Fix exception when opening preferences (#10294)

* Introduce SelfContainedSaveConfiguration

* Fix checkstyle

* Fix NPE

src/jmh/java/org/jabref/benchmarks/Benchmarks.java

@@ -13,7 +13,7 @@
 import org.jabref.logic.citationkeypattern.CitationKeyPatternPreferences;
 import org.jabref.logic.exporter.BibWriter;
 import org.jabref.logic.exporter.BibtexDatabaseWriter;
-import org.jabref.logic.exporter.SaveConfiguration;
+import org.jabref.logic.exporter.SelfContainedSaveConfiguration;
 import org.jabref.logic.formatter.bibtexfields.HtmlToLatexFormatter;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.fileformat.BibtexParser;
@@ -82,7 +82,7 @@ private StringWriter getOutputWriter() throws IOException {
         BibWriter bibWriter = new BibWriter(outputWriter, OS.NEWLINE);
         BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(
                 bibWriter,
-                mock(SaveConfiguration.class),
+                mock(SelfContainedSaveConfiguration.class),
                 mock(FieldPreferences.class),
                 mock(CitationKeyPatternPreferences.class),
                 new BibEntryTypesManager());

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

@@ -25,7 +25,7 @@
 import org.jabref.logic.exporter.EmbeddedBibFilePdfExporter;
 import org.jabref.logic.exporter.Exporter;
 import org.jabref.logic.exporter.ExporterFactory;
-import org.jabref.logic.exporter.SaveConfiguration;
+import org.jabref.logic.exporter.SelfContainedSaveConfiguration;
 import org.jabref.logic.exporter.XmpPdfExporter;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ImportException;
@@ -598,7 +598,7 @@ private void saveDatabase(BibDatabase newBase, String subName) {
             System.out.println(Localization.lang("Saving") + ": " + subName);
             try (AtomicFileWriter fileWriter = new AtomicFileWriter(Path.of(subName), StandardCharsets.UTF_8)) {
                 BibWriter bibWriter = new BibWriter(fileWriter, OS.NEWLINE);
-                SaveConfiguration saveConfiguration = new SaveConfiguration()
+                SelfContainedSaveConfiguration saveConfiguration = (SelfContainedSaveConfiguration) new SelfContainedSaveConfiguration()
                         .withReformatOnSave(preferencesService.getLibraryPreferences().shouldAlwaysReformatOnSave());
                 BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(
                         bibWriter,

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

@@ -28,7 +28,7 @@
 import org.jabref.logic.exporter.AtomicFileWriter;
 import org.jabref.logic.exporter.BibWriter;
 import org.jabref.logic.exporter.BibtexDatabaseWriter;
-import org.jabref.logic.exporter.SaveConfiguration;
+import org.jabref.logic.exporter.SelfContainedSaveConfiguration;
 import org.jabref.logic.util.BackupFileType;
 import org.jabref.logic.util.CoarseChangeFilter;
 import org.jabref.logic.util.io.BackupFileUtil;
@@ -250,7 +250,7 @@ void performBackup(Path backupPath) {
                     }
                 })
                 .orElse(SaveOrder.getDefaultSaveOrder());
-        SaveConfiguration saveConfiguration = new SaveConfiguration()
+        SelfContainedSaveConfiguration saveConfiguration = (SelfContainedSaveConfiguration) new SelfContainedSaveConfiguration()
                 .withMakeBackup(false)
                 .withSaveOrder(saveOrder)
                 .withReformatOnSave(preferences.getLibraryPreferences().shouldAlwaysReformatOnSave());

