Refactor file preferences (#6779)

* Refactored for same basic clean-up and naming consistency

* Refactored for more clean-ups and naming consistency

* Refactored and extended AutoLinkPreferences

* Refactored FilePreferences to immutable class

* Refactored two preferences from AutoLinkPreferences to FilePreferences

* Moved import linked file patterns preferences to FilePreferencesTab

* Extended FilePreferences and refactored FileTab to use it

* Checkstyle

* Fixed merge error

* Moved import-export preferences to exportSortingTab and renamed the tab

* Renamed FileTab to LinkedFilesTab

* Refactored ImportExportTab to PreferencesService

* CHANGELOG.md

* Rewording ImportExport to File

* Make FilePreferences and SavePreferences mutable, added ADR

CHANGELOG.md

@@ -17,6 +17,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Changed
 
+- We restructured the 'File' tab and extracted some parts into the 'Linked files' tab [#6779](https://github.com/JabRef/jabref/pull/6779)
 - JabRef now offers journal lists from <https://abbrv.jabref.org>. JabRef the lists which use a dot inside the abbreviations. [#5749](https://github.com/JabRef/jabref/pull/5749)
 
 ### Fixed

docs/adr/0016-mutable-preferences-objects.md

@@ -0,0 +1,16 @@
+# Mutable preferences objects
+
+## Context and Problem Statement
+
+To create an immutable preferences object every time seems to be a waste of time and computer memory. 
+
+## Considered Options
+
+* Create a new object every time a preferences object should be altered by a with*-method, similar to a Builder.
+* Alter the existing object and return it.
+
+## Decision Outcome
+
+Chosen option: 1, because the preferences objects are just wrappers around the basic preferences framework of JDK. They
+should be mutable on-the-fly similar to objects with a Builder inside and to be stored immediatly again in the
+preferences.

src/main/java/org/jabref/JabRefMain.java

@@ -11,6 +11,7 @@
 import org.jabref.cli.JabRefCLI;
 import org.jabref.gui.FXDialog;
 import org.jabref.gui.remote.JabRefMessageHandler;
+import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.ProxyAuthenticator;
@@ -168,7 +169,11 @@ private static void applyPreferences(JabRefPreferences preferences) {
                 Globals.prefs.getXMPPreferences(), Globals.getFileUpdateMonitor());
         Globals.entryTypesManager.addCustomOrModifiedTypes(preferences.loadBibEntryTypes(BibDatabaseMode.BIBTEX),
                 preferences.loadBibEntryTypes(BibDatabaseMode.BIBLATEX));
-        Globals.exportFactory = Globals.prefs.getExporterFactory(Globals.journalAbbreviationRepository);
+        Globals.exportFactory = ExporterFactory.create(
+                Globals.prefs.getCustomExportFormats(Globals.journalAbbreviationRepository),
+                Globals.prefs.getLayoutFormatterPreferences(Globals.journalAbbreviationRepository),
+                Globals.prefs.getSavePreferencesForExport(),
+                Globals.prefs.getXMPPreferences());
 
         // Initialize protected terms loader
         Globals.protectedTermsLoader = new ProtectedTermsLoader(Globals.prefs.getProtectedTermsPreferences());

