Improve serialization to fix #4877

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

@@ -16,7 +16,6 @@
 import org.jabref.logic.layout.format.HTMLChars;
 import org.jabref.logic.layout.format.LatexToUnicodeFormatter;
 import org.jabref.logic.search.SearchQuery;
-import org.jabref.model.Defaults;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
@@ -76,8 +75,7 @@ public void init() throws Exception {
     private StringWriter getOutputWriter() throws IOException {
         StringWriter outputWriter = new StringWriter();
         BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(outputWriter, mock(SavePreferences.class), new BibEntryTypesManager());
-        databaseWriter.savePartOfDatabase(
-                new BibDatabaseContext(database, new MetaData(), new Defaults()), database.getEntries());
+        databaseWriter.savePartOfDatabase(new BibDatabaseContext(database, new MetaData()), database.getEntries());
         return outputWriter;
     }
 

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

@@ -44,7 +44,6 @@
 import org.jabref.logic.shared.prefs.SharedDatabasePreferences;
 import org.jabref.logic.util.OS;
 import org.jabref.logic.xmp.XmpPreferences;
-import org.jabref.model.Defaults;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
@@ -392,8 +391,7 @@ private void saveDatabase(BibDatabase newBase, String subName) {
             SavePreferences prefs = Globals.prefs.loadForSaveFromPreferences();
             AtomicFileWriter fileWriter = new AtomicFileWriter(Paths.get(subName), prefs.getEncoding());
             BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(fileWriter, prefs, Globals.entryTypesManager);
-            Defaults defaults = new Defaults(Globals.prefs.getDefaultBibDatabaseMode());
-            databaseWriter.saveDatabase(new BibDatabaseContext(newBase, defaults));
+            databaseWriter.saveDatabase(new BibDatabaseContext(newBase));
 
             // Show just a warning message if encoding did not work for all characters:
             if (fileWriter.hasEncodingProblems()) {

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

@@ -21,7 +21,7 @@
 
 import org.jabref.Globals;
 import org.jabref.logic.bibtex.BibEntryWriter;
-import org.jabref.logic.bibtex.LatexFieldFormatter;
+import org.jabref.logic.bibtex.FieldWriter;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.ImportException;
 import org.jabref.logic.importer.ImportFormatReader;
@@ -152,7 +152,7 @@ public void setContent(String string) {
 
     public void setContent(List<BibEntry> entries) throws IOException {
         final ClipboardContent content = new ClipboardContent();
-        BibEntryWriter writer = new BibEntryWriter(new LatexFieldFormatter(Globals.prefs.getLatexFieldFormatterPreferences()), Globals.entryTypesManager);
+        BibEntryWriter writer = new BibEntryWriter(new FieldWriter(Globals.prefs.getFieldWriterPreferences()), Globals.entryTypesManager);
         String serializedEntries = writer.serializeAll(entries, BibDatabaseMode.BIBTEX);
         content.put(DragAndDropDataFormats.ENTRIES, serializedEntries);
         content.putString(serializedEntries);

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

@@ -20,7 +20,6 @@
 import org.jabref.logic.auxparser.DefaultAuxParser;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.StandardFileType;
-import org.jabref.model.Defaults;
 import org.jabref.model.auxparser.AuxParser;
 import org.jabref.model.auxparser.AuxParserResult;
 import org.jabref.model.database.BibDatabase;
@@ -59,8 +58,7 @@ public FromAuxDialog(JabRefFrame frame) {
         generateButton.defaultButtonProperty().bind(generateButton.disableProperty().not());
         setResultConverter(button -> {
             if (button == generateButtonType) {
-                Defaults defaults = new Defaults(Globals.prefs.getDefaultBibDatabaseMode());
-                BasePanel bp = new BasePanel(frame, BasePanelPreferences.from(Globals.prefs), new BibDatabaseContext(auxParserResult.getGeneratedBibDatabase(), defaults), ExternalFileTypes.getInstance());
+                BasePanel bp = new BasePanel(frame, BasePanelPreferences.from(Globals.prefs), new BibDatabaseContext(auxParserResult.getGeneratedBibDatabase()), ExternalFileTypes.getInstance());
                 frame.addTab(bp, true);
             }
             return null;