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

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

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

@@ -31,8 +31,8 @@
 import org.jabref.logic.exporter.BibDatabaseWriter;
 import org.jabref.logic.exporter.BibWriter;
 import org.jabref.logic.exporter.BibtexDatabaseWriter;
-import org.jabref.logic.exporter.SaveConfiguration;
 import org.jabref.logic.exporter.SaveException;
+import org.jabref.logic.exporter.SelfContainedSaveConfiguration;
 import org.jabref.logic.l10n.Encodings;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.shared.DatabaseLocation;
@@ -256,11 +256,8 @@ private boolean save(Path targetPath, SaveDatabaseMode mode) {
 
     private boolean saveDatabase(Path file, boolean selectedOnly, Charset encoding, BibDatabaseWriter.SaveType saveType, SelfContainedSaveOrder saveOrder) throws SaveException {
         // if this code is adapted, please also adapt org.jabref.logic.autosaveandbackup.BackupManager.performBackup
-
-        SaveConfiguration saveConfiguration = new SaveConfiguration()
-                .withSaveType(saveType)
-                .withSaveOrder(saveOrder)
-                .withReformatOnSave(preferences.getLibraryPreferences().shouldAlwaysReformatOnSave());
+        SelfContainedSaveConfiguration saveConfiguration
+                = new SelfContainedSaveConfiguration(saveOrder, false, saveType, preferences.getLibraryPreferences().shouldAlwaysReformatOnSave());
         BibDatabaseContext bibDatabaseContext = libraryTab.getBibDatabaseContext();
         synchronized (bibDatabaseContext) {
             try (AtomicFileWriter fileWriter = new AtomicFileWriter(file, encoding, saveConfiguration.shouldMakeBackup())) {

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

@@ -16,8 +16,8 @@
 import org.jabref.logic.exporter.AtomicFileWriter;
 import org.jabref.logic.exporter.BibWriter;
 import org.jabref.logic.exporter.BibtexDatabaseWriter;
-import org.jabref.logic.exporter.SaveConfiguration;
 import org.jabref.logic.exporter.SaveException;
+import org.jabref.logic.exporter.SelfContainedSaveConfiguration;
 import org.jabref.logic.git.SlrGitHandler;
 import org.jabref.logic.importer.OpenDatabase;
 import org.jabref.logic.importer.SearchBasedFetcher;
@@ -427,7 +427,7 @@ private void generateCiteKeys(BibDatabaseContext existingEntries, BibDatabase ta
 
     private void writeResultToFile(Path pathToFile, BibDatabaseContext context) throws SaveException {
         try (AtomicFileWriter fileWriter = new AtomicFileWriter(pathToFile, StandardCharsets.UTF_8)) {
-            SaveConfiguration saveConfiguration = new SaveConfiguration()
+            SelfContainedSaveConfiguration saveConfiguration = (SelfContainedSaveConfiguration) new SelfContainedSaveConfiguration()
                     .withSaveOrder(context.getMetaData().getSaveOrder().map(so -> SelfContainedSaveOrder.of(so)).orElse(SaveOrder.getDefaultSaveOrder()))
                     .withReformatOnSave(preferencesService.getLibraryPreferences().shouldAlwaysReformatOnSave());
             BibWriter bibWriter = new BibWriter(fileWriter, OS.NEWLINE);

src/main/java/org/jabref/logic/exporter/BibDatabaseWriter.java

@@ -58,13 +58,13 @@ public enum SaveType { WITH_JABREF_META_DATA, PLAIN_BIBTEX }
 
     private static final Pattern REFERENCE_PATTERN = Pattern.compile("(#[A-Za-z]+#)"); // Used to detect string references in strings
     protected final BibWriter bibWriter;
-    protected final SaveConfiguration saveConfiguration;
+    protected final SelfContainedSaveConfiguration saveConfiguration;
     protected final CitationKeyPatternPreferences keyPatternPreferences;
     protected final List<FieldChange> saveActionsFieldChanges = new ArrayList<>();
     protected final BibEntryTypesManager entryTypesManager;
 
     public BibDatabaseWriter(BibWriter bibWriter,
-                             SaveConfiguration saveConfiguration,
+                             SelfContainedSaveConfiguration saveConfiguration,
                              CitationKeyPatternPreferences keyPatternPreferences,
                              BibEntryTypesManager entryTypesManager) {
         this.bibWriter = Objects.requireNonNull(bibWriter);
@@ -181,7 +181,7 @@ public void savePartOfDatabase(BibDatabaseContext bibDatabaseContext, List<BibEn
         writeStrings(bibDatabaseContext.getDatabase());
 