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

@@ -273,7 +273,7 @@ private boolean exportMatches(List<ParserResult> loaded) {
 
             // export new database
             Optional<Exporter> exporter = Globals.exportFactory.getExporterByName(formatName);
-            if (!exporter.isPresent()) {
+            if (exporter.isEmpty()) {
                 System.err.println(Localization.lang("Unknown export format") + ": " + formatName);
             } else {
                 // We have an TemplateExporter instance:
@@ -387,7 +387,7 @@ private boolean generateAux(List<ParserResult> loaded, String[] data) {
     private void saveDatabase(BibDatabase newBase, String subName) {
         try {
             System.out.println(Localization.lang("Saving") + ": " + subName);
-            SavePreferences prefs = Globals.prefs.loadForSaveFromPreferences();
+            SavePreferences prefs = Globals.prefs.getSavePreferences();
             AtomicFileWriter fileWriter = new AtomicFileWriter(Path.of(subName), prefs.getEncoding());
             BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(fileWriter, prefs, Globals.entryTypesManager);
             databaseWriter.saveDatabase(new BibDatabaseContext(newBase));
@@ -435,7 +435,7 @@ private void exportFile(List<ParserResult> loaded, String[] data) {
                     .getFileDirectories(Globals.prefs.getFilePreferences());
             System.out.println(Localization.lang("Exporting") + ": " + data[0]);
             Optional<Exporter> exporter = Globals.exportFactory.getExporterByName(data[1]);
-            if (!exporter.isPresent()) {
+            if (exporter.isEmpty()) {
                 System.err.println(Localization.lang("Unknown export format") + ": " + data[1]);
             } else {
                 // We have an exporter:
@@ -458,9 +458,9 @@ private void importPreferences() {
             Globals.entryTypesManager.addCustomOrModifiedTypes(Globals.prefs.loadBibEntryTypes(BibDatabaseMode.BIBTEX),
                     Globals.prefs.loadBibEntryTypes(BibDatabaseMode.BIBLATEX));
             List<TemplateExporter> customExporters = Globals.prefs.getCustomExportFormats(Globals.journalAbbreviationRepository);
-            LayoutFormatterPreferences layoutPreferences = Globals.prefs
-                    .getLayoutFormatterPreferences(Globals.journalAbbreviationRepository);
-            SavePreferences savePreferences = Globals.prefs.loadForExportFromPreferences();
+            LayoutFormatterPreferences layoutPreferences =
+                    Globals.prefs.getLayoutFormatterPreferences(Globals.journalAbbreviationRepository);
+            SavePreferences savePreferences = Globals.prefs.getSavePreferencesForExport();
             XmpPreferences xmpPreferences = Globals.prefs.getXMPPreferences();
             Globals.exportFactory = ExporterFactory.create(customExporters, layoutPreferences, savePreferences, xmpPreferences);
         } catch (JabRefException ex) {
@@ -495,7 +495,11 @@ private void automaticallySetFileLinks(List<ParserResult> loaded) {
         for (ParserResult parserResult : loaded) {
             BibDatabase database = parserResult.getDatabase();
             LOGGER.info(Localization.lang("Automatically setting file links"));
-            AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(parserResult.getDatabaseContext(), Globals.prefs.getFilePreferences(), Globals.prefs.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
+            AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(
+                    parserResult.getDatabaseContext(),
+                    Globals.prefs.getFilePreferences(),
+                    Globals.prefs.getAutoLinkPreferences(),
+                    ExternalFileTypes.getInstance());
             util.linkAssociatedFiles(database.getEntries(), new NamedCompound(""));
         }
     }
@@ -534,7 +538,7 @@ private Optional<ParserResult> fetch(String fetchCommand) {
         Optional<SearchBasedFetcher> selectedFetcher = fetchers.stream()
                                                                .filter(fetcher -> fetcher.getName().equalsIgnoreCase(engine))
                                                                .findFirst();
-        if (!selectedFetcher.isPresent()) {
+        if (selectedFetcher.isEmpty()) {
             System.out.println(Localization.lang("Could not find fetcher '%0'", engine));
 
             System.out.println(Localization.lang("The following fetchers are available:"));

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

@@ -70,7 +70,7 @@ public ExporterViewModel saveExporter() {
 
         // Create a new exporter to be returned to ExportCustomizationDialogViewModel, which requested it
         LayoutFormatterPreferences layoutPreferences = preferences.getLayoutFormatterPreferences(repository);
-        SavePreferences savePreferences = preferences.loadForExportFromPreferences();
+        SavePreferences savePreferences = preferences.getSavePreferencesForExport();
         TemplateExporter format = new TemplateExporter(name.get(), layoutFile.get(), extension.get(),
                 layoutPreferences, savePreferences);
         format.setCustomExport(true);