src/main/java/org/jabref/gui/entryeditor/EntryEditor.java

@@ -252,7 +252,7 @@ private List<EntryEditorTab> createTabs() {
 
         // Source tab
         sourceTab = new SourceTab(databaseContext, undoManager,
-                entryEditorPreferences.getLatexFieldFormatterPreferences(),
+                entryEditorPreferences.getFieldWriterPreferences(),
                 entryEditorPreferences.getImportFormatPreferences(), fileMonitor, dialogService, stateManager, Globals.getKeyPrefs());
         entryEditorTabs.add(sourceTab);
 

src/main/java/org/jabref/gui/entryeditor/EntryEditorPreferences.java

@@ -5,15 +5,15 @@
 import java.util.Set;
 
 import org.jabref.gui.keyboard.KeyBindingRepository;
-import org.jabref.logic.bibtex.LatexFieldFormatterPreferences;
+import org.jabref.logic.bibtex.FieldWriterPreferences;
 import org.jabref.logic.bibtexkeypattern.BibtexKeyPatternPreferences;
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.model.entry.field.Field;
 
 public class EntryEditorPreferences {
 
     private final Map<String, Set<Field>> entryEditorTabList;
-    private final LatexFieldFormatterPreferences latexFieldFormatterPreferences;
+    private final FieldWriterPreferences fieldWriterPreferences;
     private final ImportFormatPreferences importFormatPreferences;
     private final BibtexKeyPatternPreferences bibtexKeyPatternPreferences;
     private final List<Field> customTabFieldNames;
@@ -24,9 +24,9 @@ public class EntryEditorPreferences {
     private boolean avoidOverwritingCiteKey;
     private final boolean shouldShowLatexCitationsTab;
 
-    public EntryEditorPreferences(Map<String, Set<Field>> entryEditorTabList, LatexFieldFormatterPreferences latexFieldFormatterPreferences, ImportFormatPreferences importFormatPreferences, List<Field> customTabFieldNames, boolean shouldShowRecommendationsTab, boolean isMrdlibAccepted, boolean shouldShowLatexCitationsTab, boolean showSourceTabByDefault, BibtexKeyPatternPreferences bibtexKeyPatternPreferences, KeyBindingRepository keyBindings, boolean avoidOverwritingCiteKey) {
+    public EntryEditorPreferences(Map<String, Set<Field>> entryEditorTabList, FieldWriterPreferences fieldWriterPreferences, ImportFormatPreferences importFormatPreferences, List<Field> customTabFieldNames, boolean shouldShowRecommendationsTab, boolean isMrdlibAccepted, boolean shouldShowLatexCitationsTab, boolean showSourceTabByDefault, BibtexKeyPatternPreferences bibtexKeyPatternPreferences, KeyBindingRepository keyBindings, boolean avoidOverwritingCiteKey) {
         this.entryEditorTabList = entryEditorTabList;
-        this.latexFieldFormatterPreferences = latexFieldFormatterPreferences;
+        this.fieldWriterPreferences = fieldWriterPreferences;
         this.importFormatPreferences = importFormatPreferences;
         this.customTabFieldNames = customTabFieldNames;
         this.shouldShowRecommendationsTab = shouldShowRecommendationsTab;
@@ -42,8 +42,8 @@ public Map<String, Set<Field>> getEntryEditorTabList() {
         return entryEditorTabList;
     }
 