         // Write database entries.
-        List<BibEntry> sortedEntries = getSortedEntries(entries, saveConfiguration.getSaveOrder());
+        List<BibEntry> sortedEntries = getSortedEntries(entries, saveConfiguration.getSelfContainedSaveOrder());
         List<FieldChange> saveActionChanges = applySaveActions(sortedEntries, bibDatabaseContext.getMetaData());
         saveActionsFieldChanges.addAll(saveActionChanges);
         if (keyPatternPreferences.shouldGenerateCiteKeysBeforeSaving()) {

src/main/java/org/jabref/logic/exporter/BibtexDatabaseWriter.java

@@ -35,7 +35,7 @@ public class BibtexDatabaseWriter extends BibDatabaseWriter {
     private final FieldPreferences fieldPreferences;
 
     public BibtexDatabaseWriter(BibWriter bibWriter,
-                                SaveConfiguration saveConfiguration,
+                                SelfContainedSaveConfiguration saveConfiguration,
                                 FieldPreferences fieldPreferences,
                                 CitationKeyPatternPreferences citationKeyPatternPreferences,
                                 BibEntryTypesManager entryTypesManager) {
@@ -49,7 +49,7 @@ public BibtexDatabaseWriter(BibWriter bibWriter,
 
     public BibtexDatabaseWriter(Writer writer,
                                 String newline,
-                                SaveConfiguration saveConfiguration,
+                                SelfContainedSaveConfiguration saveConfiguration,
                                 FieldPreferences fieldPreferences,
                                 CitationKeyPatternPreferences citationKeyPatternPreferences,
                                 BibEntryTypesManager entryTypesManager) {

src/main/java/org/jabref/logic/exporter/ExporterFactory.java

@@ -29,7 +29,7 @@ public static ExporterFactory create(PreferencesService preferencesService,
 
         List<TemplateExporter> customFormats = preferencesService.getExportPreferences().getCustomExporters();
         LayoutFormatterPreferences layoutPreferences = preferencesService.getLayoutFormatterPreferences();
-        SelfContainedSaveOrder saveOrder = SelfContainedSaveOrder.of(preferencesService.getExportConfiguration().getSaveOrder());
+        SelfContainedSaveOrder saveOrder = SelfContainedSaveOrder.of(preferencesService.getSelfContainedExportConfiguration().getSaveOrder());
         XmpPreferences xmpPreferences = preferencesService.getXmpPreferences();
         FieldPreferences fieldPreferences = preferencesService.getFieldPreferences();
         BibDatabaseMode bibDatabaseMode = preferencesService.getLibraryPreferences().getDefaultBibDatabaseMode();

src/main/java/org/jabref/logic/exporter/SaveConfiguration.java

@@ -2,19 +2,18 @@
 
 import org.jabref.gui.autosaveandbackup.BackupManager;
 import org.jabref.model.metadata.SaveOrder;
-import org.jabref.model.metadata.SelfContainedSaveOrder;
 
 public class SaveConfiguration {
 
     // Encoding written at the top of the .bib file.
     public static final String ENCODING_PREFIX = "Encoding: ";
 
     private boolean reformatFile;
-    private SelfContainedSaveOrder saveOrder;
+    private SaveOrder saveOrder;
     private boolean makeBackup;
     private BibDatabaseWriter.SaveType saveType;
 
-    public SaveConfiguration(SelfContainedSaveOrder saveOrder,
+    public SaveConfiguration(SaveOrder saveOrder,
                              Boolean makeBackup,
                              BibDatabaseWriter.SaveType saveType,
                              Boolean reformatFile) {
@@ -31,11 +30,11 @@ public SaveConfiguration() {
                 false);
     }
 