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

@@ -53,7 +53,7 @@ public ExportCommand(JabRefFrame frame, boolean selectedOnly, JabRefPreferences
     public void execute() {
         List<TemplateExporter> customExporters = preferences.getCustomExportFormats(Globals.journalAbbreviationRepository);
         LayoutFormatterPreferences layoutPreferences = preferences.getLayoutFormatterPreferences(Globals.journalAbbreviationRepository);
-        SavePreferences savePreferences = preferences.loadForExportFromPreferences();
+        SavePreferences savePreferences = preferences.getSavePreferencesForExport();
         XmpPreferences xmpPreferences = preferences.getXMPPreferences();
 
         // Get list of exporters and sort before adding to file dialog

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

@@ -166,7 +166,7 @@ private Optional<Path> askForSavePath() {
 
     private boolean save(BibDatabaseContext bibDatabaseContext, SaveDatabaseMode mode) {
         Optional<Path> databasePath = bibDatabaseContext.getDatabasePath();
-        if (!databasePath.isPresent()) {
+        if (databasePath.isEmpty()) {
             Optional<Path> savePath = askForSavePath();
             if (!savePath.isPresent()) {
                 return false;
@@ -216,10 +216,10 @@ private boolean save(Path targetPath, SaveDatabaseMode mode) {
     }
 
     private boolean saveDatabase(Path file, boolean selectedOnly, Charset encoding, SavePreferences.DatabaseSaveType saveType) throws SaveException {
-        SavePreferences preferences = this.preferences.loadForSaveFromPreferences()
+        SavePreferences preferences = this.preferences.getSavePreferences()
                                                       .withEncoding(encoding)
                                                       .withSaveType(saveType);
-        try (AtomicFileWriter fileWriter = new AtomicFileWriter(file, preferences.getEncoding(), preferences.makeBackup())) {
+        try (AtomicFileWriter fileWriter = new AtomicFileWriter(file, preferences.getEncoding(), preferences.shouldMakeBackup())) {
             BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(fileWriter, preferences, entryTypesManager);
 
             if (selectedOnly) {

src/main/java/org/jabref/gui/externalfiles/AutoLinkFilesAction.java

@@ -52,8 +52,12 @@ public void execute() {
         List<BibEntry> entries = stateManager.getSelectedEntries();
 
         final NamedCompound nc = new NamedCompound(Localization.lang("Automatically set file links"));
-        AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(database, preferences.getFilePreferences(), preferences.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
-        Task<List<BibEntry>> linkFilesTask = new Task<List<BibEntry>>() {
+        AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(
+                database,
+                preferences.getFilePreferences(),
+                preferences.getAutoLinkPreferences(),
+                ExternalFileTypes.getInstance());
+        Task<List<BibEntry>> linkFilesTask = new Task<>() {
 
             @Override
             protected List<BibEntry> call() {

src/main/java/org/jabref/gui/fieldeditors/LinkedFileViewModel.java

@@ -465,7 +465,7 @@ public BackgroundTask<Path> prepareDownloadTask(Path targetDirectory, URLDownloa
                     String suggestedTypeName = externalFileType.getName();
                     linkedFile.setFileType(suggestedTypeName);
                     String suggestedName = linkedFileHandler.getSuggestedFileName(externalFileType.getExtension());
-                    String fulltextDir = FileUtil.createDirNameFromPattern(databaseContext.getDatabase(), entry, filePreferences.getFileDirPattern());
+                    String fulltextDir = FileUtil.createDirNameFromPattern(databaseContext.getDatabase(), entry, filePreferences.getFileDirectoryPattern());
                     suggestedName = FileNameUniqueness.getNonOverWritingFileName(targetDirectory.resolve(fulltextDir), suggestedName);
                     return targetDirectory.resolve(fulltextDir).resolve(suggestedName);
                 })

src/main/java/org/jabref/gui/fieldeditors/LinkedFilesEditorViewModel.java

@@ -101,7 +101,15 @@ public LinkedFileViewModel fromFile(Path file) {
         List<Path> fileDirectories = databaseContext.getFileDirectoriesAsPaths(preferences.getFilePreferences());
 
