8, BibDatabaseWriter.SaveType.PLAIN_BIBTEX);
+                saveDatabase(path, true, StandardCharsets.UTF_8, BibDatabaseWriter.SaveType.PLAIN_BIBTEX,
+                        libraryTab.getBibDatabaseContext().getMetaData().getSaveOrder().orElse(SaveOrder.getDefaultSaveOrder()));
                 frame.getFileHistory().newFile(path);
                 dialogService.notify(Localization.lang("Saved selected to '%0'.", path.toString()));
             } catch (SaveException ex) {
@@ -210,7 +212,8 @@ private boolean save(Path targetPath, SaveDatabaseMode mode) {
             libraryTab.getBibDatabaseContext().getMetaData().setEncoding(encoding, ChangePropagation.DO_NOT_POST_EVENT);
 
             // Save the database
-            boolean success = saveDatabase(targetPath, false, encoding, BibDatabaseWriter.SaveType.ALL);
+            boolean success = saveDatabase(targetPath, false, encoding, BibDatabaseWriter.SaveType.WITH_JABREF_META_DATA,
+                    libraryTab.getBibDatabaseContext().getMetaData().getSaveOrder().orElse(SaveOrder.getDefaultSaveOrder()));
 
             if (success) {
                 libraryTab.getUndoManager().markUnchanged();
@@ -228,12 +231,12 @@ private boolean save(Path targetPath, SaveDatabaseMode mode) {
         }
     }
 
-    private boolean saveDatabase(Path file, boolean selectedOnly, Charset encoding, BibDatabaseWriter.SaveType saveType) throws SaveException {
+    private boolean saveDatabase(Path file, boolean selectedOnly, Charset encoding, BibDatabaseWriter.SaveType saveType, SaveOrder saveOrder) throws SaveException {
         // if this code is adapted, please also adapt org.jabref.logic.autosaveandbackup.BackupManager.performBackup
 
         SaveConfiguration saveConfiguration = new SaveConfiguration()
                 .withSaveType(saveType)
-                .withMetadataSaveOrder(true)
+                .withSaveOrder(saveOrder)
                 .withReformatOnSave(preferences.getLibraryPreferences().shouldAlwaysReformatOnSave());
         BibDatabaseContext bibDatabaseContext = libraryTab.getBibDatabaseContext();
         synchronized (bibDatabaseContext) {
@@ -255,7 +258,7 @@ private boolean saveDatabase(Path file, boolean selectedOnly, Charset encoding,
                 libraryTab.registerUndoableChanges(databaseWriter.getSaveActionsFieldChanges());
 
                 if (fileWriter.hasEncodingProblems()) {
-                    saveWithDifferentEncoding(file, selectedOnly, encoding, fileWriter.getEncodingProblems(), saveType);
+                    saveWithDifferentEncoding(file, selectedOnly, encoding, fileWriter.getEncodingProblems(), saveType, saveOrder);
                 }
             } catch (UnsupportedCharsetException ex) {
                 throw new SaveException(Localization.lang("Character encoding '%0' is not supported.", encoding.displayName()), ex);
@@ -266,7 +269,7 @@ private boolean saveDatabase(Path file, boolean selectedOnly, Charset encoding,
         }
     }
 
-    private void saveWithDifferentEncoding(Path file, boolean selectedOnly, Charset encoding, Set<Character> encodingProblems, BibDatabaseWriter.SaveType saveType) throws SaveException {
+    private void saveWithDifferentEncoding(Path file, boolean selectedOnly, Charset encoding, Set<Character> encodingProblems, BibDatabaseWriter.SaveType saveType, SaveOrder saveOrder) throws SaveException {
         DialogPane pane = new DialogPane();
         VBox vbox = new VBox();
         vbox.getChildren().addAll(
@@ -288,7 +291,7 @@ private void saveWithDifferentEncoding(Path file, boolean selectedOnly, Charset
                 // Make sure to remember which encoding we used.
                 libraryTab.getBibDatabaseContext().getMetaData().setEncoding(newEncoding.get(), ChangePropagation.DO_NOT_POST_EVENT);
 