-    public SelfContainedSaveOrder getSaveOrder() {
+    public SaveOrder getSaveOrder() {
         return saveOrder;
     }
 
-    public SaveConfiguration withSaveOrder(SelfContainedSaveOrder newSaveOrder) {
+    public SaveConfiguration withSaveOrder(SaveOrder newSaveOrder) {
         this.saveOrder = newSaveOrder;
         return this;
     }

src/main/java/org/jabref/logic/exporter/SelfContainedSaveConfiguration.java

@@ -0,0 +1,25 @@
+package org.jabref.logic.exporter;
+
+import org.jabref.model.metadata.SaveOrder;
+import org.jabref.model.metadata.SelfContainedSaveOrder;
+
+/**
+ * This is a {@link SaveOrder} where the contained saveConfiguration is a {@link org.jabref.model.metadata.SelfContainedSaveOrder}
+ */
+public class SelfContainedSaveConfiguration extends SaveConfiguration {
+    public SelfContainedSaveConfiguration() {
+        super();
+    }
+
+    public SelfContainedSaveConfiguration(
+            SelfContainedSaveOrder saveOrder,
+            Boolean makeBackup,
+            BibDatabaseWriter.SaveType saveType,
+            Boolean reformatFile) {
+        super(saveOrder, makeBackup, saveType, reformatFile);
+    }
+
+    public SelfContainedSaveOrder getSelfContainedSaveOrder() {
+        return (SelfContainedSaveOrder) getSaveOrder();
+    }
+}

src/main/java/org/jabref/model/metadata/SelfContainedSaveOrder.java

@@ -2,14 +2,23 @@
 
 import java.util.List;
 
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
 /**
  * With this class, the user of an instance can directly sort things. Without looking up anything in the preferences or in the UI.
+ *
+ * To avoid confusion at the caller, we offer ORIGINAL and SPECIFIED only. Not TABLE.
  */
 public class SelfContainedSaveOrder extends SaveOrder {
+
+    public static final Logger LOGGER = LoggerFactory.getLogger(SelfContainedSaveOrder.class);
+
     public SelfContainedSaveOrder(OrderType orderType, List<SortCriterion> sortCriteria) {
         super(orderType, sortCriteria);
         if (orderType == OrderType.TABLE) {
-            throw new IllegalArgumentException("TABLE requires external lookup.");
+            LOGGER.debug("TABLE with sort criteria {}", sortCriteria);
+            throw new IllegalArgumentException("TABLE might require external lookup.");
         }
     }
 
@@ -22,6 +31,11 @@ public static SelfContainedSaveOrder of(SaveOrder saveOrder) {
         if (saveOrder instanceof SelfContainedSaveOrder order) {
             return order;
         }
+        if ((saveOrder.getOrderType() == OrderType.TABLE) && (!saveOrder.getSortCriteria().isEmpty())) {
+            // We map from TABLE to SPECIFIED to have the users of this class just to `switch` between
+            //   ORIGINAL and SPECIFIED
+            return new SelfContainedSaveOrder(OrderType.SPECIFIED, saveOrder.getSortCriteria());
+        }
         return new SelfContainedSaveOrder(saveOrder.getOrderType(), saveOrder.getSortCriteria());
     }
 }

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

@@ -65,8 +65,9 @@
 import org.jabref.logic.citationstyle.CitationStyle;
 import org.jabref.logic.citationstyle.CitationStylePreviewLayout;
 import org.jabref.logic.cleanup.FieldFormatterCleanups;
+import org.jabref.logic.exporter.BibDatabaseWriter;
 import org.jabref.logic.exporter.MetaDataSerializer;
-import org.jabref.logic.exporter.SaveConfiguration;
+import org.jabref.logic.exporter.SelfContainedSaveConfiguration;
 import org.jabref.logic.exporter.TemplateExporter;
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.ImporterPreferences;
@@ -2256,29 +2257,33 @@ private void storeExportSaveOrder(SaveOrder saveOrder) {
         putBoolean(EXPORT_TERTIARY_SORT_DESCENDING, saveOrder.getSortCriteria().get(2).descending);
     }
 