         LinkedFile linkedFile = fromFile(file, fileDirectories, externalFileTypes);
-        return new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences.getXMPPreferences(), preferences.getFilePreferences(), externalFileTypes);
+        return new LinkedFileViewModel(
+                linkedFile,
+                entry,
+                databaseContext,
+                taskExecutor,
+                dialogService,
+                preferences.getXMPPreferences(),
+                preferences.getFilePreferences(),
+                externalFileTypes);
     }
 
     public boolean isFulltextLookupInProgress() {
@@ -114,7 +122,15 @@ public BooleanProperty fulltextLookupInProgressProperty() {
 
     private List<LinkedFileViewModel> parseToFileViewModel(String stringValue) {
         return FileFieldParser.parse(stringValue).stream()
-                              .map(linkedFile -> new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences.getXMPPreferences(), preferences.getFilePreferences(), externalFileTypes))
+                              .map(linkedFile -> new LinkedFileViewModel(
+                                      linkedFile,
+                                      entry,
+                                      databaseContext,
+                                      taskExecutor,
+                                      dialogService,
+                                      preferences.getXMPPreferences(),
+                                      preferences.getFilePreferences(),
+                                      externalFileTypes))
                               .collect(Collectors.toList());
     }
 
@@ -137,7 +153,15 @@ public void addNewFile() {
         List<Path> fileDirectories = databaseContext.getFileDirectoriesAsPaths(preferences.getFilePreferences());
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(newFile -> {
             LinkedFile newLinkedFile = fromFile(newFile, fileDirectories, externalFileTypes);
-            files.add(new LinkedFileViewModel(newLinkedFile, entry, databaseContext, taskExecutor, dialogService, preferences.getXMPPreferences(), preferences.getFilePreferences(), externalFileTypes));
+            files.add(new LinkedFileViewModel(
+                    newLinkedFile,
+                    entry,
+                    databaseContext,
+                    taskExecutor,
+                    dialogService,
+                    preferences.getXMPPreferences(),
+                    preferences.getFilePreferences(),
+                    externalFileTypes));
         });
     }
 
@@ -159,11 +183,23 @@ public void bindToEntry(BibEntry entry) {
     private List<LinkedFileViewModel> findAssociatedNotLinkedFiles(BibEntry entry) {
         List<LinkedFileViewModel> result = new ArrayList<>();
 
-        AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(databaseContext, preferences.getFilePreferences(), preferences.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
+        AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(
+                databaseContext,
+                preferences.getFilePreferences(),
+                preferences.getAutoLinkPreferences(),
+                ExternalFileTypes.getInstance());
         try {
             List<LinkedFile> linkedFiles = util.findAssociatedNotLinkedFiles(entry);
             for (LinkedFile linkedFile : linkedFiles) {
-                LinkedFileViewModel newLinkedFile = new LinkedFileViewModel(linkedFile, entry, databaseContext, taskExecutor, dialogService, preferences.getXMPPreferences(), preferences.getFilePreferences(), externalFileTypes);
+                LinkedFileViewModel newLinkedFile = new LinkedFileViewModel(
+                        linkedFile,
+                        entry,
+                        databaseContext,
+                        taskExecutor,
+                        dialogService,
+                        preferences.getXMPPreferences(),
+                        preferences.getFilePreferences(),
+                        externalFileTypes);
                 newLinkedFile.markAsAutomaticallyFound();
                 result.add(newLinkedFile);
             }
@@ -206,7 +242,15 @@ public void addFromURL() {
     }
 