-                saveDatabase(file, selectedOnly, newEncoding.get(), saveType);
+                saveDatabase(file, selectedOnly, newEncoding.get(), saveType, saveOrder);
             }
         }
     }

src/main/java/org/jabref/gui/libraryproperties/saving/SavingPropertiesViewModel.java

@@ -1,6 +1,7 @@
 package org.jabref.gui.libraryproperties.saving;
 
 import java.util.ArrayList;
+import java.util.List;
 import java.util.Optional;
 import java.util.Set;
 
@@ -18,13 +19,22 @@
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.FieldFactory;
 import org.jabref.model.entry.field.InternalField;
+import org.jabref.model.entry.field.StandardField;
 import org.jabref.model.metadata.MetaData;
 import org.jabref.model.metadata.SaveOrder;
 import org.jabref.preferences.CleanupPreferences;
 import org.jabref.preferences.PreferencesService;
 
 public class SavingPropertiesViewModel implements PropertiesTabViewModel {
 
+    private static final SaveOrder UI_DEFAULT_SAVE_ORDER = new SaveOrder(SaveOrder.OrderType.ORIGINAL, List.of(
+            new SaveOrder.SortCriterion(StandardField.AUTHOR),
+            new SaveOrder.SortCriterion(StandardField.YEAR),
+            new SaveOrder.SortCriterion(StandardField.TITLE),
+            // Pro users generate their citation keys well. They can just delete the above three proposals and get a well-sorted library.
+            new SaveOrder.SortCriterion(InternalField.KEY_FIELD)
+    ));
+
     private final BooleanProperty protectDisableProperty = new SimpleBooleanProperty();
     private final BooleanProperty libraryProtectedProperty = new SimpleBooleanProperty();
 
@@ -41,24 +51,23 @@ public class SavingPropertiesViewModel implements PropertiesTabViewModel {
 
     private final BibDatabaseContext databaseContext;
     private final MetaData initialMetaData;
-    private final SaveOrder exportSaveOrder;
+    private final SaveOrder saveOrder;
     private final PreferencesService preferencesService;
 
     public SavingPropertiesViewModel(BibDatabaseContext databaseContext, PreferencesService preferencesService) {
         this.databaseContext = databaseContext;
         this.preferencesService = preferencesService;
         this.initialMetaData = databaseContext.getMetaData();
-        this.exportSaveOrder = initialMetaData.getSaveOrderConfig()
-                                              .orElseGet(() -> preferencesService.getExportPreferences().getExportSaveOrder());
+        this.saveOrder = initialMetaData.getSaveOrder().orElse(UI_DEFAULT_SAVE_ORDER);
     }
 
     @Override
     public void setValues() {
         libraryProtectedProperty.setValue(initialMetaData.isProtected());
 
-        // SaveOrderConfigPanel
+        // SaveOrderConfigPanel, included via <?import ...> in FXML
 
-        switch (exportSaveOrder.getOrderType()) {
+        switch (saveOrder.getOrderType()) {
             case SPECIFIED -> saveInSpecifiedOrderProperty.setValue(true);
             case ORIGINAL -> saveInOriginalProperty.setValue(true);
             case TABLE -> saveInTableOrderProperty.setValue(true);
@@ -74,11 +83,11 @@ public void setValues() {
 
         sortableFieldsProperty.addAll(FieldFactory.getStandardFieldsWithCitationKey());
         sortCriteriaProperty.clear();
-        sortCriteriaProperty.addAll(exportSaveOrder.getSortCriteria().stream()
-                                                   .map(SortCriterionViewModel::new)
-                                                   .toList());
+        sortCriteriaProperty.addAll(saveOrder.getSortCriteria().stream()
+                                             .map(SortCriterionViewModel::new)
+                                             .toList());
 
-        // FieldFormatterCleanupsPanel
+        // FieldFormatterCleanupsPanel, included via <?import ...> in FXML
 
         Optional<FieldFormatterCleanups> saveActions = initialMetaData.getSaveActions();
         saveActions.ifPresentOrElse(value -> {
@@ -120,11 +129,11 @@ public void storeSettings() {
                 SaveOrder.OrderType.fromBooleans(saveInSpecifiedOrderProperty.getValue(), saveInOriginalProperty.getValue()),
                 sortCriteriaProperty.stream().map(SortCriterionViewModel::getCriterion).toList());
 