-    public LatexFieldFormatterPreferences getLatexFieldFormatterPreferences() {
-        return latexFieldFormatterPreferences;
+    public FieldWriterPreferences getFieldWriterPreferences() {
+        return fieldWriterPreferences;
     }
 
     public ImportFormatPreferences getImportFormatPreferences() {

src/main/java/org/jabref/gui/entryeditor/SourceTab.java

@@ -33,9 +33,9 @@
 import org.jabref.gui.undo.UndoableFieldChange;
 import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.logic.bibtex.BibEntryWriter;
+import org.jabref.logic.bibtex.FieldWriter;
+import org.jabref.logic.bibtex.FieldWriterPreferences;
 import org.jabref.logic.bibtex.InvalidFieldValueException;
-import org.jabref.logic.bibtex.LatexFieldFormatter;
-import org.jabref.logic.bibtex.LatexFieldFormatterPreferences;
 import org.jabref.logic.importer.ImportFormatPreferences;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.importer.fileformat.BibtexParser;
@@ -59,7 +59,7 @@
 public class SourceTab extends EntryEditorTab {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(SourceTab.class);
-    private final LatexFieldFormatterPreferences fieldFormatterPreferences;
+    private final FieldWriterPreferences fieldWriterPreferences;
     private final BibDatabaseMode mode;
     private final UndoManager undoManager;
     private final ObjectProperty<ValidationMessage> sourceIsValid = new SimpleObjectProperty<>();
@@ -100,13 +100,13 @@ public void execute() {
         }
     }
 
-    public SourceTab(BibDatabaseContext bibDatabaseContext, CountingUndoManager undoManager, LatexFieldFormatterPreferences fieldFormatterPreferences, ImportFormatPreferences importFormatPreferences, FileUpdateMonitor fileMonitor, DialogService dialogService, StateManager stateManager, KeyBindingRepository keyBindingRepository) {
+    public SourceTab(BibDatabaseContext bibDatabaseContext, CountingUndoManager undoManager, FieldWriterPreferences fieldWriterPreferences, ImportFormatPreferences importFormatPreferences, FileUpdateMonitor fileMonitor, DialogService dialogService, StateManager stateManager, KeyBindingRepository keyBindingRepository) {
         this.mode = bibDatabaseContext.getMode();
         this.setText(Localization.lang("%0 source", mode.getFormattedName()));
         this.setTooltip(new Tooltip(Localization.lang("Show/edit %0 source", mode.getFormattedName())));
         this.setGraphic(IconTheme.JabRefIcons.SOURCE.getGraphicNode());
         this.undoManager = undoManager;
-        this.fieldFormatterPreferences = fieldFormatterPreferences;
+        this.fieldWriterPreferences = fieldWriterPreferences;
         this.importFormatPreferences = importFormatPreferences;
         this.fileMonitor = fileMonitor;
         this.dialogService = dialogService;
@@ -137,10 +137,10 @@ private void highlightSearchPattern() {
         }
     }
 
-    private static String getSourceString(BibEntry entry, BibDatabaseMode type, LatexFieldFormatterPreferences fieldFormatterPreferences) throws IOException {
+    private static String getSourceString(BibEntry entry, BibDatabaseMode type, FieldWriterPreferences fieldWriterPreferences) throws IOException {
         StringWriter stringWriter = new StringWriter(200);
-        LatexFieldFormatter formatter = LatexFieldFormatter.buildIgnoreHashes(fieldFormatterPreferences);
-        new BibEntryWriter(formatter, Globals.entryTypesManager).writeWithoutPrependedNewlines(entry, stringWriter, type);
+        FieldWriter fieldWriter = FieldWriter.buildIgnoreHashes(fieldWriterPreferences);
+        new BibEntryWriter(fieldWriter, Globals.entryTypesManager).writeWithoutPrependedNewlines(entry, stringWriter, type);
 
         return stringWriter.getBuffer().toString();
     }
@@ -220,7 +220,7 @@ private void updateCodeArea() {
         DefaultTaskExecutor.runAndWaitInJavaFXThread(() -> {
             codeArea.clear();
             try {
-                codeArea.appendText(getSourceString(currentEntry, mode, fieldFormatterPreferences));
+                codeArea.appendText(getSourceString(currentEntry, mode, fieldWriterPreferences));
                 highlightSearchPattern();
             } catch (IOException ex) {
                 codeArea.setEditable(false);
@@ -300,7 +300,7 @@ private void storeSource(BibEntry outOfFocusEntry, String text) {
                 String newValue = field.getValue();
                 if (!Objects.equals(oldValue, newValue)) {
                     // Test if the field is legally set.
-                    new LatexFieldFormatter(fieldFormatterPreferences).format(newValue, fieldName);
+                    new FieldWriter(fieldWriterPreferences).write(fieldName, newValue);
 
                     compound.addEdit(new UndoableFieldChange(outOfFocusEntry, fieldName, oldValue, newValue));
                     outOfFocusEntry.setField(fieldName, newValue);