-    public SaveOrder getTableSaveOrder() {
+    /**
+     * For the export configuration, generates the SelfContainedSaveOrder having the reference to TABLE resolved.
+     */
+    public SelfContainedSaveOrder getSelfContainedTableSaveOrder() {
         List<MainTableColumnModel> sortOrder = mainTableColumnPreferences.getColumnSortOrder();
-        return new SaveOrder(
-                SaveOrder.OrderType.TABLE,
+        return new SelfContainedSaveOrder(
+                SaveOrder.OrderType.SPECIFIED,
                 sortOrder.stream().flatMap(model -> model.getSortCriteria().stream()).toList());
     }
 
     @Override
-    public SaveConfiguration getExportConfiguration() {
-        SaveOrder saveOrder = switch (getExportSaveOrder().getOrderType()) {
-            case TABLE -> this.getTableSaveOrder();
-            case SPECIFIED -> this.getExportSaveOrder();
+    public SelfContainedSaveConfiguration getSelfContainedExportConfiguration() {
+        SaveOrder exportSaveOrder = getExportSaveOrder();
+        SelfContainedSaveOrder saveOrder = switch (exportSaveOrder.getOrderType()) {
+            case TABLE -> this.getSelfContainedTableSaveOrder();
+            case SPECIFIED -> SelfContainedSaveOrder.of(exportSaveOrder);
             case ORIGINAL -> SaveOrder.getDefaultSaveOrder();
         };
 
-        return new SaveConfiguration()
-                .withSaveOrder(SelfContainedSaveOrder.of(saveOrder))
-                .withReformatOnSave(getLibraryPreferences().shouldAlwaysReformatOnSave());
+        return new SelfContainedSaveConfiguration(
+                saveOrder, false, BibDatabaseWriter.SaveType.WITH_JABREF_META_DATA, getLibraryPreferences()
+                .shouldAlwaysReformatOnSave());
     }
 
     private List<TemplateExporter> getCustomExportFormats() {
         LayoutFormatterPreferences layoutPreferences = getLayoutFormatterPreferences();
-        SaveConfiguration saveConfiguration = getExportConfiguration();
+        SelfContainedSaveConfiguration saveConfiguration = getSelfContainedExportConfiguration();
         List<TemplateExporter> formats = new ArrayList<>();
 
         for (String toImport : getSeries(CUSTOM_EXPORT_FORMAT)) {
@@ -2288,7 +2293,7 @@ private List<TemplateExporter> getCustomExportFormats() {
                     formatData.get(EXPORTER_FILENAME_INDEX),
                     formatData.get(EXPORTER_EXTENSION_INDEX),
                     layoutPreferences,
-                    saveConfiguration.getSaveOrder());
+                    saveConfiguration.getSelfContainedSaveOrder());
             format.setCustomExport(true);
             formats.add(format);
         }

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

@@ -15,7 +15,7 @@
 import org.jabref.logic.JabRefException;
 import org.jabref.logic.bibtex.FieldPreferences;
 import org.jabref.logic.citationkeypattern.CitationKeyPatternPreferences;
-import org.jabref.logic.exporter.SaveConfiguration;
+import org.jabref.logic.exporter.SelfContainedSaveConfiguration;
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.ImporterPreferences;
 import org.jabref.logic.importer.fetcher.GrobidPreferences;
@@ -73,7 +73,7 @@ public interface PreferencesService {
     /**
      * Returns the export configuration. The contained SaveConfiguration is a {@link org.jabref.model.metadata.SelfContainedSaveOrder}
      */
-    SaveConfiguration getExportConfiguration();
+    SelfContainedSaveConfiguration getSelfContainedExportConfiguration();
 
     BibEntryTypesManager getCustomEntryTypesRepository();