-        if (!newSaveOrder.equals(exportSaveOrder)) {
+        if (!newSaveOrder.equals(saveOrder)) {
             if (newSaveOrder.equals(SaveOrder.getDefaultSaveOrder())) {
-                newMetaData.clearSaveOrderConfig();
+                newMetaData.clearSaveOrder();
             } else {
-                newMetaData.setSaveOrderConfig(newSaveOrder);
+                newMetaData.setSaveOrder(newSaveOrder);
             }
         }
 

src/main/java/org/jabref/logic/autosaveandbackup/BackupManager.java

@@ -30,6 +30,7 @@
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.event.BibDatabaseContextChangedEvent;
 import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.metadata.SaveOrder;
 import org.jabref.preferences.PreferencesService;
 
 import com.google.common.eventbus.Subscribe;
@@ -225,7 +226,7 @@ void performBackup(Path backupPath) {
         // code similar to org.jabref.gui.exporter.SaveDatabaseAction.saveDatabase
         SaveConfiguration saveConfiguration = new SaveConfiguration()
                 .withMakeBackup(false)
-                .withMetadataSaveOrder(true)
+                .withSaveOrder(bibDatabaseContext.getMetaData().getSaveOrder().orElse(SaveOrder.getDefaultSaveOrder()))
                 .withReformatOnSave(preferences.getLibraryPreferences().shouldAlwaysReformatOnSave());
 
         Charset encoding = bibDatabaseContext.getMetaData().getEncoding().orElse(StandardCharsets.UTF_8);

src/main/java/org/jabref/logic/bibtex/comparator/MetaDataDiff.java

@@ -56,7 +56,7 @@ public EnumSet<Difference> getDifferences(PreferencesService preferences) {
         if (!Objects.equals(originalMetaData.getEncoding(), newMetaData.getEncoding())) {
             changes.add(Difference.ENCODING);
         }
-        if (!Objects.equals(originalMetaData.getSaveOrderConfig(), newMetaData.getSaveOrderConfig())) {
+        if (!Objects.equals(originalMetaData.getSaveOrder(), newMetaData.getSaveOrder())) {
             changes.add(Difference.SAVE_SORT_ORDER);
         }
         if (!Objects.equals(

src/main/java/org/jabref/logic/crawler/StudyRepository.java

@@ -27,6 +27,8 @@
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntryTypesManager;
+import org.jabref.model.entry.field.StandardField;
+import org.jabref.model.metadata.SaveOrder;
 import org.jabref.model.study.FetchResult;
 import org.jabref.model.study.QueryResult;
 import org.jabref.model.study.Study;
@@ -60,6 +62,11 @@ public class StudyRepository {
     private static final String WORK_BRANCH = "work";
     private static final String SEARCH_BRANCH = "search";
 
+    private static final SaveOrder SAVE_ORDER = new SaveOrder(SaveOrder.OrderType.SPECIFIED,
+            List.of(new SaveOrder.SortCriterion(StandardField.AUTHOR, false),
+                    new SaveOrder.SortCriterion(StandardField.YEAR, true),
+                    new SaveOrder.SortCriterion(StandardField.TITLE, false)));
+
     private final Path repositoryPath;
     private final Path studyDefinitionFile;
     private final SlrGitHandler gitHandler;
@@ -426,7 +433,7 @@ private void generateCiteKeys(BibDatabaseContext existingEntries, BibDatabase ta
     private void writeResultToFile(Path pathToFile, BibDatabase entries) throws SaveException {
         try (AtomicFileWriter fileWriter = new AtomicFileWriter(pathToFile, StandardCharsets.UTF_8)) {
             SaveConfiguration saveConfiguration = new SaveConfiguration()
-                    .withMetadataSaveOrder(true)
+                    .withSaveOrder(SAVE_ORDER)
                     .withReformatOnSave(preferencesService.getLibraryPreferences().shouldAlwaysReformatOnSave());
             BibWriter bibWriter = new BibWriter(fileWriter, OS.NEWLINE);
             BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(