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

@@ -114,10 +114,10 @@ private void saveWithDifferentEncoding(Path file, boolean selectedOnly, Charset
         if (saveWithDifferentEncoding) {
             Optional<Charset> newEncoding = frame.getDialogService().showChoiceDialogAndWait(Localization.lang("Save library"), Localization.lang("Select new encoding"), Localization.lang("Save library"), encoding, Encodings.getCharsets());
             if (newEncoding.isPresent()) {
-                saveDatabase(file, selectedOnly, newEncoding.get(), saveType);
-
                 // Make sure to remember which encoding we used.
                 panel.getBibDatabaseContext().getMetaData().setEncoding(newEncoding.get(), ChangePropagation.DO_NOT_POST_EVENT);
+
+                saveDatabase(file, selectedOnly, newEncoding.get(), saveType);
             }
         }
     }
@@ -126,13 +126,15 @@ private boolean doSave() {
         panel.setSaving(true);
         Path targetPath = panel.getBibDatabaseContext().getDatabasePath().get();
         try {
+            Charset encoding = panel.getBibDatabaseContext()
+                                    .getMetaData()
+                                    .getEncoding()
+                                    .orElse(prefs.getDefaultEncoding());
+            // Make sure to remember which encoding we used.
+            panel.getBibDatabaseContext().getMetaData().setEncoding(encoding, ChangePropagation.DO_NOT_POST_EVENT);
+
             // Save the database
-            boolean success = saveDatabase(targetPath, false,
-                    panel.getBibDatabaseContext()
-                         .getMetaData()
-                         .getEncoding()
-                         .orElse(prefs.getDefaultEncoding()),
-                    SavePreferences.DatabaseSaveType.ALL);
+            boolean success = saveDatabase(targetPath, false, encoding, SavePreferences.DatabaseSaveType.ALL);
 
             if (success) {
                 panel.getUndoManager().markUnchanged();

src/main/java/org/jabref/gui/importer/NewDatabaseAction.java

@@ -2,7 +2,6 @@
 
 import org.jabref.gui.JabRefFrame;
 import org.jabref.gui.actions.SimpleCommand;
-import org.jabref.model.Defaults;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
 
@@ -21,7 +20,7 @@ public NewDatabaseAction(JabRefFrame jabRefFrame, BibDatabaseMode mode) {
 
     @Override
     public void execute() {
-        BibDatabaseContext bibDatabaseContext = new BibDatabaseContext(new Defaults(BibDatabaseMode.BIBTEX));
+        BibDatabaseContext bibDatabaseContext = new BibDatabaseContext();
         bibDatabaseContext.setMode(mode);
         jabRefFrame.addTab(bibDatabaseContext, true);
     }

src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java

@@ -48,7 +48,6 @@
 import org.jabref.logic.openoffice.StyleLoader;
 import org.jabref.logic.openoffice.UndefinedParagraphFormatException;
 import org.jabref.logic.util.io.FileUtil;
-import org.jabref.model.Defaults;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.entry.BibEntry;
@@ -295,8 +294,7 @@ private void exportEntries() {
 
             }
 
-            Defaults defaults = new Defaults(jabRefPreferences.getDefaultBibDatabaseMode());
-            BibDatabaseContext databaseContext = new BibDatabaseContext(newDatabase, defaults);
+            BibDatabaseContext databaseContext = new BibDatabaseContext(newDatabase);
             this.frame.addTab(databaseContext, true);
 