     private void addFromURL(URL url) {
-        LinkedFileViewModel onlineFile = new LinkedFileViewModel(new LinkedFile(url, ""), entry, databaseContext, taskExecutor, dialogService, preferences.getXMPPreferences(), preferences.getFilePreferences(), externalFileTypes);
+        LinkedFileViewModel onlineFile = new LinkedFileViewModel(
+                new LinkedFile(url, ""),
+                entry,
+                databaseContext,
+                taskExecutor,
+                dialogService,
+                preferences.getXMPPreferences(),
+                preferences.getFilePreferences(),
+                externalFileTypes);
         files.add(onlineFile);
         onlineFile.download();
     }

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

@@ -61,7 +61,14 @@ public class ImportEntriesViewModel extends AbstractViewModel {
      * @param databaseContext the database to import into
      * @param task            the task executed for parsing the selected files(s).
      */
-    public ImportEntriesViewModel(BackgroundTask<ParserResult> task, TaskExecutor taskExecutor, BibDatabaseContext databaseContext, DialogService dialogService, UndoManager undoManager, PreferencesService preferences, StateManager stateManager, FileUpdateMonitor fileUpdateMonitor) {
+    public ImportEntriesViewModel(BackgroundTask<ParserResult> task,
+                                  TaskExecutor taskExecutor,
+                                  BibDatabaseContext databaseContext,
+                                  DialogService dialogService,
+                                  UndoManager undoManager,
+                                  PreferencesService preferences,
+                                  StateManager stateManager,
+                                  FileUpdateMonitor fileUpdateMonitor) {
         this.taskExecutor = taskExecutor;
         this.databaseContext = databaseContext;
         this.dialogService = dialogService;
@@ -94,9 +101,9 @@ public ObservableList<BibEntry> getEntries() {
     }
 
     public boolean hasDuplicate(BibEntry entry) {
-        return findInternalDuplicate(entry).isPresent()
-                ||
-                new DuplicateCheck(Globals.entryTypesManager).containsDuplicate(databaseContext.getDatabase(), entry, databaseContext.getMode()).isPresent();
+        return findInternalDuplicate(entry).isPresent() ||
+                new DuplicateCheck(Globals.entryTypesManager)
+                .containsDuplicate(databaseContext.getDatabase(), entry, databaseContext.getMode()).isPresent();
     }
 
     /**
@@ -132,8 +139,8 @@ public void importEntries(List<BibEntry> entriesToImport, boolean shouldDownload
         }
 
         // Remember the selection in the dialog
-        FilePreferences filePreferences = preferences.getFilePreferences();
-        filePreferences.setShouldDownloadLinkedFiles(shouldDownloadFiles);
+        FilePreferences filePreferences = preferences.getFilePreferences()
+                                                     .withShouldDownloadLinkedFiles(shouldDownloadFiles);
         preferences.storeFilePreferences(filePreferences);
 
         if (shouldDownloadFiles) {

src/main/java/org/jabref/gui/menus/FileHistoryMenu.java

@@ -11,16 +11,16 @@
 import org.jabref.gui.importer.actions.OpenDatabaseAction;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.io.FileHistory;
-import org.jabref.preferences.JabRefPreferences;
+import org.jabref.preferences.PreferencesService;
 
 public class FileHistoryMenu extends Menu {
 
     private final FileHistory history;
-    private final JabRefPreferences preferences;
+    private final PreferencesService preferences;
     private final DialogService dialogService;
     private final OpenDatabaseAction openDatabaseAction;
 
-    public FileHistoryMenu(JabRefPreferences preferences, DialogService dialogService, OpenDatabaseAction openDatabaseAction) {
+    public FileHistoryMenu(PreferencesService preferences, DialogService dialogService, OpenDatabaseAction openDatabaseAction) {
         setText(Localization.lang("Recent libraries"));
 
         this.preferences = preferences;