         } catch (BibEntryNotFoundException ex) {
@@ -435,7 +433,6 @@ private List<URL> findOpenOfficeJars(Path configurationPath) throws IOException
             jarURLs.add((jarPath.get().toUri().toURL()));
         }
         return jarURLs;
-
     }
 
     private OOBibBase createBibBase(List<URL> jarUrls) throws IOException, InvocationTargetException, IllegalAccessException,

src/main/java/org/jabref/gui/shared/SharedDatabaseUIManager.java

@@ -28,9 +28,7 @@
 import org.jabref.logic.shared.exception.InvalidDBMSConnectionPropertiesException;
 import org.jabref.logic.shared.exception.NotASharedDatabaseException;
 import org.jabref.logic.shared.prefs.SharedDatabasePreferences;
-import org.jabref.model.Defaults;
 import org.jabref.model.database.BibDatabaseContext;
-import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.database.shared.DatabaseNotSupportedException;
 import org.jabref.model.database.shared.DatabaseSynchronizer;
 import org.jabref.model.entry.BibEntry;
@@ -144,8 +142,8 @@ public void listen(SharedEntriesNotPresentEvent event) {
     public BasePanel openNewSharedDatabaseTab(DBMSConnectionProperties dbmsConnectionProperties)
         throws SQLException, DatabaseNotSupportedException, InvalidDBMSConnectionPropertiesException {
 
-        BibDatabaseMode selectedMode = Globals.prefs.getDefaultBibDatabaseMode();
-        BibDatabaseContext bibDatabaseContext = new BibDatabaseContext(new Defaults(selectedMode));
+        BibDatabaseContext bibDatabaseContext = new BibDatabaseContext();
+        bibDatabaseContext.setMode(Globals.prefs.getDefaultBibDatabaseMode());
         DBMSSynchronizer synchronizer = new DBMSSynchronizer(bibDatabaseContext, Globals.prefs.getKeywordDelimiter(), Globals.prefs.getKeyPattern(), Globals.getFileUpdateMonitor());
         bibDatabaseContext.convertToSharedDatabase(synchronizer);
 
@@ -169,8 +167,8 @@ public void openSharedDatabaseFromParserResult(ParserResult parserResult)
         String sharedDatabaseID = sharedDatabaseIDOptional.get();
         DBMSConnectionProperties dbmsConnectionProperties = new DBMSConnectionProperties(new SharedDatabasePreferences(sharedDatabaseID));
 
-        BibDatabaseMode selectedMode = Globals.prefs.getDefaultBibDatabaseMode();
-        BibDatabaseContext bibDatabaseContext = new BibDatabaseContext(new Defaults(selectedMode));
+        BibDatabaseContext bibDatabaseContext = new BibDatabaseContext();
+        bibDatabaseContext.setMode(Globals.prefs.getDefaultBibDatabaseMode());
         DBMSSynchronizer synchronizer = new DBMSSynchronizer(bibDatabaseContext, Globals.prefs.getKeywordDelimiter(), Globals.prefs.getKeyPattern(), Globals.getFileUpdateMonitor());
         bibDatabaseContext.convertToSharedDatabase(synchronizer);
 

src/main/java/org/jabref/gui/worker/SendAsEMailAction.java

@@ -15,7 +15,7 @@
 import org.jabref.gui.desktop.JabRefDesktop;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.logic.bibtex.BibEntryWriter;
-import org.jabref.logic.bibtex.LatexFieldFormatter;
+import org.jabref.logic.bibtex.FieldWriter;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.io.FileUtil;
 import org.jabref.model.entry.BibEntry;
@@ -72,8 +72,7 @@ private String sendEmail() throws Exception {
         List<BibEntry> bes = panel.getSelectedEntries();
 
         // write the entries using sw, which is used later to form the email content
-        BibEntryWriter bibtexEntryWriter = new BibEntryWriter(
-                new LatexFieldFormatter(Globals.prefs.getLatexFieldFormatterPreferences()), Globals.entryTypesManager);
+        BibEntryWriter bibtexEntryWriter = new BibEntryWriter(new FieldWriter(Globals.prefs.getFieldWriterPreferences()), Globals.entryTypesManager);
 
         for (BibEntry entry : bes) {
             try {